Publications using Ariadne Software
Pathway Analysis [247]
Analysis of gene expression microarray data [255]
Disease mechanism [187]
Analysis of proteomics data [42]
Drug discovery [35]
Model organisms [34]
Neuroscience [32]
Toxicogenomics [20]
Human genetics [16]
Biomarkers [12]
Plants [7]
Analysis of metabolomics data [4]
Publications by Ariadne authors [30]
Patents [35]
Text mining [17]
Databases [3]
Reviews [18]
Websites [7]
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Progranulin A-mediated MET Signaling Is Essential for Liver Morphogenesis in Zebrafish Yen-Hsing Li, Mark Hung-Chih Chen, Hong-Yi Gong, Shao-Yang Hu et al J. Biol. Chem. 2010; 285(52): p. 41001-41009 |
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Individual Stress Vulnerability Is Predicted by Short-Term Memory and AMPA Receptor Subunit Ratio in the Hippocampus Mathias V. Schmidt, Dietrich Trumbach, Peter Weber, Klaus Wagner et al J. Neurosci. 2010; 30(50): p. 16949-16958 |
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Photosynthesis and drought: can we make metabolic connections from available data? C. Pinheiro and M. M. Chaves J. Exp. Bot. 14 December 2010, 10.1093/jxb/erq340 |
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Insulin-Like Growth Factor I Suppresses Bone Morphogenetic Protein Signaling in Prostate Cancer Cells by Activating mTOR Signaling Reema S. Wahdan-Alaswad, Kyung Song, Tracy L. Krebs, Dorjee T.N. Shola, Jose A. Gomez, Shigemi Matsuyama, and David Danielpour Cancer Res. 2010; 70(22): p. 9106-9117 |
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Gene expression profiling in the stress control brain region hypothalamic paraventricular nucleus reveals a novel gene network including amyloid beta precursor protein. Tsolakidou A, Czibere L, Ptz B, Trmbach D, Panhuysen M, Deussing JM, Wurst W, Sillaber I, Landgraf R, Holsboer F, Rein T. BMC Genomics. 2010 Oct 8;11:546. |
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Tilapia Hepcidin 2-3 Peptide Modulates Lipopolysaccharide-induced Cytokines and Inhibits Tumor Necrosis Factor- through Cyclooxygenase-2 and Phosphodiesterase 4D Venugopal Rajanbabu, Chieh-Yu Pan, Shang-Chun Lee, Wei-Ju Lin, Ching-Chun Lin, Chung-Leung Li, and Jyh-Yih Chen J. Biol. Chem. |
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Akt RSK S6 Kinase Signaling Networks Activated by Oncogenic Receptor Tyrosine Kinases Albrecht Moritz et al Sci. Signal. |
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Analysis and construction of pathogenicity island regulatory pathways in Salmonella enterica serovar Typhi Su Yean Ong, Fui Ling Ng, Siti Suriawati Badai, Anton Yuryev and Maqsudul Alam Journal of Integrative Bioinformatics, 7(1):145, 2010 |
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Genomic and Proteomic Responses to Environmentally Relevant Exposures to Dieldrin: Indicators of Neurodegeneration? Christopher J. Martyniuk, Kevin J. Kroll, Nicholas J. Doperalski, David S. Barber, and Nancy D. Denslow Toxicol. Sci. |
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Identification of Early Response Genes and Pathway Activated by Androgens in the Initial Segment and Caput Regions of the Regressed Rat Epididymis Mahsa Hamzeh and Bernard Robaire Endocrinology |
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Innate immune processes are sufficient for driving silicosis in mice Celine A. Beamer, Christopher T. Migliaccio, Forrest Jessop, Melanie Trapkus, Dorothy Yuan, and Andrij Holian J. Leukoc. Biol. |
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Comparative Transcriptional Profiling and Preliminary Study on Heterosis Mechanism of Super-Hybrid Rice Gui-Sheng Song et al Mol Plant |
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Transcriptomic analysis of patients with tetralogy of Fallot reveals the effect of chronic hypoxia on myocardial gene expression Mohamed T. Ghorbel, Myriam Cherif, Emma Jenkins, Amir Mokhtari, Damien Kenny, Gianni D. Angelini, and Massimo Caputo J. Thorac. Cardiovasc. Surg. |
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Adaptive immune response in osteoclastic bone resorption induced by orally administered Aggregatibacter actinomycetemcomitans in a rat model of periodontal disease Li Y, Messina C, Bendaoud M, Fine DH, Schreiner H, Tsiagbe VK. Mol Oral Microbiol. |
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Differential Regulation of Mitogen-Activated Protein Kinase Pathways by Acetaminophen and Its Nonhepatotoxic Regioisomer 3\'-Hydroxyacetanilide in TAMH Cells Brendan D. Stamper, Theo K. Bammler, Richard P. Beyer, Frederico M. Farin, and Sidney D. Nelson Toxicol. Sci. |
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JAK-STAT Signalling Pathway Proteins are Over Expressed in Arterial Human Endothelial Cells Exposed to Oxidized Low Density Lipoproteins A. Laguna-Fernandez et al Journal of Hypertension |
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Transcriptome atlas of aromatic amino acid family metabolism-related genes in eight liver cell types uncovers the corresponding metabolic pathways in rat liver regeneration Chang, Cuifang and Xu, CunShuan The International Journal of Biochemistry & Cell Biology, 42 (10), p.1708, Oct 2010 |
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Off-pump coronary artery bypass surgery is associated with fewer gene expression changes in the human myocardium in comparison with on-pump surgery Mohamed T. Ghorbel et al, Physiol Genomics, Jun 2010 |
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Methylation profile of TP53 regulatory pathway and mtDNA alterations in breast cancer patients lacking TP53 mutations Zeinab Barekati et al Hum. Mol. Genet., May 2010 |
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Custom CGH array profiling of copy number variations (CNVs) on chromosome 6p21.32 (HLA locus) in patients with venous malformations associated with multiple sclerosis Alessandra Ferlini et al BMC Med Genetics. Apr 2010 |
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Uncovering Molecular Biomarkers That Correlate Cognitive Decline with the Changes of Hippocampus\' Gene Expression Profiles in Alzheimer\'s Disease Martn Gmez Ravetti, Osvaldo A. Rosso, Regina Berretta, Pablo Moscato PLOS One, Apr. 2010 |
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Global methylation profiling of lymphoblastoid cell lines reveals epigenetic contributions to autism spectrum disorders and a novel autism candidate gene, ORA, whose protein product is reduced in autistic brain AnhThu Nguyen, Tibor A. Rauch, Gerd P. Pfeifer, and Valerie W. Hu The FASEB Journal, Apr. 2010 |
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Identification of a Cholangiocarcinoma-Like Gene Expression Trait in Hepatocellular Carcinoma Hyun Goo Woo et al Cancer Res., Apr 2010 |
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Genome-wide analysis reveals distinct substrate specificities of Rrp6, Dis3, and core exosome subunits Daniel L. Kiss and Erik D. Andrulis RNA, Apr. 2010 |
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Modulation of Transcriptome and Metabolome of Tobacco by Arabidopsis Transcription Factor, AtMYB12, Leads to Insect Resistance Prashant Misra et al Plant Physiology, Apr 2010 |
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Comparative Analysis of the Migraine Pathway in Human and C. elegans Khurshid Ahmad et al Current research Journal of Biological Sciences, Mar. 2010 |
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Atlas of Signaling for Interpretation of Microarray Experiments Ekaterina Kotelnikova, Natalia Ivanikova, Andrey Kalinin, Anton Yuryev, Nikolai Daraselia PLoS One., Feb. 2010 |
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Investigation of Human Testis Protein Heterogeneity Using Two-Dimensional Electrophoresis Xuejiang Guo et al J Androl., Feb. 2010 |
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Testing for mean and correlation changes in microarray experiments: an application for pathway analysis Mayer Alvo, Zhongzhu Liu, Andrew Williams, Carole Yauk BMC Bioinformatics 2010 |
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Identification of tyrosine phosphoproteins in signaling pathway triggered TGF-a by using functional proteomics technology Lin Ruan, Guo-Liang Wang, Yan Chen, Hong Yi, Can-E Tang, Peng-Fei Zhang, Mao-Yu Li, Cui Li, Fang Peng, Jian-Ling Li, Zhu-Chu Chen, Zhi-Qiang Xiao Med Oncol, Jan 2010 |
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Global phosphoproteomic effects of natural tyrosine kinase Guang-Rong Yan, Chuan-Le Xiao, Gui-Wei He, Xing-Feng Yin, Nan-Peng Chen, Ya Cao, Qing-Yu He Proteomics, Jan 2010 |
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Construction of signaling pathways and identification of drug effects on the liver cancer cell HepG2. LG Alexopoulos, IN Melas, AD Chairakaki, J Saez-Rodriguez, and A Mitsos Conf Proc IEEE Eng Med Biol Soc, January 1, 2010; 1: 6717-20. |
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Time-dependent alterations of cerebral proteins following short-term normobaric hyperoxia Jochen Hinkelbein, Robert E. Feldmann Jr., Armin Kalenka Mol Cell Biochem, Jan 2010 |
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Proteomic analysis of honeybee worker (Apis mellifera) hypopharyngeal glanddevelopment Mao Feng, Yu Feng, JianKe Li BMC Genomics, Dec. 2009 |
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A mouse model of anxiety molecularly characterized by altered protein networks in the brain proteome va M. SzegQ, Tams Janky, Zoltn Szab, Attila Csorba, Hajnalka Kompagne, Gza Mller, Gyrgy Lvay, Attila Simor, Gbor Juhsz and Katalin A. Kkesi European Neuropsychopharmacology, Dec. 2009 |
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A Gene Signature Predictive for Outcome in Advanced Ovarian Cancer Identifies a Survival Factor: Microfibril-Associated Glycoprotein 2 Samuel C. Mok et al Cancer Cell, Dec. 2009 |
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Cytokine array analysis of peritoneal fluid between women with endometriosis of different stages and those without endometriosis Hou Z, Sun L, Gao L, Liao L, Mao Y, Liu J. Biomarkers, Dec. 2009 |
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Analysis of abscisic acid responsive proteins in Brassica napus guard cells by multiplexed isobaric tagging Mengmeng Zhua, Brigitte Simonsb, Ning Zhua, David G. Oppenheimera, and Sixue Chen Journal of Proteomics, Nov. 2009 |
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Next-generation sequencing in aging research: Emerging applications, problems, pitfalls and possible solutions de Magalhes JP, Finch CE, Janssens G. Ageing Res Rev., Nov. 2009 |
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Gene expression profiling of the short-term adaptive response to acute caloric restriction in liver and adipose tissues of pigs differing in feed efficiency Sender Lkhagvadorj, Long Qu, Weiguo Cai, Oliver P Couture, C. Richard Barb, Gary J Hausman, Dan Nettleton, Lloyd L. Anderson, Jack C.M. Dekkers, and Christopher K Tuggle Am J Physiol Regulatory Integrative Comp Physiol, Nov. 2009 |
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Pathway Analysis in HEK 293T Cells Overexpressing HIV-1 Tat and Nucleocapsid MJ Lee and JH Park J Microbiol Biotechnol, Oct. 2009 |
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Biological actions of curcumin on articular chondrocytes Henrotin Y, Clutterbuck AL, Allaway D, Lodwig EM, Harris P, Mathy-Hartert M, Shakibaei M, Mobasheri A. Osteoarthritis Cartilage, Oct. 2009, Product: Pathway Studio, ResNet |
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Comparative in vivo gene expression of the closely related bacteria Photorhabdus temperata and Xenorhabdus koppenhoeferi upon infection of the same insect host, Rhizotrogus majalis An R, Sreevatsan S, Grewal PS BMC Genomics, Sep. 2009 |
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Proteomic-based identification of maternal proteins in mature mouse oocytes Ping Zhang, Xiaojian Ni, Ying Guo, Xuejiang Guo, Yufeng Wang, Zuomin Zhou, Ran Huo and Jiahao Sha BMC Genomics, Product: Pathway Studio |
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Depletion of T-cell intracellular antigen proteins promotes cell proliferation Raquel Reyes, Jos Alcalde and Jos M Izquierdo Genome Biology, Product: Pathway Studio, ResNet |
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Induction of the interleukin 6/ signal transducer and activator of transcription pathway in the lungs of mice sub-chronically exposed to mainstream tobacco moke Halappanavar S, Russell M, Stampfli MR, Williams A, Yauk CL BMC Medical Genomics, 2, p.56-56, Aug 2009, Product: Pathway Studio, ResNet |
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Pathway analysis of differentially expressed genes in patients with acute aortic dissection SA Mohamed, HH Sievers, T Hanke, D Richardt, C Schmidtke, EI Charitos, G Belge, and J Bullerdiek Biomark Insights 1 Jan 2009 4: p. 81, Product: Pathway Studio |
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Pathway results from the chicken data set using GOTM, Pathway Studio and Ingenuity softwares A Bonnet, S Lagarrigue, L Liaubet, C Robert-Granie, M Sancristobal, and G Tosser-Klopp BMC Proc 1 Jan 2009 3 Suppl 4: p. S11, Product: Pathway Studio |
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Hub genes with positive feedbacks function as master switches in developmental gene regulatory networks Chang H. Seo, Jeong-Rae Kim, Man-Sun Kim, and Kwang-Hyun Cho Bioinformatics. 2009; 25(15): p. 1898-1904, Product: Pathway Studio |
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Gene expression responses in male fathead minnows exposed to binary mixtures of an estrogen and antiestrogen Garcia-Reyero et al BMC Genomics 2009, 10:308, Product: Pathway Studio |
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Uncovering the Arabidopsis thaliana nectary transcriptome: investigation of differential gene expression in floral nectariferous tissues Brian W Kram, Wayne W Xu and Clay J Carter BMC Plant Biology, Product: Pathway Studio |
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A dynamic network of transcription in LPS-treated human subjects Junhee Seok, Wenzhong Xiao, Lyle L Moldawer, Ronald W Davis and Markus W Covert BMC Systems Biology, Product: Pathway Studio |
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Zebrafish reward mutants reveal novel transcripts mediating the behavioral effects of amphetamine Webb, Katharine J, Norton, William HJ, Trmbach, Dietrich, Meijer, Annemarie H, Ninkovic, Jovica, Topp, Stefanie, Heck, Daniel, Bally-Cuif, Laure Genome Biology, Product: Pathway Studio |
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Gene Expression Profiling of Lymphoblasts from Autistic and Nonaffected Sib Pairs: Altered Pathways in Neuronal Development and Steroid Biosynthesis Hu, Valerie W., Nguyen, AnhThu, Kim, Kyung Soon, Steinberg, Mara E., Sarachana, Tewarit, Scully, Michele A., Soldin, Steven J. and Lee, Norman H. PLoS ONE, Product: Pathway Studio |
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Stress Proteins and Immunostimulatory Signaling Through Toll-Like Receptors in Glaucoma C. Luo, X. Yang, D. W. Powell, J. B. Klein, and G. Tezel Invest. Ophthalmol. Vis. Sci.,Apr 2009; 50: 4048, Product: Pathway Studio |
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Proteomics Supports Different Pathways of Complement Activity in Human Glaucoma G. Tezel, X. Yang, C. Luo, D. W. Powell, J. B. Klein, H. J. Kaplan, and M. H. Kuehn Invest. Ophthalmol. Vis. Sci.,Apr 2009; 50: 4044, Product: Pathway Studio |
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Proteomic Analysis of TNF-{alpha}Signaling in Human Glaucoma X. Yang, C. Luo, D. W. Powell, J. B. Klein, M. H. Kuehn, and G. Tezel Invest. Ophthalmol. Vis. Sci.,Apr 2009; 50: 4043, Product: Pathway Studio |
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A Modeling-Derived Hypothesis on Chronicity in Respiratory Diseases: Desensitized Pathogen Recognition Secondary to Hyperactive IRAK/TRAF6 Signaling Tingting Zhang,Kyung W. Song,Mohammad Hekmat-Nejad,David G. Morris,and Brian R. Wong PLoS ONE.2009;4(4): e5332, Product: Pathway Studio |
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Gene regulatory network inference: data integration in dynamic models-a review. Hecker M, Lambeck S, Toepfer S, van Someren E, Guthke R. Biosystems. 2009 Apr;96(1):86-103, Product: Pathway Studio |
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Proteomic analysis of salt-stressed tomato (Solanum lycposersicum) seedlings: effect of genotype and exogenous application of glycinebetaine Songbi Chen, Natan Gollop, and Bruria Heuer J. Exp. Bot., Mar 2009, Product: Pathway Studio |
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Evaluation of blastomere biopsy using mouse model indicates the potential high-risk of neurodegenerative disorders in the offspring Yang Yu, Jindao Wu, Yong Fan, Zhuo Lv, Xuejiang Guo, Chun Zhao, Rong Zhou, Zhuo Zhang, Fuqiang Wang, Min Xiao, Ling Chen, Hui Zhu, Wen Chen, Min Lin, Jiayin Liu, Zuomin Zhou, Liu Wang, Ran Huo, Qi Zhou, and Jiahao Sha Mol. Cell. Proteomics, Mar 2009, Product: Pathway Studio |
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Computational Approaches to Metabolomics David S. Wishart Book: Bioinformatics Methods in Clinical Research |
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Distinct gene subsets in pterygia formation and recurrence: dissecting complex biological phenomenon using genome wide expression data Louis Tong, Jaime Chew , Henry Yang , Leonard PK Ang , Donald TH Tan and Roger W Beuerman BMC Medical Genomics, Product: Pathway Studio |
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Thioredoxin Binding Protein-2/Thioredoxin-Interacting Protein Is a Critical Regulator of Insulin Secretion and Peroxisome Proliferator-Activated Receptor Function Shin-ichi Oka, Eiji Yoshihara, Akiko Bizen-Abe, Wenrui Liu, Mutsumi Watanabe, Junji Yodoi, and Hiroshi Masutani Endocrinology, Product: Pathway Studio |
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Genomic analyses of Musashi1 downstream targets show a strong association with cancer related processes Raquel de Sousa Abreu et al J. Biol. Chem., Mar 2009; 10.1074/jbc.M809605200, Product: Pathway Studio |
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Old target new approach: an alternate NF-B activation pathway via translation inhibition Csaba F. Lszl and Shiyong Wu Molecular and Cellular Biochemistry, Feb 2009 |
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Genome-wide Analysis of BP1 Transcriptional Targets in Breast Cancer Cell Line Hs578T Yongchun Song, Chengxue Dang1, Yebo Fu, Yi Lian, Jenny Hottel, Xuelan Li, Tim McCaffrey, Sidney W. Fu Int J Biol Sci 2009, Product: Pathway Studio |
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http://genomebiology.com/2009/10/2/R24 Immink RGH, Tonaco IAN, de Folter S, Shchennikova A, van Dijk ADJ, Busscher-Lange J, Borst JW, Angenent GC Genome Biology, Frb. 2009 |
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Comparative Mitochondrial Proteomic Analysis of Raji Cells Exposed to Adriamycin. Yu-Jie Jiang, Qing Sun, Xiao-Sheng Fang, and Xin Wang Mol Med 11 Feb 2009, Product: Pathway Studio |
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Bladder Cancer Associated Gene Expression Signatures Identified by Profiling of Exfoliated Urothelia Charles J. Rosser, Li Liu, Yijun Sun, Patrick Villicana, Molly McCullers, Stacy Porvasnik, Paul R. Young, Alexander S. Parker, and Steve Goodison Cancer Epidemiol. Biomarkers Prev., Product: Pathway Studio, ResNet |
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Comparison of Molecular and Histological Changes in Zebrafish Gills Exposed to Metallic Nanoparticles Robert J. Griffitt, Kelly Hyndman, Nancy D. Denslow, and Davis S. BarberRobert J. Griffitt, Kelly Hyndman, Nancy D. Denslow, and Davis S. BarberRobert J. Griffitt, Kelly Hyndman, Nancy D. Denslow, and Davis S. Barber Toxicol. Sci., Product: Pathway Studio |
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Critical Role of MARCO in Crystalline Silica Induced Pulmonary Inflammation Sheetal A. Thakur, Celine A. Beamer, Christopher T. Migliaccio, and Andrij Holian Toxicol. Sci., Apr 2009; 108: 462 - 471, Product: Pathway Studio |
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Dysregulated gene expression networks in human acute myelogenous leukemia stem cells Ravindra Majeti, Michael W. Becker, Qiang Tian, Tsung-Lu Michael Lee, Xiaowei Yan, Rui Liu, Jung-Hsien Chiang, Leroy Hood, Michael F. Clarke, and Irving L. Weissman PNAS, Mar 2009; 106: 3396 - 3401., Product: Pathway Studio |
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Transcriptional Profiling of Human Mesenchymal Stem Cells Transduced with Reporter Genes for Imaging Wang F, Dennis JE, Awadallah A, Solchaga LA, Molter J, Kuang Y, Salem N, Lin Y, Tian H, Kolthammer JA, Kim Y, Love ZB, Gerson SL, Lee Z. Physiol Genomics,Dec 2008; 10.1152/physiolgenomics.00300.2007 |
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Label-free mass spectrometry-based protein quantification technologies in proteomic analysis Mu Wang, Jinsam You, Kerry G. Bemis, Tony J. Tegeler, and Dawn P. G.Brown Brief Funct Genomic Proteomic. 2008; 7(5): p. 329-339, Product: Pathway Studio |
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Interaction analyses of human monocytes co-cultured with different forms of Aspergillus fumigatus Juergen Loeffler et al J. Med. Microbiol. 2009; 58(1): p. 49-58, Product: PathwayAssist |
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Mucosal cytokine imbalance in irritable bowel syndrome John Macsharry et al Scandinavian Journal of Gastroenterology, Dec. 2008 |
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Shortest-path network analysis is a useful approach toward identifying genetic determinants of longevity. Managbanag JR, Witten TM, Bonchev D, Fox LA, Tsuchiya M, Kennedy BK, Kaeberlein M. PLoS One. 2008;3(11):e3802. Epub 2008 Nov 25, Product: Pathway Studio |
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Ageing, oxidative stress and cancer: paradigms in parallax Christopher C. Benz& Christina Yau Nature Reviews Cancer8,875-879, Product: Pathway Studio |
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The Rat Genome Database 2009: variation, ontologies and pathways Melinda R. Dwinell, Elizabeth A. Worthey, Mary Shimoyama, Burcu, Bakir-Gungor, Jeffrey DePons, Stanley Laulederkind, Timothy Lowry, Rajni Nigram, Victoria Petri, Jennifer Smith, Alexander Stoddard, Simon, N. Twigger, Howard J. Jacob and the RGD Team Nucleic Acids Research Advance Access published on November 7, 2008, DOI 10.1093/nar/gkn842., Product: Pathway Studio |
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Assessing chronic liver toxicity based on relative gene expression data Kedar Kulkarni, Peter Larsen and Andreas A. Linninger Journal of Theoretical Biology, V254(2),21:308-318, Product: Pathway Studio |
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Mitochondrial dysregulation of osteoarthritic human articular chondrocytes analyzed by proteomics: A decrease in mitochondrial superoxide dismutase points to a redox imbalance Cristina Ruiz-Romero, Valentina Calamia, Jesus Mateos, Vanesa Carreira, Montserrat Martnez-Gomariz, Mercedes Fernndez, and Francisco J. Blanco Mol. Cell. Proteomics, Sep 2008; 10.1074/mcp.M800292-MCP200., Product: Pathway Studio |
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Identification of cold-shock protein RBM3 as a possible regulator of skeletal muscle size through expression profiling Esther E. Dupont-Versteegden, Radhakrishnan Nagarajan, Marjorie L Beggs, Edward D Bearden, Pippa M Simpson, and Charlotte A. Peterson Am J Physiol Regulatory Integrative Comp Physiol, Aug 2008; 10.1152/ajpregu.90455.2008, Product: PathwayAssist |
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Different signaling pathways expressed by chicken naive CD4(+) T cells, CD4(+) lymphocytes activated with staphylococcal enterotoxin B, and those malignantly transformed by Marek\'s disease virus. Buza JJ, Burgess SC Journal of proteome research, 7 (6), p.2380-2387, Product: Pathway Studio |
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Gene expression analysis of terminal differentiation of human melanoma cells highlights global reductions in cell cycle-associated genes. Huynh KM, Kim G, Kim DJ, Yang SJ, Park SM, Yeom YI, Fisher PB, Kang D. Gene. 2009 Mar 15;433(1-2):32-9, Product: Pathway Studio |
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Genomic Insights into Acute Alcohol Tolerance Wei Hu, Laura Saba, Katherina Kechris, Sanjiv V Bhave, Paula L Hoffman, and Boris Tabakoff J. Pharmacol. Exp. Ther., Jun 2008; 10.1124/jpet.108.137521, Product: PathwayAssist, ResNet |
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A copula method for modeling directional dependence of genes Kim JM, Jung YS, Sungur EA, Han KH, Park C, Sohn I. BMC Bioinformatics. 2008 May 1;9:225, Product: PathwayAssist |
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Effects of Subminimum Inhibitory Concentrations of Antibiotics on the Pasteurella multocida Proteome: A Systems Approach. Nanduri B, Lawrence ML, Peddinti DS, Burgess SC. Comp Funct Genomics. 2008:254836, Product: Pathway Studio |
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Quantitative analysis of Streptococcus pneumoniae TIGR4 response to in vitro iron restriction by 2-D LC ESI MS/MS. B Nanduri, P Shah, M Ramkumar, EB Allen, E Swiatlo, SC Burgess, and ML Lawrence Proteomics, May 2008; 8(10): 2104-14, Product: Pathway Studio |
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The first five years of the Wnt targetome Vlad, A.,Rohrs, S.,Klein-Hitpass, L.,Muller, O. Cellular Signalling, 20 (5), p.795-802, Product: Pathway Studio |
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Drinking-Water Arsenic Exposure Modulates Gene Expression in Human Lymphocytes from a U.S. Population Angeline S. Andrew, David A. Jewell, Rebecca A. Mason, Michael L. Whitfield, Jason H. Moore, and Margaret R. Karagas Environmental Health Perspectivesm Apr 20008, Product: Pathway Studio, ResNet |
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Phenotype reversion in fetal human liver epithelial cells identifies the role of an intermediate meso-endodermal stage before hepatic maturation Mari Inada, Antonia Follenzi, Kang Cheng, Manju Surana, Brigid Joseph, Daniel Benten, Sriram Bandi, Hong Qian, and Sanjeev Gupta J. Cell Sci., Mar 2008; 10.1242/jcs.019315, Product: Pathway Studio |
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Transcriptional Adaptation to Clcn5 Knockout in Proximal Tubules of the Mouse Kidney Jerry Wright, Marcelo M. Morales, Jackson Sousa-Menzes, Debora Ornellas, Jennifer Sipes, and Sandra E. Guggino Physiol Genomics, Mar 2008; 10.1152/physiolgenomics.00024.2008, Product: PathwayAssist |
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Chemical rescue of DF508-CFTR mimics genetic repair in cystic fibrosis bronchial epithelial cells Om V. Singh, Harvey B. Pollard, and Pamela L. Zeitlin Mol. Cell. Proteomics, Feb 2008; 10.1074/mcp.M700303-MCP200, Product: Pathway Studio |
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Scan of 977 nonsynonymous SNPs in CLL4 trial patients for the identification of genetic variants influencing prognosis Gabrielle S. Sellick, Rachel Wade, Susan Richards, David G. Oscier, Daniel Catovsky, and Richard S. Houlston Blood, Feb 2008; 111: 1625 - 1633, Product: PathwayAssist |
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Bioinformatics applications for pathway analysis of microarray data Werner, T Current Opinion in Biotechnology, 19 (1), p.50-54, Product: Pathway Studio |
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Harnessing genetically engineered mouse models for preclinical testing Robles, A.I., Varticovski, L. Chemico-Biological Interactions, 171 (2), p.159-164, Product: Pathway Studio |
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cAMP Response Element-Binding Protein-Mediated Gene Expression Increases the Intrinsic Excitability of CA1 Pyramidal Neurons Mikel Lopez de Armentia, Dragana Jancic, Roman Olivares, Juan M. Alarcon, Eric R. Kandel, and Angel Barco J. Neurosci., Dec 2007; 27: 13909 - 13918., Product: Pathway Studio |
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Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia Peter F. Dunfield, Anton Yuryev, Pavel Senin, Angela V. Smirnova, Matthew B. Stott, Shaobin Hou, Binh Ly, Jimmy H. Saw, Zhemin Zhou, Yan Ren, Jianmei Wang, Bruce W. Mountain, Michelle A. Crowe, Tina M. Weatherby, Paul L. E. Bodelier, Werner Liesack, Lu Feng, Lei Wang, Maqsudul Alam Nature 450, 879 - 882 (06 Dec 2007), Product: Pathway Studio, Topic: Applications of pathway analysis |
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A network-based approach to the analysis of acute wound healing N.B. Menke, K.R. Ward and R.F. Diegelmann Journal of Critical Care, Vol.22(4) 2007 p332, Product: Pathway Studio |
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Gene expression and biological processes influenced by deletion of Stat3 in pulmonary type II epithelial cells Yan Xu , Machiko Ikegami , Yanhua Wang , Yohei Matsuzaki and Jeffrey A Whitsett BMC Genomics 2007, 8:455, Product: Pathway Studio |
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Predicting aging/longevity-related genes in the nematode Caenorhabditis elegans. Witten TM, Bonchev D. Chem Biodivers. 2007 Nov;4(11):2639-55., Product: Pathway Studio |
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Genomic Changes in Regenerated Porcine Coronary Arterial Endothelial Cells Mary Y.K. Lee, Hung-Fat Tse, Chung-Wah Siu, Shu-Guang Zhu, Ricky Y.K. Man, and Paul M. Vanhoutte Arterioscler. Thromb. Vasc. Biol., Nov 2007; 27: 2443 - 2449, Product: PathwayAssist |
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Genomic and Nongenomic Effects of Estrogen Signaling in Human Endometrial Cells: Involvement of the Growth Factor Receptor Signaling Downstream AKT Pathway Sussane C. J. P. Gielen, Lindy A. M. Santegoets, Liesbeth C. M. Khne, Wilfred F. J. Van IJcken, Bianca Boers-Sijmons, Payman Hanifi-Moghaddam, Theo J. M. Helmerhorst, Leen J. Blok, and Curt W. Burger Reproductive Sciences, Vol. 14, No. 7, 646-654 (2007), Product: Pathway Studio |
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Automatic extraction of gene ontology annotation and its correlation with clusters in protein networks. Daraselia N, Yuryev A, Egorov S, Mazo I, Ispolatov I. BMC Bioinformatics. 2007 Jul 10;8(1):243, Product: MedScan, Topic: MedScan, Pathway and function |
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Regulation of the gonadal transcriptome during sex determination and testis morphogenesis: comparative candidate genes Tracy M Clement, Matthew D Anway, Mehmet Uzumcu, and Michael K Skinner Reproduction, Sep 2007; 134: 455 - 472, Product: PathwayAssist |
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The PPAR resource page John P. Vanden Heuvel BBA - Molecular and Cell Biology of Lipids, 1771 (8), p.1108-1112, Aug 2007, Product: Pathway Studio |
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A novel computational approach to the genetics of polycystic ovarian syndrome (PCOS) M. Nam Menke, N.B. Menke, D.G. Bonchev, T.M. Witten, J.R. Wood and J.F. Straussa Fertility and Sterility, v. 88, Supp.1, Page S73, Product: Pathway Studio |
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Molecular signatures of trauma-hemorrhagic shock-induced lung injury: hemorrhage- and injury-associated genes. R Feinman, EA Deitch, V Aris, HB Chu, B Abungu, FJ Caputo, A Galante, D Xu, Q Lu, I Colorado, D Streck, J Dermody, and P Soteropoulos Shock. 2007 Sep;28(3):360-8, Product: PathwayAssist |
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Propagation of large concentration changes in reversible protein-binding networks Maslov S, Ispolatov I. Proc Natl Acad Sci U S A. 2007, Product: None, Topic: Network topology and dynamics |
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Prediction of Protein-protein Interactions on the Basis of Evolutionary Conservation of Protein Functions Ekaterina Kotelnikova, Andrey Kalinin, Anton Yuryev, and Sergei Maslov Evolutionary Bioinformatics, Product: MedScan, Topic: Network evolution |
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Transcriptome teleonomy and scavenger lipidomics of albumin and alpha 1-acid glycoproteins: contextual genome-wide ontology enrichment as evidence for the epigenetic code? Pauli Ojala, , Sami Kilpinen, Lotta Arola, Petri Trnen, Elmar Bucher, Kalle Ojala, Kristiina Iljin, Mari Peltonen, Rolf Skotheim, Kristine Kleivi, Martti Tolvanen, Reija Autio, Pentti Somerharju, Olli Kallioniemi and Saara Laitinen Physics of Lipids, 149, p.S86-S86, Sep 2007, Product: Pathway Studio |
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Profiling Studies in Ovarian Cancer: A Review Rudolf S. N. Fehrmann, Xiang-yi Li, Ate G. J. van der Zee, Steven de Jong, Gerard J. te Meerman, Elisabeth G. E. de Vries, and Anne P. G. Crijns Oncologist, Aug 2007; 12: 960 - 966, Product: PathwayAssist |
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Gene Systems Network Inferred from Expression Profiles in Hepatocellular Carcinogenesis by Graphical Gaussian Model Sachiyo Aburatani, Fuyan Sun, Shigeru Saito, Masao Honda, Shu-Ichi Kaneko, and Katsuhisa Horimoto EURASIP J Bioinform Syst Biol. 2007; 2007: 47214, Product: PathwayAssist |
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Induction of a unique gene expression profile in primary human hepatocytes by hepatitis C virus core, NS3 and NS5A proteins A Budhu, Y Chen, J.W. Kim, M Forgues, K Valerie, C.C. Harris, and X.W. Wang Carcinogenesis, Product: PathwayAssist |
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Transcriptional network governing the angiogenic switch in human pancreatic cancer Abdollahi A, Schwager C, Kleeff J, Esposito I, Domhan S, Peschke P, Hauser K, Hahnfeldt P, Hlatky L, Debus J, Peters JM, Friess H, Folkman J, Huber PE. Proc Natl Acad Sci U S A. 2007 Jul 24, Product: Pathway Studio |
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Exenatide blocks JAK1-STAT1 in pancreatic beta cells Couto FM, Minn AH, Pise-Masison CA, Radonovich M, Brady JN, Hanson M, Fernandez LA, Wang P, Kendziorski C, Shalev A Metabolism. 2007 Jul;56(7):915-8, Product: Pathway Studio |
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Neutrophils: the forgotten cell in JIA disease pathogenesis James N Jarvis, Kaiyu Jiang, Howard R Petty, and Michael Centola Pediatr Rheumatol Online J. 2007; 5: 13., Product: Pathway Studio |
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Identification of human cell responses to benzene and benzene metabolites Bruce Gillis, Igor M. Gavin, Zarema Arbieva, Stephen T. King, Sundararajan Jayaraman, Bellur S. Prabhakar Genomics, Product: Pathway Studio, ResNet |
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Gap junction and purinergic P2 receptor proteins as a functional unit: insights from transcriptomics. Iacobas DA, Suadicani SO, Iacobas S, Chrisman C, Cohen MA, Spray DC, Scemes E. J Membr Biol. 2007 Jun;217(1-3):83-91, Product: Pathway Studio |
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Pathway analysis for design of promiscuous drugs and selective drug mixtures. Sivachenko A, Kalinin A, Yuryev A. Curr Drug Discov Technol. 2006 Dec;3(4):269-77., Product: Pathway Studio, Topic: Applications of pathway analysis |
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Molecular networks in microarray analysis. Sivachenko AY, Yuryev A, Daraselia N, Mazo I. J Bioinform Comput Biol., Product: Pathway Studio, Topic: Gene expression analysis |
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Specific Activation of the Glucocorticoid Receptor and Modulation of Signal Transduction Pathways in Human Lens Epithelial Cells Vanita Gupta, Niranjan Awasthi, and B. J. Wagner Invest. Ophthalmol. Vis. Sci., Apr 2007; 48: 1724 - 1734., Product: PathwayAssist |
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Functional genomics and proteomics of the cellular osmotic stress response in `non-model\' organisms Dietmar Kltz, Diego Fiol, Nelly Valkova, Silvia Gomez-Jimenez, Stephanie Y. Chan, and Jinoo Lee J. Exp. Biol., May 2007; 210: 1593 - 1601, Product: Pathway Studio |
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Pathway analysis software as a tool for drug target selection, prioritization and validation of drug mechanism Sivachenko A & Yuryev A Expert Opinion on Therapeutic Targets, v.11(3), pp.411-421, Product: Pathway Studio, Topic: Applications of pathway analysis |
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Comparative, genome-scale transcriptional analysis of CHRF-288-11 and primary human megakaryocytic cell cultures provides novel insights into lineage-specific differentiation Peter G. Fuhrken, Chi Chen, William M. Millera, and Eleftherios T. Papoutsakis Experimental Hematology,V.35(3):476-489.e23, Product: Pathway Studio |
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The microglial gene regulatory network activated by interferon-gamma Moran, L.B.,Duke, D.C.,Graeber, M.B. Journal of Neuroimmunology, Feb 2007, Product: Pathway Studio |
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A cassette system to study ES cell differentiation by inducible RNA interference Daniel Wegmller, Ines Raineri, Brigitte Gross, Edward J. Oakeley, and Christoph Moroni Stem Cells, Jan 2007; 10.1634/stemcells.2006-0106., Product: Pathway Studio |
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Overexpression of Angiopoietin-like Protein 4 Alters Mitochondria Activities and Modulates Methionine Metabolic Cycle in the Liver Tissues of db/db Diabetic Mice Yu Wang, Karen SL Lam, Janice BB Lam, Michael C Lam, Priscilla TY Leung, Mingyan Zhou, and Aimin Xu Molecular Endocrinology, doi:10.1210/me.2006-0249, Product: Pathway Studio |
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Microarrays in breast cancer research and clinical practice the future lies ahead Sofia K Gruvberger-Saal, Heather E Cunliffe, Kristen M Carr and Ingrid A Hedenfalk Endocrine-Related Cancer, Product: Pathway Studio |
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Phenotypic and global gene expression profile changes between low passage and high passage MIN-6 cells Lorraine O Driscoll, Patrick Gammell, Eadaoin McKiernan, Eoin Ryan, Per Bendix Jeppesen, Sweta Rani, and Martin Clynes J. Endocrinol., Dec 2006; 191: 665 - 676, Product: PathwayAssist |
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Data Mining for Gene Networks Relevant to Poor Prognosis in Lung Cancer Via Backward-Chaining Rule Induction Mary E. Edgerton, Douglas H. Fisher, Lianhong Tang,Lewis J. Frey, Zhihua Chen Cancer Informatics 2006:2, Product: Pathway Studio |
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RET oncoproteins induce tyrosine phosphorylation changes of proteins involved in RNA metabolism L. Gorlaa, M. Canta, F. Miccicha, C. Patellia, P. Mondellinia, M.A. Pierottia, and I. Bongarzonea Cellular Signalling V.18(12):2272-2282, Product: Pathway Studio |
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Integrated molecular profiling of SOD2 expression in multiple myeloma Elaine M Hurt, Suneetha B Thomas, Benjamin Peng, and William L Farrar Blood, Dec 2006; 10.1182/blood-2006-07-035162., Product: PathwayAssist |
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Identification of the Proliferation/Differentiation Switch in the Cellular Network of Multicellular Organisms Kai Xia, Huiling Xue, Dong Dong, Shanshan Zhu, Jiamu Wang, Qingpeng Zhang, Lei Hou, Hua Chen, Ran Tao, Zheng Huang, Zheng Fu, Ye-Guang Chen, Jing-Dong J. Han PLoS Comput Biol, Product: Pathway Studio |
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A Sex-Specific Role of Type VII Adenylyl Cyclase in Depression Hines LM, Hoffman PL, Bhave S, Saba L, Kaiser A, Snell L, Goncharov I, LeGault L, Dongier M, Grant B, Pronko S, Martinez L, Yoshimura M, Tabakoff B; World Health Organization/International Society for Biomedical Research on Alcoholism Study on State and Trait Markers of Alcohol Use and Dependence Investigators. The Journal of Neuroscience, Product: PathwayAssist |
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Transcriptional Profiling of the Human Monocyte-to-Macrophage Differentiation and Polarization: New Molecules and Patterns of Gene Expression Fernando O. Martinez, Siamon Gordon, Massimo Locati, and Alberto Mantovani J. Immunol., Nov 2006; 177: 7303 - 7311, Product: Pathway Studio |
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Peroxisome Proliferator-Activated Receptor Is Highly Expressed in Pancreatic Cancer and Is Associated With Shorter Overall Survival Times Glen Kristiansen, Juliane Jacob, Ann-Christin Buckendahl, Robert Grtzmann, Ingo Alldinger, Bence Sipos, Gnter Klppel, Marcus Bahra, Jan M. Langrehr, Peter Neuhaus, Manfred Dietel, and Christian Pilarsky Clin. Cancer Res., Nov 2006; 12: 6444 - 6451., Product: PathwayAssist |
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Essential role of Jun family transcription factors in PU.1 knockdown induced leukemic stem cells Ulrich Steidl, Frank Rosenbauer, Roel G W Verhaak, Xuesong Gu, Alexander Ebralidze, Hasan H Otu, Steffen Klippel, Christian Steidl, Ingmar Bruns, Daniel B Costa, Katharina Wagner, Manuel Aivado, Guido Kobbe, Peter J M Valk, Emmanuelle Passegu, Towia A Libermann, Ruud Delwel, Daniel G Tenen Nature Genetics 38, 1269 - 1277 (01 Nov 2006), Product: Pathway Studio |
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Molecular Network and Chromosomal Clustering of Genes Involved in Synaptic Plasticity in the Hippocampus Chang Sin Park, Ruomu Gong, Joshua Stuart, and Shao-Jun Tang J. Biol. Chem, Product: Pathway Studio |
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Time dependent rescue of gene expression by androgens in the mouse proximal caput epididymidis (PC-1) cell line after androgen withdrawal Shayesta Seenundun and Bernard Robaire Endocrinology, Product: Pathway Studio |
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Characterization of differential gene expression profiles in diabetic embryopathy using DNA microarray analysis. Reece EA, Ji I, Wu YK, Zhao Z. Am J Obstet Gynecol. 2006 Oct;195(4):1075-80., Product: Pathway Studio |
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Identification of molecular markers and signaling pathway in endometrial cancer in Hong Kong Chinese women by genome-wide gene expression profiling Y F Wong, T H Cheung, K W K Lo, S F Yim, N S S Siu, S C S Chan, T W F Ho, K W Y Wong, M Y Yu, V W Wang, C Li, G J Gardner, T Bonome, W B Johnson, D I Smith, T K H Chung, M J Birrer Oncogene. 2006 Oct 16, Product: Pathway Studio |
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Candidate genes, pathways and mechanisms for alcoholism: an expanded convergent functional genomics approach Z A Rodd, B A Bertsch, W N Strother, H Le-Niculescu, Y Balaraman, E Hayden, R E Jerome, L Lumeng, J I Nurnberger, H J Edenberg, W J McBride, A B Niculescu The Pharmacogenomics Journal (10 Oct 2006), Product: Pathway Studio |
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Search for low penetrance alleles for colorectal cancer through a scan of 1,467 non-synonymous SNPs in 2,575 cases and 2,707 controls with validation by kin-cohort analysis of 14,704 first-degree relatives Webb EL, Rudd MF, Sellick GS, El Galta R, Bethke L, Wood W, Fletcher O, Penegar S, Withey L, Qureshi M, Johnson N, Tomlinson I, Gray R, Peto J, Houlston RS. Hum Mol Genet, Product: PathwayAssist |
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Exercise affects the gene expression profiles of human white blood cells Buettner P, Mosig S, Lechtermann A, Funke H, Mooren FC. J Appl Physiol., Product: PathwayAssist |
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Cluster-based network model for time-course gene expression data Inoue LY, Neira M, Nelson C, Gleave M, Etzioni R. Biostatistics, Product: Pathway Studio |
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Transgenerational Epigenetic Imprinting of the Male Germ-Line by Endocrine Disruptor Exposure During Gonadal Sex Determination Hung-Shu Chang, Matthew D. Anway, Stephen S. Rekow, and Michael K. Skinner Endocrinology, Product: PathwayAssist |
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Systems Biology of AGC Kinases in Fungi Alex Sobko Sci. STKE, Product: Pathway Studio |
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Identification and pathway analysis of immediate hyperosmotic stress responsive molecular mechanisms in tilapia (Oreochromis mossambicus) gill Diego F. Fiola, Stephanie Y. Chana and Dietmar Kltz Comparative Biochemistry and Physiology Part D: Genomics and Proteomics V1(3):344-356, Product: Pathway Studio |
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Cigarette smoke condensate induces cytochromes P450 and aldo-keto reductases in oral cancer cells Nagaraj, N.S. Beckers, S. Mensah, J.K. Waigel, S. Vigneswaran, N. Zacharias, W. Toxicology Letters, Aug 2006, Product: Pathway Studio |
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Molecular network and chromosomal clustering of genes involved in synaptic plasticity in the hippocampus Chang Sin Park, Ruomu Gong, Joshua Stuart, and Shao-Jun Tang J. Biol. Chem., Jul 2006; 10.1074/jbc.M605876200., Product: PathwayAssist |
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BiologicalNetworks: visualization and analysis tool for systems biology Michael Baitaluk, Mayya Sedova, Animesh Ray, and Amarnath Gupta Nucleic Acids Res., Jul 2006; 34: W466 - W471., Product: PathwayAssist |
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Intrinsic disorder in transcription factors Jiangang Liu et al Biochemistry, Jun 2006 |
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Targeting transcription factors in cell regulation. Anton Yuryev Expert Opinion on Therapeutic Targets, Product: Pathway Studio, Topic: Applications of pathway analysis |
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Characterization of cell-type specific profiles in tissues and isolated cells from squamous cell carcinomas of the lung Lesleyann Hawthorn, Leighton Stein, Jenniffer Panzarella, Gregory M. Loewen and Heinz Baumann Lung Cancer, 04, 2006, Product: Pathway Studio |
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Signatures of human regulatory T cells: an encounter with old friends and new players. Pfoertner S, Jeron A, Probst-Kepper M, Guzman CA, Hansen W, Westendorf AM, Toepfer T, Schrader AJ, Franzke A, Buer J, Geffers R Genome Biol. 2006 Jun 12;7(7):, Product: Pathway Studio |
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Transcriptional Signatures of Cellular Plasticity in Mice Lacking the {alpha}1 Subunit of GABA-A Receptors Igor Ponomarev, Rajani Maiya, Mark T. Harnett, Gwen L. Schafer, Andrey E. Ryabinin, Yuri A. Blednov, Hitoshi Morikawa, Stephen L. Boehm, II, Gregg E. Homanics, Ari Berman, Kerrie H. Lodowski, Susan E. Bergeson, and R. Adron Harris J. Neurosci., May 2006; 26: 5673 - 5683, Product: PathwayAssist |
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Bioinformatics Models In Drug Abuse And NeuroAIDS: Using And Developing Databases Shapshak Paul, Robert Duncan, Jadwiga Turchan, Avindra Nath, Alireza Minagar, Pandjassarame Kangueane, Wade Davis, Francesco Chiappelli, Fatten Elkomy, Raman Seth, Toni Kazic BIOINFORMATION, Product: Pathway Studio |
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Gene chromosomal organization and expression in cultured human neurons exposed to cocaine and HIV-1 proteins gp120 and tat: drug abuse and NeuroAIDS. Shapshak P, Duncan R, Nath A, Turchan J, Pandjassarame K, Rodriguez H, Duran EM, Ziegler F, Amaro E, Lewis A, Rodriguez A, Minagar A, Davis W, Seth R, Elkomy FF, Chiappelli F, Kazic T. Front Biosci., Product: Pathway Studio |
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A novel prognostic subclass of hepatocellular carcinoma derived from hepatic stem cells. Lee, J-S., Heo, J., Libbrecht, L., Chu, I-S., Kaposi-Novak, P., Calvisi, D. C., Mikaelyan, A., Roberts, L. R., Demetris, A. J., Sun, Z., Nevens, F., Roskams, T., and Thorgeirsson, S. S. Nature Medicine 12(4):410-416, Product: Pathway Studio |
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Variants in the ATM-BRCA2-CHEK2 axis predispose to chronic lymphocytic leukaemia Rudd MF, Sellick GS, Webb EL, Catovsky D, Houlston RS. Blood. 2006 Mar 30, Product: PathwayAssist |
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Quantitative phosphotyrosine proteomics of EphB2 signaling by stable isotope labeling with amino acids in cell culture (SILAC). Zhang G, Spellman DS, Skolnik EY, Neubert TA. J Proteome Res. 2006 Mar;5(3):581-8., Product: Pathway Studio |
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An effective structure learning method for constructing gene networks Xue-wen Chen, Gopalakrishna Anantha, and Xinkun Wang Bioinformatics, Product: PathwayAssist |
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Gene Expression Profiling Reveals the Profound Up-regulation of Hypoxia-Responsive Genes in Primary Human Astrocytes S. M Mense, A. Sengupta, M. Zhou, C. Lan, G. Bentsman, D. J Volsky, and L. Zhang Physiol. Genomics (February 28, 2006)., Product: PathwayAssist |
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A Pathway Analysis of Poly (I:C)-Induced Global Gene Expression Change in Human Peripheral Blood Mononuclear Cells Huang CC, Duffy KE, San Mateo LR, Amegadzie BY, Sarisky RT, Mbow ML. Physiol Genomics. 2006 Mar 22, Product: PathwayAssist |
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Targeted disruption of glycerol kinase gene in mice: expression analysis in liver shows alterations in network partners related to glycerol kinase activity Nicole K. MacLennan, Lola Rahib, Cynthia Shin, Zixing Fang, Steve Horvath, Jason Dean, James C. Liao, Edward R.B. McCabe, and Katrina M. Dipple Hum. Mol. Genet., Feb 2006; 15: 405 - 415., Product: PathwayAssist |
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PathSys: integrating molecular interaction graphs for systems biology Baitaluk, Michael Qian, Xufei Godbole, Shubhada Raval, Alpan Ray, Animesh Gupta, Amarnath BMC Bioinformatics, Feb 2006, Product: Pathway Studio |
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The neuroprotective WldS gene regulates expression of PTTG1 and erythroid differentiation regulator 1-like gene in mice and human cells Gillingwater TH, Wishart TM, Chen PE, Haley JE, Robertson K, MacDonald SH, Middleton S, Wawrowski K, Shipston MJ, Melmed S, Wyllie DJ, Skehel PA, Coleman MP, Ribchester RR. Hum Mol Genet. 2006 Feb 15;15(4):625-35., Product: PathwayAssist |
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Microarray Analysis of Immobilization Stress Triggered Changes in Gene Expression in Rat Adrenal Medulla Esther Louise Sabban, Xiaoping Liu, Richard Kvetnansky, and Lidia I Serova FASEB J, Product: PathwayAssist |
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Pathway Analysis in Drug Development Azat Badretdinov, Anton Yuryev Pharma & Bio Ingridients March 2006, Product: Pathway Studio, Topic: Applications of pathway analysis |
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Automatic pathway building in biological association networks Anton Yuryev, Zufar Mulyukov, Ekaterina Kotelnikova, Sergei Maslov, Sergei Egorov, Alexander Nikitin, Nikolai Daraselia and Ilya Mazo BMC Bioinformatics 2006, 7:171, Product: Pathway Studio, Topic: Pathways and function |
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Androgens Regulate the Immune/Inflammatory Response and Cell Survival Pathways in Rat Ventral Prostate Epithelial Cells A. J. Asirvatham, M. Schmidt, B. Gao, and J. Chaudhary Endocrinology, Jan 2006; 147: 257 - 271., Product: PathwayAssist |
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WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data Yi, Ming Horton, Jay D. Cohen, Jonathan C. Hobbs, Helen H. Stephens, Robert M. BMC Bioinformatics, Jan 2006, Product: Pathway Studio |
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InCeP: Intracellular Pathway Based on mKIAA Protein-Protein Interactions Masatoshi Murakami, Kiyo Shimada, Makoto Kawai, and Hisashi Koga DNA Res, Jan 2006; 10.1093/dnares/dsi014., Product: PathwayAssist |
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Sparse Multitask Regression for Identifying Common Mechanism of Response to Therapeutic Targets Kai Zhang, Joe W. Gray, and Bahram Parvin Bioinformatics, 2005 |
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Binding properties and evolution of homodimers in protein-protein interaction networks Ispolatov, Iaroslav; Yuryev, Anton; Mazo, Ilya; Maslov, Sergei Nucleic Acids Research 2005 33(11):3629-3635, Product: PathwayAssist, Topic: Network evolution |
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Gene expression profiling in INS-1 cells overexpressing thioredoxin-interacting protein. Minn AH, Pise-Masison CA, Radonovich M, Brady JN, Wang P, Kendziorski C, Shalev A. Biochem Biophys Res Commun. 2005 Oct 28;336(3):770-8., Product: Pathway Studio |
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Analysis off Estrogen Agonism and Antagonism of Tamoxifen, Raloxifene, and ICI182780 in Endometrial Cancer Cells: A Putative Role for the Epidermal Growth Factor Receptor Ligand Amphiregulin Susanne C.J.P. Gielen, Curt W. Burger, Liesbeth C.M. Khne, Payman Hanifi-Moghaddam, and Leen J. Blok Journal of the Society for Gynecologic Investigation, Product: PathwayAssist |
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Nova regulates brain-specific splicing to shape the synapse Ule J, Ule A, Spencer J, Williams A, Hu JS, Cline M, Wang H, Clark T, Fraser C, Ruggiu M, Zeeberg BR, Kane D, Weinstein JN, Blume J, Darnell RB. Nature Genetics 37, 844-852, Product: Pathway Studio |
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Oncogenic H-Ras Up-regulates Expression of Ku80 to Protect Cells from -Ray Irradiation in NIH3T3 Cells In-Youb Chang, Cha-Kyung Youn, Hong-Beum Kim, Mi-Hwa Kim, Hyun-Ju Cho, Young Yoon, Yun-Sil Lee, Myung-Hee Chung, and Ho Jin You Cancer Res., Aug 2005; 65: 6811 - 6819., Product: PathwayAssist |
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Extension of the Visualization Tool MapMan to Allow Statistical Analysis of Arrays, Display of Coresponding Genes, and Comparison with Known Responses Bjrn Usadel, Axel Nagel, Oliver Thimm, Henning Redestig, Oliver E. Blaesing, Natalia Palacios-Rojas, Joachim Selbig, Jan Hannemann, Maria Conceio Piques, Dirk Steinhauser, Wolf-Rdiger Scheible, Yves Gibon, Rosa Morcuende, Daniel Weicht, Svenja Meyer, and Mark Stitt Plant Physiology, Jul 2005; 138: 1195 - 1204., Product: PathwayAssist |
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Sp1 and NFkappaB pathways are regulated in brain in response to acute and chronic ethanol. Rulten SL, Ripley TL, Hunt CL, Stephens DN, Mayne LV. Genes, Brain and Behavior, 2006, Product: Pathway Studio |
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Identification of GAS-dependent interferon-sensitive target genes whose transcription is STAT2-dependent but ISGF3-independent Melissa M Brierley, Katie L Marchington, Igor Jurisica and Eleanor N Fish FEBS Journal 273 (2006) 1569-1581, Product: Pathway Studio |
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Duplication-divergence model of protein interaction network I.Ispolatov, P.L.Krapivsky, A.Yuryev Phys. Rev. E 71, 061911 (2005), Product: Pathway Studio, Topic: Network evolution |
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Transcriptional Basis for Exercise Limitation in Male eNOS Knockout Mice with Age: Heart Failure and the Fetal Phenotype Caroline Ojaimi, Wei Li, Shintaro Kinugawa, Heiner Post, Anna Csiszar, Pal Pacher, Gabor Kaley, and Thomas H Hintze Am J Physiol Heart Circ Physiol, May 2005, Product: PathwayAssist |
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Persistent Nuclear Factor-Kappa-B Activation in Ucp2-/- Mice Leads to Enhanced Nitric Oxide and Inflammatory Cytokine Production Yushi Bai, Hiroki Onuma, Xu Bai, Alexander V. Medvedev, Mary Misukonis, J. Brice Weinberg, Wenhong Cao, Jacques Robidoux, Lisa M. Floering, Kiefer W. Daniel, and Sheila Collins J. Biol. Chem., May 2005, Product: PathwayAssist |
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Comparative gene expression profile of mouse carotid body and adrenal medulla under physiological hypoxia Maria D Ganfornina, M. Teresa Prez-Garca, Gabriel Gutierrez, Eduardo Miguel-Velado, Jos Ramn Lpez-Lpez, Antonio Marin, Diego Sanchez, and Constancio Gonzalez J. Physiol., May 2005, Product: PathwayAssist |
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Pathway analysis of whole genomic expression profiles of colorectal cancer biopsy samples Orsolya Galamb, Ferenc Sipos, Sndor Spisk, Bla Molnr, Andrea Ladnyi, and Zsolt Tulassay AACR Meeting Abstracts, Product: PathwayAssist |
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Alterations of apoptosis in a rhabdomyosarcoma patient with Li-Fraumeni syndrome, familial syndactyly, and absence of germline p53 mutation. Malgorzata Pienkowska, Rika Tsuchida, Elizabeth Sexsmith, Jane Bayani, Gloria Lim, Jeremy A. Squire, and David Malkin AACR Meeting Abstracts, Product: PathwayAssist |
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Identification of genes related to cisplatin-resistance in four isogenic human ovarian cancer cell lines, which only differ in their degree of cisplatin resistance Anne P. G. Crijns, Gert Jan Meersma, Steven De Jong, Gerard J. Te Meerman, Frans Gerbens, Robert M. W. Hofstra, Elisabeth G. E. De Vries and Ate G. J. Van der Zee AACR Meeting Abstracts, Product: PathwayAssist |
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The links between axin and carcinogenesis S Salahshor and J R Woodgett J. Clin. Pathol., Mar 2005; 58: 225 236, Product: PathwayAssist |
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Identifying Local Gene Expression Patterns in Biomolecular Networks A. Y. Sivachenko, A. Yuryev, N. Daraselia, I. Mazo IEEE Computational Systems Bioinformatics Conference, Aug. 8-11, 2005, Product: Pathway Studio, Topic: Gene expression analysis |
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Cliques and duplication-divergence network growth Ispolatov, I ; Krapivsky, P L ; Mazo, I ; Yuryev, A New J.Phys. 7(2005) 145, Product: Pathway Studio, Topic: Network evolution |
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Finding mesoscopic communities in sparse networks I. Ispolatov, I. Mazo, and A. Yuryev J. Stat. Mech. (2006) P09014, Product: Pathway Studio, Topic: Pathways and fucntion |
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Alterations in the Ovarian Transcriptome During Primordial Follicle Assembly and Development Phillip R. Kezele, Jacquelyn M. Ague, Eric Nilsson, and Michael K. Skinner Biol Reprod, Jan 2005, Product: PathwayAssist |
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Osteocyte and Osteoblast Cell Models have Unique Patterns of Gene Expression and Responses to Mechanical Loading Wuchen Yang, Marie A. Harris, Dayong Guo, Lynda F. Bonewald, Stephen E. Harris Department of Periodontics, University of Texas Health Science Center at San Antonio, School of Dentistry, Product: Pathway Studio |
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Microarray analysis of androgen-regulated gene expression in testis: the use of the androgen-binding protein (ABP)-transgenic mouse as a model. Petrusz P, Jeyaraj DA, Grossman G. Reprod Biol Endocrinol. 2005; 3: 70., Product: Pathway Studio |
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Identification of mouse retinal genes differentially regulated by dim and bright cyclic light rearing Hu Huang, Mark Barton Frank, Igor Dozmorov, Wei Cao, Craig Cadwell, Nick Knowlton, Michael Centola and Robert E. Anderson Experimental Eye Research, 2005, Product: Pathway Studio |
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Global Genomic Approaches to the Iron-Regulated Proteome Ying Liu, Zvezdana Popovich and Douglas M. Templeton Ann. Clin. Lab. Sci., Jan 2005; 35: 230 - 239., Product: PathwayAssist |
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Visualizing biological pathways: requirements analysis, systems evaluation and research agenda Purvi Saraiya, Chris North, Karen Duca Information Visualization (2005), 1 15, Product: Pathway Studio |
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Cancer-related pathway collection Tetsuya Shiraishi Sony Computer Science Laboratories, Product: Pathway Studio |
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Impact of Adenoviral Transduction With SREBP1c or AMPK on Pancreatic Islet Gene Expression Profile: Analysis With Oligonucleotide Microarrays Frederique Diraison, Efthimios Motakis, Laura E. Parton, Guy P. Nason, Isabelle Leclerc, and Guy A. Rutter Diabetes, Dec 2004, Product: PathwayAssist |
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Identification of the CREB-binding Protein/p300-interacting Protein CITED2 as a Peroxisome Proliferator-activated Receptor a Coregulator Eric S. Tien, John W. Davis, and John P. Vanden Heuvel J. Biol. Chem., Vol. 279, Issue 23, 24053-24063, June 4, 2004., Product: PathwayAssist |
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Making Mechanistic Connections between Cell Signaling Pathways and Pathological Endpoints Myrtle A. Davis Toxicologic Pathology,Volume 32, Supplement 1 / March-April 2004: 131 135, Product: Pathway Studio |
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Whole genome expression profiling of advance stage papillary serous ovarian cancer reveals activated pathways. Donninger H, Bonome T, Radonovich M, Pise-Masison CA, Brady J, Shih JH, Barrett JC, Birrer MJ. Oncogene. 2004 Sep 13, Product: Pathway Studio |
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FGF-2 enhances the mitotic and chondrogenic potentials of human adult bone marrow-derived mesenchymal stem cells Luis A. Solchaga, Kitsie Penick, John D. Porter, Victor M.Goldberg, Arnold I. Caplan, Jean F. Welter Journal of Cellular Physiology Volume 203, Issue 2, Pages 398 - 409, Nov. 2004, Product: Pathway Studio |
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Long term modulation of gene expression in the mouse eye following laser photocoagulation N. Binz, K. Simpson, W. Y. Shen, C. M. Lai, T. Speed and E.P. Rakoczy Invest Ophthalmol Vis Sci 2004; 45: E-Abstract 2504., Product: PathwayAssist |
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Can Theoretical Analysis of Cellular Regulatory Networks Improve Drug Target Identification and Validation? Burkhard Haefner BUSINESS BRIEFING: FUTURE Drug discovery 2004, Product: Pathway Studio |
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Microarray Data Analysis and Pathway Visualization of Murine Cochlear Ear Hair Cell Differentiation Eric S. Allen & Kris Barbee Submitted on December 4th, 2003, Product: Pathway Studio |
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Pathway studio the analysis and navigation of molecular networks Alexander Nikitin, Sergei Egorov, Nikolai Daraselia, and Ilya Mazo Bioinformatics. 2003 Nov 1;19(16):2155-7, Product: PathwayAssist, Pathway Studio, Topic: Pathway Studio |
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Phospholipidosis Induced by PPAR Signaling in Human Bronchial Epithelial (BEAS-2B) Cells Exposed to Amiodarone Mee Song, Youn-Jung Kim, and Jae-Chun Ryu Toxicol. Sci. |
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Pathway Analysis in Microarray Data: A Comparison of Two Different Pathway Analysis Devices in the Same Data Set Bogner, Viktoria et al SHOCK |
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Comprehensive Analysis of Alternative Splicing and Functionality in Neuronal Differentiation of P19 Cells Hitoshi Suzuki et al PLoS One |
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Metabolic and Genomic Response to Dietary Isocaloric Protein Restriction in the Rat Satish C. Kalhan et alSatish C. Kalhan, Sonal O. Uppal, Jillian L. Moorman, Carole Bennett, Lourdes L. Gruca, Prabhu S. Parimi, Srinivasan Dasarathy, David Serre, and Richard W. Hanson J. Biol. Chem. |
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Growth Hormone Receptor Deficiency Is Associated with a Major Reduction in Pro-Aging Signaling, Cancer, and Diabetes in Humans Jaime Guevara-Aguirre, Priya Balasubramanian, Marco Guevara-Aguirre, Min Wei, Federica Madia, Chia-Wei Cheng, David Hwang, Alejandro Martin-Montalvo, Jannette Saavedra, Sue Ingles, Rafael de Cabo, Pinchas Cohen, and Valter D. Longo Science Translational Medicine |
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Activation of cytokine expression occurs through the TNF/NF-B-mediated pathway in birnavirus-infected cells Wang WL, Liu W, Gong HY, Hong JR, Lin CC, Wu JL. Fish Shellfish Immunol. |
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Down-regulation of intra-hepatic T-cell signaling associated with GB virus C in a HCV/HIV co-infected group with reduced liver disease Berzsenyi MD, Woollard DJ, McLean CA, Preiss S, Perreau VM, Beard MR, Bowden DS, Cowie BC, Li S, Mijch AM, Roberts SK. J Hepatol. |
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Stage-Specific Expression of TNF Regulates Bad/Bid-Mediated Apoptosis and RIP1/ROS-Mediated Secondary Necrosis in Birnavirus-Infected Fish Cells Wei-Lun Wang et al PLoS One |
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Evaluation of the effects of naproxen in human colon polyp cells using gene expression and pathway analysis Eugene Elmore, Vernon E. Steele, and John L. Redpath Cancer Prevention Research |
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Aging Causes Alterations in the Base Excision Repair Pathway in Pachytene Spermatocytes in the Brown Norway Rat Catriona Paul , Makoto Nagano , and Bernard Robaire Biol Reprod |
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Transcriptome Analysis Indicates an Enhanced Activation of Adaptive and Innate Immunity by Chlamydia-Infected Murine Epithelial Cells Treated with Interferon Katalin Burian, Valeria Endresz, Judit Deak, Zsolt Kormanyos, Attila Pal, David Nelson, and Dezso P. Virok The Journal of Infectious Disease |
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Tracheal occlusion modulates the gene expression profile of the medial thalamus in anesthetized rats Vipa Bernhardt, Natlia Garcia-Reyero, Andrea Vovk, Nancy Denslow, and Paul W. Davenport J Appl Physiol |
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Analysis of EGFR signaling pathway in nasopharyngeal carcinoma cells by quantitative phosphoproteomics L Ruan, XH Li, XX Wan, H Yi, C Li, MY Li, PF Zhang, GQ Zeng, JQ Qu, QY He, JH Li, Y Chen, ZC Chen, and ZQ Xiao Proteome Sci |
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Cortisol is a potent modulator of lipopolysaccharide-induced interferon signaling in macrophages Anja M. Billing, Fred Fack, Jonathan D. Turner, and Claude P. Muller Innate Immunity |
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Estrogen Receptor Induces Antiinflammatory and Antitumorigenic Networks in Colon Cancer Cells Karin Edvardsson, Anders Strm, Philip Jonsson, Jan-ke Gustafsson, and Cecilia Williams Mol. Endocrinol. |
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miR-33a/b contribute to the regulation of fatty acid metabolism and insulin signaling Alberto Dvalos et al PNAS |
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Pathway analysis of primary human non-small cell lung cancer (NSCLC) N. Daraselia, Y. Wang, A. Budoff, A. Lituev, O. Potapova, J. Monforte, and V. Ossovskaya ASCO Meeting Abstracts |
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Identification of new autoantibody specificities directed at proteins involved in the transforming growth factor beta pathway in patients with systemic sclerosis G Bussone, H Dib, MC Tamby, C Broussard, C Federici, G Woimant, L Camoin, L Guillevin, and L Mouthon Arthritis Res Ther |
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Cardiac ATP-sensitive K+ channel associates with the glycolytic enzyme complex Miyoun Hong, Eirini Kefaloyianni, Li Bao, Brian Malester, Diane Delaroche, Thomas A. Neubert, and William A. Coetzee FASEB J |
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Two-tiered Approach Identifies a Network of Cancer and Liver Disease-related Genes Regulated by miR-122 Daniel R. Boutz, Patrick J. Collins, Uthra Suresh, Mingzhu Lu, Cristina M. Ramrez, Carlos Fernndez-Hernando, Yufei Huang, Raquel de Sousa Abreu, Shu-Yun Le, Bruce A. Shapiro, Angela M. Liu, John M. Luk, Shelley Force Aldred, Nathan D. Trinklein, Edward M. Marcotte, and Luiz O. F. Penalva J. Biol. Chem., May 2011; 286: 18066 - 18078 |
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Serum Autoantibodies Following Laser Induced Retinal Injury in Rabbits Sarah E. Scott, Rachida Bouhenni, Anthony Chomyk, Jayaprakash Patil, Michael Hart, Hiroshi Nakamura, and Deepak P. Edward Invest. Ophthalmol. Vis. Sci., Apr 2011; 52: 2919. |
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The Impact of MicroRNAs on Nr2e3 Associated Retinal Disease Austin S. Jelcick, James Reinecke, Yang Yuan, and Neena B. Haider Invest. Ophthalmol. Vis. Sci., Apr 2011; 52: 5416. |
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The Rat Genome Database Pathway Portal Victoria Petri, Mary Shimoyama, G. Thomas Hayman, Jennifer R. Smith, Marek Tutaj, Jeff de Pons, Melinda R. Dwinell, Diane H. Munzenmaier, Simon N. Twigger, Howard J. Jacob, and RGD Team Database, Apr 2011; 2011: bar010. |
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PITX2c Is Expressed in the Adult Left Atrium, and Reducing Pitx2c Expression Promotes Atrial Fibrillation Inducibility and Complex Changes in Gene Expression Paulus Kirchhof, Peter C. Kahr, Sven Kaese, Ilaria Piccini, Ismail Vokshi, Hans-Heinrich Scheld, Heinrich Rotering, Lisa Fortmueller, Sandra Laakmann, Sander Verheule, Ulrich Schotten, Larissa Fabritz, and Nigel A. Brown Circ Cardiovasc Genet, Apr 2011; 4: 123 - 133 |
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Pathway analysis in microarray data: a comparison of two different pathway analysis devices in the same data set. V Bogner, BA Leidel, KG Kanz, W Mutschler, EA Neugebauer, and P Biberthaler Shock, Mar 2011; 35(3): 245-51. |
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Metabolic and Genomic Response to Dietary Isocaloric Protein Restriction in the Rat Satish C. Kalhan, Sonal O. Uppal, Jillian L. Moorman, Carole Bennett, Lourdes L. Gruca, Prabhu S. Parimi, Srinivasan Dasarathy, David Serre, and Richard W. Hanson J. Biol. Chem. |
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Global response of Plasmodium falciparum to hyperoxia: a combined transcriptomic and proteomic approach Torrentino-Madamet M, Almras L, Desplans J, Le Priol Y, Belghazi M, Pophillat M, Fourquet P, Jammes Y, Parzy D. Malar J. 2011 Jan 11;10:4 |
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Induction of Metastatic Gastric Cancer by Peroxisome Proliferator-Activated Receptor Activation Claire B. Pollock et al PPAR Res. |
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Aging Causes Alterations in the Base Excision Repair Pathway in Pachytene Spermatocytes in the Brown Norway Rat Catriona Paul, Makoto Nagano , and Bernard Robaire Biol Reprod |
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Ariadne s ChemEffect and Pathway Studio knowledge base Anton Yuryev, Ekaterina Kotelnikova & Nikolai Daraselia Opinion on Drug Discovery |
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In silico pathway analysis: the final frontier towards completely rational drug design Yuryev A. Expert Opinion on Drug Discovery |
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Immune and Inflammatory Gene Expression Profiles of Chronological(Intrinsic) Skin Aging and Photo-Aging M K Robinson et al 21st World Congress of Dermatology in Buenos Aires, Argentina |
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Rhythmic Diel Pattern of Gene Expression in Juvenile Maize Leaf Maciej JoDczyk, Alicja Sobkowiak, PaweB Siedlecki, PrzemysBaw Biecek, Joanna Trzcinska-Danielewicz, Jerzy Tiuryn, Jan Fronk, PaweB SowiDski PLoS One. 2011; 6(8): e23628 |
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Ginkgo may prevent genetic-associated ovarian cancer risk: multiple biomarkers and anticancer pathways induced by ginkgolide B in BRCA1-mutant ovarian epithelial cells W Jiang, W Qiu, Y Wang, Q Cong, D Edwards, B Ye, and C Xu Eur J Cancer Prev |
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Integrated Transcriptional and Proteomic Analysis with In Vitro Biochemical Assay Reveal the Important Role of CYP3A46 in T-2 Toxin Hydroxylation in Porcine Primary Hepatocytes Jianshe Wang et al Mol. Cell. Proteomics |
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Candidate gene association analysis of acute lymphoblastic leukemia identifies new susceptibility locus at 11p15 (LMO1) Joke Beuten, Jonathan A.L. Gelfond, Duangjai Piwkham, Brad H. Pollock, Naomi J. Winick, Anderson B. Collier, III, and Gail E. Tomlinson Carcinogenesis, Sep 2011; 32: 1349 - 1353 |
| Analysis of gene expression microarray data | Go to top | |
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Molecular signatures and new candidates to target the pathogenesis of rheumatoid arthritis U. Ungethuem, T. Haeupl, H. Witt, D, et al Physiol Genomics. 2010; 42A(4): p. 267-282 |
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Role of NFKB2 on the early myeloid differentiation of CD34+ hematopoietic stem/progenitor cells. De Molfetta GA, Lucola Zanette D, Alexandre Panepucci R, Dos Santos AR, da Silva WA Jr, Antonio Zago M. Differentiation. 2010 Nov-Dec;80(4-5):195-203. Epub 2010 Aug 14 |
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Insulin-Like Growth Factor I Suppresses Bone Morphogenetic Protein Signaling in Prostate Cancer Cells by Activating mTOR Signaling Reema S. Wahdan-Alaswad, Kyung Song, Tracy L. Krebs, Dorjee T.N. Shola, Jose A. Gomez, Shigemi Matsuyama, and David Danielpour Cancer Res. 2010; 70(22): p. 9106-9117 |
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Gene expression profiling in the stress control brain region hypothalamic paraventricular nucleus reveals a novel gene network including amyloid beta precursor protein. Tsolakidou A, Czibere L, Ptz B, Trmbach D, Panhuysen M, Deussing JM, Wurst W, Sillaber I, Landgraf R, Holsboer F, Rein T. BMC Genomics. 2010 Oct 8;11:546. |
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Tilapia Hepcidin 2-3 Peptide Modulates Lipopolysaccharide-induced Cytokines and Inhibits Tumor Necrosis Factor- through Cyclooxygenase-2 and Phosphodiesterase 4D Venugopal Rajanbabu, Chieh-Yu Pan, Shang-Chun Lee, Wei-Ju Lin, Ching-Chun Lin, Chung-Leung Li, and Jyh-Yih Chen J. Biol. Chem. |
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Akt RSK S6 Kinase Signaling Networks Activated by Oncogenic Receptor Tyrosine Kinases Albrecht Moritz et al Sci. Signal. |
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Innate immune processes are sufficient for driving silicosis in mice Celine A. Beamer, Christopher T. Migliaccio, Forrest Jessop, Melanie Trapkus, Dorothy Yuan, and Andrij Holian J. Leukoc. Biol. |
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Transcriptomic analysis of patients with tetralogy of Fallot reveals the effect of chronic hypoxia on myocardial gene expression Mohamed T. Ghorbel, Myriam Cherif, Emma Jenkins, Amir Mokhtari, Damien Kenny, Gianni D. Angelini, and Massimo Caputo J. Thorac. Cardiovasc. Surg. |
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Differential Regulation of Mitogen-Activated Protein Kinase Pathways by Acetaminophen and Its Nonhepatotoxic Regioisomer 3\'-Hydroxyacetanilide in TAMH Cells Brendan D. Stamper, Theo K. Bammler, Richard P. Beyer, Frederico M. Farin, and Sidney D. Nelson Toxicol. Sci. |
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JAK-STAT Signalling Pathway Proteins are Over Expressed in Arterial Human Endothelial Cells Exposed to Oxidized Low Density Lipoproteins A. Laguna-Fernandez et al Journal of Hypertension |
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Gene expression profiling and cancer-related pathways in type I endometrial carcinoma. FS Saghir, IM Rose, AZ Dali, Z Shamsuddin, AR Jamal, and NM Mokhtar Int J Gynecol Cancer 1 Jul 2010 20(5): p. 724 |
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Off-pump coronary artery bypass surgery is associated with fewer gene expression changes in the human myocardium in comparison with on-pump surgery Mohamed T. Ghorbel et al, Physiol Genomics, Jun 2010 |
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Identification of Unique Differentially Expressed Proteins in the Aqueous Humor of Patients With Primary Congenital Glaucoma (PCG) R. Bouhenni, D.P. Edward, S. Al Shahwan, J. Morales, B. Wakim ARVO 2010 presentation abstract |
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Substance P in Polymicrobial Sepsis: Molecular Fingerprint ofLung Injury in Preprotachykinin-A / Mice Akhil Hegde et al Molecular Medicine, May 2010 |
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Expression profiling of microdissected serous ovarian cancers and matched Fallopian tube identifies a gene signature of clinicopathologic importance Vinod Vathipadiekal, Karishma K. Mehra, Sunghoon Kim, Christopher P. Crum, Xian Wa, Michael J. Birrer AACR 101 presentation abstract |
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Uncovering Molecular Biomarkers That Correlate Cognitive Decline with the Changes of Hippocampus\' Gene Expression Profiles in Alzheimer\'s Disease Martn Gmez Ravetti, Osvaldo A. Rosso, Regina Berretta, Pablo Moscato PLOS One, Apr. 2010 |
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Microarray Analysis of Chick Retina/RPE/Choroid During Recovery From Form Deprivation Myopia (FDM) L. Giummarra, M. J. Murphy, M. J. Goodyear, and S. G. Crewther Invest. Ophthalmol. Vis. Sci., Apr 2010 |
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Inhibition of c-Jun N-terminal Kinase by SP600125: A cDNA Microarray Analysis Pierre Champelovier, Michele El Atifi-Borel, Jean Paul Issartel, Jean Boutonnat, Franois Berger and Daniel Seigneurin Cancer Genomics Proteomics, Mar 2010 |
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Atlas of Signaling for Interpretation of Microarray Experiments Ekaterina Kotelnikova, Natalia Ivanikova, Andrey Kalinin, Anton Yuryev, Nikolai Daraselia PLoS One., Feb. 2010 |
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The Transcriptional Programme of Human Heart Valves Reveals the Natural History of Infective Endocarditis Marie Benoit et al PLoS One. 2010 |
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Testing for mean and correlation changes in microarray experiments: an application for pathway analysis Mayer Alvo, Zhongzhu Liu, Andrew Williams, Carole Yauk BMC Bioinformatics 2010 |
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Transcriptional Profiling of the Caloric Restriction in Key Metabolic Tissues of Pigs Differing in Feed Efficiency Sender Lkhagvadorj et al Iowa State University Animal Industry Report 2010 |
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Zebrafish Spotted-Microarray for Genome-Wide Expression Profiling Experiments: Data Acquisition and Analysis Siew Hong Lam, R. Krishna Murthy Karuturi, Zhiyuan Gong Book Title: Zebrafish: Methods and Protocols, Jan 2010 |
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Reactivation of adiponectin expression in obese patients after bariatric surgery A. Katharine Hindle, Claire Edwards, Tim McCaffrey, Sidney W. Fu and Fred Brody Surgical Endoscopy, Dec. 2009 |
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A Gene Signature Predictive for Outcome in Advanced Ovarian Cancer Identifies a Survival Factor: Microfibril-Associated Glycoprotein 2 Samuel C. Mok et al Cancer Cell, Dec. 2009 |
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Gene expression profiling of the short-term adaptive response to acute caloric restriction in liver and adipose tissues of pigs differing in feed efficiency Sender Lkhagvadorj, Long Qu, Weiguo Cai, Oliver P Couture, C. Richard Barb, Gary J Hausman, Dan Nettleton, Lloyd L. Anderson, Jack C.M. Dekkers, and Christopher K Tuggle Am J Physiol Regulatory Integrative Comp Physiol, Nov. 2009 |
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Pathway Analysis in HEK 293T Cells Overexpressing HIV-1 Tat and Nucleocapsid MJ Lee and JH Park J Microbiol Biotechnol, Oct. 2009 |
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Comparative in vivo gene expression of the closely related bacteria Photorhabdus temperata and Xenorhabdus koppenhoeferi upon infection of the same insect host, Rhizotrogus majalis An R, Sreevatsan S, Grewal PS BMC Genomics, Sep. 2009 |
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Gene expression profiling in the aging ovary Eyster KM, Brannian JD. Methods Mol Biol. 2009 |
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Depletion of T-cell intracellular antigen proteins promotes cell proliferation Raquel Reyes, Jos Alcalde and Jos M Izquierdo Genome Biology, Product: Pathway Studio, ResNet |
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Pathway analysis of differentially expressed genes in patients with acute aortic dissection SA Mohamed, HH Sievers, T Hanke, D Richardt, C Schmidtke, EI Charitos, G Belge, and J Bullerdiek Biomark Insights 1 Jan 2009 4: p. 81, Product: Pathway Studio |
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Methods for interpreting lists of affected genes obtained in a DNA microarray experiment Hedegaard et al BMC Proc 1 Jan 2009 3 Suppl 4: p. S5, Product: Pathway Studio |
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The transcriptional response of Pasteurella multocida to three classes of antibiotics. B Nanduri, LA Shack, SC Burgess, and ML Lawrence BMC Genomics 1 Jan 2009 10 Suppl 2: p. S4, Product: Pathway Studio |
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Pathway results from the chicken data set using GOTM, Pathway Studio and Ingenuity softwares A Bonnet, S Lagarrigue, L Liaubet, C Robert-Granie, M Sancristobal, and G Tosser-Klopp BMC Proc 1 Jan 2009 3 Suppl 4: p. S11, Product: Pathway Studio |
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The Constitutive Active/Androstane Receptor Facilitates Unique Phenobarbital-Induced Expression Changes of Genes Involved in Key Pathways in Precancerous Liver and Liver Tumors Jennifer M. Phillips, Lyle D. Burgoon, and Jay I. Goodman Toxicol. Sci. 2009; 110(2): p. 319-333, Product: Pathway Studio |
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Gene expression responses in male fathead minnows exposed to binary mixtures of an estrogen and antiestrogen Garcia-Reyero et al BMC Genomics 2009, 10:308, Product: Pathway Studio |
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Uncovering the Arabidopsis thaliana nectary transcriptome: investigation of differential gene expression in floral nectariferous tissues Brian W Kram, Wayne W Xu and Clay J Carter BMC Plant Biology, Product: Pathway Studio |
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Zebrafish reward mutants reveal novel transcripts mediating the behavioral effects of amphetamine Webb, Katharine J, Norton, William HJ, Trmbach, Dietrich, Meijer, Annemarie H, Ninkovic, Jovica, Topp, Stefanie, Heck, Daniel, Bally-Cuif, Laure Genome Biology, Product: Pathway Studio |
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Modulation of the E2F1-Driven Cancer Cell Fate by the DNA Damage Response Machinery and Potential Novel E2F1 Targets in Osteosarcomas Liontos et al Am. J. Pathol. 2009; 175(1): p. 376-391, Product: Pathway Studio |
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Gene Expression Profiling of Lymphoblasts from Autistic and Nonaffected Sib Pairs: Altered Pathways in Neuronal Development and Steroid Biosynthesis Hu, Valerie W., Nguyen, AnhThu, Kim, Kyung Soon, Steinberg, Mara E., Sarachana, Tewarit, Scully, Michele A., Soldin, Steven J. and Lee, Norman H. PLoS ONE, Product: Pathway Studio |
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Bioinformatic Analysis Identified Upstream Transcription Factors and Indirect Regulators of Differentially Expressed Mouse Retinal Genes During Gestational Lead Exposure (GLE) W. Xiao, X. Wang, A. Giddabasappa, and D. A. Fox Invest. Ophthalmol. Vis. Sci.,Apr 2009; 50: 3995, Product: Pathway Studio |
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New Microbicidal Functions of Tracheal Glands: Defective Anti-Infectious Response toPseudomonas aeruginosain Cystic Fibrosis Bastonero S, Le Priol Y, Armand M, Bernard CS, Reynaud-Gaubert M, Olive D, Parzy D, de Bentzmann S, Capo C, Mege JL. PLoS ONE.2009;4(4): e5357, Product: Pathway Studio |
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Phenobarbital Elicits Unique, Early Changes in the Expression of Hepatic Genes that Affect Critical Pathways in Tumor-Prone B6C3F1 Mice Jennifer M. Phillips, Lyle D. Burgoon, and Jay I. Goodman Toxicol. Sci.,Jun 2009; 109: 193 - 205, Product: Pathway Studio |
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Gene expression profiling of ATL patients: compilation of disease-related genes and evidence for TCF4 involvement in BIRC5 gene expression and cell viability Cynthia A. Pise-Masison, Michael Radonovich, Kathleen Dohoney, John C. Morris, Deirdre O\'Mahony, Min-Jung Lee, Jane Trepel, Thomas A. Waldmann, John E. Janik, and John N. Brady Blood,Apr 2009; 113: 4016 - 4026, Product: Pathway Studio |
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Core Exosome-independent Roles for Rrp6 in Cell Cycle Progression Amy C. Graham, Daniel L. Kiss, and Erik D. Andrulis Mol. Biol. Cell, Apr 2009; 20: 2242 - 2253, Product: Pathway Studio |
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Microarray gene expression profiles of fasting induced changes in liver and adipose tissues of pigs expressing the melanocortin-4 receptor D298N variant Sender Lkhagvadorj, Long Qu, Weiguo Cai, Oliver P Couture, C Richard Barb, Gary J Hausman, Dan Nettleton, Lloyd L. Anderson, Jack C.M. Dekkers, and Christopher K Tuggle Physiol Genomics, Apr 2009, Product: Pathway Studio |
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Central Role of c-Myc during Malignant Conversion in Human Hepatocarcinogenesis Pal Kaposi-Novak, Louis Libbrecht, Hyun Goo Woo, Yun-Han Lee, Nathaniel C. Sears, Elizabeth A. Conner, Valentina M. Factor, Tania Roskams, and Snorri S. Thorgeirsson Cancer Res., Apr 2009; 69: 2775 - 2782, Product: PathwayAssist |
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Distinct gene subsets in pterygia formation and recurrence: dissecting complex biological phenomenon using genome wide expression data Louis Tong, Jaime Chew , Henry Yang , Leonard PK Ang , Donald TH Tan and Roger W Beuerman BMC Medical Genomics, Product: Pathway Studio |
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Bladder Cancer Associated Gene Expression Signatures Identified by Profiling of Exfoliated Urothelia Charles J. Rosser, Li Liu, Yijun Sun, Patrick Villicana, Molly McCullers, Stacy Porvasnik, Paul R. Young, Alexander S. Parker, and Steve Goodison Cancer Epidemiol. Biomarkers Prev., Product: Pathway Studio, ResNet |
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Dysregulated gene expression networks in human acute myelogenous leukemia stem cells Ravindra Majeti, Michael W. Becker, Qiang Tian, Tsung-Lu Michael Lee, Xiaowei Yan, Rui Liu, Jung-Hsien Chiang, Leroy Hood, Michael F. Clarke, and Irving L. Weissman PNAS, Mar 2009; 106: 3396 - 3401., Product: Pathway Studio |
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Gene expression profiling of ATL patients: compilation of disease related genes and evidence for TCF-4 involvement in BIRC5 gene expression and cell viability Cynthia A. Pise-Masison, Michael Radonovich, Kathleen Dohoney, John C. Morris, Deirdre O\'Mahony, Min-Jung Lee, Jane Trepel, Thomas A. Waldmann, John E. Janik, and John N. Brady Blood, Product: Pathway Studio |
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Transcriptional Profiling of Human Mesenchymal Stem Cells Transduced with Reporter Genes for Imaging Wang F, Dennis JE, Awadallah A, Solchaga LA, Molter J, Kuang Y, Salem N, Lin Y, Tian H, Kolthammer JA, Kim Y, Love ZB, Gerson SL, Lee Z. Physiol Genomics,Dec 2008; 10.1152/physiolgenomics.00300.2007 |
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Microarray RNA Expression Analysis of Cerebral White Matter Lesions Reveals Changes in Multiple Functional Pathways Simpson et al Stroke,Dec 2008; 10.1161/STROKEAHA.108.529214., Product: PathwayAssist |
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Time-dependent gene expression changes in a human colon polyp cell line induced by a clinically relevant concentration of atorvastatin Eugene Elmore, Aarti Jain, Vernon Steele, and J. Leslie Redpath Cancer Prevention Research. 2008; 1(7_MeetingAbstracts): p. A133, Product: Pathway Studio |
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Interaction analyses of human monocytes co-cultured with different forms of Aspergillus fumigatus Juergen Loeffler et al J. Med. Microbiol. 2009; 58(1): p. 49-58, Product: PathwayAssist |
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Mucosal cytokine imbalance in irritable bowel syndrome John Macsharry et al Scandinavian Journal of Gastroenterology, Dec. 2008 |
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Impact of the Chemotherapy Cocktail Used to Treat Testicular Cancer on the Gene Expression Profile of Germ Cells from Male Brown-Norway Rats Delbs G,Chan D,Pakarinen P,Trasler JM,Hales BF,Robaire B. Biol Reprod, 10.1095/biolreprod.108.072108, Product: Pathway Studio, ResNet |
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Global analysis of gene expression changes during retinoic acid-induced growth arrest and differentiation of melanoma: comparison to differentially expressed genes in melanocytes vs melanoma Mary Estler, Goran Boskovic, James Denvir, Sarah Miles, Donald A Primerano and Richard M Niles BMC Genomics, Oct 2008, Product: Pathway Studio |
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Identification of a 5-Protein Biomarker Molecular Signature for Predicting Alzheimer\'s Disease Martn Gmez Ravetti, Pablo Moscato PLoS ONE 3(9): e3111, Product: Pathway Studio |
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Identification of cold-shock protein RBM3 as a possible regulator of skeletal muscle size through expression profiling Esther E. Dupont-Versteegden, Radhakrishnan Nagarajan, Marjorie L Beggs, Edward D Bearden, Pippa M Simpson, and Charlotte A. Peterson Am J Physiol Regulatory Integrative Comp Physiol, Aug 2008; 10.1152/ajpregu.90455.2008, Product: PathwayAssist |
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Hint to Biomarkers of Acute Aortic Dissection by Pathway Analysis Salah A Mohamed BCVS Conference 2008 Abstracts, Product: MedScan |
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Kruppel-like factor 5 is required for perinatal lung morphogenesis and function Huajing Wan, Fengming Luo, Susan E. Wert, Liqian Zhang, Yan Xu, Machiko Ikegami, Yutaka Maeda, Sheila M. Bell, and Jeffrey A. Whitsett Development, Aug 2008; 135: 2563 - 2572, Product: Pathway Studio |
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Data-driven Networking Reveals 5-Genes Signature for Early Detection of Lung Cancer Vladimir Kuznetsov, Sterling Thomas, Danail Bonchev bmei,pp. 413-417,2008, Product: Pathway Studio |
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Molecular mechanisms of the antiangiogenic and antitumor effects of mycophenolic acid Sophie Domhan, Stefan Muschal, Christian Schwager, Christian Morath, Ute Wirkner, Wilhelm Ansorge, Christian Maercker, Martin Zeier, Peter E. Huber, and Amir Abdollahi Mol. Cancer Ther., Jun 2008; 7: 1656 - 1668, Product: PathwayAssist |
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Transcriptomic analysis of nephrotoxicity induced by cephaloridine, a representative cephalosporin antibiotic. Rokushima M, Fujisawa K, Furukawa N, Itoh F, Yanagimoto T, Fukushima R, Araki A, Okada M, Torii M, Kato I, Ishizaki J, Omi K. Chem Res Toxicol. 2008 Jun;21(6):1186-96. Epub 2008 May 23., Product: Pathway Studio |
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Constructing disease-specific gene networks using pair-wise relevance metric: application to colon cancer identifies interleukin 8, desmin and enolase 1 as the central elements. Jiang W, Li X, Rao S, Wang L, Du L, Li C, Wu C, Wang H, Wang Y, Yang B. BMC Syst Biol. 2008 Aug 10;2:72, Product: PathwayAssist |
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A Gene Signature Predicting for Survival in Suboptimally Debulked Patients with Ovarian Cancer Tomas Bonome, Douglas A. Levine, Joanna Shih, Mike Randonovich, Cindy A. Pise-Masison, Faina Bogomolniy, Laurent Ozbun, John Brady, J. Carl Barrett, Jeff Boyd, and Michael J. Birrer Cancer Res., Jul 2008; 68: 5478 - 5486., Product: PathwayAssist |
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Cancer stem cell gene signature of ovarian tumor side populations L. Ozbun, V. Vathipadiekal, M. E. Radonovich, C. Pise-Masison, D. Saxena, P. V. Hauschka, S. C. Mok, and M. J. Birrer ASCO Meeting Abstracts, May 2008; 26: 5546., Product: Pathway Studio |
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Gene expression profile for metastatic melanoma and patient survival D. Bogunovic, D. O Neill, S. Adams, J. Wang, F. Darvishian, A. C. Pavlick, R. L. Shapiro, J. Zavadil, I. Osman, and N. Bhardwaj ASCO Meeting Abstracts, May 2008; 26: 9049, Product: PathwayAssist |
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Gene expression analysis of embryonic stem cells expressing VE-cadherin (CD144) during endothelial differentiation. Nikolova-Krstevski V, Bhasin M, Otu HH, Libermann T, Oettgen P. BMC Genomics. 2008 May 22;9:240., Product: Pathway Studio |
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Parasite burden and CD36-mediated sequestration are determinants of acute lung injury in an experimental malaria model. Lovegrove FE, Gharib SA, Pea-Castillo L, Patel SN, Ruzinski JT, Hughes TR, Liles WC, Kain KC. PLoS Pathog. 2008 May 16;4(5):e1000068, Product: Pathway Studio |
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Genomic Insights into Acute Alcohol Tolerance Wei Hu, Laura Saba, Katherina Kechris, Sanjiv V Bhave, Paula L Hoffman, and Boris Tabakoff J. Pharmacol. Exp. Ther., Jun 2008; 10.1124/jpet.108.137521, Product: PathwayAssist, ResNet |
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A copula method for modeling directional dependence of genes Kim JM, Jung YS, Sungur EA, Han KH, Park C, Sohn I. BMC Bioinformatics. 2008 May 1;9:225, Product: PathwayAssist |
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Parasite burden and CD36-mediated sequestration are determinants of acute lung injury in an experimental malaria model. Lovegrove FE, Gharib SA, Pea-Castillo L, Patel SN, Ruzinski JT, Hughes TR, Liles WC, Kain KC. PLoS Pathog. 2008 May 16;4(5):e1000068, Product: Pathway Studio |
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Gene Profiling and Patterning in the Mouse Retina During Gestational Lead Exposure (GLE) A. Giddabasappa, W. Xiao, B. Xu, S. Mukherjee, S. Chaney, M. Brooks, R. Khanna, A. Swaroop, and D. A. Fox Invest. Ophthalmol. Vis. Sci., Apr 2008; 49: 3086, Product: Pathway Studio |
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Phenotype reversion in fetal human liver epithelial cells identifies the role of an intermediate meso-endodermal stage before hepatic maturation Mari Inada, Antonia Follenzi, Kang Cheng, Manju Surana, Brigid Joseph, Daniel Benten, Sriram Bandi, Hong Qian, and Sanjeev Gupta J. Cell Sci., Apr 2008; 121: 1002 - 1013, Product: Pathway Studio |
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The first five years of the Wnt targetome Vlad, A.,Rohrs, S.,Klein-Hitpass, L.,Muller, O. Cellular Signalling, 20 (5), p.795-802, Product: Pathway Studio |
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Tumor-stroma interactions in ovarian cancer: The role of CTGF in ovarian tumor biology Goli Samimi, Tomas Bonome, Sue Ghosh, Shu-wing Ng, Samuel Mok, and Michael Birrer AACR Meeting Abstracts, Apr 2008; 2008: 5379., Product: Pathway Studio |
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Cancer stem cell gene signature identified from advanced stage papillary serous ovarian adenocarcinoma side populations Laurent Ozbun, Vinod Vathipadiekal, Michael Radonovich, Cindy Pise-Masison, Deepa Saxena, Peter Hauschka, Samuel Mok, and Michael Birrer AACR Meeting Abstracts, Apr 2008; 2008: 5005., Product: Pathway Studio |
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Gene Expression Based Recurrence Prediction of Hepatitis B Virus Related Human Hepatocellular Carcinoma Hyun Goo Woo et al Clin. Cancer Res., Apr 2008; 14: 2056 - 2064, Product: Pathway Studio |
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Intestinal tumors adapt to excess dietary iron by altering expression of lipocalin-2 and divalent metal ion transporter James Swain, Chunbiao Li, and Patrick Leahy FASEB J, Mar 2008; 22: 694.3., Product: Pathway Studio |
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Iron supplementation modulates genes involved in oxidoreductase activity, including prostaglandin-endoperoxide synthase 2 in intestinal tumors James Swain, Chunbiao Li, and Patrick Leahy FASEB J, Mar 2008; 22: 692.4, Product: Pathway Studio |
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Network of Paraventricular Nucleus Gene Expression in Angiotensin-salt Hypertension Lihui Yuan, Xia Li, Judith Sved, Alan Sved, Li Liu, and Mohan Raizada FASEB J, Mar 2008; 22: 1168.9, Product: Pathway Studio |
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Gene Expression Networks in Rostral Ventrolateral Medulla (RVLM) of Rats with Angiotensin-salt Hypertension Lihui Yuan, Xia Li, Judith Sved, Alan Sved, Mohan Raizada, and Li Liu FASEB J, Mar 2008; 22: 1168.10, Product: Pathway Studio |
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Phenotype reversion in fetal human liver epithelial cells identifies the role of an intermediate meso-endodermal stage before hepatic maturation Mari Inada, Antonia Follenzi, Kang Cheng, Manju Surana, Brigid Joseph, Daniel Benten, Sriram Bandi, Hong Qian, and Sanjeev Gupta J. Cell Sci., Mar 2008; 10.1242/jcs.019315, Product: Pathway Studio |
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Towards a pathway definition of Parkinson s disease: a complex disorder with links to cancer, diabetes and inflammation Linda B. Moran and Manuel B. Graeber Neurogenetics, Vol.9(1)2008, Product: Pathway Studio |
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IFN-beta-regulated genes show abnormal expression in therapy-nave relapsing remitting MS mononuclear cells: Gene expression analysis employing all reported protein protein interactions Ken D. Yamaguchi, Daniel L. Ruderman, Ed Croze, T. Charis Wagner, Sharlene Velichko, Anthony T. Reder, Hugh Salamon J Neuroimmunol. 2008 Feb 13, Product: Pathway Studio, ResNet |
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Bioinformatics applications for pathway analysis of microarray data Werner, T Current Opinion in Biotechnology, 19 (1), p.50-54, Product: Pathway Studio |
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Early Events in the Pathogenesis of Epithelial Ovarian Cancer Charles N. Landen, Jr, Michael J. Birrer, and Anil K. Sood J. Clin. Oncol., Jan 2008; 10.1200/JCO.2006.07.9970., Product: Pathway Studio |
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cAMP Response Element-Binding Protein-Mediated Gene Expression Increases the Intrinsic Excitability of CA1 Pyramidal Neurons Mikel Lopez de Armentia, Dragana Jancic, Roman Olivares, Juan M. Alarcon, Eric R. Kandel, and Angel Barco J. Neurosci., Dec 2007; 27: 13909 - 13918., Product: Pathway Studio |
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The tale of two domains: Proteomic and genomic analysis of SMYD2, a new histone methyltransferase Mohamed Abu-Farha, Jean-Philippe Lambert, Ashraf S. Al-Madhoun, Fred Elisma, Ilona S. Skerjanc, and Daniel Figeys Mol. Cell. Proteomics, Dec 2007; 10.1074/mcp.M700271-MCP200, Product: Pathway Studio |
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Dexamethasone Sensitizes the Neonatal Intestine to Fructose Induction of Intestinal Fructose Transporter (Slc2A5) Function Veronique Douard, Xue-Lin Cui, Patricia Soteropoulos, and Ronaldo P. Ferraris Endocrinology, Jan 2008; 149: 409 - 423, Product: PathwayAssist |
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Gene Expression in Human Hippocampus from Cocaine Abusers Identifies Genes which Regulate Extracellular Matrix Remodeling Deborah C. Mash, Jarlath ffrench-Mullen, Nikhil Adi, Yujing Qin, Andrew Buck, and John Pablo PLoS ONE. 2007; 2(11): e1187, Product: Pathway Studio |
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Microarray data analysis and mining approaches Francesca Cordero, Marco Botta, and Raffaele A. Calogero Brief Funct Genomic Proteomic, Dec 2007; 6: 265 - 281, Product: Pathway Studio |
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Gene expression and biological processes influenced by deletion of Stat3 in pulmonary type II epithelial cells Yan Xu , Machiko Ikegami , Yanhua Wang , Yohei Matsuzaki and Jeffrey A Whitsett BMC Genomics 2007, 8:455, Product: Pathway Studio |
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Vascular microarray profiling in two models of hypertension identifies caveolin-1, Rgs2 and Rgs5 as antihypertensive targets. Grayson TH, Ohms SJ, Brackenbury TD, Meaney KR, Peng K, Pittelkow YE, Wilson SR, Sandow SL, Hill CE. BMC Genomics. 2007 Nov 7;8:404., Product: Pathway Studio |
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Dexamethasone sensitizes the neonatal intestine to fructose-induction of GLUT5 transport function Veronique Douard, Xue-Lin Cui, Patricia Soteropoulos, and Ronaldo P. Ferraris Endocrinology, Oct 2007; 10.1210/en.2007-0906, Product: PathwayAssist |
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Genomic Changes in Regenerated Porcine Coronary Arterial Endothelial Cells Mary Y.K. Lee, Hung-Fat Tse, Chung-Wah Siu, Shu-Guang Zhu, Ricky Y.K. Man, and Paul M. Vanhoutte Arterioscler. Thromb. Vasc. Biol., Nov 2007; 27: 2443 - 2449, Product: PathwayAssist |
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Exposure to Arsenic at Levels Found in U.S. Drinking Water Modifies Expression in the Mouse Lung Angeline S. Andrew, Viviane Bernardo, Linda A. Warnke, Jennifer C. Davey, Thomas Hampton, Rebecca A. Mason, Jessica E.Thorpe, Michael A. Ihnat, and Joshua W. Hamilton Toxicol. Sci., Nov 2007; 100: 75 - 87, Product: Pathway Studio |
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Regulation of the gonadal transcriptome during sex determination and testis morphogenesis: comparative candidate genes Tracy M Clement, Matthew D Anway, Mehmet Uzumcu, and Michael K Skinner Reproduction, Sep 2007; 134: 455 - 472, Product: PathwayAssist |
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Candidate genes, pathways and mechanisms for alcoholism: an expanded convergent functional genomics approach Z A Rodd, B A Bertsch, W N Strother, H Le-Niculescu, Y Balaraman, E Hayden, R E Jerome, L Lumeng, J I Nurnberger, H J Edenberg, W J McBride, A B Niculescu The Pharmacogenomics Journal (2007) 7, 222 256, Product: PathwayAssist |
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Transcriptome teleonomy and scavenger lipidomics of albumin and alpha 1-acid glycoproteins: contextual genome-wide ontology enrichment as evidence for the epigenetic code? Pauli Ojala, , Sami Kilpinen, Lotta Arola, Petri Trnen, Elmar Bucher, Kalle Ojala, Kristiina Iljin, Mari Peltonen, Rolf Skotheim, Kristine Kleivi, Martti Tolvanen, Reija Autio, Pentti Somerharju, Olli Kallioniemi and Saara Laitinen Physics of Lipids, 149, p.S86-S86, Sep 2007, Product: Pathway Studio |
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Profiling Studies in Ovarian Cancer: A Review Rudolf S. N. Fehrmann, Xiang-yi Li, Ate G. J. van der Zee, Steven de Jong, Gerard J. te Meerman, Elisabeth G. E. de Vries, and Anne P. G. Crijns Oncologist, Aug 2007; 12: 960 - 966, Product: PathwayAssist |
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Big Results from Small Samples: Evaluation of Amplification Protocols for Gene Expression Profiling Agnes Viale, Juan Li, Jay Tiesman, Susan Hester, Aldo Massimi, Chandi Griffin, George Grills, Greg Khitrov, Kathryn Lilley, Kevin Knudtson, Bill Ward, Karl Kornacker, Chin-yi Chu, Herbert Auer, and Andrew I. Brooks Journal of Biomolecular Techniques, Product: PathwayAssist |
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Early gene expression profiles during intraoperative myocardial ischemia-reperfusion in cardiac surgery Sara Arab, Igor E. Konstantinov, Cathy Boscarino, Eva Cukerman, Alessandro Mori, Jia Li, Peter P. Liu, Andrew N. Redington, and John G. Coles J. Thorac. Cardiovasc. Surg., Jul 2007; 134: 74 - 81., Product: PathwayAssist |
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Induction of a unique gene expression profile in primary human hepatocytes by hepatitis C virus core, NS3 and NS5A proteins A Budhu, Y Chen, J.W. Kim, M Forgues, K Valerie, C.C. Harris, and X.W. Wang Carcinogenesis, Product: PathwayAssist |
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Transcriptional network governing the angiogenic switch in human pancreatic cancer Abdollahi A, Schwager C, Kleeff J, Esposito I, Domhan S, Peschke P, Hauser K, Hahnfeldt P, Hlatky L, Debus J, Peters JM, Friess H, Folkman J, Huber PE. Proc Natl Acad Sci U S A. 2007 Jul 24, Product: Pathway Studio |
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Exenatide blocks JAK1-STAT1 in pancreatic beta cells Couto FM, Minn AH, Pise-Masison CA, Radonovich M, Brady JN, Hanson M, Fernandez LA, Wang P, Kendziorski C, Shalev A Metabolism. 2007 Jul;56(7):915-8, Product: Pathway Studio |
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Neutrophils: the forgotten cell in JIA disease pathogenesis James N Jarvis, Kaiyu Jiang, Howard R Petty, and Michael Centola Pediatr Rheumatol Online J. 2007; 5: 13., Product: Pathway Studio |
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Use of predictive gene expression signature from advanced-stage serous papillary ovarian cancer to identify biologically relevant molecular targets for chemoresponse L. Ozbun, T. Bonome, M. Radonovich, C. Pise-Masison, J. Brady, N. Caplen, M. Johnson, S. C. Mok, and M. J. Birrer ASCO Meeting Abstracts, Product: Pathway Studio |
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Gene expression profiling of human primary astrocytes exposed to manganese chloride indicates selective effects on several functions of the cells Amitabha Sengupta, Sarah M. Mense, Changgui Lana, Mei Zhou, Rory E. Mauro, Lisa Kellerman, Galina Bentsman, David J. Volsky, Elan D. Louis, Joseph H. Graziano and Li Zhang Neurotoxicology, 28 (3), p.478-489, May 2007, Product: Pathway Studio |
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Endothelial Cells\' Activation and Apoptosis Induced by a Subset of Antibodies against Human Cytomegalovirus: Relevance to the Pathogenesis of Atherosclerosis Lunardi C, Dolcino M, Peterlana D, Bason C, Navone R, Tamassia N, Tinazzi E, Beri R, Corrocher R, Puccetti A. PLoS ONE. 2007 May 30;2:e473, Product: Pathway Studio |
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Tumor number and comparative micro-array analysis of tumor and adjacent non-tumor intestinal tissue after iron supplementation in ApcMin/+ mice James H. Swain, Adam M. Kresak, and Theresa P. Pretlow FASEB J, Apr 2007; 21: A384., Product: Pathway Studio |
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Global analysis of differentially expressed genes in androgen-independent prostate cancer Q Wei, M Li, X Fu, R Tang, Y Na, M Jiang, Y Li Prostate Cancer and Prostatic Diseases 10, 167 - 174, Product: Pathway Studio |
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Arthritis suppression by NADPH activation operates through an interferon- pathway Olofsson P, Nerstedt A, Hultqvist M, Nilsson EC, Andersson S, Bergelin A, Holmdahl R. BMC Biol. 2007 May 9;5:19, Product: Pathway Studio |
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C13-11 neovascularization in bland-white-garland syndrome A.A. Fokin, T.N. Masters, C. Gregory, F. Robicsek Interactive CardioVascular and Thoracic Surgery, 6: S1 - S172, Product: Pathway Studio |
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Identification of human cell responses to benzene and benzene metabolites Bruce Gillis, Igor M. Gavin, Zarema Arbieva, Stephen T. King, Sundararajan Jayaraman, Bellur S. Prabhakar Genomics, Product: Pathway Studio, ResNet |
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Gap junction and purinergic P2 receptor proteins as a functional unit: insights from transcriptomics. Iacobas DA, Suadicani SO, Iacobas S, Chrisman C, Cohen MA, Spray DC, Scemes E. J Membr Biol. 2007 Jun;217(1-3):83-91, Product: Pathway Studio |
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Expression changes in mouse brains following nicotine-induced seizures; the modulation of transcription factor networks Merav Kedmi and Avi Orr-Urtreger Physiol Genomics, Apr 2007; 10.1152/physiolgenomics.00288.2006, Product: Pathway Studio |
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Molecular networks in microarray analysis. Sivachenko AY, Yuryev A, Daraselia N, Mazo I. J Bioinform Comput Biol., Product: Pathway Studio, Topic: Gene expression analysis |
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Success and failure in human spermatogenesis as revealed by teratozoospermic RNAs Adrian E. Platts, David J. Dix, Hector E. Chemes, Kary E. Thompson, Robert Goodrich, John C. Rockett, Vanesa Y. Rawe, Silvina Quintana, Michael P. Diamond, Lillian F. Strader, and Stephen A. Krawetz Hum. Mol. Genet., Apr 2007; 16: 763 - 773., Product: Pathway Studio |
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Glycerol kinase deficiency alters expression of genes involved in lipid metabolism, carbohydrate metabolism, and insulin signaling Rahib L, Maclennan NK, Horvath S, Liao JC, Dipple KM. Eur J Hum Genet. 2007 Apr 4, Product: Pathway Studio |
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Highly purified CD38+ and CD38- sub-clones derived from the same chronic lymphocytic leukemia patient have distinct gene expression signatures despite their monoclonal origin C Pepper, R Ward, T T Lin, P Brennan, J Starczynski, M Musson, C Rowntree, P Bentley, K Mills, G Pratt, C Fegan Leukemia 21, 687 - 696 (01 Apr 2007), Product: Pathway Studio |
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Comparative, genome-scale transcriptional analysis of CHRF-288-11 and primary human megakaryocytic cell cultures provides novel insights into lineage-specific differentiation Peter G. Fuhrken, Chi Chen, William M. Millera, and Eleftherios T. Papoutsakis Experimental Hematology,V.35(3):476-489.e23, Product: Pathway Studio |
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The microglial gene regulatory network activated by interferon-gamma Moran, L.B.,Duke, D.C.,Graeber, M.B. Journal of Neuroimmunology, Feb 2007, Product: Pathway Studio |
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Heterologous Tissue Culture Expression Signature Predicts Human Breast Cancer Prognosis Eun Sung Park, Ju-Seog Lee, Hyun Goo Woo, Fenghuang Zhan, Joanna H. Shih, John D. Shaughnessy, Jr., and J. Frederic Mushinski PLoS ONE. 2007; 2(1): e145, Product: Pathway Studio |
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Gene Alterations Identified by Expression Profiling in Tumor-Associated Endothelial Cells from Invasive Ovarian Carcinoma Chunhua Lu, Tomas Bonome, Yang Li, Aparna A. Kamat, Liz Y. Han, Rosemarie Schmandt, Robert L. Coleman, David M. Gershenson, Robert B. Jaffe, Michael J. Birrer, and Anil K. Sood Cancer Res., Feb 2007; 67: 1757 - 1768, Product: PathwayAssist |
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Ventral Tegmental Transcriptome Response to Intermittent Nicotine Treatment and Withdrawal in BALB/cJ, C57BL/6ByJ,and Quasi-Congenic RQI Mice Csaba Vadasz, Mariko Saito, Danielle O Brien,Jiri Zavadil, Grant Morahan, Goutam Chakraborty, Ray Wang Neurochem Res (2007) 32:457 480, Product: Pathway Studio |
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Interplay of Genes Regulated by Estrogen and Diindolylmethane in Breast Cancer Cell Lines Laura Mulvey, Alamelu Chandrasekaran, Kai Liu, Sarah Lombardi, Xue-Ping Wang, Karen J Auborn, and Leslie Goodwin Mol Med. 2007 Jan Feb; 13(1-2): 69 78, Product: Pathway Studio |
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Pre- and postnatal hepatic gene expression profiles of two pig breeds differing in body composition: insight into pathways of metabolic regulation Siriluck Ponsuksili, Eduard Murani, Christina Walz, Manfred Schwerin, and Klaus Wimmers Physiol Genomics, Jan 2007; 10.1152/physiolgenomics.00178.2006, Product: PathwayAssist |
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A cassette system to study ES cell differentiation by inducible RNA interference Daniel Wegmller, Ines Raineri, Brigitte Gross, Edward J. Oakeley, and Christoph Moroni Stem Cells, Jan 2007; 10.1634/stemcells.2006-0106., Product: Pathway Studio |
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Bioinformatics analysis of the early inflammatory response in a rat thermal injury model Eric Yang, Timothy Maguire, Martin L Yarmush, Francois Berthiaume, and Ioannis P Androulakis BMC Bioinformatics. 2007; 8: 10, Product: Pathway Studio |
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Time-Dependent Rescue of Gene Expression by Androgens in the Mouse Proximal Caput Epididymidis-1 Cell Line after Androgen Withdrawal. Shayesta Seenundun and Bernard Robaire Endocrinology Vol. 148, No. 1 173-188, Product: Pathway Studio |
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Phenotypic and global gene expression profile changes between low passage and high passage MIN-6 cells Lorraine O Driscoll, Patrick Gammell, Eadaoin McKiernan, Eoin Ryan, Per Bendix Jeppesen, Sweta Rani, and Martin Clynes J. Endocrinol., Dec 2006; 191: 665 - 676, Product: PathwayAssist |
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Molecular Diagnostics in Sepsis: From Bedside to Bench T. Philip Chung et al J Am Coll Surg., Nov. 2006 |
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Systems Analysis Of Pasteurella Multocida Response To Sub-Minimum Inhibitory Concentrations Of Antibiotics Bindu Nanduri, Mark L Lawrence,Shane C Burgess Mississippi Academy Of Sciences, Product: Pathway Studio |
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Transcriptional Profiling of the Human Monocyte-to-Macrophage Differentiation and Polarization: New Molecules and Patterns of Gene Expression Fernando O. Martinez, Siamon Gordon, Massimo Locati, and Alberto Mantovani J. Immunol., Nov 2006; 177: 7303 - 7311, Product: Pathway Studio |
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Peroxisome Proliferator-Activated Receptor Is Highly Expressed in Pancreatic Cancer and Is Associated With Shorter Overall Survival Times Glen Kristiansen, Juliane Jacob, Ann-Christin Buckendahl, Robert Grtzmann, Ingo Alldinger, Bence Sipos, Gnter Klppel, Marcus Bahra, Jan M. Langrehr, Peter Neuhaus, Manfred Dietel, and Christian Pilarsky Clin. Cancer Res., Nov 2006; 12: 6444 - 6451., Product: PathwayAssist |
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Essential role of Jun family transcription factors in PU.1 knockdown induced leukemic stem cells Ulrich Steidl, Frank Rosenbauer, Roel G W Verhaak, Xuesong Gu, Alexander Ebralidze, Hasan H Otu, Steffen Klippel, Christian Steidl, Ingmar Bruns, Daniel B Costa, Katharina Wagner, Manuel Aivado, Guido Kobbe, Peter J M Valk, Emmanuelle Passegu, Towia A Libermann, Ruud Delwel, Daniel G Tenen Nature Genetics 38, 1269 - 1277 (01 Nov 2006), Product: Pathway Studio |
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Molecular Network and Chromosomal Clustering of Genes Involved in Synaptic Plasticity in the Hippocampus Chang Sin Park, Ruomu Gong, Joshua Stuart, and Shao-Jun Tang J. Biol. Chem, Product: Pathway Studio |
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Time dependent rescue of gene expression by androgens in the mouse proximal caput epididymidis (PC-1) cell line after androgen withdrawal Shayesta Seenundun and Bernard Robaire Endocrinology, Product: Pathway Studio |
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Characterization of differential gene expression profiles in diabetic embryopathy using DNA microarray analysis. Reece EA, Ji I, Wu YK, Zhao Z. Am J Obstet Gynecol. 2006 Oct;195(4):1075-80., Product: Pathway Studio |
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Identification of molecular markers and signaling pathway in endometrial cancer in Hong Kong Chinese women by genome-wide gene expression profiling Y F Wong, T H Cheung, K W K Lo, S F Yim, N S S Siu, S C S Chan, T W F Ho, K W Y Wong, M Y Yu, V W Wang, C Li, G J Gardner, T Bonome, W B Johnson, D I Smith, T K H Chung, M J Birrer Oncogene. 2006 Oct 16, Product: Pathway Studio |
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Candidate genes, pathways and mechanisms for alcoholism: an expanded convergent functional genomics approach Z A Rodd, B A Bertsch, W N Strother, H Le-Niculescu, Y Balaraman, E Hayden, R E Jerome, L Lumeng, J I Nurnberger, H J Edenberg, W J McBride, A B Niculescu The Pharmacogenomics Journal (10 Oct 2006), Product: Pathway Studio |
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Exercise affects the gene expression profiles of human white blood cells Buettner P, Mosig S, Lechtermann A, Funke H, Mooren FC. J Appl Physiol., Product: PathwayAssist |
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Cluster-based network model for time-course gene expression data Inoue LY, Neira M, Nelson C, Gleave M, Etzioni R. Biostatistics, Product: Pathway Studio |
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Agonist and Antagonist of Retinoic Acid Receptors Cause Similar Changes in Gene Expression and Induce Senescence-like Growth Arrest in MCF-7 Breast Carcinoma Cells Yuhong Chen, Milos Dokmanovic, Wilfred D. Stein, Robert J. Ardecky, and Igor B. Roninson Cancer Res., Sep 2006; 66: 8749 - 8761, Product: PathwayAssist |
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Respiratory Epithelial Gene Expression in Patients with Mild and Severe Cystic Fibrosis Lung Disease Jerry M. Wright, Christian A. Merlo, Jeffrey B. Reynolds, Pamela L. Zeitlin, Joe G. N. Garcia, William B. Guggino, and Michael P. Boyle Am. J. Respir. Cell Mol. Biol., Sep 2006; 35: 327 - 336., Product: Pathway Studio |
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Evidence for chronic, peripheral activation of neutrophils in polyarticular juvenile rheumatoid arthritis. Jarvis JN, Petty HR, Tang Y, Frank MB, Tessier PA, Dozmorov I, Jiang K, Kindzelski A, Chen Y, Cadwell C, Turner M, Szodoray P, McGhee JL, Centola M. Arthritis Res Ther. 2006; 8(5): R154, Product: Pathway Studio |
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Physiologic and Genomic Analyses of Nutrition-Ethanol Interactions During Gestation: Implications for Fetal Ethanol Toxicity Kartik Shankar, Mats Hidestrand, Xiaoli Liu, Rijin Xiao, Charles M. Skinner, Frank A. Simmen, Thomas M. Badger, and Martin J. J. Ronis Experimental Biology and Medicine, Sep 2006; 231: 1379 - 1397., Product: PathwayAssist |
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Identification of Cell Cycle Regulatory and Inflammatory Genes As Predominant Targets of p38 Mitogen-Activated Protein Kinase in the Heart Olli Tenhunen, Jaana Rys, Mika Ilves, Ylermi Soini, Heikki Ruskoaho, and Hanna Leskinen Circ. Res., Sep 2006; 99: 485 - 493., Product: PathwayAssist |
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Expression Profiling Identifies Altered Expression of Genes That Contribute to the Inhibition of Transforming Growth Factor- Signaling in Ovarian Cancer Jan S. Sunde, Howard Donninger, Kongming Wu, Michael E. Johnson, Richard G. Pestell, G. Scott Rose, Samuel C. Mok, John Brady, Tomas Bonome, and Michael J. Birrer Cancer Res.; 66: 8404 - 8412., Product: PathwayAssist |
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Text mining of full-text journal articles combined with gene expression analysis reveals a relationship between sphingosine-1-phosphate and invasiveness of a glioblastoma cell line Jeyakumar Natarajan, Daniel Berrar, Werner Dubitzky, Catherine Hack, Yonghong Zhang, Catherine DeSesa, James R Van Brocklyn and Eric G Bremer BMC Bioinformatics 2006, 7:373, Product: Pathway Studio |
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Identification and pathway analysis of immediate hyperosmotic stress responsive molecular mechanisms in tilapia (Oreochromis mossambicus) gill Diego F. Fiola, Stephanie Y. Chana and Dietmar Kltz Comparative Biochemistry and Physiology Part D: Genomics and Proteomics V1(3):344-356, Product: Pathway Studio |
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Phenotype-Based Screening of Mechanistically Annotated Compounds in Combination with Gene Expression and Pathway Analysis Identifies Candidate Drug Targets in a Human Squamous Carcinoma Cell Model Mrten Frykns, Linda Rickardson, Malin Wickstrm, Sumeer Dhar, Henrik Lvborg, Joachim Gullbo, Peter Nygren, Mats G. Gustafsson, Anders Isaksson, and Rolf Larsson J Biomol Screen., 11: 457 - 468, Product: PathwayAssist |
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The Microarray Data Analysis Process: From Raw Data to Biological Significance Olson, N.E. NeuroRX, Product: Pathway Studio |
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Stat3 Is Required for Cytoprotection of the Respiratory Epithelium during Adenoviral Infection Yohei Matsuzaki, Yan Xu, Machiko Ikegami, Valrie Besnard, Kwon-Sik Park, William M. Hull, Susan E. Wert and Jeffrey A. Whitsett2 The Journal of Immunology, 2006, 177: 527-537., Product: PathwayAssist |
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Celecoxib Treatment Alters the Gene Expression Profile of Normal Colonic Mucosa Oleg K. Glebov, Luz M. Rodriguez, Patrick Lynch, Sherri Patterson, Henry Lynch, Kenneth Nakahara, Jean Jenkins, Janet Cliatt, Casey-Jo Humbyrd, John DeNobile, Peter Soballe, Steven Gallinger, Aby Buchbinder, Gary Gordon, Ernest Hawk, and Ilan R. Kirsch Cancer Epidemiol. Biomarkers Prev., Jul 2006; 15: 1382 - 1391., Product: PathwayAssist, MedScan |
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Molecular network and chromosomal clustering of genes involved in synaptic plasticity in the hippocampus Chang Sin Park, Ruomu Gong, Joshua Stuart, and Shao-Jun Tang J. Biol. Chem., Jul 2006; 10.1074/jbc.M605876200., Product: PathwayAssist |
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Characterization of cell-type specific profiles in tissues and isolated cells from squamous cell carcinomas of the lung Lesleyann Hawthorn, Leighton Stein, Jenniffer Panzarella, Gregory M. Loewen and Heinz Baumann Lung Cancer, 04, 2006, Product: Pathway Studio |
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The Common Insecticides Cyfluthrin and Chlorpyrifos Alter the Expression of a Subset of Genes with Diverse Functions in Primary Human Astrocytes Sarah M. Mense, Amitabha Sengupta, Changgui Lan, Mei Zhou, Galina Bentsman, David J. Volsky, Robin M. Whyatt, Frederica P. Perera, and Li Zhang Toxicol. Sci., Jun 2006, Product: PathwayAssist |
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Signatures of human regulatory T cells: an encounter with old friends and new players. Pfoertner S, Jeron A, Probst-Kepper M, Guzman CA, Hansen W, Westendorf AM, Toepfer T, Schrader AJ, Franzke A, Buer J, Geffers R Genome Biol. 2006 Jun 12;7(7):, Product: Pathway Studio |
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Parallel analysis of transcript and translation profiles: identification of metastasis-related signal pathways differentially regulated by drug and genetic modifications Yang H, Yu LR, Yi M, Lucas DA, Lukes L, Lancaster M, Chan KC, Issaq HJ, Stephens RM, Conrads TP, Veenstra TD, Hunter KW. J Proteome Res. 2006 July 7; 5(7): 1555 1567., Product: Pathway Studio |
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Transcriptional Signatures of Cellular Plasticity in Mice Lacking the {alpha}1 Subunit of GABA-A Receptors Igor Ponomarev, Rajani Maiya, Mark T. Harnett, Gwen L. Schafer, Andrey E. Ryabinin, Yuri A. Blednov, Hitoshi Morikawa, Stephen L. Boehm, II, Gregg E. Homanics, Ari Berman, Kerrie H. Lodowski, Susan E. Bergeson, and R. Adron Harris J. Neurosci., May 2006; 26: 5673 - 5683, Product: PathwayAssist |
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Gene expression alterations in brains of mice infected with three strains of scrapie. Skinner PJ, Abbassi H, Chesebro B, Race RE, Reilly C, Haase AT. BMC Genomics. 2006; 7: 114., Product: Pathway Studio |
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Mechanisms and Effects of Loss of Human Leukocyte Antigen Class II Expression in Immune-Privileged Site-Associated B-Cell Lymphoma Marije Booman, Jenny Douwes, Annuska M. Glas, Sietske A. Riemersma, Ekaterina S. Jordanova, Klaas Kok, Andreas Rosenwald, Daphne de Jong, Ed Schuuring, and Philip M. Kluin Clin. Cancer Res., May 2006; 12: 2698 - 2705, Product: PathwayAssist |
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DNA microarray analysis of striatal gene expression in symptomatic transgenic Huntington\'s mice (R6/2) reveals... Crocker, S.F. Costain, W.J. Robertson, H.A. Brain Research, May 2006, Product: Pathway Studio |
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cis-Regulatory sequences of the genes involved in apoptosis, cell growth, and proliferation may provide a target for some of the effects of acute ethanol exposure Uddin, R.K. Singh, S.M. Brain Research, May 2006, Product: Pathway Studio |
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Functional Genomic Responses to Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) and CFTR508 in the Lung Xu Y, Liu C, Clark JC, Whitsett JA. J Biol Chem. 2006 Apr 21;281(16):11279-11291, Product: PathwayAssist |
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Respiratory Epithelial Gene Expression in Cystic Fibrosis Patients with Mild and Severe Lung Disease. Wright JM, Merlo CA, Reynolds JB, Zeitlin PL, Garcia JG, Guggino WB, Boyle MP. Am J Respir Cell Mol Biol. 2006 Apr 13, Product: PathwayAssist |
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Gene Expression Profiling of Acute Liver Stress During Living Donor Liver Transplantation Borozan, I; Chen, L; Sun, J; Tannis, L.-L; Guindi, M; Rotstein, OD; Heathcote, J; Edwards, AM; Grant, D; McGilvray, ID American Journal of Transplantation, 6(4):806-824, 2006, Product: Pathway Studio |
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A genome-scale assessment of peripheral blood B-cell molecular homeostasis in patients with rheumatoid arthritis Szodoray P, Alex P, Frank MB, Turner M, Turner S, Knowlton N, Cadwell C, Dozmorov I, Tang Y, Wilson PC, Jonsson R, Centola M. Rheumatology (Oxford). 2006 Apr 25;, Product: PathwayAssist |
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Gingival epithelial cells heterozygous for Toll-like receptor 4 polymorphisms Asp299Gly and Thr399ile are hypo-responsive to Porphyromonas gingivalis Kinane DF, Shiba H, Stathopoulou PG, Zhao H, Lappin DF, Singh A, Eskan MA, Beckers S, Waigel S, Alpert B, Knudsen TB. Genes and Immunity (2006) 7,, Product: Pathway Studio |
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A novel prognostic subtype of human hepatocellular carcinoma derived from hepatic progenitor cells Ju-Seog Lee, Jeonghoon Heo, Louis Libbrecht, In-Sun Chu, Pal Kaposi-Novak, Diego F Calvisi, Arsen Mikaelyan, Lewis R Roberts, Anthony J Demetris, Zongtang Sun, Frederik Nevens, Tania Roskams & Snorri S Thorgeirsson Nature Medicine 12, 410 - 416 (2006), Product: Pathway Studio |
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Identification of novel prognostic subtype of hepatocellular carcinoma derived from hepatic stem cells by comparative functional genomic approach. Ju-Seog Lee, Jeonghoon Heo, Louis Libbrecht, In-Sun Chu, Pal Kaposi-Novak, Diego F. Calvisi, Arsen Mikaelyan, Lewis R. Roberts, Anthony J. Demetris, Zongtang Sun, Frederik Nevens, Tania Roskams, and Snorri S. Thorgeirsson ACR Meeting Abstracts, 2006: 1338 - 1339., Product: PathwayAssist |
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Global gene expression profiling of mucinous ovarian tumors and cystadenomas identifies genes of clinicopathologic importance Fred W. A. Wamunyokoli, Tomas Bonome, Ji-Young Lee, Colleen M. Feltmate, William R. Welch, Mike Radonovich, Cindy Pise-Masison, John Brady, Ke Hao, Ross S. Berkowitz, Samuel Mok, and Michael J. Birrer AACR Meeting Abstracts, 2006: 1057 - 1058, Product: PathwayAssist |
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Expression profiling of peripheral blood cells for early detection of breast cancer Jrgen M. Aare, Torbjrn Lindahl, Solve Sb, Per Skaane, Simen Myhre, Turid Reiersen, Anders Lnneborg, Anne-Lise Brresen-Dale, and Praveen Sharma AACR Meeting Abstracts,2006: 29 - 30., Product: PathwayAssist |
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Variants in the ATM-BRCA2-CHEK2 axis predispose to chronic lymphocytic leukaemia Rudd MF, Sellick GS, Webb EL, Catovsky D, Houlston RS. Blood. 2006 Mar 30, Product: PathwayAssist |
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Gene Expression Arrays in Juvenile Rheumatoid Arthritis: Will the Blind Men Finally See the Elephant? Jarvis, J.N. Current Problems in Pediatric and Adolescent Health Care, Mar 2006, Product: Pathway Studio |
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Activation of IFN pathways and plasmacytoid dendritic cell recruitment in target organs of primary Sjgren s syndrome Gottenberg JE, Cagnard N, Lucchesi C, Letourneur F, Mistou S, Lazure T, Jacques S, Ba N, Ittah M, Lepajolec C, Labetoulle M, Ardizzone M, Sibilia J, Fournier C, Chiocchia G, Mariette X. Proc Natl Acad Sci U S A. 2006 Feb 13, Product: PathwayAssist |
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Gene Expression Profiling Reveals the Profound Up-regulation of Hypoxia-Responsive Genes in Primary Human Astrocytes S. M Mense, A. Sengupta, M. Zhou, C. Lan, G. Bentsman, D. J Volsky, and L. Zhang Physiol. Genomics (February 28, 2006)., Product: PathwayAssist |
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A Pathway Analysis of Poly (I:C)-Induced Global Gene Expression Change in Human Peripheral Blood Mononuclear Cells Huang CC, Duffy KE, San Mateo LR, Amegadzie BY, Sarisky RT, Mbow ML. Physiol Genomics. 2006 Mar 22, Product: PathwayAssist |
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Expression profiling of mucinous tumors of the ovary identifies genes of clinicopathologic importance. Wamunyokoli FW, Bonome T, Lee JY, Feltmate CM, Welch WR, Radonovich M, Pise-Masison C, Brady J, Hao K, Berkowitz RS, Mok S, Birrer MJ. Clin Cancer Res. 2006 Feb 1;12(3 Pt 1):690-700., Product: PathwayAssist |
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Targeted disruption of glycerol kinase gene in mice: expression analysis in liver shows alterations in network partners related to glycerol kinase activity Nicole K. MacLennan, Lola Rahib, Cynthia Shin, Zixing Fang, Steve Horvath, Jason Dean, James C. Liao, Edward R.B. McCabe, and Katrina M. Dipple Hum. Mol. Genet., Feb 2006; 15: 405 - 415., Product: PathwayAssist |
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The neuroprotective WldS gene regulates expression of PTTG1 and erythroid differentiation regulator 1-like gene in mice and human cells Gillingwater TH, Wishart TM, Chen PE, Haley JE, Robertson K, MacDonald SH, Middleton S, Wawrowski K, Shipston MJ, Melmed S, Wyllie DJ, Skehel PA, Coleman MP, Ribchester RR. Hum Mol Genet. 2006 Feb 15;15(4):625-35., Product: PathwayAssist |
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Adaptation and increased susceptibility to infection associated with constitutive expression of misfolded SP-C James P. Bridges, Yan Xu, Cheng-Lun Na, Hector R. Wong, and Timothy E. Weaver The Rockefeller University Press, 0021-9525, Product: PathwayAssist |
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Transcriptional targets of hepatocyte growth factor signaling and Ki-ras oncogene activation in colorectal cancer Seiden-Long IM, Brown KR, Shih W, Wigle DA, Radulovich N, Jurisica I, Tsao MS. Oncogene. 2006 Jan 5;25(1):91-102., Product: Pathway Studio |
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Microarray Analysis of Immobilization Stress Triggered Changes in Gene Expression in Rat Adrenal Medulla Esther Louise Sabban, Xiaoping Liu, Richard Kvetnansky, and Lidia I Serova FASEB J, Product: PathwayAssist |
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Rapid parallel evolutionary changes of gene transcription profiles in farmed Atlantic salmon Christian Roberge, Sigurd Einum, Helga Guderley, Louis Bernatchez Molecular Ecology Volume 15, Issue 1, Page 9-20, Jan 2006, Product: Pathway Studio |
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Androgens Regulate the Immune/Inflammatory Response and Cell Survival Pathways in Rat Ventral Prostate Epithelial Cells A. J. Asirvatham, M. Schmidt, B. Gao, and J. Chaudhary Endocrinology, Jan 2006; 147: 257 - 271., Product: PathwayAssist |
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Transcriptional analysis of protective antigen-stimulated PBMC from non-human primates vaccinated with the anthrax vaccine absorbed James V. Rogersa, Stacy L. Casbohma, Lenore F. Giannunzioa, Loraine T. Sinnotta, Steven W. Rusta, April M. Brysa, Joyce M. Durnforda, Conrad P. Quinnb, David M. Robinsona, Robert E. Hunta, James E. Estepa and Carol L.K. Sabourin Vaccine, Apr 2006, Product: Pathway Studio |
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Gene expression profile of activated microglia under conditions associated with dopamine neuronal damage David M. Thomas, Dina M. Francescutti-Verbeem, and Donald M. Kuhn FASEB J, Dec 2005, Product: PathwayAssist |
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Gene expression microarray studies in polygenic psychiatric disorders: Applications and data analysis Konradi, C. Brain Research Reviews, Dec 2005, Product: Pathway Studio |
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Tamoxifen treatment for breast cancer enforces a distinct gene-expression profile on the human endometrium: an exploratory study S C J P Gielen, L C M Kuhne, P C Ewing, L J Blok, and C W Burger Endocr. Relat. Cancer, Dec 2005; 12: 1037 - 1049., Product: PathwayAssist |
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Validating Molecular Targets of Thalidomide in CLL: Net Effect of Increased Apoptosis through the Intrinsic Pathway and down Regulation of NF-kB Signaling- Validation Using Gene Expression Profile from the Phase I/II Clinical Trial of Thalidomide and Fludarabine. Asher Alban Chanan-Khan, Swaminathan Padmanabhan, Leighton Stein, Jennifer Panzarella, Kena C. Miller, and Leslie Hawthorne Blood (ASH Annual Meeting Abstracts), Nov 2005; 106: 5043., Product: PathwayAssist |
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Expression Profiling of Serous Low Malignant Potential, Low-Grade, and High-Grade Tumors of the Ovary Tomas Bonome, Ji-Young Lee, Dong-Choon Park, Mike Radonovich, Cindy Pise-Masison, John Brady, Ginger J. Gardner, Ke Hao, Wing H. Wong, J. Carl Barrett, Karen H. Lu, Anil K. Sood, David M. Gershenson, Samuel C. Mok and Michael J. Birrer Cancer Research 65, 10602-10612, November 15, 2005, Product: PathwayAssist |
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Identification of potential caloric restriction mimetics by microarray profiling Joseph M. Dhahbi, Patricia L. Mote, Gregory M. Fahy, and Stephen R. Spindler Physiol Genomics, Nov 2005; 23: 343 - 350., Product: PathwayAssist |
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Discovering causes and cures for cancer from gene expression analysis Weeraratna, A.T. Ageing Research Reviews, Nov 2005, Product: Pathway Studio |
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Gene expression profiling in INS-1 cells overexpressing thioredoxin-interacting protein. Minn AH, Pise-Masison CA, Radonovich M, Brady JN, Wang P, Kendziorski C, Shalev A. Biochem Biophys Res Commun. 2005 Oct 28;336(3):770-8., Product: Pathway Studio |
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Relationships between genomic, cell cycle, and mutagenic responses of TK6 cells exposed to DNA damaging chemicals Mohammed Islaih, Bartley W. Halstead, Ibrahim A. Kadura, Baohui Li, Jaclyn L. Reid-Hubbard, Leah Flick, Julie L. Altizer, J. Thom Deahl, David K. Monteith, Ronald K. Newton and David E. Watson Mutation Research Regular Papers, Oct 2005, Product: Pathway Studio |
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Complex Genetics of Interactions of Alcohol and CNS Function and Behavior. Matthews, Douglas B.; Bhave, Sanjiv V.; Belknap, John K.; Brittingham, Cynthia; Chesler, Elissa J.; Hitzemann, Robert J.; Hoffmann, Paula L.; Lu, Lu; McWeeney, Shannon; Miles, Michael F.; Tabakoff, Boris; Williams, Robert W. Alcoholism: Clinical & Experimental Research. 29(9):1706-1719, Product: Pathway Studio |
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Characterization of human fibrocytes as circulating adipocyte progenitors and the formation of human adipose tissue in SCID mice Kurt M. Hong, Marie D. Burdick, Roderick J. Phillips& FASEB J, Sep 2005; 10.1096/fj.05-4295fje, Product: PathwayAssist |
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Nova regulates brain-specific splicing to shape the synapse Ule J, Ule A, Spencer J, Williams A, Hu JS, Cline M, Wang H, Clark T, Fraser C, Ruggiu M, Zeeberg BR, Kane D, Weinstein JN, Blume J, Darnell RB. Nature Genetics 37, 844-852, Product: Pathway Studio |
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Gene expression profiling of mantle cell lymphoma cells reveals aberrant expression of genes from the PI3K-AKT, WNT and TGF signalling pathways Edgar Gil Rizzatti, Roberto Passetto Falcao, Rodrigo Alexandre Panepucci, Rodrigo Proto-Siqueira, Wilma Terezinha Anselmo-Lima, Oswaldo Keith Okamoto, Marco Antonio Zago British Journal of Haematology, Volume 130, Issue 4, Page 516-526, Aug 2005, Product: Pathway Studio |
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Oncogenic H-Ras Up-regulates Expression of Ku80 to Protect Cells from -Ray Irradiation in NIH3T3 Cells In-Youb Chang, Cha-Kyung Youn, Hong-Beum Kim, Mi-Hwa Kim, Hyun-Ju Cho, Young Yoon, Yun-Sil Lee, Myung-Hee Chung, and Ho Jin You Cancer Res., Aug 2005; 65: 6811 - 6819., Product: PathwayAssist |
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Pharmacogenomic profiling of an oxidative stress-mediated spongiform encephalopathy Golden, T.R. Hubbard, A. Morten, K.J. Hinerfeld, D. Melov, S. Free Radical Biology and Medicine, Jul 2005, Product: Pathway Studio |
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Response rate of fibrosarcoma cells to cytotoxic drugs on the expression level correlates to the therapeutic response rate of fibrosarcomas and is mediated by regulation of apoptotic pathways. Marcus Lehnhardt, Ludger Klein-Hitpass, Cornelius Kuhnen, Heinz Herbert Homann, Adrien Daigeler, Hans Ulrich Steinau, Sonja Roehrs, Laura Schnoor, Lars Steinstraesser and Oliver Mueller BioMed Central 7 July 2005, Product: Pathway Studio |
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Identification of molecular mechanisms for cellular drug resistance by combining drug activity and gene expression profiles. Rickardson L, Fryknas M, Dhar S, Lovborg H, Gullbo J, Rydaker M, Nygren P, Gustafsson MG, Larsson R, Isaksson A. British Journal of Cancer (2005) 93, 483-492. doi:10.1038/sj.bjc.6602699, Product: Pathway Studio |
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Sp1 and NFkappaB pathways are regulated in brain in response to acute and chronic ethanol. Rulten SL, Ripley TL, Hunt CL, Stephens DN, Mayne LV. Genes, Brain and Behavior, 2006, Product: Pathway Studio |
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Diabetes Enhances mRNA Levels of Proapoptotic Genes and Caspase Activity, Which Contribute to Impaired Healing Hesham A. Al-Mashat, Suneel Kandru, Rongkun Liu, Yugal Behl, Tesfahun Desta, and Dana T. Graves Diabetes 55:487-495, 2006, Product: PathwayAssist |
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Identification of GAS-dependent interferon-sensitive target genes whose transcription is STAT2-dependent but ISGF3-independent Melissa M Brierley, Katie L Marchington, Igor Jurisica and Eleanor N Fish FEBS Journal 273 (2006) 1569-1581, Product: Pathway Studio |
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Proteomic analysis of protein expression and oxidative modification in R6/2 transgenic mice - A model of Huntington\'s disease Marzia Perluigi, H. Fai Poon, William Maragos, William M. Pierce, Jon B. Klein, Vittoriio Calabrese, Chiara Cini, Carlo De Marco, and D. Allan Butterfield Mol. Cell. Proteomics, Jun 2005, Product: PathwayAssist |
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High-Resolution Mapping of Genomic Imbalance and Identification of Gene Expression Profiles Associated with Differential Chemotherapy Response in Serous Epithelial Ovarian Cancer. Bernardini M, Lee CH, Beheshti B, Prasad M, Albert M, Marrano P, Begley H, Shaw P, Covens A, Murphy J, Rosen B, Minkin S, Squire JA, Macgregor PF. Neoplasia. 2005 Jun; 7(6): 603-613, Product: Pathway Studio |
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Genetic association, post-translational modification and protein-protein interactions in type 2 diabetes mellitus Amitabh Sharma, Sreenivas Chavali, Anubha Mahajan, Rubina Tabassum, Vijaya Banerjee, Nikhil Tandon, and Dwaipayan Bharadwaj Mol. Cell. Proteomics, May 2005, Product: PathwayAssist |
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Gene Expression in Glaucomatous Retinas Implicate the TNF Mediated Pathway in Retinal Ganglion Cell Death N. Piri, J.M. K. Kwong, M. Song, and J. Caprioli Invest. Ophthalmol. Vis. Sci., May 2005, Product: PathwayAssist |
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Comparative Host Gene Transcription by Microarray Analysis Early after Infection of the Huh7 Cell Line by Severe Acute Respiratory Syndrome Coronavirus and Human Coronavirus 229E Bone S. F. Tang, Kwok-hung Chan, Vincent C. C. Cheng, Patrick C. Y. Woo, Susanna K. P. Lau, Clarence C. K. Lam, Tsun-leung Chan, Alan K. L. Wu, Ivan F. N. Hung, Suet-yi Leung, and Kwok-yung Yuen J. Virol., May 2005, Product: PathwayAssist |
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Dexamethasone Induces Changes in Glucocorticoid Receptor Phosphorylation and Gene Expression in Human Lens Epithelial Cells V.K. Gupta and B.J. Wagner Invest. Ophthalmol. Vis. Sci., May 2005, Product: PathwayAssist |
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Transcriptional Basis for Exercise Limitation in Male eNOS Knockout Mice with Age: Heart Failure and the Fetal Phenotype Caroline Ojaimi, Wei Li, Shintaro Kinugawa, Heiner Post, Anna Csiszar, Pal Pacher, Gabor Kaley, and Thomas H Hintze Am J Physiol Heart Circ Physiol, May 2005, Product: PathwayAssist |
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Persistent Nuclear Factor-Kappa-B Activation in Ucp2-/- Mice Leads to Enhanced Nitric Oxide and Inflammatory Cytokine Production Yushi Bai, Hiroki Onuma, Xu Bai, Alexander V. Medvedev, Mary Misukonis, J. Brice Weinberg, Wenhong Cao, Jacques Robidoux, Lisa M. Floering, Kiefer W. Daniel, and Sheila Collins J. Biol. Chem., May 2005, Product: PathwayAssist |
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Comparative gene expression profile of mouse carotid body and adrenal medulla under physiological hypoxia Maria D Ganfornina, M. Teresa Prez-Garca, Gabriel Gutierrez, Eduardo Miguel-Velado, Jos Ramn Lpez-Lpez, Antonio Marin, Diego Sanchez, and Constancio Gonzalez J. Physiol., May 2005, Product: PathwayAssist |
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Global Gene Expression Analysis of Keloid Fibroblasts in Response to Electron Beam Irradiation Reveals the Involvement of Interleukin-6 Pathway Tosa M, Ghazizadeh M, Shimizu H, Hirai T, Hyakusoku H, Kawanami O. Journal of Investigative Dermatology 124, 704-713, Product: Pathway Studio |
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Transcripts from a human primordial follicle cDNA library Maria D. Serafica, Tetsuya Goto, and Alan O. Trounson Hum. Reprod., Apr 2005, Product: PathwayAssist |
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Pathway analysis of whole genomic expression profiles of colorectal cancer biopsy samples Orsolya Galamb, Ferenc Sipos, Sndor Spisk, Bla Molnr, Andrea Ladnyi, and Zsolt Tulassay AACR Meeting Abstracts, Product: PathwayAssist |
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Alterations of apoptosis in a rhabdomyosarcoma patient with Li-Fraumeni syndrome, familial syndactyly, and absence of germline p53 mutation. Malgorzata Pienkowska, Rika Tsuchida, Elizabeth Sexsmith, Jane Bayani, Gloria Lim, Jeremy A. Squire, and David Malkin AACR Meeting Abstracts, Product: PathwayAssist |
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Molecular Portrait of the Progestagenic and Estrogenic Actions of Tibolone: Behavior of Cellular Networks in Response to Tibolone P. Hanifi-Moghaddam, S. C. J. P. Gielen, H. J. Kloosterboer, M. E. De Gooyer, A. M. Sijbers, A. J. van Gool, M. Smid, M. Moorhouse, F. H. van Wijk, C. W. Burger, and L. J. Blok J. Clin. Endocrinol. Metab., Feb 2005, Product: PathwayAssist |
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Functional Genomic Relationships in HIV-1 Disease Revealed by Gene-Expression Profiling of Primary Human Peripheral Blood Mononuclear Cells Christian F. Ockenhouse, Wendy B. Bernstein,2 Zhining Wang, and Maryanne T. Vahey The Journal of Infectious Diseases 2005 Jun 15; 191(12):2064-74., Product: Pathway Studio |
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Genetic pathway analysis of expression microarray data S Spisak, O Galamb, F Sipos, B Molnar, Z Tulassay British Journal of Haematology, Z Gastroenterol 2005; 43, DOI: 10.1055/s-2005-869766, Product: PathwayAssist |
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The p53 Tumor Suppressor Network Is a Key Responder to Microenvironmental Components of Chronic Inflammatory Stress Frank Staib, Ana I. Robles, Lyuba Varticovski, Xin W. Wang, Barry R. Zeeberg, Michail Sirotin, Victor B. Zhurkin, Lorne J. Hofseth, S. Perwez Hussain, John N. Weinstein, Peter R. Galle and Curtis C. Harris Cancer Research 65, 10255-10264, November 15, 2005, Product: PathwayAssist |
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Alterations in the Ovarian Transcriptome During Primordial Follicle Assembly and Development Phillip R. Kezele, Jacquelyn M. Ague, Eric Nilsson, and Michael K. Skinner Biol Reprod, Jan 2005, Product: PathwayAssist |
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Osteocyte and Osteoblast Cell Models have Unique Patterns of Gene Expression and Responses to Mechanical Loading Wuchen Yang, Marie A. Harris, Dayong Guo, Lynda F. Bonewald, Stephen E. Harris Department of Periodontics, University of Texas Health Science Center at San Antonio, School of Dentistry, Product: Pathway Studio |
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Microarray analysis of androgen-regulated gene expression in testis: the use of the androgen-binding protein (ABP)-transgenic mouse as a model. Petrusz P, Jeyaraj DA, Grossman G. Reprod Biol Endocrinol. 2005; 3: 70., Product: Pathway Studio |
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Identification of mouse retinal genes differentially regulated by dim and bright cyclic light rearing Hu Huang, Mark Barton Frank, Igor Dozmorov, Wei Cao, Craig Cadwell, Nick Knowlton, Michael Centola and Robert E. Anderson Experimental Eye Research, 2005, Product: Pathway Studio |
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Global Genomic Approaches to the Iron-Regulated Proteome Ying Liu, Zvezdana Popovich and Douglas M. Templeton Ann. Clin. Lab. Sci., Jan 2005; 35: 230 - 239., Product: PathwayAssist |
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Microarrays: a monitoring tool for transplant patients? Lauren A. Weintraub, Minnie M. Sarwal Transplant International, Product: Pathway Studio |
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Using microarrays to predict resistance to chemotherapy in cancer patients Chung-Hae Lee, Pascale F Macgregor Pharmacogenomics, Volume: 5, Issue: 6; September 2004, Product: Pathway Studio |
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Impact of Adenoviral Transduction With SREBP1c or AMPK on Pancreatic Islet Gene Expression Profile: Analysis With Oligonucleotide Microarrays Frederique Diraison, Efthimios Motakis, Laura E. Parton, Guy P. Nason, Isabelle Leclerc, and Guy A. Rutter Diabetes, Dec 2004, Product: PathwayAssist |
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Identification of the CREB-binding Protein/p300-interacting Protein CITED2 as a Peroxisome Proliferator-activated Receptor a Coregulator Eric S. Tien, John W. Davis, and John P. Vanden Heuvel J. Biol. Chem., Vol. 279, Issue 23, 24053-24063, June 4, 2004., Product: PathwayAssist |
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Cocaine-induced changes in the expression of apoptosis-related genes in the fetal mouse cerebral wall Svetlana I. Novikova, Fang He, Jie Bai, Irina Badan, Irina A. Lidow, Michael S. Lidow Neurotoxicology and Teratology, 2004, Product: Pathway Studio |
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Novel approaches to gene expression analysis of active polyarticular juvenile rheumatoid arthritis James N Jarvis, Igor Dozmorov, Kaiyu Jiang, Mark Barton Frank, Peter Szodoray, Philip Alex and Michael Centola Arthritis Res. Ther. 2004, 6:R15 - R32, Product: Pathway Studio |
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Gene profile changes after Pseudomonas aeruginosa exposure in immortalized airway epithelial cells Aura Perez, Pamela B. Davis Journal of Structural and Functional Genomics 5 (3): 179-194, 2004, Product: Pathway Studio |
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Whole genome expression profiling of advance stage papillary serous ovarian cancer reveals activated pathways. Donninger H, Bonome T, Radonovich M, Pise-Masison CA, Brady J, Shih JH, Barrett JC, Birrer MJ. Oncogene. 2004 Sep 13, Product: Pathway Studio |
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FGF-2 enhances the mitotic and chondrogenic potentials of human adult bone marrow-derived mesenchymal stem cells Luis A. Solchaga, Kitsie Penick, John D. Porter, Victor M.Goldberg, Arnold I. Caplan, Jean F. Welter Journal of Cellular Physiology Volume 203, Issue 2, Pages 398 - 409, Nov. 2004, Product: Pathway Studio |
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Long term modulation of gene expression in the mouse eye following laser photocoagulation N. Binz, K. Simpson, W. Y. Shen, C. M. Lai, T. Speed and E.P. Rakoczy Invest Ophthalmol Vis Sci 2004; 45: E-Abstract 2504., Product: PathwayAssist |
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Microarray Data Analysis and Pathway Visualization of Murine Cochlear Ear Hair Cell Differentiation Eric S. Allen & Kris Barbee Submitted on December 4th, 2003, Product: Pathway Studio |
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Hnrnpk, a Protein Differentially Expressed in Immature Rat Ovarian Development, Is Required for Normal Primordial Follicle Assembly and Development Ningling Wang, Ping Zhang, Xuejiang Guo, Zuomin Zhou, and Jiahao Sha Endocrinology |
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Pathway Analysis in Microarray Data: A Comparison of Two Different Pathway Analysis Devices in the Same Data Set Bogner, Viktoria et al SHOCK |
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Stage-Specific Expression of TNF Regulates Bad/Bid-Mediated Apoptosis and RIP1/ROS-Mediated Secondary Necrosis in Birnavirus-Infected Fish Cells Wei-Lun Wang et al PLoS One |
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Tracheal occlusion modulates the gene expression profile of the medial thalamus in anesthetized rats Vipa Bernhardt, Natlia Garcia-Reyero, Andrea Vovk, Nancy Denslow, and Paul W. Davenport J Appl Physiol |
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Gene expression profiling predicts nonresponders to chemoradiation in HPV16-positive head and neck squamous cell carcinoma B. J. Thibodeau, T. J. Geddes, S. Ahmed, B. L. Pruetz, P. Y. Chen, G. D. Wilson, and J. A. Akervall ASCO Meeting Abstracts |
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PITX2c Is Expressed in the Adult Left Atrium, and Reducing Pitx2c Expression Promotes Atrial Fibrillation Inducibility and Complex Changes in Gene Expression Paulus Kirchhof, Peter C. Kahr, Sven Kaese, Ilaria Piccini, Ismail Vokshi, Hans-Heinrich Scheld, Heinrich Rotering, Lisa Fortmueller, Sandra Laakmann, Sander Verheule, Ulrich Schotten, Larissa Fabritz, and Nigel A. Brown Circ Cardiovasc Genet, Apr 2011; 4: 123 - 133 |
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TMPRSS2/ERG fusion gene expression alters chemo- and radio-responsiveness in cell culture models of androgen independent prostate cancer. TA Swanson, SA Krueger, S Galoforo, BJ Thibodeau, AA Martinez, GD Wilson, and B Marples Prostate, Mar 2011 |
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Global response of Plasmodium falciparum to hyperoxia: a combined transcriptomic and proteomic approach Torrentino-Madamet M, Almras L, Desplans J, Le Priol Y, Belghazi M, Pophillat M, Fourquet P, Jammes Y, Parzy D. Malar J. 2011 Jan 11;10:4 |
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Use of a bovine genome array to identify new biological pathways for beef marbling in Hanwoo (Korean Cattle) Lee SH,Gondro C,van der Werf J,Kim NK,Lim DJ,Park EW,Oh SJ,Gibson JP,Thompson JM. BMC Genomics.2010 Nov 9;11:623 |
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Immune and Inflammatory Gene Expression Profiles of Chronological(Intrinsic) Skin Aging and Photo-Aging M K Robinson et al 21st World Congress of Dermatology in Buenos Aires, Argentina |
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Calcium Prevents Tumorigenesis in a Mouse Model of Colorectal Cancer Ji-Lin Wang, Yan-Wei Lin, Hui-Min Chen, Xuan Kong, Hua Xiong, Nan Shen, Jie Hong, Jing-Yuan Fang PLoS One. 2011; 6(8): e22566 |
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Proteomic analysis of myocardial tissue from the border zone during early stage post-infarct remodelling in rats Fei Xiang, Zhonghua Shi, Xuejiang Guo, Zhibing Qiu, Xujun Chen, Fuhua Huang, Jiahao Sha, and Xin Chen Eur J Heart Fail. 10 December 2010, 10.1093/eurjhf/hfq196 |
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Molecular signatures and new candidates to target the pathogenesis of rheumatoid arthritis U. Ungethuem, T. Haeupl, H. Witt, D, et al Physiol Genomics. 2010; 42A(4): p. 267-282 |
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Genomic and Proteomic Responses to Environmentally Relevant Exposures to Dieldrin: Indicators of Neurodegeneration? Christopher J. Martyniuk, Kevin J. Kroll, Nicholas J. Doperalski, David S. Barber, and Nancy D. Denslow Toxicol. Sci. |
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Adaptive immune response in osteoclastic bone resorption induced by orally administered Aggregatibacter actinomycetemcomitans in a rat model of periodontal disease Li Y, Messina C, Bendaoud M, Fine DH, Schreiner H, Tsiagbe VK. Mol Oral Microbiol. |
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Gene expression profiling and cancer-related pathways in type I endometrial carcinoma. FS Saghir, IM Rose, AZ Dali, Z Shamsuddin, AR Jamal, and NM Mokhtar Int J Gynecol Cancer 1 Jul 2010 20(5): p. 724 |
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Identification of Unique Differentially Expressed Proteins in the Aqueous Humor of Patients With Primary Congenital Glaucoma (PCG) R. Bouhenni, D.P. Edward, S. Al Shahwan, J. Morales, B. Wakim ARVO 2010 presentation abstract |
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Substance P in Polymicrobial Sepsis: Molecular Fingerprint ofLung Injury in Preprotachykinin-A / Mice Akhil Hegde et al Molecular Medicine, May 2010 |
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Methylation profile of TP53 regulatory pathway and mtDNA alterations in breast cancer patients lacking TP53 mutations Zeinab Barekati et al Hum. Mol. Genet., May 2010 |
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Custom CGH array profiling of copy number variations (CNVs) on chromosome 6p21.32 (HLA locus) in patients with venous malformations associated with multiple sclerosis Alessandra Ferlini et al BMC Med Genetics. Apr 2010 |
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Expression profiling of microdissected serous ovarian cancers and matched Fallopian tube identifies a gene signature of clinicopathologic importance Vinod Vathipadiekal, Karishma K. Mehra, Sunghoon Kim, Christopher P. Crum, Xian Wa, Michael J. Birrer AACR 101 presentation abstract |
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Uncovering Molecular Biomarkers That Correlate Cognitive Decline with the Changes of Hippocampus\' Gene Expression Profiles in Alzheimer\'s Disease Martn Gmez Ravetti, Osvaldo A. Rosso, Regina Berretta, Pablo Moscato PLOS One, Apr. 2010 |
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Investigation of post-transcriptional gene regulatory networks associated with autism spectrum disorders by microRNA expression profiling of lymphoblastoid cell lines Tewarit Sarachana et al Genome Medicine, Apr 2010 |
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Global methylation profiling of lymphoblastoid cell lines reveals epigenetic contributions to autism spectrum disorders and a novel autism candidate gene, ORA, whose protein product is reduced in autistic brain AnhThu Nguyen, Tibor A. Rauch, Gerd P. Pfeifer, and Valerie W. Hu The FASEB Journal, Apr. 2010 |
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Identification of a Cholangiocarcinoma-Like Gene Expression Trait in Hepatocellular Carcinoma Hyun Goo Woo et al Cancer Res., Apr 2010 |
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Microarray Analysis of Chick Retina/RPE/Choroid During Recovery From Form Deprivation Myopia (FDM) L. Giummarra, M. J. Murphy, M. J. Goodyear, and S. G. Crewther Invest. Ophthalmol. Vis. Sci., Apr 2010 |
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The use of proteomics as a research methodology for studying cancer-related fatigue: a review Ollie Minton Palliative Medicine, Vol. 24, No. 3, Apr. 2010 |
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Comparative Analysis of the Migraine Pathway in Human and C. elegans Khurshid Ahmad et al Current research Journal of Biological Sciences, Mar. 2010 |
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Inhibition of c-Jun N-terminal Kinase by SP600125: A cDNA Microarray Analysis Pierre Champelovier, Michele El Atifi-Borel, Jean Paul Issartel, Jean Boutonnat, Franois Berger and Daniel Seigneurin Cancer Genomics Proteomics, Mar 2010 |
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The Transcriptional Programme of Human Heart Valves Reveals the Natural History of Infective Endocarditis Marie Benoit et al PLoS One. 2010 |
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Time-dependent alterations of cerebral proteins following short-term normobaric hyperoxia Jochen Hinkelbein, Robert E. Feldmann Jr., Armin Kalenka Mol Cell Biochem, Jan 2010 |
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Reactivation of adiponectin expression in obese patients after bariatric surgery A. Katharine Hindle, Claire Edwards, Tim McCaffrey, Sidney W. Fu and Fred Brody Surgical Endoscopy, Dec. 2009 |
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A mouse model of anxiety molecularly characterized by altered protein networks in the brain proteome va M. SzegQ, Tams Janky, Zoltn Szab, Attila Csorba, Hajnalka Kompagne, Gza Mller, Gyrgy Lvay, Attila Simor, Gbor Juhsz and Katalin A. Kkesi European Neuropsychopharmacology, Dec. 2009 |
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A Gene Signature Predictive for Outcome in Advanced Ovarian Cancer Identifies a Survival Factor: Microfibril-Associated Glycoprotein 2 Samuel C. Mok et al Cancer Cell, Dec. 2009 |
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Cytokine array analysis of peritoneal fluid between women with endometriosis of different stages and those without endometriosis Hou Z, Sun L, Gao L, Liao L, Mao Y, Liu J. Biomarkers, Dec. 2009 |
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Comparative proteomic analysis to discover potential therapeutic targets in human multiple myeloma. Proteomics Clin Appl 1 Nov 2009 3(11): p. 1348. |
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Biological actions of curcumin on articular chondrocytes Henrotin Y, Clutterbuck AL, Allaway D, Lodwig EM, Harris P, Mathy-Hartert M, Shakibaei M, Mobasheri A. Osteoarthritis Cartilage, Oct. 2009, Product: Pathway Studio, ResNet |
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Depletion of T-cell intracellular antigen proteins promotes cell proliferation Raquel Reyes, Jos Alcalde and Jos M Izquierdo Genome Biology, Product: Pathway Studio, ResNet |
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Involvement of potential pathways in malignant transformation from Oral Leukoplakia to Oral Squamous Cell Carcinoma revealed by proteomic analysis Zhi Wang , Xiaodong Feng, Xinyu Liu , Lu Jiang , Xin Zeng , Ning Ji , Jing Li1, Longjiang Li and Qianming Chen BMC Genomics, 10 (1), p.383, Aug 2009, Product: Pathway Studio, ResNet |
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Induction of the interleukin 6/ signal transducer and activator of transcription pathway in the lungs of mice sub-chronically exposed to mainstream tobacco moke Halappanavar S, Russell M, Stampfli MR, Williams A, Yauk CL BMC Medical Genomics, 2, p.56-56, Aug 2009, Product: Pathway Studio, ResNet |
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Evaluation of Blastomere Biopsy Using a Mouse Model Indicates the Potential High Risk of Neurodegenerative Disorders in the Offspring Yu et al Mol. Cell. Proteomics. 2009; 8(7): p. 1490-1500, Product: Pathway Studio |
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Pathway analysis of differentially expressed genes in patients with acute aortic dissection SA Mohamed, HH Sievers, T Hanke, D Richardt, C Schmidtke, EI Charitos, G Belge, and J Bullerdiek Biomark Insights 1 Jan 2009 4: p. 81, Product: Pathway Studio |
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A dynamic network of transcription in LPS-treated human subjects Junhee Seok, Wenzhong Xiao, Lyle L Moldawer, Ronald W Davis and Markus W Covert BMC Systems Biology, Product: Pathway Studio |
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Positional identification of variants of Adamts16 linked to inherited hypertension Joe et al Hum. Mol. Genet. 2009; 18(15): p. 2825-2838, Product: Pathway Studio |
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Modulation of the E2F1-Driven Cancer Cell Fate by the DNA Damage Response Machinery and Potential Novel E2F1 Targets in Osteosarcomas Liontos et al Am. J. Pathol. 2009; 175(1): p. 376-391, Product: Pathway Studio |
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Gene Expression Profiling of Lymphoblasts from Autistic and Nonaffected Sib Pairs: Altered Pathways in Neuronal Development and Steroid Biosynthesis Hu, Valerie W., Nguyen, AnhThu, Kim, Kyung Soon, Steinberg, Mara E., Sarachana, Tewarit, Scully, Michele A., Soldin, Steven J. and Lee, Norman H. PLoS ONE, Product: Pathway Studio |
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Proteome analysis of haptoglobin in cerebrospinal fluid of neuromyelitis optica. Shumei Bai, Shilian Liu, Xuxiao Guo, Zhaoyu Qin, Banqin Wang, Xiaohong Li, and Yanjiang Qin Mol Biol Rep,May 15, 2009, Product: Pathway Studio |
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Stress Proteins and Immunostimulatory Signaling Through Toll-Like Receptors in Glaucoma C. Luo, X. Yang, D. W. Powell, J. B. Klein, and G. Tezel Invest. Ophthalmol. Vis. Sci.,Apr 2009; 50: 4048, Product: Pathway Studio |
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Proteomics Supports Different Pathways of Complement Activity in Human Glaucoma G. Tezel, X. Yang, C. Luo, D. W. Powell, J. B. Klein, H. J. Kaplan, and M. H. Kuehn Invest. Ophthalmol. Vis. Sci.,Apr 2009; 50: 4044, Product: Pathway Studio |
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Proteomic Analysis of TNF-{alpha}Signaling in Human Glaucoma X. Yang, C. Luo, D. W. Powell, J. B. Klein, M. H. Kuehn, and G. Tezel Invest. Ophthalmol. Vis. Sci.,Apr 2009; 50: 4043, Product: Pathway Studio |
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New Microbicidal Functions of Tracheal Glands: Defective Anti-Infectious Response toPseudomonas aeruginosain Cystic Fibrosis Bastonero S, Le Priol Y, Armand M, Bernard CS, Reynaud-Gaubert M, Olive D, Parzy D, de Bentzmann S, Capo C, Mege JL. PLoS ONE.2009;4(4): e5357, Product: Pathway Studio |
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A Modeling-Derived Hypothesis on Chronicity in Respiratory Diseases: Desensitized Pathogen Recognition Secondary to Hyperactive IRAK/TRAF6 Signaling Tingting Zhang,Kyung W. Song,Mohammad Hekmat-Nejad,David G. Morris,and Brian R. Wong PLoS ONE.2009;4(4): e5332, Product: Pathway Studio |
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Gene expression profiling of ATL patients: compilation of disease-related genes and evidence for TCF4 involvement in BIRC5 gene expression and cell viability Cynthia A. Pise-Masison, Michael Radonovich, Kathleen Dohoney, John C. Morris, Deirdre O\'Mahony, Min-Jung Lee, Jane Trepel, Thomas A. Waldmann, John E. Janik, and John N. Brady Blood,Apr 2009; 113: 4016 - 4026, Product: Pathway Studio |
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Central Role of c-Myc during Malignant Conversion in Human Hepatocarcinogenesis Pal Kaposi-Novak, Louis Libbrecht, Hyun Goo Woo, Yun-Han Lee, Nathaniel C. Sears, Elizabeth A. Conner, Valentina M. Factor, Tania Roskams, and Snorri S. Thorgeirsson Cancer Res., Apr 2009; 69: 2775 - 2782, Product: PathwayAssist |
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Genome-wide Analysis of BP1 Transcriptional Targets in Breast Cancer Cell Line Hs578T Yongchun Song, Chengxue Dang1, Yebo Fu, Yi Lian, Jenny Hottel, Xuelan Li, Tim McCaffrey, Sidney W. Fu Int J Biol Sci 2009, Product: Pathway Studio |
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Bladder Cancer Associated Gene Expression Signatures Identified by Profiling of Exfoliated Urothelia Charles J. Rosser, Li Liu, Yijun Sun, Patrick Villicana, Molly McCullers, Stacy Porvasnik, Paul R. Young, Alexander S. Parker, and Steve Goodison Cancer Epidemiol. Biomarkers Prev., Product: Pathway Studio, ResNet |
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Dysregulated gene expression networks in human acute myelogenous leukemia stem cells Ravindra Majeti, Michael W. Becker, Qiang Tian, Tsung-Lu Michael Lee, Xiaowei Yan, Rui Liu, Jung-Hsien Chiang, Leroy Hood, Michael F. Clarke, and Irving L. Weissman PNAS, Mar 2009; 106: 3396 - 3401., Product: Pathway Studio |
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Gene expression profiling of ATL patients: compilation of disease related genes and evidence for TCF-4 involvement in BIRC5 gene expression and cell viability Cynthia A. Pise-Masison, Michael Radonovich, Kathleen Dohoney, John C. Morris, Deirdre O\'Mahony, Min-Jung Lee, Jane Trepel, Thomas A. Waldmann, John E. Janik, and John N. Brady Blood, Product: Pathway Studio |
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Microarray RNA Expression Analysis of Cerebral White Matter Lesions Reveals Changes in Multiple Functional Pathways Simpson et al Stroke,Dec 2008; 10.1161/STROKEAHA.108.529214., Product: PathwayAssist |
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Time-dependent gene expression changes in a human colon polyp cell line induced by a clinically relevant concentration of atorvastatin Eugene Elmore, Aarti Jain, Vernon Steele, and J. Leslie Redpath Cancer Prevention Research. 2008; 1(7_MeetingAbstracts): p. A133, Product: Pathway Studio |
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Ageing, oxidative stress and cancer: paradigms in parallax Christopher C. Benz& Christina Yau Nature Reviews Cancer8,875-879, Product: Pathway Studio |
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Global analysis of gene expression changes during retinoic acid-induced growth arrest and differentiation of melanoma: comparison to differentially expressed genes in melanocytes vs melanoma Mary Estler, Goran Boskovic, James Denvir, Sarah Miles, Donald A Primerano and Richard M Niles BMC Genomics, Oct 2008, Product: Pathway Studio |
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Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival. Van Ness B, Ramos C, Haznadar M, Hoering A, Haessler J, Crowley J, Jacobus S, Oken M, Rajkumar V, Greipp P, Barlogie B, Durie B, Katz M, Atluri G, Fang G, Gupta R, Steinbach M, Kumar V, Mushlin R, Johnson D, Morgan G. BMC Med. 2008 Sep 8;6:26, Product: PathwayAssist |
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Genetic associations with thalidomide mediated venous thrombotic events in myeloma identified using targeted genotyping David C Johnson, Sophie Corthals, Christine Ramos, Antje Hoering, Kim Cocks, Nicholas J Dickens, Jeff Haessler, Harmut Goldschmidt, J. Anthony Child, Sue E Bell, Graham Jackson, Dalsu Baris, S. Vincent Rajkumar, Faith E Davies, Brian G.M. Durie, John Crowley, Pieter Sonneveld, Brian Van Ness, and Gareth J Morgan Blood, Sep 2008; 10.1182/blood-2008-02-140434., Product: PathwayAssist |
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Mitochondrial dysregulation of osteoarthritic human articular chondrocytes analyzed by proteomics: A decrease in mitochondrial superoxide dismutase points to a redox imbalance Cristina Ruiz-Romero, Valentina Calamia, Jesus Mateos, Vanesa Carreira, Montserrat Martnez-Gomariz, Mercedes Fernndez, and Francisco J. Blanco Mol. Cell. Proteomics, Sep 2008; 10.1074/mcp.M800292-MCP200., Product: Pathway Studio |
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DnaJB6 is present in the core of Lewy bodies and is highly up-regulated in parkinsonian astrocytes. Durrenberger PF, Filiou MD, Moran LB, Michael GJ, Novoselov S, Cheetham ME, Clark P, Pearce RK, Graeber MB. J Neurosci Res. 2008 Aug 18, Product: Pathway Studio |
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Constructing disease-specific gene networks using pair-wise relevance metric: application to colon cancer identifies interleukin 8, desmin and enolase 1 as the central elements. Jiang W, Li X, Rao S, Wang L, Du L, Li C, Wu C, Wang H, Wang Y, Yang B. BMC Syst Biol. 2008 Aug 10;2:72, Product: PathwayAssist |
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Cancer stem cell gene signature of ovarian tumor side populations L. Ozbun, V. Vathipadiekal, M. E. Radonovich, C. Pise-Masison, D. Saxena, P. V. Hauschka, S. C. Mok, and M. J. Birrer ASCO Meeting Abstracts, May 2008; 26: 5546., Product: Pathway Studio |
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Gene expression profile for metastatic melanoma and patient survival D. Bogunovic, D. O Neill, S. Adams, J. Wang, F. Darvishian, A. C. Pavlick, R. L. Shapiro, J. Zavadil, I. Osman, and N. Bhardwaj ASCO Meeting Abstracts, May 2008; 26: 9049, Product: PathwayAssist |
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Parasite burden and CD36-mediated sequestration are determinants of acute lung injury in an experimental malaria model. Lovegrove FE, Gharib SA, Pea-Castillo L, Patel SN, Ruzinski JT, Hughes TR, Liles WC, Kain KC. PLoS Pathog. 2008 May 16;4(5):e1000068, Product: Pathway Studio |
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Gene expression analysis of terminal differentiation of human melanoma cells highlights global reductions in cell cycle-associated genes. Huynh KM, Kim G, Kim DJ, Yang SJ, Park SM, Yeom YI, Fisher PB, Kang D. Gene. 2009 Mar 15;433(1-2):32-9, Product: Pathway Studio |
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Parasite burden and CD36-mediated sequestration are determinants of acute lung injury in an experimental malaria model. Lovegrove FE, Gharib SA, Pea-Castillo L, Patel SN, Ruzinski JT, Hughes TR, Liles WC, Kain KC. PLoS Pathog. 2008 May 16;4(5):e1000068, Product: Pathway Studio |
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Investigating copper-regulated protein expression in Menkes fibroblasts using antibody microarrays. T Du, SL La Fontaine, M Abdo, SA Bellingham, M Greenough, I Volitakis, RA Cherny, AI Bush, PJ Hudson, J Camakaris, JF Mercer, PJ Crouch, CL Masters, VM Perreau, and AR White Proteomics, May 2008; 8(9): 1819-31, Product: Pathway Studio |
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Drinking-Water Arsenic Exposure Modulates Gene Expression in Human Lymphocytes from a U.S. Population Angeline S. Andrew, David A. Jewell, Rebecca A. Mason, Michael L. Whitfield, Jason H. Moore, and Margaret R. Karagas Environmental Health Perspectivesm Apr 20008, Product: Pathway Studio, ResNet |
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Tumor-stroma interactions in ovarian cancer: The role of CTGF in ovarian tumor biology Goli Samimi, Tomas Bonome, Sue Ghosh, Shu-wing Ng, Samuel Mok, and Michael Birrer AACR Meeting Abstracts, Apr 2008; 2008: 5379., Product: Pathway Studio |
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Gene Expression Based Recurrence Prediction of Hepatitis B Virus Related Human Hepatocellular Carcinoma Hyun Goo Woo et al Clin. Cancer Res., Apr 2008; 14: 2056 - 2064, Product: Pathway Studio |
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Intestinal tumors adapt to excess dietary iron by altering expression of lipocalin-2 and divalent metal ion transporter James Swain, Chunbiao Li, and Patrick Leahy FASEB J, Mar 2008; 22: 694.3., Product: Pathway Studio |
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Iron supplementation modulates genes involved in oxidoreductase activity, including prostaglandin-endoperoxide synthase 2 in intestinal tumors James Swain, Chunbiao Li, and Patrick Leahy FASEB J, Mar 2008; 22: 692.4, Product: Pathway Studio |
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Network of Paraventricular Nucleus Gene Expression in Angiotensin-salt Hypertension Lihui Yuan, Xia Li, Judith Sved, Alan Sved, Li Liu, and Mohan Raizada FASEB J, Mar 2008; 22: 1168.9, Product: Pathway Studio |
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Gene Expression Networks in Rostral Ventrolateral Medulla (RVLM) of Rats with Angiotensin-salt Hypertension Lihui Yuan, Xia Li, Judith Sved, Alan Sved, Mohan Raizada, and Li Liu FASEB J, Mar 2008; 22: 1168.10, Product: Pathway Studio |
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Transcriptional Adaptation to Clcn5 Knockout in Proximal Tubules of the Mouse Kidney Jerry Wright, Marcelo M. Morales, Jackson Sousa-Menzes, Debora Ornellas, Jennifer Sipes, and Sandra E. Guggino Physiol Genomics, Mar 2008; 10.1152/physiolgenomics.00024.2008, Product: PathwayAssist |
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Towards a pathway definition of Parkinson s disease: a complex disorder with links to cancer, diabetes and inflammation Linda B. Moran and Manuel B. Graeber Neurogenetics, Vol.9(1)2008, Product: Pathway Studio |
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IFN-beta-regulated genes show abnormal expression in therapy-nave relapsing remitting MS mononuclear cells: Gene expression analysis employing all reported protein protein interactions Ken D. Yamaguchi, Daniel L. Ruderman, Ed Croze, T. Charis Wagner, Sharlene Velichko, Anthony T. Reder, Hugh Salamon J Neuroimmunol. 2008 Feb 13, Product: Pathway Studio, ResNet |
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Scan of 977 nonsynonymous SNPs in CLL4 trial patients for the identification of genetic variants influencing prognosis Gabrielle S. Sellick, Rachel Wade, Susan Richards, David G. Oscier, Daniel Catovsky, and Richard S. Houlston Blood, Feb 2008; 111: 1625 - 1633, Product: PathwayAssist |
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Early Events in the Pathogenesis of Epithelial Ovarian Cancer Charles N. Landen, Jr, Michael J. Birrer, and Anil K. Sood J. Clin. Oncol., Jan 2008; 10.1200/JCO.2006.07.9970., Product: Pathway Studio |
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Signaling networks assembled by oncogenic EGFR and c-Met Ailan Guo, Judit Villn, Jon Kornhauser, Kimberly A. Lee, Matthew P. Stokes, Klarisa Rikova, Anthony Possemato, Julie Nardone, Gregory Innocenti, Randall Wetzel, Yi Wang, Joan MacNeill, Jeffrey Mitchell, Steven P. Gygi, John Rush, Roberto D. Polakiewicz, and Michael J. Comb PNAS, Jan 2008; 105: 692 - 697, Product: Pathway Studio |
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Harnessing genetically engineered mouse models for preclinical testing Robles, A.I., Varticovski, L. Chemico-Biological Interactions, 171 (2), p.159-164, Product: Pathway Studio |
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Gene Expression in Human Hippocampus from Cocaine Abusers Identifies Genes which Regulate Extracellular Matrix Remodeling Deborah C. Mash, Jarlath ffrench-Mullen, Nikhil Adi, Yujing Qin, Andrew Buck, and John Pablo PLoS ONE. 2007; 2(11): e1187, Product: Pathway Studio |
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A network-based approach to the analysis of acute wound healing N.B. Menke, K.R. Ward and R.F. Diegelmann Journal of Critical Care, Vol.22(4) 2007 p332, Product: Pathway Studio |
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Vascular microarray profiling in two models of hypertension identifies caveolin-1, Rgs2 and Rgs5 as antihypertensive targets. Grayson TH, Ohms SJ, Brackenbury TD, Meaney KR, Peng K, Pittelkow YE, Wilson SR, Sandow SL, Hill CE. BMC Genomics. 2007 Nov 7;8:404., Product: Pathway Studio |
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Frontiers in Nephrology: Genomic Approaches to Understanding the Molecular Basis of Atherosclerosis Euan A. Ashley, Joshua M. Spin, Raymond Tabibiazar, and Thomas Quertermous J. Am. Soc. Nephrol., Oct 2007; 10.1681/ASN.2007040514, Product: Pathway Studio |
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Differential expression of novel tyrosine kinase substrates during breast cancer development Yunhao Chen, Lee Yee Choong, Qingsong Lin, Robin Philps, Chee Hong Wong, Boon Keong Ang, Yee Ling Tan, Marie Chiew Shia Loh, Choy Leong Hew, Nilesh Shah, Brian J. Druker, Poh Kuan Chong, and Yoon Pin Lim Mol Cell Proteomics. 2007 Sep 12, Product: PathwayAssist |
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A novel computational approach to the genetics of polycystic ovarian syndrome (PCOS) M. Nam Menke, N.B. Menke, D.G. Bonchev, T.M. Witten, J.R. Wood and J.F. Straussa Fertility and Sterility, v. 88, Supp.1, Page S73, Product: Pathway Studio |
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Molecular signatures of trauma-hemorrhagic shock-induced lung injury: hemorrhage- and injury-associated genes. R Feinman, EA Deitch, V Aris, HB Chu, B Abungu, FJ Caputo, A Galante, D Xu, Q Lu, I Colorado, D Streck, J Dermody, and P Soteropoulos Shock. 2007 Sep;28(3):360-8, Product: PathwayAssist |
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Candidate genes, pathways and mechanisms for alcoholism: an expanded convergent functional genomics approach Z A Rodd, B A Bertsch, W N Strother, H Le-Niculescu, Y Balaraman, E Hayden, R E Jerome, L Lumeng, J I Nurnberger, H J Edenberg, W J McBride, A B Niculescu The Pharmacogenomics Journal (2007) 7, 222 256, Product: PathwayAssist |
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Profiling Studies in Ovarian Cancer: A Review Rudolf S. N. Fehrmann, Xiang-yi Li, Ate G. J. van der Zee, Steven de Jong, Gerard J. te Meerman, Elisabeth G. E. de Vries, and Anne P. G. Crijns Oncologist, Aug 2007; 12: 960 - 966, Product: PathwayAssist |
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Gene Systems Network Inferred from Expression Profiles in Hepatocellular Carcinogenesis by Graphical Gaussian Model Sachiyo Aburatani, Fuyan Sun, Shigeru Saito, Masao Honda, Shu-Ichi Kaneko, and Katsuhisa Horimoto EURASIP J Bioinform Syst Biol. 2007; 2007: 47214, Product: PathwayAssist |
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Early gene expression profiles during intraoperative myocardial ischemia-reperfusion in cardiac surgery Sara Arab, Igor E. Konstantinov, Cathy Boscarino, Eva Cukerman, Alessandro Mori, Jia Li, Peter P. Liu, Andrew N. Redington, and John G. Coles J. Thorac. Cardiovasc. Surg., Jul 2007; 134: 74 - 81., Product: PathwayAssist |
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Transcriptional network governing the angiogenic switch in human pancreatic cancer Abdollahi A, Schwager C, Kleeff J, Esposito I, Domhan S, Peschke P, Hauser K, Hahnfeldt P, Hlatky L, Debus J, Peters JM, Friess H, Folkman J, Huber PE. Proc Natl Acad Sci U S A. 2007 Jul 24, Product: Pathway Studio |
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Use of predictive gene expression signature from advanced-stage serous papillary ovarian cancer to identify biologically relevant molecular targets for chemoresponse L. Ozbun, T. Bonome, M. Radonovich, C. Pise-Masison, J. Brady, N. Caplen, M. Johnson, S. C. Mok, and M. J. Birrer ASCO Meeting Abstracts, Product: Pathway Studio |
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Endothelial Cells\' Activation and Apoptosis Induced by a Subset of Antibodies against Human Cytomegalovirus: Relevance to the Pathogenesis of Atherosclerosis Lunardi C, Dolcino M, Peterlana D, Bason C, Navone R, Tamassia N, Tinazzi E, Beri R, Corrocher R, Puccetti A. PLoS ONE. 2007 May 30;2:e473, Product: Pathway Studio |
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Tumor number and comparative micro-array analysis of tumor and adjacent non-tumor intestinal tissue after iron supplementation in ApcMin/+ mice James H. Swain, Adam M. Kresak, and Theresa P. Pretlow FASEB J, Apr 2007; 21: A384., Product: Pathway Studio |
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Global analysis of differentially expressed genes in androgen-independent prostate cancer Q Wei, M Li, X Fu, R Tang, Y Na, M Jiang, Y Li Prostate Cancer and Prostatic Diseases 10, 167 - 174, Product: Pathway Studio |
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Arthritis suppression by NADPH activation operates through an interferon- pathway Olofsson P, Nerstedt A, Hultqvist M, Nilsson EC, Andersson S, Bergelin A, Holmdahl R. BMC Biol. 2007 May 9;5:19, Product: Pathway Studio |
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Counting potentially functional variants in BRCA1, BRCA2 and ATM predicts breast cancer susceptibility Nichola Johnson, Olivia Fletcher, Claire Palles, Matthew Rudd, Emily Webb, Gabrielle Sellick, Isabel dos Santos Silva, Valerie McCormack, Lorna Gibson, Agnes Fraser, Angela Leonard, Clare Gilham, Sean V. Tavtigian, Alan Ashworth, Richard Houlston, and Julian Peto Hum. Mol. Genet., May 2007; 16: 1051 - 1057., Product: PathwayAssist |
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Applied information retrieval and multidisciplinary research: new mechanistic hypotheses in Complex Regional Pain Syndrome Hettne KM, de Mos M, de Bruijn AG, Weeber M, Boyer S, van Mulligen EM, Cases M, Mestres J, van der Lei J. J Biomed Discov Collab. 2007 May 4;2:2, Product: Pathway Studio |
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Expression changes in mouse brains following nicotine-induced seizures; the modulation of transcription factor networks Merav Kedmi and Avi Orr-Urtreger Physiol Genomics, Apr 2007; 10.1152/physiolgenomics.00288.2006, Product: Pathway Studio |
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Glycerol kinase deficiency alters expression of genes involved in lipid metabolism, carbohydrate metabolism, and insulin signaling Rahib L, Maclennan NK, Horvath S, Liao JC, Dipple KM. Eur J Hum Genet. 2007 Apr 4, Product: Pathway Studio |
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Highly purified CD38+ and CD38- sub-clones derived from the same chronic lymphocytic leukemia patient have distinct gene expression signatures despite their monoclonal origin C Pepper, R Ward, T T Lin, P Brennan, J Starczynski, M Musson, C Rowntree, P Bentley, K Mills, G Pratt, C Fegan Leukemia 21, 687 - 696 (01 Apr 2007), Product: Pathway Studio |
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Heterologous Tissue Culture Expression Signature Predicts Human Breast Cancer Prognosis Eun Sung Park, Ju-Seog Lee, Hyun Goo Woo, Fenghuang Zhan, Joanna H. Shih, John D. Shaughnessy, Jr., and J. Frederic Mushinski PLoS ONE. 2007; 2(1): e145, Product: Pathway Studio |
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Gene Alterations Identified by Expression Profiling in Tumor-Associated Endothelial Cells from Invasive Ovarian Carcinoma Chunhua Lu, Tomas Bonome, Yang Li, Aparna A. Kamat, Liz Y. Han, Rosemarie Schmandt, Robert L. Coleman, David M. Gershenson, Robert B. Jaffe, Michael J. Birrer, and Anil K. Sood Cancer Res., Feb 2007; 67: 1757 - 1768, Product: PathwayAssist |
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Bioinformatics analysis of the early inflammatory response in a rat thermal injury model Eric Yang, Timothy Maguire, Martin L Yarmush, Francois Berthiaume, and Ioannis P Androulakis BMC Bioinformatics. 2007; 8: 10, Product: Pathway Studio |
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Time-Dependent Rescue of Gene Expression by Androgens in the Mouse Proximal Caput Epididymidis-1 Cell Line after Androgen Withdrawal. Shayesta Seenundun and Bernard Robaire Endocrinology Vol. 148, No. 1 173-188, Product: Pathway Studio |
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Molecular Diagnostics in Sepsis: From Bedside to Bench T. Philip Chung et al J Am Coll Surg., Nov. 2006 |
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A Sex-Specific Role of Type VII Adenylyl Cyclase in Depression Hines LM, Hoffman PL, Bhave S, Saba L, Kaiser A, Snell L, Goncharov I, LeGault L, Dongier M, Grant B, Pronko S, Martinez L, Yoshimura M, Tabakoff B; World Health Organization/International Society for Biomedical Research on Alcoholism Study on State and Trait Markers of Alcohol Use and Dependence Investigators. The Journal of Neuroscience, Product: PathwayAssist |
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Essential role of Jun family transcription factors in PU.1 knockdown induced leukemic stem cells Ulrich Steidl, Frank Rosenbauer, Roel G W Verhaak, Xuesong Gu, Alexander Ebralidze, Hasan H Otu, Steffen Klippel, Christian Steidl, Ingmar Bruns, Daniel B Costa, Katharina Wagner, Manuel Aivado, Guido Kobbe, Peter J M Valk, Emmanuelle Passegu, Towia A Libermann, Ruud Delwel, Daniel G Tenen Nature Genetics 38, 1269 - 1277 (01 Nov 2006), Product: Pathway Studio |
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Search for low penetrance alleles for colorectal cancer through a scan of 1467 non-synonymous SNPs in 2575 cases and 2707 controls with validation by kin-cohort analysis of 14704 first-degree relatives Emily L. Webb, Matthew F. Rudd, Gabrielle S. Sellick, Rachid El Galta, Lara Bethke, Wendy Wood, Olivia Fletcher, Steven Penegar, Laura Withey, Mobshra Qureshi, Nichola Johnson, Ian Tomlinson, Richard Gray, Julian Peto and Richard S. Houlston Hum. Mol. Genetics, Product: Pathway Studio |
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Characterization of differential gene expression profiles in diabetic embryopathy using DNA microarray analysis. Reece EA, Ji I, Wu YK, Zhao Z. Am J Obstet Gynecol. 2006 Oct;195(4):1075-80., Product: Pathway Studio |
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Identification of molecular markers and signaling pathway in endometrial cancer in Hong Kong Chinese women by genome-wide gene expression profiling Y F Wong, T H Cheung, K W K Lo, S F Yim, N S S Siu, S C S Chan, T W F Ho, K W Y Wong, M Y Yu, V W Wang, C Li, G J Gardner, T Bonome, W B Johnson, D I Smith, T K H Chung, M J Birrer Oncogene. 2006 Oct 16, Product: Pathway Studio |
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Candidate genes, pathways and mechanisms for alcoholism: an expanded convergent functional genomics approach Z A Rodd, B A Bertsch, W N Strother, H Le-Niculescu, Y Balaraman, E Hayden, R E Jerome, L Lumeng, J I Nurnberger, H J Edenberg, W J McBride, A B Niculescu The Pharmacogenomics Journal (10 Oct 2006), Product: Pathway Studio |
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Search for low penetrance alleles for colorectal cancer through a scan of 1,467 non-synonymous SNPs in 2,575 cases and 2,707 controls with validation by kin-cohort analysis of 14,704 first-degree relatives Webb EL, Rudd MF, Sellick GS, El Galta R, Bethke L, Wood W, Fletcher O, Penegar S, Withey L, Qureshi M, Johnson N, Tomlinson I, Gray R, Peto J, Houlston RS. Hum Mol Genet, Product: PathwayAssist |
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Agonist and Antagonist of Retinoic Acid Receptors Cause Similar Changes in Gene Expression and Induce Senescence-like Growth Arrest in MCF-7 Breast Carcinoma Cells Yuhong Chen, Milos Dokmanovic, Wilfred D. Stein, Robert J. Ardecky, and Igor B. Roninson Cancer Res., Sep 2006; 66: 8749 - 8761, Product: PathwayAssist |
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Respiratory Epithelial Gene Expression in Patients with Mild and Severe Cystic Fibrosis Lung Disease Jerry M. Wright, Christian A. Merlo, Jeffrey B. Reynolds, Pamela L. Zeitlin, Joe G. N. Garcia, William B. Guggino, and Michael P. Boyle Am. J. Respir. Cell Mol. Biol., Sep 2006; 35: 327 - 336., Product: Pathway Studio |
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Evidence for chronic, peripheral activation of neutrophils in polyarticular juvenile rheumatoid arthritis. Jarvis JN, Petty HR, Tang Y, Frank MB, Tessier PA, Dozmorov I, Jiang K, Kindzelski A, Chen Y, Cadwell C, Turner M, Szodoray P, McGhee JL, Centola M. Arthritis Res Ther. 2006; 8(5): R154, Product: Pathway Studio |
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Physiologic and Genomic Analyses of Nutrition-Ethanol Interactions During Gestation: Implications for Fetal Ethanol Toxicity Kartik Shankar, Mats Hidestrand, Xiaoli Liu, Rijin Xiao, Charles M. Skinner, Frank A. Simmen, Thomas M. Badger, and Martin J. J. Ronis Experimental Biology and Medicine, Sep 2006; 231: 1379 - 1397., Product: PathwayAssist |
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Identification of Cell Cycle Regulatory and Inflammatory Genes As Predominant Targets of p38 Mitogen-Activated Protein Kinase in the Heart Olli Tenhunen, Jaana Rys, Mika Ilves, Ylermi Soini, Heikki Ruskoaho, and Hanna Leskinen Circ. Res., Sep 2006; 99: 485 - 493., Product: PathwayAssist |
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Expression Profiling Identifies Altered Expression of Genes That Contribute to the Inhibition of Transforming Growth Factor- Signaling in Ovarian Cancer Jan S. Sunde, Howard Donninger, Kongming Wu, Michael E. Johnson, Richard G. Pestell, G. Scott Rose, Samuel C. Mok, John Brady, Tomas Bonome, and Michael J. Birrer Cancer Res.; 66: 8404 - 8412., Product: PathwayAssist |
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Text mining of full-text journal articles combined with gene expression analysis reveals a relationship between sphingosine-1-phosphate and invasiveness of a glioblastoma cell line Jeyakumar Natarajan, Daniel Berrar, Werner Dubitzky, Catherine Hack, Yonghong Zhang, Catherine DeSesa, James R Van Brocklyn and Eric G Bremer BMC Bioinformatics 2006, 7:373, Product: Pathway Studio |
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Histology-Based Expression Profiling Yields Novel Prognostic Markers in Human Glioblastoma Shumin Dong, MB, PhD, Catherine L. Nutt, PhD, Rebecca A. Betensky, PhD, Anat O. Stemmer-Rachamimov, MD, Nicholas C. Denko, MD, PhD, Keith L. Ligon, MD, PhD, David H. Rowitch, MD, PhD, and David N. Louis, MD J Neuropathol Exp Neurol. 2005 November; 64(11): 948 955., Product: Pathway Studio |
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Stat3 Is Required for Cytoprotection of the Respiratory Epithelium during Adenoviral Infection Yohei Matsuzaki, Yan Xu, Machiko Ikegami, Valrie Besnard, Kwon-Sik Park, William M. Hull, Susan E. Wert and Jeffrey A. Whitsett2 The Journal of Immunology, 2006, 177: 527-537., Product: PathwayAssist |
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de Novo biosynthetic profiling of high abundance proteinsin cystic fibrosis lung epithelial cells Harvey B. Pollard, Ofer Eidelman, Catherine Jozwik, Wei Huang, Meera Srivastava, X-D Ji, Bridget McGowan, Christine Formas Norris, Sutoshi Todo, Thomas Darling, Peter J. Mogayzel, Pamela L. Zeitlin, Jerry Wright, William B. Guggino, Eleanore Metcalf, William Driscoll, Greg Mueller, Cloud Paweletz, and David M. Jacobowitz Mol. Cell. Proteomics, Jul 2006; 10.1074/mcp.M600091-MCP200., Product: PathwayAssist |
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Characterization of cell-type specific profiles in tissues and isolated cells from squamous cell carcinomas of the lung Lesleyann Hawthorn, Leighton Stein, Jenniffer Panzarella, Gregory M. Loewen and Heinz Baumann Lung Cancer, 04, 2006, Product: Pathway Studio |
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Characterization of cell-type specific profiles in tissues and isolated cells from squamous cell carcinomas of the lung Lesleyann Hawthorn, Leighton Stein, Jenniffer Panzarella, Gregory M. Loewen and Heinz Baumann Lung Cancer, 04, 2006, Product: Pathway Studio |
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Variants in the GH-IGF axis confer susceptibility to lung cancer Rudd MF, Webb EL, Matakidou A, Sellick GS, Williams RD, Bridle H, Eisen T, Houlston RS; GELCAPS Consortium. Genome Research, Product: PathwayAssist |
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Signatures of human regulatory T cells: an encounter with old friends and new players. Pfoertner S, Jeron A, Probst-Kepper M, Guzman CA, Hansen W, Westendorf AM, Toepfer T, Schrader AJ, Franzke A, Buer J, Geffers R Genome Biol. 2006 Jun 12;7(7):, Product: Pathway Studio |
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Parallel analysis of transcript and translation profiles: identification of metastasis-related signal pathways differentially regulated by drug and genetic modifications Yang H, Yu LR, Yi M, Lucas DA, Lukes L, Lancaster M, Chan KC, Issaq HJ, Stephens RM, Conrads TP, Veenstra TD, Hunter KW. J Proteome Res. 2006 July 7; 5(7): 1555 1567., Product: Pathway Studio |
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Gene expression alterations in brains of mice infected with three strains of scrapie. Skinner PJ, Abbassi H, Chesebro B, Race RE, Reilly C, Haase AT. BMC Genomics. 2006; 7: 114., Product: Pathway Studio |
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Mechanisms and Effects of Loss of Human Leukocyte Antigen Class II Expression in Immune-Privileged Site-Associated B-Cell Lymphoma Marije Booman, Jenny Douwes, Annuska M. Glas, Sietske A. Riemersma, Ekaterina S. Jordanova, Klaas Kok, Andreas Rosenwald, Daphne de Jong, Ed Schuuring, and Philip M. Kluin Clin. Cancer Res., May 2006; 12: 2698 - 2705, Product: PathwayAssist |
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DNA microarray analysis of striatal gene expression in symptomatic transgenic Huntington\'s mice (R6/2) reveals... Crocker, S.F. Costain, W.J. Robertson, H.A. Brain Research, May 2006, Product: Pathway Studio |
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cis-Regulatory sequences of the genes involved in apoptosis, cell growth, and proliferation may provide a target for some of the effects of acute ethanol exposure Uddin, R.K. Singh, S.M. Brain Research, May 2006, Product: Pathway Studio |
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Functional Genomic Responses to Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) and CFTR508 in the Lung Xu Y, Liu C, Clark JC, Whitsett JA. J Biol Chem. 2006 Apr 21;281(16):11279-11291, Product: PathwayAssist |
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Respiratory Epithelial Gene Expression in Cystic Fibrosis Patients with Mild and Severe Lung Disease. Wright JM, Merlo CA, Reynolds JB, Zeitlin PL, Garcia JG, Guggino WB, Boyle MP. Am J Respir Cell Mol Biol. 2006 Apr 13, Product: PathwayAssist |
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A genome-scale assessment of peripheral blood B-cell molecular homeostasis in patients with rheumatoid arthritis Szodoray P, Alex P, Frank MB, Turner M, Turner S, Knowlton N, Cadwell C, Dozmorov I, Tang Y, Wilson PC, Jonsson R, Centola M. Rheumatology (Oxford). 2006 Apr 25;, Product: PathwayAssist |
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Gingival epithelial cells heterozygous for Toll-like receptor 4 polymorphisms Asp299Gly and Thr399ile are hypo-responsive to Porphyromonas gingivalis Kinane DF, Shiba H, Stathopoulou PG, Zhao H, Lappin DF, Singh A, Eskan MA, Beckers S, Waigel S, Alpert B, Knudsen TB. Genes and Immunity (2006) 7,, Product: Pathway Studio |
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A novel prognostic subtype of human hepatocellular carcinoma derived from hepatic progenitor cells Ju-Seog Lee, Jeonghoon Heo, Louis Libbrecht, In-Sun Chu, Pal Kaposi-Novak, Diego F Calvisi, Arsen Mikaelyan, Lewis R Roberts, Anthony J Demetris, Zongtang Sun, Frederik Nevens, Tania Roskams & Snorri S Thorgeirsson Nature Medicine 12, 410 - 416 (2006), Product: Pathway Studio |
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Identification of novel prognostic subtype of hepatocellular carcinoma derived from hepatic stem cells by comparative functional genomic approach. Ju-Seog Lee, Jeonghoon Heo, Louis Libbrecht, In-Sun Chu, Pal Kaposi-Novak, Diego F. Calvisi, Arsen Mikaelyan, Lewis R. Roberts, Anthony J. Demetris, Zongtang Sun, Frederik Nevens, Tania Roskams, and Snorri S. Thorgeirsson ACR Meeting Abstracts, 2006: 1338 - 1339., Product: PathwayAssist |
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Global gene expression profiling of mucinous ovarian tumors and cystadenomas identifies genes of clinicopathologic importance Fred W. A. Wamunyokoli, Tomas Bonome, Ji-Young Lee, Colleen M. Feltmate, William R. Welch, Mike Radonovich, Cindy Pise-Masison, John Brady, Ke Hao, Ross S. Berkowitz, Samuel Mok, and Michael J. Birrer AACR Meeting Abstracts, 2006: 1057 - 1058, Product: PathwayAssist |
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Expression profiling of peripheral blood cells for early detection of breast cancer Jrgen M. Aare, Torbjrn Lindahl, Solve Sb, Per Skaane, Simen Myhre, Turid Reiersen, Anders Lnneborg, Anne-Lise Brresen-Dale, and Praveen Sharma AACR Meeting Abstracts,2006: 29 - 30., Product: PathwayAssist |
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A Myeloma-specific panel of 3,500 SNP-based functional genetic variants relevant to the etiology and treatment outcome in multiple myeloma David C. Johnson, Suzanne M. Grindle, David Gonzalez, Christine Ramos, Faith Davies, Brian A. Walker, Brian G. Durie, Brian G. Van Ness, and Gareth J. Morgan AACR Meeting Abstracts, Apr 2006; 2006: 40., Product: PathwayAssist |
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Gene Expression Arrays in Juvenile Rheumatoid Arthritis: Will the Blind Men Finally See the Elephant? Jarvis, J.N. Current Problems in Pediatric and Adolescent Health Care, Mar 2006, Product: Pathway Studio |
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Activation of IFN pathways and plasmacytoid dendritic cell recruitment in target organs of primary Sjgren s syndrome Gottenberg JE, Cagnard N, Lucchesi C, Letourneur F, Mistou S, Lazure T, Jacques S, Ba N, Ittah M, Lepajolec C, Labetoulle M, Ardizzone M, Sibilia J, Fournier C, Chiocchia G, Mariette X. Proc Natl Acad Sci U S A. 2006 Feb 13, Product: PathwayAssist |
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Expression profiling of mucinous tumors of the ovary identifies genes of clinicopathologic importance. Wamunyokoli FW, Bonome T, Lee JY, Feltmate CM, Welch WR, Radonovich M, Pise-Masison C, Brady J, Hao K, Berkowitz RS, Mok S, Birrer MJ. Clin Cancer Res. 2006 Feb 1;12(3 Pt 1):690-700., Product: PathwayAssist |
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Use of microarray biomarkers to identify longevity therapeutics Stephen R. Spindler Aging Cell, Volume 5 Page 39, Product: Pathway Studio |
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Adaptation and increased susceptibility to infection associated with constitutive expression of misfolded SP-C James P. Bridges, Yan Xu, Cheng-Lun Na, Hector R. Wong, and Timothy E. Weaver The Rockefeller University Press, 0021-9525, Product: PathwayAssist |
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Transcriptional targets of hepatocyte growth factor signaling and Ki-ras oncogene activation in colorectal cancer Seiden-Long IM, Brown KR, Shih W, Wigle DA, Radulovich N, Jurisica I, Tsao MS. Oncogene. 2006 Jan 5;25(1):91-102., Product: Pathway Studio |
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Transcriptional Profiling of Reporter Genes Used for Molecular Imaging of Embryonic Stem Cell Transplantation Joseph C Wu, Joshua M Spin, Feng Cao, Shuan Lin, Xiaoyan Xie, Olivier Gheysens, Ian Y Chen, Ahmad Y Sheikh, Robert C Robbins, Anya Tsalenko, Sanjiv S. Gambhir, and Tom Quertermous Physiol Genomics, Jan 2006; 10.1152/physiolgenomics.00254.2005., Product: PathwayAssist |
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Gene expression profile of activated microglia under conditions associated with dopamine neuronal damage David M. Thomas, Dina M. Francescutti-Verbeem, and Donald M. Kuhn FASEB J, Dec 2005, Product: PathwayAssist |
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Gene expression microarray studies in polygenic psychiatric disorders: Applications and data analysis Konradi, C. Brain Research Reviews, Dec 2005, Product: Pathway Studio |
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Expression Profiling of Serous Low Malignant Potential, Low-Grade, and High-Grade Tumors of the Ovary Tomas Bonome, Ji-Young Lee, Dong-Choon Park, Mike Radonovich, Cindy Pise-Masison, John Brady, Ginger J. Gardner, Ke Hao, Wing H. Wong, J. Carl Barrett, Karen H. Lu, Anil K. Sood, David M. Gershenson, Samuel C. Mok and Michael J. Birrer Cancer Research 65, 10602-10612, November 15, 2005, Product: PathwayAssist |
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Discovering causes and cures for cancer from gene expression analysis Weeraratna, A.T. Ageing Research Reviews, Nov 2005, Product: Pathway Studio |
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Characterization of human fibrocytes as circulating adipocyte progenitors and the formation of human adipose tissue in SCID mice Kurt M. Hong, Marie D. Burdick, Roderick J. Phillips& FASEB J, Sep 2005; 10.1096/fj.05-4295fje, Product: PathwayAssist |
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Gene expression profiling of mantle cell lymphoma cells reveals aberrant expression of genes from the PI3K-AKT, WNT and TGF signalling pathways Edgar Gil Rizzatti, Roberto Passetto Falcao, Rodrigo Alexandre Panepucci, Rodrigo Proto-Siqueira, Wilma Terezinha Anselmo-Lima, Oswaldo Keith Okamoto, Marco Antonio Zago British Journal of Haematology, Volume 130, Issue 4, Page 516-526, Aug 2005, Product: Pathway Studio |
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Pharmacogenomic profiling of an oxidative stress-mediated spongiform encephalopathy Golden, T.R. Hubbard, A. Morten, K.J. Hinerfeld, D. Melov, S. Free Radical Biology and Medicine, Jul 2005, Product: Pathway Studio |
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Sp1 and NFkappaB pathways are regulated in brain in response to acute and chronic ethanol. Rulten SL, Ripley TL, Hunt CL, Stephens DN, Mayne LV. Genes, Brain and Behavior, 2006, Product: Pathway Studio |
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Diabetes Enhances mRNA Levels of Proapoptotic Genes and Caspase Activity, Which Contribute to Impaired Healing Hesham A. Al-Mashat, Suneel Kandru, Rongkun Liu, Yugal Behl, Tesfahun Desta, and Dana T. Graves Diabetes 55:487-495, 2006, Product: PathwayAssist |
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Proteomic analysis of protein expression and oxidative modification in R6/2 transgenic mice - A model of Huntington\'s disease Marzia Perluigi, H. Fai Poon, William Maragos, William M. Pierce, Jon B. Klein, Vittoriio Calabrese, Chiara Cini, Carlo De Marco, and D. Allan Butterfield Mol. Cell. Proteomics, Jun 2005, Product: PathwayAssist |
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High-Resolution Mapping of Genomic Imbalance and Identification of Gene Expression Profiles Associated with Differential Chemotherapy Response in Serous Epithelial Ovarian Cancer. Bernardini M, Lee CH, Beheshti B, Prasad M, Albert M, Marrano P, Begley H, Shaw P, Covens A, Murphy J, Rosen B, Minkin S, Squire JA, Macgregor PF. Neoplasia. 2005 Jun; 7(6): 603-613, Product: Pathway Studio |
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Genetic association, post-translational modification and protein-protein interactions in type 2 diabetes mellitus Amitabh Sharma, Sreenivas Chavali, Anubha Mahajan, Rubina Tabassum, Vijaya Banerjee, Nikhil Tandon, and Dwaipayan Bharadwaj Mol. Cell. Proteomics, May 2005, Product: PathwayAssist |
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Gene Expression in Glaucomatous Retinas Implicate the TNF Mediated Pathway in Retinal Ganglion Cell Death N. Piri, J.M. K. Kwong, M. Song, and J. Caprioli Invest. Ophthalmol. Vis. Sci., May 2005, Product: PathwayAssist |
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Comparative Host Gene Transcription by Microarray Analysis Early after Infection of the Huh7 Cell Line by Severe Acute Respiratory Syndrome Coronavirus and Human Coronavirus 229E Bone S. F. Tang, Kwok-hung Chan, Vincent C. C. Cheng, Patrick C. Y. Woo, Susanna K. P. Lau, Clarence C. K. Lam, Tsun-leung Chan, Alan K. L. Wu, Ivan F. N. Hung, Suet-yi Leung, and Kwok-yung Yuen J. Virol., May 2005, Product: PathwayAssist |
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Global Gene Expression Analysis of Keloid Fibroblasts in Response to Electron Beam Irradiation Reveals the Involvement of Interleukin-6 Pathway Tosa M, Ghazizadeh M, Shimizu H, Hirai T, Hyakusoku H, Kawanami O. Journal of Investigative Dermatology 124, 704-713, Product: Pathway Studio |
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Pathway analysis of whole genomic expression profiles of colorectal cancer biopsy samples Orsolya Galamb, Ferenc Sipos, Sndor Spisk, Bla Molnr, Andrea Ladnyi, and Zsolt Tulassay AACR Meeting Abstracts, Product: PathwayAssist |
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Alterations of apoptosis in a rhabdomyosarcoma patient with Li-Fraumeni syndrome, familial syndactyly, and absence of germline p53 mutation. Malgorzata Pienkowska, Rika Tsuchida, Elizabeth Sexsmith, Jane Bayani, Gloria Lim, Jeremy A. Squire, and David Malkin AACR Meeting Abstracts, Product: PathwayAssist |
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Identification of genes related to cisplatin-resistance in four isogenic human ovarian cancer cell lines, which only differ in their degree of cisplatin resistance Anne P. G. Crijns, Gert Jan Meersma, Steven De Jong, Gerard J. Te Meerman, Frans Gerbens, Robert M. W. Hofstra, Elisabeth G. E. De Vries and Ate G. J. Van der Zee AACR Meeting Abstracts, Product: PathwayAssist |
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Functional Genomic Relationships in HIV-1 Disease Revealed by Gene-Expression Profiling of Primary Human Peripheral Blood Mononuclear Cells Christian F. Ockenhouse, Wendy B. Bernstein,2 Zhining Wang, and Maryanne T. Vahey The Journal of Infectious Diseases 2005 Jun 15; 191(12):2064-74., Product: Pathway Studio |
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The p53 Tumor Suppressor Network Is a Key Responder to Microenvironmental Components of Chronic Inflammatory Stress Frank Staib, Ana I. Robles, Lyuba Varticovski, Xin W. Wang, Barry R. Zeeberg, Michail Sirotin, Victor B. Zhurkin, Lorne J. Hofseth, S. Perwez Hussain, John N. Weinstein, Peter R. Galle and Curtis C. Harris Cancer Research 65, 10255-10264, November 15, 2005, Product: PathwayAssist |
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Cocaine-induced changes in the expression of apoptosis-related genes in the fetal mouse cerebral wall Svetlana I. Novikova, Fang He, Jie Bai, Irina Badan, Irina A. Lidow, Michael S. Lidow Neurotoxicology and Teratology, 2004, Product: Pathway Studio |
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Novel approaches to gene expression analysis of active polyarticular juvenile rheumatoid arthritis James N Jarvis, Igor Dozmorov, Kaiyu Jiang, Mark Barton Frank, Peter Szodoray, Philip Alex and Michael Centola Arthritis Res. Ther. 2004, 6:R15 - R32, Product: Pathway Studio |
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Gene profile changes after Pseudomonas aeruginosa exposure in immortalized airway epithelial cells Aura Perez, Pamela B. Davis Journal of Structural and Functional Genomics 5 (3): 179-194, 2004, Product: Pathway Studio |
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Whole genome expression profiling of advance stage papillary serous ovarian cancer reveals activated pathways. Donninger H, Bonome T, Radonovich M, Pise-Masison CA, Brady J, Shih JH, Barrett JC, Birrer MJ. Oncogene. 2004 Sep 13, Product: Pathway Studio |
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CANDIDATE GENE SELECTION FOR DEVELOPMENTAL DYSLEXIA: A BIOINFORMATICS APPROACH Orourke J, Platko JV, and Pauls D , Product: Pathway Studio |
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Growth Hormone Receptor Deficiency Is Associated with a Major Reduction in Pro-Aging Signaling, Cancer, and Diabetes in Humans Jaime Guevara-Aguirre, Priya Balasubramanian, Marco Guevara-Aguirre, Min Wei, Federica Madia, Chia-Wei Cheng, David Hwang, Alejandro Martin-Montalvo, Jannette Saavedra, Sue Ingles, Rafael de Cabo, Pinchas Cohen, and Valter D. Longo Science Translational Medicine |
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Stage-Specific Expression of TNF Regulates Bad/Bid-Mediated Apoptosis and RIP1/ROS-Mediated Secondary Necrosis in Birnavirus-Infected Fish Cells Wei-Lun Wang et al PLoS One |
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Analysis of EGFR signaling pathway in nasopharyngeal carcinoma cells by quantitative phosphoproteomics L Ruan, XH Li, XX Wan, H Yi, C Li, MY Li, PF Zhang, GQ Zeng, JQ Qu, QY He, JH Li, Y Chen, ZC Chen, and ZQ Xiao Proteome Sci |
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Estrogen Receptor Induces Antiinflammatory and Antitumorigenic Networks in Colon Cancer Cells Karin Edvardsson, Anders Strm, Philip Jonsson, Jan-ke Gustafsson, and Cecilia Williams Mol. Endocrinol. |
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Pathway analysis of primary human non-small cell lung cancer (NSCLC) N. Daraselia, Y. Wang, A. Budoff, A. Lituev, O. Potapova, J. Monforte, and V. Ossovskaya ASCO Meeting Abstracts |
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Gene expression profiling predicts nonresponders to chemoradiation in HPV16-positive head and neck squamous cell carcinoma B. J. Thibodeau, T. J. Geddes, S. Ahmed, B. L. Pruetz, P. Y. Chen, G. D. Wilson, and J. A. Akervall ASCO Meeting Abstracts |
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Identification of new autoantibody specificities directed at proteins involved in the transforming growth factor beta pathway in patients with systemic sclerosis G Bussone, H Dib, MC Tamby, C Broussard, C Federici, G Woimant, L Camoin, L Guillevin, and L Mouthon Arthritis Res Ther |
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Two-tiered Approach Identifies a Network of Cancer and Liver Disease-related Genes Regulated by miR-122 Daniel R. Boutz, Patrick J. Collins, Uthra Suresh, Mingzhu Lu, Cristina M. Ramrez, Carlos Fernndez-Hernando, Yufei Huang, Raquel de Sousa Abreu, Shu-Yun Le, Bruce A. Shapiro, Angela M. Liu, John M. Luk, Shelley Force Aldred, Nathan D. Trinklein, Edward M. Marcotte, and Luiz O. F. Penalva J. Biol. Chem., May 2011; 286: 18066 - 18078 |
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Serum Autoantibodies Following Laser Induced Retinal Injury in Rabbits Sarah E. Scott, Rachida Bouhenni, Anthony Chomyk, Jayaprakash Patil, Michael Hart, Hiroshi Nakamura, and Deepak P. Edward Invest. Ophthalmol. Vis. Sci., Apr 2011; 52: 2919. |
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The Impact of MicroRNAs on Nr2e3 Associated Retinal Disease Austin S. Jelcick, James Reinecke, Yang Yuan, and Neena B. Haider Invest. Ophthalmol. Vis. Sci., Apr 2011; 52: 5416. |
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TMPRSS2/ERG fusion gene expression alters chemo- and radio-responsiveness in cell culture models of androgen independent prostate cancer. TA Swanson, SA Krueger, S Galoforo, BJ Thibodeau, AA Martinez, GD Wilson, and B Marples Prostate, Mar 2011 |
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Global response of Plasmodium falciparum to hyperoxia: a combined transcriptomic and proteomic approach Torrentino-Madamet M, Almras L, Desplans J, Le Priol Y, Belghazi M, Pophillat M, Fourquet P, Jammes Y, Parzy D. Malar J. 2011 Jan 11;10:4 |
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Induction of Metastatic Gastric Cancer by Peroxisome Proliferator-Activated Receptor Activation Claire B. Pollock et al PPAR Res. |
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Calcium Prevents Tumorigenesis in a Mouse Model of Colorectal Cancer Ji-Lin Wang, Yan-Wei Lin, Hui-Min Chen, Xuan Kong, Hua Xiong, Nan Shen, Jie Hong, Jing-Yuan Fang PLoS One. 2011; 6(8): e22566 |
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Ginkgo may prevent genetic-associated ovarian cancer risk: multiple biomarkers and anticancer pathways induced by ginkgolide B in BRCA1-mutant ovarian epithelial cells W Jiang, W Qiu, Y Wang, Q Cong, D Edwards, B Ye, and C Xu Eur J Cancer Prev |
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Candidate gene association analysis of acute lymphoblastic leukemia identifies new susceptibility locus at 11p15 (LMO1) Joke Beuten, Jonathan A.L. Gelfond, Duangjai Piwkham, Brad H. Pollock, Naomi J. Winick, Anderson B. Collier, III, and Gail E. Tomlinson Carcinogenesis, Sep 2011; 32: 1349 - 1353 |
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Deletion of a subgroup of ribosome-related genes minimizes hypoxia-induced changes and confers hypoxia tolerance Ajit N. Shah, Daniela Cadinu, R. Michael Henke, Xiantong Xin, Ranita Ghosh Dastidar, and Li Zhang Physiol Genomics, Jul 2011; 43: 855 - 872 |
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Proteomic analysis of myocardial tissue from the border zone during early stage post-infarct remodelling in rats Fei Xiang, Zhonghua Shi, Xuejiang Guo, Zhibing Qiu, Xujun Chen, Fuhua Huang, Jiahao Sha, and Xin Chen Eur J Heart Fail. 10 December 2010, 10.1093/eurjhf/hfq196 |
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The use of proteomics as a research methodology for studying cancer-related fatigue: a review Ollie Minton Palliative Medicine, Vol. 24, No. 3, Apr. 2010 |
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Investigation of Human Testis Protein Heterogeneity Using Two-Dimensional Electrophoresis Xuejiang Guo et al J Androl., Feb. 2010 |
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Identification of tyrosine phosphoproteins in signaling pathway triggered TGF-a by using functional proteomics technology Lin Ruan, Guo-Liang Wang, Yan Chen, Hong Yi, Can-E Tang, Peng-Fei Zhang, Mao-Yu Li, Cui Li, Fang Peng, Jian-Ling Li, Zhu-Chu Chen, Zhi-Qiang Xiao Med Oncol, Jan 2010 |
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Global phosphoproteomic effects of natural tyrosine kinase Guang-Rong Yan, Chuan-Le Xiao, Gui-Wei He, Xing-Feng Yin, Nan-Peng Chen, Ya Cao, Qing-Yu He Proteomics, Jan 2010 |
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Proteomic analysis of honeybee worker (Apis mellifera) hypopharyngeal glanddevelopment Mao Feng, Yu Feng, JianKe Li BMC Genomics, Dec. 2009 |
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Comparative proteomic analysis to discover potential therapeutic targets in human multiple myeloma. Proteomics Clin Appl 1 Nov 2009 3(11): p. 1348. |
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Involvement of potential pathways in malignant transformation from Oral Leukoplakia to Oral Squamous Cell Carcinoma revealed by proteomic analysis Zhi Wang , Xiaodong Feng, Xinyu Liu , Lu Jiang , Xin Zeng , Ning Ji , Jing Li1, Longjiang Li and Qianming Chen BMC Genomics, 10 (1), p.383, Aug 2009, Product: Pathway Studio, ResNet |
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Evaluation of Blastomere Biopsy Using a Mouse Model Indicates the Potential High Risk of Neurodegenerative Disorders in the Offspring Yu et al Mol. Cell. Proteomics. 2009; 8(7): p. 1490-1500, Product: Pathway Studio |
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Proteome analysis of biomarkers in the cerebrospinal fluid of neuromyelitis optica patients S Bai, S Liu, X Guo, Z Qin, B Wang, X Li, Y Qin, and YH Liu Mol Vis 1 Jan 2009 15: p. 1638, Product: Pathway Studio |
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Proteome analysis of haptoglobin in cerebrospinal fluid of neuromyelitis optica. Shumei Bai, Shilian Liu, Xuxiao Guo, Zhaoyu Qin, Banqin Wang, Xiaohong Li, and Yanjiang Qin Mol Biol Rep,May 15, 2009, Product: Pathway Studio |
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Stress Proteins and Immunostimulatory Signaling Through Toll-Like Receptors in Glaucoma C. Luo, X. Yang, D. W. Powell, J. B. Klein, and G. Tezel Invest. Ophthalmol. Vis. Sci.,Apr 2009; 50: 4048, Product: Pathway Studio |
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Proteomics Supports Different Pathways of Complement Activity in Human Glaucoma G. Tezel, X. Yang, C. Luo, D. W. Powell, J. B. Klein, H. J. Kaplan, and M. H. Kuehn Invest. Ophthalmol. Vis. Sci.,Apr 2009; 50: 4044, Product: Pathway Studio |
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Proteomic Analysis of TNF-{alpha}Signaling in Human Glaucoma X. Yang, C. Luo, D. W. Powell, J. B. Klein, M. H. Kuehn, and G. Tezel Invest. Ophthalmol. Vis. Sci.,Apr 2009; 50: 4043, Product: Pathway Studio |
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Proteomic analysis of salt-stressed tomato (Solanum lycposersicum) seedlings: effect of genotype and exogenous application of glycinebetaine Songbi Chen, Natan Gollop, and Bruria Heuer J. Exp. Bot., Mar 2009, Product: Pathway Studio |
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Evaluation of blastomere biopsy using mouse model indicates the potential high-risk of neurodegenerative disorders in the offspring Yang Yu, Jindao Wu, Yong Fan, Zhuo Lv, Xuejiang Guo, Chun Zhao, Rong Zhou, Zhuo Zhang, Fuqiang Wang, Min Xiao, Ling Chen, Hui Zhu, Wen Chen, Min Lin, Jiayin Liu, Zuomin Zhou, Liu Wang, Ran Huo, Qi Zhou, and Jiahao Sha Mol. Cell. Proteomics, Mar 2009, Product: Pathway Studio |
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Genomic analyses of Musashi1 downstream targets show a strong association with cancer related processes Raquel de Sousa Abreu et al J. Biol. Chem., Mar 2009; 10.1074/jbc.M809605200, Product: Pathway Studio |
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Comparative Mitochondrial Proteomic Analysis of Raji Cells Exposed to Adriamycin. Yu-Jie Jiang, Qing Sun, Xiao-Sheng Fang, and Xin Wang Mol Med 11 Feb 2009, Product: Pathway Studio |
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Label-free mass spectrometry-based protein quantification technologies in proteomic analysis Mu Wang, Jinsam You, Kerry G. Bemis, Tony J. Tegeler, and Dawn P. G.Brown Brief Funct Genomic Proteomic. 2008; 7(5): p. 329-339, Product: Pathway Studio |
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Mitochondrial dysregulation of osteoarthritic human articular chondrocytes analyzed by proteomics: A decrease in mitochondrial superoxide dismutase points to a redox imbalance Cristina Ruiz-Romero, Valentina Calamia, Jesus Mateos, Vanesa Carreira, Montserrat Martnez-Gomariz, Mercedes Fernndez, and Francisco J. Blanco Mol. Cell. Proteomics, Sep 2008; 10.1074/mcp.M800292-MCP200., Product: Pathway Studio |
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Identification of early responsive genes in human amnion epithelial FL cells induced by N-methyl-N2 -nitro-N-nitrosoguanidine using oligonucleotide microarray and quantitative real-time RT-PCR approaches Li H, Shao J, Lu X, Gao Z, Yu Y Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis, 644 (1), p.1-10, Product: Pathway Studio |
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Different signaling pathways expressed by chicken naive CD4(+) T cells, CD4(+) lymphocytes activated with staphylococcal enterotoxin B, and those malignantly transformed by Marek\'s disease virus. Buza JJ, Burgess SC Journal of proteome research, 7 (6), p.2380-2387, Product: Pathway Studio |
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Label-free mass spectrometry-based protein quantification technologies in proteomic analysis Mu Wang, Jinsam You, Kerry G. Bemis, Tony J. Tegeler, and Dawn P. G. Brown Brief Funct Genomic Proteomic, Jun 2008; 10.1093/bfgp/eln031, Product: Pathway Studio |
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Gene expression analysis of terminal differentiation of human melanoma cells highlights global reductions in cell cycle-associated genes. Huynh KM, Kim G, Kim DJ, Yang SJ, Park SM, Yeom YI, Fisher PB, Kang D. Gene. 2009 Mar 15;433(1-2):32-9, Product: Pathway Studio |
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Effects of Subminimum Inhibitory Concentrations of Antibiotics on the Pasteurella multocida Proteome: A Systems Approach. Nanduri B, Lawrence ML, Peddinti DS, Burgess SC. Comp Funct Genomics. 2008:254836, Product: Pathway Studio |
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Investigating copper-regulated protein expression in Menkes fibroblasts using antibody microarrays. T Du, SL La Fontaine, M Abdo, SA Bellingham, M Greenough, I Volitakis, RA Cherny, AI Bush, PJ Hudson, J Camakaris, JF Mercer, PJ Crouch, CL Masters, VM Perreau, and AR White Proteomics, May 2008; 8(9): 1819-31, Product: Pathway Studio |
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Quantitative analysis of Streptococcus pneumoniae TIGR4 response to in vitro iron restriction by 2-D LC ESI MS/MS. B Nanduri, P Shah, M Ramkumar, EB Allen, E Swiatlo, SC Burgess, and ML Lawrence Proteomics, May 2008; 8(10): 2104-14, Product: Pathway Studio |
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Chemical rescue of DF508-CFTR mimics genetic repair in cystic fibrosis bronchial epithelial cells Om V. Singh, Harvey B. Pollard, and Pamela L. Zeitlin Mol. Cell. Proteomics, Feb 2008; 10.1074/mcp.M700303-MCP200, Product: Pathway Studio |
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Signaling networks assembled by oncogenic EGFR and c-Met Ailan Guo, Judit Villn, Jon Kornhauser, Kimberly A. Lee, Matthew P. Stokes, Klarisa Rikova, Anthony Possemato, Julie Nardone, Gregory Innocenti, Randall Wetzel, Yi Wang, Joan MacNeill, Jeffrey Mitchell, Steven P. Gygi, John Rush, Roberto D. Polakiewicz, and Michael J. Comb PNAS, Jan 2008; 105: 692 - 697, Product: Pathway Studio |
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The tale of two domains: Proteomic and genomic analysis of SMYD2, a new histone methyltransferase Mohamed Abu-Farha, Jean-Philippe Lambert, Ashraf S. Al-Madhoun, Fred Elisma, Ilona S. Skerjanc, and Daniel Figeys Mol. Cell. Proteomics, Dec 2007; 10.1074/mcp.M700271-MCP200, Product: Pathway Studio |
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Differential expression of novel tyrosine kinase substrates during breast cancer development Yunhao Chen, Lee Yee Choong, Qingsong Lin, Robin Philps, Chee Hong Wong, Boon Keong Ang, Yee Ling Tan, Marie Chiew Shia Loh, Choy Leong Hew, Nilesh Shah, Brian J. Druker, Poh Kuan Chong, and Yoon Pin Lim Mol Cell Proteomics. 2007 Sep 12, Product: PathwayAssist |
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Specific Activation of the Glucocorticoid Receptor and Modulation of Signal Transduction Pathways in Human Lens Epithelial Cells Vanita Gupta, Niranjan Awasthi, and B. J. Wagner Invest. Ophthalmol. Vis. Sci., Apr 2007; 48: 1724 - 1734., Product: PathwayAssist |
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Large-scale mapping of human protein protein interactions by mass spectrometry Ewing RM et al Mol Syst Biol. 2007; 3: 89., Product: Pathway Studio |
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Overexpression of Angiopoietin-like Protein 4 Alters Mitochondria Activities and Modulates Methionine Metabolic Cycle in the Liver Tissues of db/db Diabetic Mice Yu Wang, Karen SL Lam, Janice BB Lam, Michael C Lam, Priscilla TY Leung, Mingyan Zhou, and Aimin Xu Molecular Endocrinology, doi:10.1210/me.2006-0249, Product: Pathway Studio |
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RET oncoproteins induce tyrosine phosphorylation changes of proteins involved in RNA metabolism L. Gorlaa, M. Canta, F. Miccicha, C. Patellia, P. Mondellinia, M.A. Pierottia, and I. Bongarzonea Cellular Signalling V.18(12):2272-2282, Product: Pathway Studio |
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Integrated molecular profiling of SOD2 expression in multiple myeloma Elaine M Hurt, Suneetha B Thomas, Benjamin Peng, and William L Farrar Blood, Dec 2006; 10.1182/blood-2006-07-035162., Product: PathwayAssist |
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de Novo biosynthetic profiling of high abundance proteinsin cystic fibrosis lung epithelial cells Harvey B. Pollard, Ofer Eidelman, Catherine Jozwik, Wei Huang, Meera Srivastava, X-D Ji, Bridget McGowan, Christine Formas Norris, Sutoshi Todo, Thomas Darling, Peter J. Mogayzel, Pamela L. Zeitlin, Jerry Wright, William B. Guggino, Eleanore Metcalf, William Driscoll, Greg Mueller, Cloud Paweletz, and David M. Jacobowitz Mol. Cell. Proteomics, Jul 2006; 10.1074/mcp.M600091-MCP200., Product: PathwayAssist |
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Proteomic Phenotyping And Functional Genomics Of Shark (Squalus Acanthias) Tissues Dietmar Kltz, Jinoo Lee, Nelly Valkova and Mark White VIIth International Congress on the Biology of Fish, Product: Pathway Studio |
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Parallel analysis of transcript and translation profiles: identification of metastasis-related signal pathways differentially regulated by drug and genetic modifications Yang H, Yu LR, Yi M, Lucas DA, Lukes L, Lancaster M, Chan KC, Issaq HJ, Stephens RM, Conrads TP, Veenstra TD, Hunter KW. J Proteome Res. 2006 July 7; 5(7): 1555 1567., Product: Pathway Studio |
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Global response of Plasmodium falciparum to hyperoxia: a combined transcriptomic and proteomic approach Torrentino-Madamet M, Almras L, Desplans J, Le Priol Y, Belghazi M, Pophillat M, Fourquet P, Jammes Y, Parzy D. Malar J. 2011 Jan 11;10:4 |
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Integrated Transcriptional and Proteomic Analysis with In Vitro Biochemical Assay Reveal the Important Role of CYP3A46 in T-2 Toxin Hydroxylation in Porcine Primary Hepatocytes Jianshe Wang et al Mol. Cell. Proteomics |
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Deletion of a subgroup of ribosome-related genes minimizes hypoxia-induced changes and confers hypoxia tolerance Ajit N. Shah, Daniela Cadinu, R. Michael Henke, Xiantong Xin, Ranita Ghosh Dastidar, and Li Zhang Physiol Genomics, Jul 2011; 43: 855 - 872 |
| Drug discovery | Go to top | |
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Systems biology visualization tools for drug target discovery T. Huan et al Expert Opinion on Drug Discovery, May 2010 |
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Running tranSMART for the Drug Development Marathon Kevin Davies BioIT World |
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Construction of signaling pathways and identification of drug effects on the liver cancer cell HepG2. LG Alexopoulos, IN Melas, AD Chairakaki, J Saez-Rodriguez, and A Mitsos Conf Proc IEEE Eng Med Biol Soc, January 1, 2010; 1: 6717-20. |
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The transcriptional response of Pasteurella multocida to three classes of antibiotics. B Nanduri, LA Shack, SC Burgess, and ML Lawrence BMC Genomics 1 Jan 2009 10 Suppl 2: p. S4, Product: Pathway Studio |
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The Constitutive Active/Androstane Receptor Facilitates Unique Phenobarbital-Induced Expression Changes of Genes Involved in Key Pathways in Precancerous Liver and Liver Tumors Jennifer M. Phillips, Lyle D. Burgoon, and Jay I. Goodman Toxicol. Sci. 2009; 110(2): p. 319-333, Product: Pathway Studio |
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Time-dependent gene expression changes in a human colon polyp cell line induced by a clinically relevant concentration of atorvastatin Eugene Elmore, Aarti Jain, Vernon Steele, and J. Leslie Redpath Cancer Prevention Research. 2008; 1(7_MeetingAbstracts): p. A133, Product: Pathway Studio |
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Impact of the Chemotherapy Cocktail Used to Treat Testicular Cancer on the Gene Expression Profile of Germ Cells from Male Brown-Norway Rats Delbs G,Chan D,Pakarinen P,Trasler JM,Hales BF,Robaire B. Biol Reprod, 10.1095/biolreprod.108.072108, Product: Pathway Studio, ResNet |
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In silico pathway analysis: the final frontier towards completely rational drug design Anton Yuryev Expert Opinion on Drug Discovery; August 2008, V.3(8):867-876, Product: Pathway Studio |
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Molecular mechanisms of the antiangiogenic and antitumor effects of mycophenolic acid Sophie Domhan, Stefan Muschal, Christian Schwager, Christian Morath, Ute Wirkner, Wilhelm Ansorge, Christian Maercker, Martin Zeier, Peter E. Huber, and Amir Abdollahi Mol. Cancer Ther., Jun 2008; 7: 1656 - 1668, Product: PathwayAssist |
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Transcriptomic analysis of nephrotoxicity induced by cephaloridine, a representative cephalosporin antibiotic. Rokushima M, Fujisawa K, Furukawa N, Itoh F, Yanagimoto T, Fukushima R, Araki A, Okada M, Torii M, Kato I, Ishizaki J, Omi K. Chem Res Toxicol. 2008 Jun;21(6):1186-96. Epub 2008 May 23., Product: Pathway Studio |
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Dexamethasone Sensitizes the Neonatal Intestine to Fructose Induction of Intestinal Fructose Transporter (Slc2A5) Function Veronique Douard, Xue-Lin Cui, Patricia Soteropoulos, and Ronaldo P. Ferraris Endocrinology, Jan 2008; 149: 409 - 423, Product: PathwayAssist |
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Dexamethasone sensitizes the neonatal intestine to fructose-induction of GLUT5 transport function Veronique Douard, Xue-Lin Cui, Patricia Soteropoulos, and Ronaldo P. Ferraris Endocrinology, Oct 2007; 10.1210/en.2007-0906, Product: PathwayAssist |
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Connecting Small Molecules to Nuclear Receptor Pathways Kristina Hettne, Montserrat Cases, Scott Boyer and Jordi Mestres Curr Top Med Chem. 2007;7(15):1530-6, Product: PathwayAssist |
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Exenatide blocks JAK1-STAT1 in pancreatic beta cells Couto FM, Minn AH, Pise-Masison CA, Radonovich M, Brady JN, Hanson M, Fernandez LA, Wang P, Kendziorski C, Shalev A Metabolism. 2007 Jul;56(7):915-8, Product: Pathway Studio |
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Pathway analysis for design of promiscuous drugs and selective drug mixtures. Sivachenko A, Kalinin A, Yuryev A. Curr Drug Discov Technol. 2006 Dec;3(4):269-77., Product: Pathway Studio, Topic: Applications of pathway analysis |
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Pathway analysis software as a tool for drug target selection, prioritization and validation of drug mechanism Sivachenko A & Yuryev A Expert Opinion on Therapeutic Targets, v.11(3), pp.411-421, Product: Pathway Studio, Topic: Applications of pathway analysis |
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Interplay of Genes Regulated by Estrogen and Diindolylmethane in Breast Cancer Cell Lines Laura Mulvey, Alamelu Chandrasekaran, Kai Liu, Sarah Lombardi, Xue-Ping Wang, Karen J Auborn, and Leslie Goodwin Mol Med. 2007 Jan Feb; 13(1-2): 69 78, Product: Pathway Studio |
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Phenotype-Based Screening of Mechanistically Annotated Compounds in Combination with Gene Expression and Pathway Analysis Identifies Candidate Drug Targets in a Human Squamous Carcinoma Cell Model Mrten Frykns, Linda Rickardson, Malin Wickstrm, Sumeer Dhar, Henrik Lvborg, Joachim Gullbo, Peter Nygren, Mats G. Gustafsson, Anders Isaksson, and Rolf Larsson J Biomol Screen., 11: 457 - 468, Product: PathwayAssist |
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Celecoxib Treatment Alters the Gene Expression Profile of Normal Colonic Mucosa Oleg K. Glebov, Luz M. Rodriguez, Patrick Lynch, Sherri Patterson, Henry Lynch, Kenneth Nakahara, Jean Jenkins, Janet Cliatt, Casey-Jo Humbyrd, John DeNobile, Peter Soballe, Steven Gallinger, Aby Buchbinder, Gary Gordon, Ernest Hawk, and Ilan R. Kirsch Cancer Epidemiol. Biomarkers Prev., Jul 2006; 15: 1382 - 1391., Product: PathwayAssist, MedScan |
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The Common Insecticides Cyfluthrin and Chlorpyrifos Alter the Expression of a Subset of Genes with Diverse Functions in Primary Human Astrocytes Sarah M. Mense, Amitabha Sengupta, Changgui Lan, Mei Zhou, Galina Bentsman, David J. Volsky, Robin M. Whyatt, Frederica P. Perera, and Li Zhang Toxicol. Sci., Jun 2006, Product: PathwayAssist |
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E2F1-induced apoptosis: turning killers into therapeutics Stanelle, J. Putzer, B.M. Trends in Molecular Medicine, Apr 2006, Product: Pathway Studio |
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Microarray Analysis of Immobilization Stress Triggered Changes in Gene Expression in Rat Adrenal Medulla Esther Louise Sabban, Xiaoping Liu, Richard Kvetnansky, and Lidia I Serova FASEB J, Product: PathwayAssist |
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Pathway Analysis in Drug Development Azat Badretdinov, Anton Yuryev Pharma & Bio Ingridients March 2006, Product: Pathway Studio, Topic: Applications of pathway analysis |
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Tamoxifen treatment for breast cancer enforces a distinct gene-expression profile on the human endometrium: an exploratory study S C J P Gielen, L C M Kuhne, P C Ewing, L J Blok, and C W Burger Endocr. Relat. Cancer, Dec 2005; 12: 1037 - 1049., Product: PathwayAssist |
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Validating Molecular Targets of Thalidomide in CLL: Net Effect of Increased Apoptosis through the Intrinsic Pathway and down Regulation of NF-kB Signaling- Validation Using Gene Expression Profile from the Phase I/II Clinical Trial of Thalidomide and Fludarabine. Asher Alban Chanan-Khan, Swaminathan Padmanabhan, Leighton Stein, Jennifer Panzarella, Kena C. Miller, and Leslie Hawthorne Blood (ASH Annual Meeting Abstracts), Nov 2005; 106: 5043., Product: PathwayAssist |
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Identification of potential caloric restriction mimetics by microarray profiling Joseph M. Dhahbi, Patricia L. Mote, Gregory M. Fahy, and Stephen R. Spindler Physiol Genomics, Nov 2005; 23: 343 - 350., Product: PathwayAssist |
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Response rate of fibrosarcoma cells to cytotoxic drugs on the expression level correlates to the therapeutic response rate of fibrosarcomas and is mediated by regulation of apoptotic pathways. Marcus Lehnhardt, Ludger Klein-Hitpass, Cornelius Kuhnen, Heinz Herbert Homann, Adrien Daigeler, Hans Ulrich Steinau, Sonja Roehrs, Laura Schnoor, Lars Steinstraesser and Oliver Mueller BioMed Central 7 July 2005, Product: Pathway Studio |
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Identification of molecular mechanisms for cellular drug resistance by combining drug activity and gene expression profiles. Rickardson L, Fryknas M, Dhar S, Lovborg H, Gullbo J, Rydaker M, Nygren P, Gustafsson MG, Larsson R, Isaksson A. British Journal of Cancer (2005) 93, 483-492. doi:10.1038/sj.bjc.6602699, Product: Pathway Studio |
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Dexamethasone Induces Changes in Glucocorticoid Receptor Phosphorylation and Gene Expression in Human Lens Epithelial Cells V.K. Gupta and B.J. Wagner Invest. Ophthalmol. Vis. Sci., May 2005, Product: PathwayAssist |
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Molecular Portrait of the Progestagenic and Estrogenic Actions of Tibolone: Behavior of Cellular Networks in Response to Tibolone P. Hanifi-Moghaddam, S. C. J. P. Gielen, H. J. Kloosterboer, M. E. De Gooyer, A. M. Sijbers, A. J. van Gool, M. Smid, M. Moorhouse, F. H. van Wijk, C. W. Burger, and L. J. Blok J. Clin. Endocrinol. Metab., Feb 2005, Product: PathwayAssist |
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Illuminating Drug discovery with biological pathways Gordana Apic, Tijana Ignjatovic, Scott Boyer, Robert B. Russell FEBS Letters 579 (2005) 1872-1877, Product: Pathway Studio |
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Using microarrays to predict resistance to chemotherapy in cancer patients Chung-Hae Lee, Pascale F Macgregor Pharmacogenomics, Volume: 5, Issue: 6; September 2004, Product: Pathway Studio |
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The role of bioinformatics in target validation Whittaker, P.A. Drug Discovery Today: Technologies, Oct 2004, Product: Pathway Studio |
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Can Theoretical Analysis of Cellular Regulatory Networks Improve Drug Target Identification and Validation? Burkhard Haefner BUSINESS BRIEFING: FUTURE Drug discovery 2004, Product: Pathway Studio |
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TMPRSS2/ERG fusion gene expression alters chemo- and radio-responsiveness in cell culture models of androgen independent prostate cancer. TA Swanson, SA Krueger, S Galoforo, BJ Thibodeau, AA Martinez, GD Wilson, and B Marples Prostate, Mar 2011 |
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Progranulin A-mediated MET Signaling Is Essential for Liver Morphogenesis in Zebrafish Yen-Hsing Li, Mark Hung-Chih Chen, Hong-Yi Gong, Shao-Yang Hu et al J. Biol. Chem. 2010; 285(52): p. 41001-41009 |
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Genome-wide analysis reveals distinct substrate specificities of Rrp6, Dis3, and core exosome subunits Daniel L. Kiss and Erik D. Andrulis RNA, Apr. 2010 |
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Modulation of Transcriptome and Metabolome of Tobacco by Arabidopsis Transcription Factor, AtMYB12, Leads to Insect Resistance Prashant Misra et al Plant Physiology, Apr 2010 |
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Comparative Analysis of the Migraine Pathway in Human and C. elegans Khurshid Ahmad et al Current research Journal of Biological Sciences, Mar. 2010 |
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Transcriptional Profiling of the Caloric Restriction in Key Metabolic Tissues of Pigs Differing in Feed Efficiency Sender Lkhagvadorj et al Iowa State University Animal Industry Report 2010 |
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Zebrafish Spotted-Microarray for Genome-Wide Expression Profiling Experiments: Data Acquisition and Analysis Siew Hong Lam, R. Krishna Murthy Karuturi, Zhiyuan Gong Book Title: Zebrafish: Methods and Protocols, Jan 2010 |
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Proteomic analysis of honeybee worker (Apis mellifera) hypopharyngeal glanddevelopment Mao Feng, Yu Feng, JianKe Li BMC Genomics, Dec. 2009 |
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Analysis of abscisic acid responsive proteins in Brassica napus guard cells by multiplexed isobaric tagging Mengmeng Zhua, Brigitte Simonsb, Ning Zhua, David G. Oppenheimera, and Sixue Chen Journal of Proteomics, Nov. 2009 |
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Comparative in vivo gene expression of the closely related bacteria Photorhabdus temperata and Xenorhabdus koppenhoeferi upon infection of the same insect host, Rhizotrogus majalis An R, Sreevatsan S, Grewal PS BMC Genomics, Sep. 2009 |
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Methods for interpreting lists of affected genes obtained in a DNA microarray experiment Hedegaard et al BMC Proc 1 Jan 2009 3 Suppl 4: p. S5, Product: Pathway Studio |
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The transcriptional response of Pasteurella multocida to three classes of antibiotics. B Nanduri, LA Shack, SC Burgess, and ML Lawrence BMC Genomics 1 Jan 2009 10 Suppl 2: p. S4, Product: Pathway Studio |
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Pathway results from the chicken data set using GOTM, Pathway Studio and Ingenuity softwares A Bonnet, S Lagarrigue, L Liaubet, C Robert-Granie, M Sancristobal, and G Tosser-Klopp BMC Proc 1 Jan 2009 3 Suppl 4: p. S11, Product: Pathway Studio |
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Gene expression responses in male fathead minnows exposed to binary mixtures of an estrogen and antiestrogen Garcia-Reyero et al BMC Genomics 2009, 10:308, Product: Pathway Studio |
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Uncovering the Arabidopsis thaliana nectary transcriptome: investigation of differential gene expression in floral nectariferous tissues Brian W Kram, Wayne W Xu and Clay J Carter BMC Plant Biology, Product: Pathway Studio |
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Zebrafish reward mutants reveal novel transcripts mediating the behavioral effects of amphetamine Webb, Katharine J, Norton, William HJ, Trmbach, Dietrich, Meijer, Annemarie H, Ninkovic, Jovica, Topp, Stefanie, Heck, Daniel, Bally-Cuif, Laure Genome Biology, Product: Pathway Studio |
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Core Exosome-independent Roles for Rrp6 in Cell Cycle Progression Amy C. Graham, Daniel L. Kiss, and Erik D. Andrulis Mol. Biol. Cell, Apr 2009; 20: 2242 - 2253, Product: Pathway Studio |
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Microarray gene expression profiles of fasting induced changes in liver and adipose tissues of pigs expressing the melanocortin-4 receptor D298N variant Sender Lkhagvadorj, Long Qu, Weiguo Cai, Oliver P Couture, C Richard Barb, Gary J Hausman, Dan Nettleton, Lloyd L. Anderson, Jack C.M. Dekkers, and Christopher K Tuggle Physiol Genomics, Apr 2009, Product: Pathway Studio |
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Silver Diamine Fluoride: A Caries A. Rosenblatt, T.C.M. Stamford, and R. Niederman Journal of Dental Research. 2009; 88(2): p. 116-125, Product: Pathway Studio |
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http://genomebiology.com/2009/10/2/R24 Immink RGH, Tonaco IAN, de Folter S, Shchennikova A, van Dijk ADJ, Busscher-Lange J, Borst JW, Angenent GC Genome Biology, Frb. 2009 |
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Different signaling pathways expressed by chicken naive CD4(+) T cells, CD4(+) lymphocytes activated with staphylococcal enterotoxin B, and those malignantly transformed by Marek\'s disease virus. Buza JJ, Burgess SC Journal of proteome research, 7 (6), p.2380-2387, Product: Pathway Studio |
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Effects of Subminimum Inhibitory Concentrations of Antibiotics on the Pasteurella multocida Proteome: A Systems Approach. Nanduri B, Lawrence ML, Peddinti DS, Burgess SC. Comp Funct Genomics. 2008:254836, Product: Pathway Studio |
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Quantitative analysis of Streptococcus pneumoniae TIGR4 response to in vitro iron restriction by 2-D LC ESI MS/MS. B Nanduri, P Shah, M Ramkumar, EB Allen, E Swiatlo, SC Burgess, and ML Lawrence Proteomics, May 2008; 8(10): 2104-14, Product: Pathway Studio |
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Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia Peter F. Dunfield, Anton Yuryev, Pavel Senin, Angela V. Smirnova, Matthew B. Stott, Shaobin Hou, Binh Ly, Jimmy H. Saw, Zhemin Zhou, Yan Ren, Jianmei Wang, Bruce W. Mountain, Michelle A. Crowe, Tina M. Weatherby, Paul L. E. Bodelier, Werner Liesack, Lu Feng, Lei Wang, Maqsudul Alam Nature 450, 879 - 882 (06 Dec 2007), Product: Pathway Studio, Topic: Applications of pathway analysis |
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Predicting aging/longevity-related genes in the nematode Caenorhabditis elegans. Witten TM, Bonchev D. Chem Biodivers. 2007 Nov;4(11):2639-55., Product: Pathway Studio |
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Genetic Determinants of Mitochondrial Response to Arsenic in Yeast Saccharomyces cerevisiae Marija Vujcic, Meghna Shroff, and Keshav K. Singh Cancer Res., Oct 2007; 67: 9740 - 9749, Product: PathwayAssist |
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C13-11 neovascularization in bland-white-garland syndrome A.A. Fokin, T.N. Masters, C. Gregory, F. Robicsek Interactive CardioVascular and Thoracic Surgery, 6: S1 - S172, Product: Pathway Studio |
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Functional genomics and proteomics of the cellular osmotic stress response in `non-model\' organisms Dietmar Kltz, Diego Fiol, Nelly Valkova, Silvia Gomez-Jimenez, Stephanie Y. Chan, and Jinoo Lee J. Exp. Biol., May 2007; 210: 1593 - 1601, Product: Pathway Studio |
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Pre- and postnatal hepatic gene expression profiles of two pig breeds differing in body composition: insight into pathways of metabolic regulation Siriluck Ponsuksili, Eduard Murani, Christina Walz, Manfred Schwerin, and Klaus Wimmers Physiol Genomics, Jan 2007; 10.1152/physiolgenomics.00178.2006, Product: PathwayAssist |
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Systems Analysis Of Pasteurella Multocida Response To Sub-Minimum Inhibitory Concentrations Of Antibiotics Bindu Nanduri, Mark L Lawrence,Shane C Burgess Mississippi Academy Of Sciences, Product: Pathway Studio |
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Systems Biology of AGC Kinases in Fungi Alex Sobko Sci. STKE, Product: Pathway Studio |
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Identification and pathway analysis of immediate hyperosmotic stress responsive molecular mechanisms in tilapia (Oreochromis mossambicus) gill Diego F. Fiola, Stephanie Y. Chana and Dietmar Kltz Comparative Biochemistry and Physiology Part D: Genomics and Proteomics V1(3):344-356, Product: Pathway Studio |
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Proteomic Phenotyping And Functional Genomics Of Shark (Squalus Acanthias) Tissues Dietmar Kltz, Jinoo Lee, Nelly Valkova and Mark White VIIth International Congress on the Biology of Fish, Product: Pathway Studio |
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Rapid parallel evolutionary changes of gene transcription profiles in farmed Atlantic salmon Christian Roberge, Sigurd Einum, Helga Guderley, Louis Bernatchez Molecular Ecology Volume 15, Issue 1, Page 9-20, Jan 2006, Product: Pathway Studio |
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Use of a bovine genome array to identify new biological pathways for beef marbling in Hanwoo (Korean Cattle) Lee SH,Gondro C,van der Werf J,Kim NK,Lim DJ,Park EW,Oh SJ,Gibson JP,Thompson JM. BMC Genomics.2010 Nov 9;11:623 |
| Neuroscience | Go to top | |
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Individual Stress Vulnerability Is Predicted by Short-Term Memory and AMPA Receptor Subunit Ratio in the Hippocampus Mathias V. Schmidt, Dietrich Trumbach, Peter Weber, Klaus Wagner et al J. Neurosci. 2010; 30(50): p. 16949-16958 |
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Gene expression profiling in the stress control brain region hypothalamic paraventricular nucleus reveals a novel gene network including amyloid beta precursor protein. Tsolakidou A, Czibere L, Ptz B, Trmbach D, Panhuysen M, Deussing JM, Wurst W, Sillaber I, Landgraf R, Holsboer F, Rein T. BMC Genomics. 2010 Oct 8;11:546. |
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Evaluation of Blastomere Biopsy Using a Mouse Model Indicates the Potential High Risk of Neurodegenerative Disorders in the Offspring Yu et al Mol. Cell. Proteomics. 2009; 8(7): p. 1490-1500, Product: Pathway Studio |
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Proteome analysis of biomarkers in the cerebrospinal fluid of neuromyelitis optica patients S Bai, S Liu, X Guo, Z Qin, B Wang, X Li, Y Qin, and YH Liu Mol Vis 1 Jan 2009 15: p. 1638, Product: Pathway Studio |
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Proteome analysis of haptoglobin in cerebrospinal fluid of neuromyelitis optica. Shumei Bai, Shilian Liu, Xuxiao Guo, Zhaoyu Qin, Banqin Wang, Xiaohong Li, and Yanjiang Qin Mol Biol Rep,May 15, 2009, Product: Pathway Studio |
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Identification of Candidate Genes and Gene Networks Specifically Associated with Analgesic Tolerance to Morphine Jenica D. Tapocik, Noah Letwin, Cheryl L. Mayo, Bryan Frank, Troung Luu, Ovokeraye Achinike, Carrie House, Russell Williams, Greg I. Elmer,and Norman H. Lee J. Neurosci.,Apr 2009; 29: 5295 - 5307, Product: Pathway Studio |
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Methodology for Discovery of Alzheimer s Disease Blood-Based Biomarkers Olivier C. Maes, Hyman M. Schipper, Howard M. Chertkow, and Eugenia Wang J Gerontol A Biol Sci Med Sci, Apr 2009, Product: Pathway Studio |
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Evaluation of blastomere biopsy using mouse model indicates the potential high-risk of neurodegenerative disorders in the offspring Yang Yu, Jindao Wu, Yong Fan, Zhuo Lv, Xuejiang Guo, Chun Zhao, Rong Zhou, Zhuo Zhang, Fuqiang Wang, Min Xiao, Ling Chen, Hui Zhu, Wen Chen, Min Lin, Jiayin Liu, Zuomin Zhou, Liu Wang, Ran Huo, Qi Zhou, and Jiahao Sha Mol. Cell. Proteomics, Mar 2009, Product: Pathway Studio |
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Biomarkers for Parkinson\'s disease Manuel B. Graeber Experimental Neurology 216 (2009) 249 253, Product: Pathway Studio |
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Microarray RNA Expression Analysis of Cerebral White Matter Lesions Reveals Changes in Multiple Functional Pathways Simpson et al Stroke,Dec 2008; 10.1161/STROKEAHA.108.529214., Product: PathwayAssist |
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Identification of a 5-Protein Biomarker Molecular Signature for Predicting Alzheimer\'s Disease Martn Gmez Ravetti, Pablo Moscato PLoS ONE 3(9): e3111, Product: Pathway Studio |
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DnaJB6 is present in the core of Lewy bodies and is highly up-regulated in parkinsonian astrocytes. Durrenberger PF, Filiou MD, Moran LB, Michael GJ, Novoselov S, Cheetham ME, Clark P, Pearce RK, Graeber MB. J Neurosci Res. 2008 Aug 18, Product: Pathway Studio |
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Towards a pathway definition of Parkinson s disease: a complex disorder with links to cancer, diabetes and inflammation Linda B. Moran and Manuel B. Graeber Neurogenetics, Vol.9(1)2008, Product: Pathway Studio |
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IFN-beta-regulated genes show abnormal expression in therapy-nave relapsing remitting MS mononuclear cells: Gene expression analysis employing all reported protein protein interactions Ken D. Yamaguchi, Daniel L. Ruderman, Ed Croze, T. Charis Wagner, Sharlene Velichko, Anthony T. Reder, Hugh Salamon J Neuroimmunol. 2008 Feb 13, Product: Pathway Studio, ResNet |
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cAMP Response Element-Binding Protein-Mediated Gene Expression Increases the Intrinsic Excitability of CA1 Pyramidal Neurons Mikel Lopez de Armentia, Dragana Jancic, Roman Olivares, Juan M. Alarcon, Eric R. Kandel, and Angel Barco J. Neurosci., Dec 2007; 27: 13909 - 13918., Product: Pathway Studio |
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Gene expression profiling of human primary astrocytes exposed to manganese chloride indicates selective effects on several functions of the cells Amitabha Sengupta, Sarah M. Mense, Changgui Lana, Mei Zhou, Rory E. Mauro, Lisa Kellerman, Galina Bentsman, David J. Volsky, Elan D. Louis, Joseph H. Graziano and Li Zhang Neurotoxicology, 28 (3), p.478-489, May 2007, Product: Pathway Studio |
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Expression changes in mouse brains following nicotine-induced seizures; the modulation of transcription factor networks Merav Kedmi and Avi Orr-Urtreger Physiol Genomics, Apr 2007; 10.1152/physiolgenomics.00288.2006, Product: Pathway Studio |
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The microglial gene regulatory network activated by interferon-gamma Moran, L.B.,Duke, D.C.,Graeber, M.B. Journal of Neuroimmunology, Feb 2007, Product: Pathway Studio |
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Ventral Tegmental Transcriptome Response to Intermittent Nicotine Treatment and Withdrawal in BALB/cJ, C57BL/6ByJ,and Quasi-Congenic RQI Mice Csaba Vadasz, Mariko Saito, Danielle O Brien,Jiri Zavadil, Grant Morahan, Goutam Chakraborty, Ray Wang Neurochem Res (2007) 32:457 480, Product: Pathway Studio |
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A Sex-Specific Role of Type VII Adenylyl Cyclase in Depression Hines LM, Hoffman PL, Bhave S, Saba L, Kaiser A, Snell L, Goncharov I, LeGault L, Dongier M, Grant B, Pronko S, Martinez L, Yoshimura M, Tabakoff B; World Health Organization/International Society for Biomedical Research on Alcoholism Study on State and Trait Markers of Alcohol Use and Dependence Investigators. The Journal of Neuroscience, Product: PathwayAssist |
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Histology-Based Expression Profiling Yields Novel Prognostic Markers in Human Glioblastoma Shumin Dong, MB, PhD, Catherine L. Nutt, PhD, Rebecca A. Betensky, PhD, Anat O. Stemmer-Rachamimov, MD, Nicholas C. Denko, MD, PhD, Keith L. Ligon, MD, PhD, David H. Rowitch, MD, PhD, and David N. Louis, MD J Neuropathol Exp Neurol. 2005 November; 64(11): 948 955., Product: Pathway Studio |
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The Microarray Data Analysis Process: From Raw Data to Biological Significance Olson, N.E. NeuroRX, Product: Pathway Studio |
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Transcriptional Signatures of Cellular Plasticity in Mice Lacking the {alpha}1 Subunit of GABA-A Receptors Igor Ponomarev, Rajani Maiya, Mark T. Harnett, Gwen L. Schafer, Andrey E. Ryabinin, Yuri A. Blednov, Hitoshi Morikawa, Stephen L. Boehm, II, Gregg E. Homanics, Ari Berman, Kerrie H. Lodowski, Susan E. Bergeson, and R. Adron Harris J. Neurosci., May 2006; 26: 5673 - 5683, Product: PathwayAssist |
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Gene expression alterations in brains of mice infected with three strains of scrapie. Skinner PJ, Abbassi H, Chesebro B, Race RE, Reilly C, Haase AT. BMC Genomics. 2006; 7: 114., Product: Pathway Studio |
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Bioinformatics Models In Drug Abuse And NeuroAIDS: Using And Developing Databases Shapshak Paul, Robert Duncan, Jadwiga Turchan, Avindra Nath, Alireza Minagar, Pandjassarame Kangueane, Wade Davis, Francesco Chiappelli, Fatten Elkomy, Raman Seth, Toni Kazic BIOINFORMATION, Product: Pathway Studio |
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Gene chromosomal organization and expression in cultured human neurons exposed to cocaine and HIV-1 proteins gp120 and tat: drug abuse and NeuroAIDS. Shapshak P, Duncan R, Nath A, Turchan J, Pandjassarame K, Rodriguez H, Duran EM, Ziegler F, Amaro E, Lewis A, Rodriguez A, Minagar A, Davis W, Seth R, Elkomy FF, Chiappelli F, Kazic T. Front Biosci., Product: Pathway Studio |
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The neuroprotective WldS gene regulates expression of PTTG1 and erythroid differentiation regulator 1-like gene in mice and human cells Gillingwater TH, Wishart TM, Chen PE, Haley JE, Robertson K, MacDonald SH, Middleton S, Wawrowski K, Shipston MJ, Melmed S, Wyllie DJ, Skehel PA, Coleman MP, Ribchester RR. Hum Mol Genet. 2006 Feb 15;15(4):625-35., Product: PathwayAssist |
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Gene expression profile of activated microglia under conditions associated with dopamine neuronal damage David M. Thomas, Dina M. Francescutti-Verbeem, and Donald M. Kuhn FASEB J, Dec 2005, Product: PathwayAssist |
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Complex Genetics of Interactions of Alcohol and CNS Function and Behavior. Matthews, Douglas B.; Bhave, Sanjiv V.; Belknap, John K.; Brittingham, Cynthia; Chesler, Elissa J.; Hitzemann, Robert J.; Hoffmann, Paula L.; Lu, Lu; McWeeney, Shannon; Miles, Michael F.; Tabakoff, Boris; Williams, Robert W. Alcoholism: Clinical & Experimental Research. 29(9):1706-1719, Product: Pathway Studio |
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Nova regulates brain-specific splicing to shape the synapse Ule J, Ule A, Spencer J, Williams A, Hu JS, Cline M, Wang H, Clark T, Fraser C, Ruggiu M, Zeeberg BR, Kane D, Weinstein JN, Blume J, Darnell RB. Nature Genetics 37, 844-852, Product: Pathway Studio |
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Sp1 and NFkappaB pathways are regulated in brain in response to acute and chronic ethanol. Rulten SL, Ripley TL, Hunt CL, Stephens DN, Mayne LV. Genes, Brain and Behavior, 2006, Product: Pathway Studio |
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Cocaine-induced changes in the expression of apoptosis-related genes in the fetal mouse cerebral wall Svetlana I. Novikova, Fang He, Jie Bai, Irina Badan, Irina A. Lidow, Michael S. Lidow Neurotoxicology and Teratology, 2004, Product: Pathway Studio |
| Toxicogenomics | Go to top | |
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Construction of signaling pathways and identification of drug effects on the liver cancer cell HepG2. LG Alexopoulos, IN Melas, AD Chairakaki, J Saez-Rodriguez, and A Mitsos Conf Proc IEEE Eng Med Biol Soc, January 1, 2010; 1: 6717-20. |
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The Constitutive Active/Androstane Receptor Facilitates Unique Phenobarbital-Induced Expression Changes of Genes Involved in Key Pathways in Precancerous Liver and Liver Tumors Jennifer M. Phillips, Lyle D. Burgoon, and Jay I. Goodman Toxicol. Sci. 2009; 110(2): p. 319-333, Product: Pathway Studio |
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Bioinformatic Analysis Identified Upstream Transcription Factors and Indirect Regulators of Differentially Expressed Mouse Retinal Genes During Gestational Lead Exposure (GLE) W. Xiao, X. Wang, A. Giddabasappa, and D. A. Fox Invest. Ophthalmol. Vis. Sci.,Apr 2009; 50: 3995, Product: Pathway Studio |
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Phenobarbital Elicits Unique, Early Changes in the Expression of Hepatic Genes that Affect Critical Pathways in Tumor-Prone B6C3F1 Mice Jennifer M. Phillips, Lyle D. Burgoon, and Jay I. Goodman Toxicol. Sci.,Jun 2009; 109: 193 - 205, Product: Pathway Studio |
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Multiple Genes Exhibit Phenobarbital-Induced Constitutive Active/Androstane Receptor Mediated DNA Methylation Changes during Liver Tumorigenesis and in Liver Tumors Jennifer M. Phillips and Jay I. Goodman Toxicol. Sci., Apr 2009; 108: 273 - 289, Product: Pathway Studio |
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Comparison of Molecular and Histological Changes in Zebrafish Gills Exposed to Metallic Nanoparticles Robert J. Griffitt, Kelly Hyndman, Nancy D. Denslow, and Davis S. BarberRobert J. Griffitt, Kelly Hyndman, Nancy D. Denslow, and Davis S. BarberRobert J. Griffitt, Kelly Hyndman, Nancy D. Denslow, and Davis S. Barber Toxicol. Sci., Product: Pathway Studio |
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Critical Role of MARCO in Crystalline Silica Induced Pulmonary Inflammation Sheetal A. Thakur, Celine A. Beamer, Christopher T. Migliaccio, and Andrij Holian Toxicol. Sci., Apr 2009; 108: 462 - 471, Product: Pathway Studio |
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Identification of early responsive genes in human amnion epithelial FL cells induced by N-methyl-N2 -nitro-N-nitrosoguanidine using oligonucleotide microarray and quantitative real-time RT-PCR approaches Li H, Shao J, Lu X, Gao Z, Yu Y Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis, 644 (1), p.1-10, Product: Pathway Studio |
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Transcriptomic analysis of nephrotoxicity induced by cephaloridine, a representative cephalosporin antibiotic. Rokushima M, Fujisawa K, Furukawa N, Itoh F, Yanagimoto T, Fukushima R, Araki A, Okada M, Torii M, Kato I, Ishizaki J, Omi K. Chem Res Toxicol. 2008 Jun;21(6):1186-96. Epub 2008 May 23., Product: Pathway Studio |
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Identification of Genes that May Play Critical Roles in Phenobarbital (PB)-Induced Liver Tumorigenesis due to Altered DNA Methylation Jennifer M. Phillips and Jay I. Goodman Toxicol. Sci., Jul 2008; 104: 86 - 99, Product: Pathway Studio |
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Gene Profiling and Patterning in the Mouse Retina During Gestational Lead Exposure (GLE) A. Giddabasappa, W. Xiao, B. Xu, S. Mukherjee, S. Chaney, M. Brooks, R. Khanna, A. Swaroop, and D. A. Fox Invest. Ophthalmol. Vis. Sci., Apr 2008; 49: 3086, Product: Pathway Studio |
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Genetic Determinants of Mitochondrial Response to Arsenic in Yeast Saccharomyces cerevisiae Marija Vujcic, Meghna Shroff, and Keshav K. Singh Cancer Res., Oct 2007; 67: 9740 - 9749, Product: PathwayAssist |
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Exposure to Arsenic at Levels Found in U.S. Drinking Water Modifies Expression in the Mouse Lung Angeline S. Andrew, Viviane Bernardo, Linda A. Warnke, Jennifer C. Davey, Thomas Hampton, Rebecca A. Mason, Jessica E.Thorpe, Michael A. Ihnat, and Joshua W. Hamilton Toxicol. Sci., Nov 2007; 100: 75 - 87, Product: Pathway Studio |
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Gene expression profiling of human primary astrocytes exposed to manganese chloride indicates selective effects on several functions of the cells Amitabha Sengupta, Sarah M. Mense, Changgui Lana, Mei Zhou, Rory E. Mauro, Lisa Kellerman, Galina Bentsman, David J. Volsky, Elan D. Louis, Joseph H. Graziano and Li Zhang Neurotoxicology, 28 (3), p.478-489, May 2007, Product: Pathway Studio |
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Genomic Profiling in Nuclear Receptor-Mediated Toxicity Woods CG, Heuvel JP, Rusyn I. Toxicol Pathol. 2007;35(4):474-94, Product: Pathway Studio |
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Cigarette smoke condensate induces cytochromes P450 and aldo-keto reductases in oral cancer cells Nagaraj, N.S. Beckers, S. Mensah, J.K. Waigel, S. Vigneswaran, N. Zacharias, W. Toxicology Letters, Aug 2006, Product: Pathway Studio |
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Transcriptional analysis of protective antigen-stimulated PBMC from non-human primates vaccinated with the anthrax vaccine absorbed James V. Rogersa, Stacy L. Casbohma, Lenore F. Giannunzioa, Loraine T. Sinnotta, Steven W. Rusta, April M. Brysa, Joyce M. Durnforda, Conrad P. Quinnb, David M. Robinsona, Robert E. Hunta, James E. Estepa and Carol L.K. Sabourin Vaccine, Apr 2006, Product: Pathway Studio |
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Relationships between genomic, cell cycle, and mutagenic responses of TK6 cells exposed to DNA damaging chemicals Mohammed Islaih, Bartley W. Halstead, Ibrahim A. Kadura, Baohui Li, Jaclyn L. Reid-Hubbard, Leah Flick, Julie L. Altizer, J. Thom Deahl, David K. Monteith, Ronald K. Newton and David E. Watson Mutation Research Regular Papers, Oct 2005, Product: Pathway Studio |
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Making Mechanistic Connections between Cell Signaling Pathways and Pathological Endpoints Myrtle A. Davis Toxicologic Pathology,Volume 32, Supplement 1 / March-April 2004: 131 135, Product: Pathway Studio |
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Integrated Transcriptional and Proteomic Analysis with In Vitro Biochemical Assay Reveal the Important Role of CYP3A46 in T-2 Toxin Hydroxylation in Porcine Primary Hepatocytes Jianshe Wang et al Mol. Cell. Proteomics |
| Human genetics | Go to top | |
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Positional identification of variants of Adamts16 linked to inherited hypertension Joe et al Hum. Mol. Genet. 2009; 18(15): p. 2825-2838, Product: Pathway Studio |
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Identification of Candidate Genes and Gene Networks Specifically Associated with Analgesic Tolerance to Morphine Jenica D. Tapocik, Noah Letwin, Cheryl L. Mayo, Bryan Frank, Troung Luu, Ovokeraye Achinike, Carrie House, Russell Williams, Greg I. Elmer,and Norman H. Lee J. Neurosci.,Apr 2009; 29: 5295 - 5307, Product: Pathway Studio |
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Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival. Van Ness B, Ramos C, Haznadar M, Hoering A, Haessler J, Crowley J, Jacobus S, Oken M, Rajkumar V, Greipp P, Barlogie B, Durie B, Katz M, Atluri G, Fang G, Gupta R, Steinbach M, Kumar V, Mushlin R, Johnson D, Morgan G. BMC Med. 2008 Sep 8;6:26, Product: PathwayAssist |
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Genetic associations with thalidomide mediated venous thrombotic events in myeloma identified using targeted genotyping David C Johnson, Sophie Corthals, Christine Ramos, Antje Hoering, Kim Cocks, Nicholas J Dickens, Jeff Haessler, Harmut Goldschmidt, J. Anthony Child, Sue E Bell, Graham Jackson, Dalsu Baris, S. Vincent Rajkumar, Faith E Davies, Brian G.M. Durie, John Crowley, Pieter Sonneveld, Brian Van Ness, and Gareth J Morgan Blood, Sep 2008; 10.1182/blood-2008-02-140434., Product: PathwayAssist |
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Genomic Insights into Acute Alcohol Tolerance Wei Hu, Laura Saba, Katherina Kechris, Sanjiv V Bhave, Paula L Hoffman, and Boris Tabakoff J. Pharmacol. Exp. Ther., Jun 2008; 10.1124/jpet.108.137521, Product: PathwayAssist, ResNet |
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The estrogen hypothesis of schizophrenia implicates glucose metabolism: association study in three independent samples. Olsen L, Hansen T, Jakobsen KD, Djurovic S, Melle I, Agartz I, Hall H, Ullum H, Timm S, Wang AG, Jnsson EG, Andreassen OA, Werge T. BMC Med Genet. 2008 May 6;9:39, Product: PathwayAssist |
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Scan of 977 non-synonymous SNPs in CLL4 trial patients for the identification of genetic variants influencing prognosis. Gabrielle S Sellick, Rachel Wade, Susan Richards, David G. Oscier, Daniel Catovsky, and Richard S Houlston Blood, Nov 2007; 10.1182/blood-2007-08-110130, Product: PathwayAssist |
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Counting potentially functional variants in BRCA1, BRCA2 and ATM predicts breast cancer susceptibility Nichola Johnson, Olivia Fletcher, Claire Palles, Matthew Rudd, Emily Webb, Gabrielle Sellick, Isabel dos Santos Silva, Valerie McCormack, Lorna Gibson, Agnes Fraser, Angela Leonard, Clare Gilham, Sean V. Tavtigian, Alan Ashworth, Richard Houlston, and Julian Peto Hum. Mol. Genet., May 2007; 16: 1051 - 1057., Product: PathwayAssist |
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Search for low penetrance alleles for colorectal cancer through a scan of 1467 non-synonymous SNPs in 2575 cases and 2707 controls with validation by kin-cohort analysis of 14704 first-degree relatives Emily L. Webb, Matthew F. Rudd, Gabrielle S. Sellick, Rachid El Galta, Lara Bethke, Wendy Wood, Olivia Fletcher, Steven Penegar, Laura Withey, Mobshra Qureshi, Nichola Johnson, Ian Tomlinson, Richard Gray, Julian Peto and Richard S. Houlston Hum. Mol. Genetics, Product: Pathway Studio |
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Candidate genes, pathways and mechanisms for alcoholism: an expanded convergent functional genomics approach Z A Rodd, B A Bertsch, W N Strother, H Le-Niculescu, Y Balaraman, E Hayden, R E Jerome, L Lumeng, J I Nurnberger, H J Edenberg, W J McBride, A B Niculescu The Pharmacogenomics Journal (10 Oct 2006), Product: Pathway Studio |
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Variants in the GH-IGF axis confer susceptibility to lung cancer Rudd MF, Webb EL, Matakidou A, Sellick GS, Williams RD, Bridle H, Eisen T, Houlston RS; GELCAPS Consortium. Genome Research, Product: PathwayAssist |
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A Myeloma-specific panel of 3,500 SNP-based functional genetic variants relevant to the etiology and treatment outcome in multiple myeloma David C. Johnson, Suzanne M. Grindle, David Gonzalez, Christine Ramos, Faith Davies, Brian A. Walker, Brian G. Durie, Brian G. Van Ness, and Gareth J. Morgan AACR Meeting Abstracts, Apr 2006; 2006: 40., Product: PathwayAssist |
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Development of a Panel of 3,500 SNP Based Functional Genetic Variants Relevant to the Etiology and Outcome in Multiple Myeloma. David C. Johnson, Suzanne M. Grindle, Christine Ramos, Faith Davies, David Gonzalez, Brian A. Walker, Brian G.M. Durie, Brian G. Van Ness, and Gareth J. Morgan Blood (ASH Annual Meeting Abstracts), Nov 2005; 106: 620., Product: PathwayAssist |
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High-Resolution Mapping of Genomic Imbalance and Identification of Gene Expression Profiles Associated with Differential Chemotherapy Response in Serous Epithelial Ovarian Cancer. Bernardini M, Lee CH, Beheshti B, Prasad M, Albert M, Marrano P, Begley H, Shaw P, Covens A, Murphy J, Rosen B, Minkin S, Squire JA, Macgregor PF. Neoplasia. 2005 Jun; 7(6): 603-613, Product: Pathway Studio |
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CANDIDATE GENE SELECTION FOR DEVELOPMENTAL DYSLEXIA: A BIOINFORMATICS APPROACH Orourke J, Platko JV, and Pauls D , Product: Pathway Studio |
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Bioinformatic analysis of autism positional candidate genes using biological databases and computational gene network prediction A. L. Yonan, A. A. Palmer, K. C. Smith, I. Feldman, H. K. Lee, J. M. Yonan, S. G. Fischer, P. Pavlidis and T. C. Gilliam Genes, Brain and Behavior (2003) 2: 303 320, Product: Pathway Studio |
| Biomarkers | Go to top | |
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Cytokine array analysis of peritoneal fluid between women with endometriosis of different stages and those without endometriosis Hou Z, Sun L, Gao L, Liao L, Mao Y, Liu J. Biomarkers, Dec. 2009 |
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Proteome analysis of biomarkers in the cerebrospinal fluid of neuromyelitis optica patients S Bai, S Liu, X Guo, Z Qin, B Wang, X Li, Y Qin, and YH Liu Mol Vis 1 Jan 2009 15: p. 1638, Product: Pathway Studio |
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Methodology for Discovery of Alzheimer s Disease Blood-Based Biomarkers Olivier C. Maes, Hyman M. Schipper, Howard M. Chertkow, and Eugenia Wang J Gerontol A Biol Sci Med Sci, Apr 2009, Product: Pathway Studio |
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Biomarkers for Parkinson\'s disease Manuel B. Graeber Experimental Neurology 216 (2009) 249 253, Product: Pathway Studio |
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Identification of a 5-Protein Biomarker Molecular Signature for Predicting Alzheimer\'s Disease Martn Gmez Ravetti, Pablo Moscato PLoS ONE 3(9): e3111, Product: Pathway Studio |
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Hint to Biomarkers of Acute Aortic Dissection by Pathway Analysis Salah A Mohamed BCVS Conference 2008 Abstracts, Product: MedScan |
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Data-driven Networking Reveals 5-Genes Signature for Early Detection of Lung Cancer Vladimir Kuznetsov, Sterling Thomas, Danail Bonchev bmei,pp. 413-417,2008, Product: Pathway Studio |
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A Gene Signature Predicting for Survival in Suboptimally Debulked Patients with Ovarian Cancer Tomas Bonome, Douglas A. Levine, Joanna Shih, Mike Randonovich, Cindy A. Pise-Masison, Faina Bogomolniy, Laurent Ozbun, John Brady, J. Carl Barrett, Jeff Boyd, and Michael J. Birrer Cancer Res., Jul 2008; 68: 5478 - 5486., Product: PathwayAssist |
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Cancer stem cell gene signature identified from advanced stage papillary serous ovarian adenocarcinoma side populations Laurent Ozbun, Vinod Vathipadiekal, Michael Radonovich, Cindy Pise-Masison, Deepa Saxena, Peter Hauschka, Samuel Mok, and Michael Birrer AACR Meeting Abstracts, Apr 2008; 2008: 5005., Product: Pathway Studio |
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Towards a pathway definition of Parkinson s disease: a complex disorder with links to cancer, diabetes and inflammation Linda B. Moran and Manuel B. Graeber Neurogenetics, Vol.9(1)2008, Product: Pathway Studio |
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Heterologous Tissue Culture Expression Signature Predicts Human Breast Cancer Prognosis Eun Sung Park, Ju-Seog Lee, Hyun Goo Woo, Fenghuang Zhan, Joanna H. Shih, John D. Shaughnessy, Jr., and J. Frederic Mushinski PLoS ONE. 2007; 2(1): e145, Product: Pathway Studio |
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Using prior knowledge and rule induction methods to discover molecular markers of prognosis in lung cancer. Frey L, Edgerton ME, Fisher DH, Tang L, Chen Z. AMIA Annu Symp Proc. 2005;:256-60., Product: Pathway Studio |
| Plants | Go to top | |
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Photosynthesis and drought: can we make metabolic connections from available data? C. Pinheiro and M. M. Chaves J. Exp. Bot. 14 December 2010, 10.1093/jxb/erq340 |
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Comparative Transcriptional Profiling and Preliminary Study on Heterosis Mechanism of Super-Hybrid Rice Gui-Sheng Song, Hong-Li Zhai, Yong-Gang Peng, Lei Zhang, Gang Wei et al Mol Plant. 2010; 3(6): p. 1012-1025 |
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Proteomic analysis of salt-stressed tomato (Solanum lycposersicum) seedlings: effect of genotype and exogenous application of glycinebetaine Songbi Chen, Natan Gollop, and Bruria Heuer J. Exp. Bot., Mar 2009, Product: Pathway Studio |
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Comparative transcriptome analysis of arsenate and arsenite stresses in rice seedlings Debasis Chakrabarty, Prabodh Kumar Trivedi, Prashant Misra, Manish Tiwari, Manju Shri, Devesh Shukla, Smita Kumar, Arti Rai, Ashutosh Pandey, Deepti Nigam, Rudra Dev Tripathi, Rakesh Tuli Chemosphere. 2008 Nov 7, Product: Pathway Studio |
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A draft gene regulatory network for cellular totipotency reprogramming during plant somatic embryogenesis. Zeng F, Zhang X, Cheng L, Hu L, Zhu L, Cao J, Guo X. Genomics. 2007 Nov;90(5):620-8, Product: Pathway Studio |
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Poplar maintains zinc homeostasis with heavy metal genes HMA4 and PCS1 Joshua P. Adams, Ardeshir Adeli, Chuan-Yu Hsu, Richard L. Harkess, Grier P. Page, Claude W. dePamphilis, Emily B. Schultz, and Cetin Yuceer J. Exp. Bot., Apr 2011; 10.1093/jxb/err025. |
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Rhythmic Diel Pattern of Gene Expression in Juvenile Maize Leaf Maciej JoDczyk, Alicja Sobkowiak, PaweB Siedlecki, PrzemysBaw Biecek, Joanna Trzcinska-Danielewicz, Jerzy Tiuryn, Jan Fronk, PaweB SowiDski PLoS One. 2011; 6(8): e23628 |
| Analysis of metabolomics data | Go to top | |
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Photosynthesis and drought: can we make metabolic connections from available data? C. Pinheiro and M. M. Chaves J. Exp. Bot. 14 December 2010, 10.1093/jxb/erq340 |
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Transcriptome atlas of aromatic amino acid family metabolism-related genes in eight liver cell types uncovers the corresponding metabolic pathways in rat liver regeneration Chang, Cuifang and Xu, CunShuan The International Journal of Biochemistry & Cell Biology, 42 (10), p.1708, Oct 2010 |
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Modulation of Transcriptome and Metabolome of Tobacco by Arabidopsis Transcription Factor, AtMYB12, Leads to Insect Resistance Prashant Misra et al Plant Physiology, Apr 2010 |
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Computational Approaches to Metabolomics David S. Wishart Book: Bioinformatics Methods in Clinical Research |
| Publications by Ariadne authors | Go to top | |
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Analysis and construction of pathogenicity island regulatory pathways in Salmonella enterica serovar Typhi Su Yean Ong, Fui Ling Ng, Siti Suriawati Badai, Anton Yuryev and Maqsudul Alam Journal of Integrative Bioinformatics, 7(1):145, 2010 |
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Custom CGH array profiling of copy number variations (CNVs) on chromosome 6p21.32 (HLA locus) in patients with venous malformations associated with multiple sclerosis Alessandra Ferlini et al BMC Med Genetics. Apr 2010 |
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Atlas of Signaling for Interpretation of Microarray Experiments Ekaterina Kotelnikova, Natalia Ivanikova, Andrey Kalinin, Anton Yuryev, Nikolai Daraselia PLoS One., Feb. 2010 |
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In silico pathway analysis: the final frontier towards completely rational drug design Anton Yuryev Expert Opinion on Drug Discovery; August 2008, V.3(8):867-876, Product: Pathway Studio |
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Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia Peter F. Dunfield, Anton Yuryev, Pavel Senin, Angela V. Smirnova, Matthew B. Stott, Shaobin Hou, Binh Ly, Jimmy H. Saw, Zhemin Zhou, Yan Ren, Jianmei Wang, Bruce W. Mountain, Michelle A. Crowe, Tina M. Weatherby, Paul L. E. Bodelier, Werner Liesack, Lu Feng, Lei Wang, Maqsudul Alam Nature 450, 879 - 882 (06 Dec 2007), Product: Pathway Studio, Topic: Applications of pathway analysis |
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Prediction and verification of indirect interactions in densely interconnected regulatory networks Koon-Kiu Yan, Sergei Maslov, Ilya Mazo, Anton Yuryev arXiv:0710.0892v2 [q-bio.QM], Product: None, Topic: Network topology and dynamics |
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Automatic extraction of gene ontology annotation and its correlation with clusters in protein networks. Daraselia N, Yuryev A, Egorov S, Mazo I, Ispolatov I. BMC Bioinformatics. 2007 Jul 10;8(1):243, Product: MedScan, Topic: MedScan, Pathway and function |
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Spreading out of perturbations in reversible reaction networks Sergei Maslov, Kim Sneppen and I Ispolatov New Journal of Physics 9 (2007) 273, Product: None, Topic: Network topology and dynamics |
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Propagation of large concentration changes in reversible protein-binding networks Maslov S, Ispolatov I. Proc Natl Acad Sci U S A. 2007, Product: None, Topic: Network topology and dynamics |
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Prediction of Protein-protein Interactions on the Basis of Evolutionary Conservation of Protein Functions Ekaterina Kotelnikova, Andrey Kalinin, Anton Yuryev, and Sergei Maslov Evolutionary Bioinformatics, Product: MedScan, Topic: Network evolution |
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Pathway analysis for design of promiscuous drugs and selective drug mixtures. Sivachenko A, Kalinin A, Yuryev A. Curr Drug Discov Technol. 2006 Dec;3(4):269-77., Product: Pathway Studio, Topic: Applications of pathway analysis |
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Molecular networks in microarray analysis. Sivachenko AY, Yuryev A, Daraselia N, Mazo I. J Bioinform Comput Biol., Product: Pathway Studio, Topic: Gene expression analysis |
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Pathway analysis software as a tool for drug target selection, prioritization and validation of drug mechanism Sivachenko A & Yuryev A Expert Opinion on Therapeutic Targets, v.11(3), pp.411-421, Product: Pathway Studio, Topic: Applications of pathway analysis |
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Targeting transcription factors in cell regulation. Anton Yuryev Expert Opinion on Therapeutic Targets, Product: Pathway Studio, Topic: Applications of pathway analysis |
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Pathway Analysis in Drug Development Azat Badretdinov, Anton Yuryev Pharma & Bio Ingridients March 2006, Product: Pathway Studio, Topic: Applications of pathway analysis |
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Automatic pathway building in biological association networks Anton Yuryev, Zufar Mulyukov, Ekaterina Kotelnikova, Sergei Maslov, Sergei Egorov, Alexander Nikitin, Nikolai Daraselia and Ilya Mazo BMC Bioinformatics 2006, 7:171, Product: Pathway Studio, Topic: Pathways and function |
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Binding properties and evolution of homodimers in protein-protein interaction networks Ispolatov, Iaroslav; Yuryev, Anton; Mazo, Ilya; Maslov, Sergei Nucleic Acids Research 2005 33(11):3629-3635, Product: PathwayAssist, Topic: Network evolution |
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Duplication-divergence model of protein interaction network I.Ispolatov, P.L.Krapivsky, A.Yuryev Phys. Rev. E 71, 061911 (2005), Product: Pathway Studio, Topic: Network evolution |
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Identifying Local Gene Expression Patterns in Biomolecular Networks A. Y. Sivachenko, A. Yuryev, N. Daraselia, I. Mazo IEEE Computational Systems Bioinformatics Conference, Aug. 8-11, 2005, Product: Pathway Studio, Topic: Gene expression analysis |
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Cliques and duplication-divergence network growth Ispolatov, I ; Krapivsky, P L ; Mazo, I ; Yuryev, A New J.Phys. 7(2005) 145, Product: Pathway Studio, Topic: Network evolution |
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Finding mesoscopic communities in sparse networks I. Ispolatov, I. Mazo, and A. Yuryev J. Stat. Mech. (2006) P09014, Product: Pathway Studio, Topic: Pathways and fucntion |
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Extracting Protein Function Information from MEDLINE Using a Full-Sentence Parser Nikolai Daraselia, Sergei Egorov, Andrey Yazhuk, Svetlana Novichkova, Anton Yuryev, Ilya Mazo Proceeding of the Second European Workshop on Data Mining and Text Mining for Bioinformatics, pp11-18, 2004, Product: Pathway Studio, Topic: MedScan |
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A Simple and Practical Dictionary-Based Approach for Identification of Proteins in MEDLINE Abstracts Sergei Egorov PhD, Anton Yuryev PhD, and Nikolai Daraselia PhD Journal of the American Medical Informatics Association 2004, Product: PathwayAssist, Topic: MedScan |
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Pathway studio the analysis and navigation of molecular networks Alexander Nikitin, Sergei Egorov, Nikolai Daraselia, and Ilya Mazo Bioinformatics. 2003 Nov 1;19(16):2155-7, Product: PathwayAssist, Pathway Studio, Topic: Pathway Studio |
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MedScan, a natural language processing engine for MEDLINE abstracts Svetlana Novichkova, Sergei Egorov and Nikolai Daraselia Bioinformatics 2003, v.19(13) p.1699-706, Product: Pathway Studio, Topic: MedScan |
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Extracting human protein interactions from MEDLINE using a full-sentence parser Nikolai Daraselia, Anton Yuryev, Sergei Egorov, Svetalana Novichkova, Alexander Nikitin and Ilya Mazo Bioinformatics 2004, v.20(5):604-11, Product: Pathway Studio, Topic: MedScan |
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Integrating fragmented software applications into holistic solutions: focus on drug discovery Anton Yuryev Expert Opinion on Drug Discovery, Volume 6,Number 4, April 2011 , pp. 383-392(10) |
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Global response of Plasmodium falciparum to hyperoxia: a combined transcriptomic and proteomic approach Torrentino-Madamet M, Almras L, Desplans J, Le Priol Y, Belghazi M, Pophillat M, Fourquet P, Jammes Y, Parzy D. Malar J. 2011 Jan 11;10:4 |
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Ariadne s ChemEffect and Pathway Studio knowledge base Anton Yuryev, Ekaterina Kotelnikova & Nikolai Daraselia Opinion on Drug Discovery |
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In silico pathway analysis: the final frontier towards completely rational drug design Yuryev A. Expert Opinion on Drug Discovery |
| Patents | Go to top | |
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Treatment and diagnosis of metastatic prostate cancer with inhibitors of epidermal growth factor receptor (egfr) Ree Anne Hansen; Bratland Ase; Boender Pieter Jacob; Ruijtenbeek Robby , Product: Pathway Studio |
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A gene expression signature identifying pro-angiogenic genes in ovarian tumor endothelial cell isolates Birrer Michael J; Bonome Tomas A; Sood Anil; Lu Chunhua , Product: Pathway Studio |
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Method for the molecular characterization of old-age hair Grdl, Sabine ; Giesen, Melanie ; Holtktter, Olaf ; Petersohn, Dirk; Patent cooperation treaty application, Product: PathwayAssist |
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Conditioned cell immunization Schreiner, George F. Patent cooperation treaty application, Product: PathwayAssist |
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Global Gene Expression Analysis of Human Bronchial Epithelial Cells Exposed to Cigarette Smoke, Smoke Condensates, or Components Thereof Jorgensen, Ellen D ; Albino, Anthony P. ; Jin, Wendy; United states patent and trademark office pre-grant publication, Product: PathwayAssist |
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Diagnosis and prognosis of infectious diseases clinical phenotypes and other physiologic states using host gene expression biomarkers in blood Agan, Brian K. ; Hanson, Eric H. ; Jenkins, Michael J. ; Lin, Baochuan ; Olsen, Chris C. ; Rowley, Robb K. ; Stenger, David A. ; Thach, Dzung C. ; Tibbetts, Clark J. ; Walter, Elizabeth A. ; Liu, Jinny Lin; United states patent and trademark office pre-grant publication, Product: PathwayAssist |
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Method for identifying therapeutical targets in secondary tumors, the use of thereof and means for identifying, labelling and targeting secondary tumors Borlak, Jrgen ; Lehner, Frank ; Klempnauer, Jrgen; Patent cooperation treaty application, Product: Pathway Studio |
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Induction of intracellular and secreted growth inhibitors and paracrine tumor-suppressive activity by rar ligands Chen, Yuhong ; Roninson, Igor B.; Patent cooperation treaty application, Product: PathwayAssist |
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Toxicology and cellular effect of manufactured nanomaterials Chen, Fanqing; Patent cooperation treaty application, Product: PathwayAssist |
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Cassette system for expression control and cell differentiation by inducible rna interference and uses thereof Moroni, Christoph ; Wegmueller, Daniel; Patent cooperation treaty application, Product: Pathway Studio |
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Modulation of mesenchymal and metastatic cell growth Spicer, Douglas B.; Patent cooperation treaty application, Product: PathwayAssist |
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Methods to analyze biological networks Iyengar, Ravi ; Ma\'ayan, Avi; Patent cooperation treaty application, Product: Pathway Studio |
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Diagnosis and prognosis of infectious diesease clinical phenotypes and other physiologic states using host gene expresion biomarkers in blood Agan, Brian K. ; Hanson, Eric H. ; Jenkins, Michael, J ; Lin, Baochuan ; Olsen, Chris C. ; Rowley, Robb K. ; Stenger, David A. ; Thach, Dzung C. ; Tibbetts, Clark J. ; Walter, Elizabeth A. ; Liu, Jinny, Lin; Patent cooperation treaty application, Product: PathwayAssist |
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Methods for identification of compounds that mimic the senescence-inducing activity of retinoic acid receptor ligands Chen, Yuhong ; Roninson, Igor B.; United states patent and trademark office pre-grant publication, Product: PathwayAssist |
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Transgenic TIEG non-human animals Spelsberg, Thomas C. ; Subramaniam, Malayannan ; Velasquez, Merry Jo ; Rajamannan, Nalini M.; United states patent and trademark office granted patent, Product: PathwayAssist |
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System and method for prediction of drug metabolism, toxicity, mode of action, and side effects of novel small molecule compounds Ekins, Sean ; Bugrim, Andrej ; Nikolskaya, Tatiana ; Nikolsky, Yuri; United states patent and trademark office pre-grant publication, Product: PathwayAssist |
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Identifying off-target effects and hidden phenotypes of drugs in human cells MacDonald, Marnie L. ; Lamerdin, Jane ; Owens, Stephen ; Keon, Brigitte ; Bilter, Graham K. ; Shang, Zhidi ; Huang, Zhengping ; Yu, Helen ; Dias, Jennifer ; Minami, Tomoe ; Michnick, Stephen W. ; Westwick, John K.; United states patent and trademark office pre-grant publication, Product: PathwayAssist |
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Network-based approaches to identifying significant molecules based on high-throughput data analysis Vailaya, Aditya ; Kuchinsky, Allan ; Ashley, Euan Angus ; King, Jennifer Y. ; Ferrara, Rossella ; Quertermous, Thomas; United states patent and trademark office pre-grant publication, Product: PathwayAssist |
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Modulation of mesenchymal and metastatic cell growth Spicer, Douglas B.; United states patent and trademark office pre-grant publication, Product: PathwayAssist |
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Methods for identification of novel protein drug targets and biomarkers utilizing functional networks Nikolskaya, Tatiana ; Bugrim, Andrej ; Nikolsky, Yuri; United states patent and trademark office pre-grant publication, Product: PathwayAssist |
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Methods for identifying parkinson\'s disease therapeutics Isacson, Ole; Patent cooperation treaty application, Product: PathwayAssist |
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Methods for identifying parkinson\'s disease therapeutics Isacson, Ole; United states patent and trademark office pre-grant publication, Product: PathwayAssist |
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Network-based approaches to identifying significant molecules based on high-throughput data analysis Vailaya, Aditya ; Kuchinsky, Allan ; King, Jennifer Y. ; Ferrara, Rossella ; Quertermous, Thomas; European Patent Application, Product: PathwayAssist |
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Methods for diagnosing epigenetic, transgenerational effects of environmental toxicants on mammalian germ-lines and treating associated diseases Skinner, Michael K.; Patent cooperation treaty application, Product: PathwayAssist |
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Reduced risk tobacco products and methods of making same Albino, Anthony ; Jin, Wendy ; Jorgensen, Ellen; Patent cooperation treaty application, Product: PathwayAssist |
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Cancer vaccines and therapeutic methods Cohen, Edward P.; Patent cooperation treaty application, Product: PathwayAssist |
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Chemical interaction with metabolites in organism Ekins, Sean ; Bugrim, Andrej ; Nikolskaya, Tatiana ; Nikolsky, Yuri; Patent cooperation treaty application, Product: PathwayAssist |
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Harnessing network biology to improve drug discovery Macdonald, Marnie L. ; Westwick, John K. ; Keon, Brigitte ; Lamerdin, Jane ; Michnick, Stephen W.; Patent cooperation treaty application, Product: PathwayAssist |
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Microarray data normalization using nonparametric variable reduction and approximation Ni, Terri T.; Patent cooperation treaty application, Product: PathwayAssist |
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Methods for diagnosing epigenetic, transgenerational effects of environmental toxicants on mammalian germ-lines and treating associated diseases Skinner, Michael K.; United states patent and trademark office pre-grant publication, Product: PathwayAssist |
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Harnessing network biology to improve drug discovery MacDonald, Marnie L. ; Westwick, John K. ; Keon, Brigitte ; Lamerdin, Jane ; Michnick, Stephen W.; United states patent and trademark office pre-grant publication, Product: PathwayAssist |
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Transgenic TIEG non-human animals Spelsberg, Thomas C. ; Subramaniam, Malayannan ; Velasquez, Merry Jo ; Rajamannan, Nalini M.; United states patent and trademark office pre-grant publication, Product: PathwayAssist |
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Global gene expression analysis of human bronchial epithelial cells exposed to cigarette smoke, smoke condensates, or components thereof Jorgensen, Ellen D. ; Albino, Anthony P. ; Jin, Wendy; Patent cooperation treaty application, Product: PathwayAssist |
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Transgenic TIEG non-human animals Spelsberg, Thomas C. ; Subramaniam, Malayannan; Patent cooperation treaty application, Product: PathwayAssist |
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Methods for predicting the course of a malignant disease Rowe, Michael W. ; Moler, Edward J. ; Randazzo, Filippo; Patent cooperation treaty application, Product: PathwayAssist |
| Epigenetic studies | Go to top | |
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Multiple Genes Exhibit Phenobarbital-Induced Constitutive Active/Androstane Receptor Mediated DNA Methylation Changes during Liver Tumorigenesis and in Liver Tumors Jennifer M. Phillips and Jay I. Goodman Toxicol. Sci., Apr 2009; 108: 273 - 289, Product: Pathway Studio |
| Text mining | Go to top | |
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Analysis and construction of pathogenicity island regulatory pathways in Salmonella enterica serovar Typhi Su Yean Ong, Fui Ling Ng, Siti Suriawati Badai, Anton Yuryev and Maqsudul Alam Journal of Integrative Bioinformatics, 7(1):145, 2010 |
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Induction of the interleukin 6/ signal transducer and activator of transcription pathway in the lungs of mice sub-chronically exposed to mainstream tobacco moke Halappanavar S, Russell M, Stampfli MR, Williams A, Yauk CL BMC Medical Genomics, 2, p.56-56, Aug 2009, Product: Pathway Studio, ResNet |
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A Modeling-Derived Hypothesis on Chronicity in Respiratory Diseases: Desensitized Pathogen Recognition Secondary to Hyperactive IRAK/TRAF6 Signaling Tingting Zhang,Kyung W. Song,Mohammad Hekmat-Nejad,David G. Morris,and Brian R. Wong PLoS ONE.2009;4(4): e5332, Product: Pathway Studio |
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Gene regulatory network inference: data integration in dynamic models-a review. Hecker M, Lambeck S, Toepfer S, van Someren E, Guthke R. Biosystems. 2009 Apr;96(1):86-103, Product: Pathway Studio |
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Silver Diamine Fluoride: A Caries A. Rosenblatt, T.C.M. Stamford, and R. Niederman Journal of Dental Research. 2009; 88(2): p. 116-125, Product: Pathway Studio |
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Old target new approach: an alternate NF-B activation pathway via translation inhibition Csaba F. Lszl and Shiyong Wu Molecular and Cellular Biochemistry, Feb 2009 |
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Developmental gene regulatory networks in the zebrafish embryo. Chan TM, Longabaugh W, Bolouri H, Chen HL, Tseng WF, Chao CH, Jang TH, Lin YI, Hung SC, Wang HD, Yuh CH. Biochim Biophys Acta. 2008 Oct 8, Product: MedScan |
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Automatic extraction of gene ontology annotation and its correlation with clusters in protein networks. Daraselia N, Yuryev A, Egorov S, Mazo I, Ispolatov I. BMC Bioinformatics. 2007 Jul 10;8(1):243, Product: MedScan, Topic: MedScan, Pathway and function |
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Applied information retrieval and multidisciplinary research: new mechanistic hypotheses in Complex Regional Pain Syndrome Hettne KM, de Mos M, de Bruijn AG, Weeber M, Boyer S, van Mulligen EM, Cases M, Mestres J, van der Lei J. J Biomed Discov Collab. 2007 May 4;2:2, Product: Pathway Studio |
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Text mining of full-text journal articles combined with gene expression analysis reveals a relationship between sphingosine-1-phosphate and invasiveness of a glioblastoma cell line Jeyakumar Natarajan, Daniel Berrar, Werner Dubitzky, Catherine Hack, Yonghong Zhang, Catherine DeSesa, James R Van Brocklyn and Eric G Bremer BMC Bioinformatics 2006, 7:373, Product: Pathway Studio |
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Extracting Protein Function Information from MEDLINE Using a Full-Sentence Parser Nikolai Daraselia, Sergei Egorov, Andrey Yazhuk, Svetlana Novichkova, Anton Yuryev, Ilya Mazo Proceeding of the Second European Workshop on Data Mining and Text Mining for Bioinformatics, pp11-18, 2004, Product: Pathway Studio, Topic: MedScan |
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A Simple and Practical Dictionary-Based Approach for Identification of Proteins in MEDLINE Abstracts Sergei Egorov PhD, Anton Yuryev PhD, and Nikolai Daraselia PhD Journal of the American Medical Informatics Association 2004, Product: PathwayAssist, Topic: MedScan |
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Metadata: A Fundamental Component of the Semantic Web Jane Greenberg, Stuart Sutton and D. Grant Campbell Bulletin of the American Society for Information Science and Technology, Vol. 9, No. 4; April/May 2003, Product: Pathway Studio |
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MedScan, a natural language processing engine for MEDLINE abstracts Svetlana Novichkova, Sergei Egorov and Nikolai Daraselia Bioinformatics 2003, v.19(13) p.1699-706, Product: Pathway Studio, Topic: MedScan |
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Extracting human protein interactions from MEDLINE using a full-sentence parser Nikolai Daraselia, Anton Yuryev, Sergei Egorov, Svetalana Novichkova, Alexander Nikitin and Ilya Mazo Bioinformatics 2004, v.20(5):604-11, Product: Pathway Studio, Topic: MedScan |
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Comprehensive Analysis of Alternative Splicing and Functionality in Neuronal Differentiation of P19 Cells Hitoshi Suzuki et al PLoS One |
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Ariadne s ChemEffect and Pathway Studio knowledge base Anton Yuryev, Ekaterina Kotelnikova & Nikolai Daraselia Opinion on Drug Discovery |
| Databases | Go to top | |
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The predicted impact of coding single nucleotide polymorphisms database. Rudd MF, Williams RD, Webb EL, Schmidt S, Sellick GS, Houlston RS. Cancer Epidemiol Biomarkers Prev. 2005 Nov;14(11 Pt 1):2598-604., Product: PathwayAssist |
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HAGR: the Human Ageing Genomic Resources Joo Pedro de Magalhes, Joana Costa, and Olivier Toussaint Nucleic Acids Res., Jan 2005; 33: 537 - 543., Product: PathwayAssist |
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GenAge: a genomic and proteomic network map of human ageing Joo Pedro de Magalhes, Olivier Toussaint FEBS Letters 571 (2004) 243 247, Product: Pathway Studio |
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A survey of current software for network analysis in molecular biology S Thomas and D Bonchev Hum Genomics |
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Computational methods for discovering gene networks from expression data Wei-Po Lee and Wen-Shyong Tzou Brief Bioinform,Jul 2009; 10: 408 - 423, Product: Pathway Studio |
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Genomic analysis of epithelial ovarian cancer John Farley, Laurent L Ozbun, Michael J Birrer Cell Research (2008) 18:538 548, Product: PathwayAssist |
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Logic models of pathway biology Steven Watterson, Stephen Marshall and Peter Ghazal Drug Discovery Today, 13 (9), p.447-456, May 2008, Product: Pathway Studio |
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Bioinformatics applications for pathway analysis of microarray data Werner, T Current Opinion in Biotechnology, 19 (1), p.50-54, Product: Pathway Studio |
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Genomic Profiling in Nuclear Receptor-Mediated Toxicity Woods CG, Heuvel JP, Rusyn I. Toxicol Pathol. 2007;35(4):474-94, Product: Pathway Studio |
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Pathway analysis for design of promiscuous drugs and selective drug mixtures. Sivachenko A, Kalinin A, Yuryev A. Curr Drug Discov Technol. 2006 Dec;3(4):269-77., Product: Pathway Studio, Topic: Applications of pathway analysis |
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Molecular networks in microarray analysis. Sivachenko AY, Yuryev A, Daraselia N, Mazo I. J Bioinform Comput Biol., Product: Pathway Studio, Topic: Gene expression analysis |
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Pathway analysis software as a tool for drug target selection, prioritization and validation of drug mechanism Sivachenko A & Yuryev A Expert Opinion on Therapeutic Targets, v.11(3), pp.411-421, Product: Pathway Studio, Topic: Applications of pathway analysis |
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Microarrays in breast cancer research and clinical practice the future lies ahead Sofia K Gruvberger-Saal, Heather E Cunliffe, Kristen M Carr and Ingrid A Hedenfalk Endocrine-Related Cancer, Product: Pathway Studio |
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Pathway Analysis in Drug Development Azat Badretdinov, Anton Yuryev Pharma & Bio Ingridients March 2006, Product: Pathway Studio, Topic: Applications of pathway analysis |
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The Pathways Promise Malorye Blanca Bio-IT World, July 2004, Vol. 3, No 7, Product: Pathway Studio |
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Expanding Options in Data Analysis Emma Hitt The Scientist, Volume 18, Issue 13, 44, Jul. 5, 2004, Product: Pathway Studio |
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Making Mechanistic Connections between Cell Signaling Pathways and Pathological Endpoints Myrtle A. Davis Toxicologic Pathology,Volume 32, Supplement 1 / March-April 2004: 131 135, Product: Pathway Studio |
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From bioarrays to diagnostics: a systemomics approach Krishnarao Appasani Expert Rev. Mol. Diagn. 4(1), 1-5 (2004), Product: Pathway Studio |
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Bioinformatics from genes to pathways Laura Bonetta Nature Methods 1, 169 - 176 (2004) doi:10.1038/nmeth1104-169, Product: Pathway Studio |
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Drug discovery and Biotechnology Trends - Bioinformatics: Feeling the Forward Momentum Mike May, Gary Heebner Science e-Marketplace, September 26, 2003, Product: Pathway Studio |
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Drug discovery and Biotechnology Trends - DNA and Biochips 2: Arrays of Diagnostics Mike May, Gary Heebner Science e-Marketplace, May 3, 2003, Product: Pathway Studio |
| Websites | Go to top | |
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Rat Genome Database pathway ontology Victoria Petri Medical College of Wisconsin, Bioinformatics Research Center, Product: Pathway Studio |
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The PPAR resource page Jack Vanden Heuvel Penn State University, Center for Molecular Toxicology, Product: Pathway Studio |
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p53 knowledege base Felicia NG Bioinformatics Institute (BII), Singapore, Product: Pathway Studio |
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Research in scleroderma Zhou X, Tan FK, Guo X, Wallis D, Milewicz DM, Xue S, Arnett FC University of Texas, Health Science Center at Huston, Product: PathwayAssist |
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Cancer-related pathway collection Tetsuya Shiraishi Sony Computer Science Laboratories, Product: Pathway Studio |
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Nova-2 regulated network Jernej Ule The Rockefeller University, Product: PathwayAssist |
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The Rat Genome Database Pathway Portal Victoria Petri, Mary Shimoyama, G. Thomas Hayman, Jennifer R. Smith, Marek Tutaj, Jeff de Pons, Melinda R. Dwinell, Diane H. Munzenmaier, Simon N. Twigger, Howard J. Jacob, and RGD Team Database, Apr 2011; 2011: bar010. |
Publication Policy for Pathway Studio
Ariadne provides a publication policy to encourage publication and to explain the conditions by which Licensed Users may publish from Pathway Studio without requiring special approval by Ariadne.
