Bayer HealthCare AG
Pfizer
Gene Network Sciences
Genstruct
Institut Curie
Murex Pharmaceuticals
University of Oklahoma
Vanderbilt University
Elan Pharmaceuticals
Freiburg University
Finnish Red Cross
The Rat Genome Database
University of Florida
Illumina
Affymetrix
Cornell University
M.D. Anderson Cancer Center
Euro Neuromuscular Disease Consortium
Case Western Reserve University
ExonHit Therapeutics

A sample of scientific publications made using Ariadne products is available in Publications.

“Bayer HealthCare recognizes the importance of using pathway analysis tools for interpretation of experimental results and hypotheses validation. But to make these tools truly efficient, we need an internal integrated database of pathways and molecular networks, containing all most recent information. We have chosen MedScan for its advanced natural language processing algorithm, well known for high recovery rate and accuracy, and its ease of integration with our bioinformatics systems.” - Michael Seewald, Bioinformatician.

"Pathway Studio provides Pfizer researchers with easy access to publicly available scientific information, and a way to integrate our proprietary data along with third party high-confidence data such as the Human Interaction Database from Prolexys. We can also integrate Pathway Studio with in-house tools to assemble targeted data sets for research in specific disease, biomarker, and drug related topics." - Giles Day, Senior Director, Target and Mechanism Informatics at Pfizer.

“PathwayStudio Central is an efficient and effective tool to help integrate the latest pathway-related knowledge scattered throughout scientific publications with our pre-clinical and clinical models,” - Jeffrey Fox, Ph.D., vice president of research of GNS.

“The accuracy of our assertions is one of our highest priorities. MedScan TextMiner, with its unique Natural Language Processing engine, will improve our ability to apply Knowledge Assembly to the extraction of molecular interaction information from the scientific literature.” - Keith O. Elliston, Ph.D., President and CEO of Genstruct.

“PathwayStudio will be utilized in our research projects aimed at understanding and stopping tumoral progression, in particular for the elucidation of the biological pathways that are responsible of cell deregulation, such as perturbation in apoptosis, proliferation, and differentiation. One of our main purposes is to better classify, diagnose and prognose tumors, and to adapt treatments to individual patients.” - Emmanuel Barillot, Director of Bioinformatics at Institut Curie.

“It’s hard to overestimate the importance of Pathway Studio in our development of cancer therapies based on patients’ individual gene expression data. Pathway Studio will accelerate our development efforts as well as help to further increase the safety of our products.” -David Shanahan, President and CEO of Murex Pharmaceuticals.

"We will perform scientific evaluation of pathway expansion and microarray data analysis algorithms available in Pathway Studio. Then we will build up a collection of cancer-related pathways using its built-in ResNet database and advanced pathway reconstruction and literature mining tools." - Dr. Dee Wu, an associate professor at the OU Health Sciences Center.

“We evaluated various pathway analysis packages and were impressed by Pathway Studio’s graphics and ease of use. Most impressive is the MedScan Technology that allows our researchers to extract relationships from the latest publications and add them to the large body of knowledge in the packaged database. The ability to instantly update the database with selected information is of paramount importance in cancer research." - Dr. Lynn Matrisian, Chair of the Department of Cancer Biology at Vanderbilt University.

"Ariadne's Pathway Studio, MedScan, and ResNet complement the tools already in use at Elan for pathway investigation and gene expression analysis. The MedScan module, in particular, gives a scientist the capability to quickly create pathways from the newest literature sources in a matter of minutes." - Jim Miller, Principal Scientist at Elan Pharmaceuticals.

"Instant availability of knowledge extracted from peer-reviewed publications in the ResNet Mammalian and especially ResNet Plant database along with Pathway Studio's powerful mechanism for visualization makes Ariadne's Pathway Studio uniquely suited for our use," - Stefan Rensing, head of the Data Management Core Facility within the Freiburg Initiative for Systems Biology.

"MedScan is the only existing tool that allows flexible concentration of biomedical text and extraction of knowledge, e.g., after a batch download of full-text articles or Google Scholar full text queries into a database amenable for further analysis. Pathway Studio Enterprise allows us to easily add and update databases, expand the database content, and work with our own and third party data. The first step in reviewing a manuscript now is to make a quick and flat mind-map of its relations to visualize the bulk text. Even in a trivial topic, it is handy to count the contradicting claims in a self correcting process." - Pauli Ojala, Bioinformatician at Finnish Red Cross.

"Ariadne Pathway Studio is a uniquely powerful tool to create public pathway collections. Besides the largest collection of molecular interactions referenced by original literature sources, it includes powerful visualization tools and can produce interactive HTML pathways with underlying reference information in just one click." - Victoria Petri, The Rat Genome Database.

"We work on many of non-model organisms and create microarrays for them using 454 and Agilent technologies. After mapping genes from these non-model organisms to model organisms, we use Pathway Studio to explore the gene networks." - Li Liu, Bioinformatics Director at the ICBR Bioinformatics Core, University of Florida.

"Ariadne is the first to offer a plug-in with our newly launched GenomeStudio Software program. By providing a graphical representation of Illumina's microarray data, Pathway Studio offers researchers a unique way to complete advanced downstream analysis. Illumina and its software partners continue to improve tools that aid in the interpretation of data across multiple applications." - Omoshile Clement, Ph.D., Senior Product Manager of Software Informatics at Illumina.

“Pathway-level annotation and functional analysis is fast becoming a standard part of gene expression microarray data analysis. The integration between the Affymetrix GeneChip platform and Ariadne’s Pathway Studio allows our mutual customers to extract the greatest value from their microarray data.” - Steve Lincoln, vice president of Informatics at Affymetrix.

"Pathway Studio with ResNet Plant Database will enable researchers to identify relationships among proteins, small molecules, and cell processes; to look at for example regulation by plant hormones and the effects of different environmental conditions on small molecule and metabolite synthesis. I think ResNet Plant is very good, probably the best in the market at this point since it can be frequently updated". - Magnolia Ariza-Nieto Ph.D., US Plant, Soil and Nutrition Lab, Cornell University.

"L-ASP is a standard component of chemotherapy regimens for leukemia and is also being tested against solid tumors, but efficacy is observed in only a subset of patients. We're looking for protein and small molecule biomarkers that predict L-ASP response and for small molecules that exhibit synergistic anticancer activity with L-ASP. Our laboratory employs a systems pharmacology approach to identifying novel mechanisms of action, biomarkers that predict drug effect, and synergistic combination therapies. Pathway Studio helps us integrate those strategies." - Dr. Phil Lorenzi, supervisor of Laboratory and Research, Department of Bioinformatics and Computational Biology at M.D. Anderson 

"Together with data from siRNA screening and metabolomic profiling experiments, Pathway Studio and ChemEffect will facilitate a systems-wide approach to prioritizing candidate biomarkers and potentially synergistic drug combinations. If successful, an advantage of trying to re-position approved drugs, rather than bring a new one to the table, is that we don't have to wait 14 years or have a billion dollars in spare change to make it happen." - Dr. John Weinstein, Chair of the department and principal investigator.

"The participation of Ariadne as partners together with INSERM is crucial for the project. Developing bioinformatic tools for OMIC studies analysis is essential and guarantees success to the project. In addition, it reinforces collaboration between academics and industries, again a key point for successful research to be translated into clinics." - BIO-NMD's coordinator and chair of the steering committee, Professor Alessandra Ferlini (University of Ferrara, Italy)

“I have been a PathwayAssist user since its very first version. The ability to mine the myriad of functional relationships extracted from publications, and match the result to the change observed in one’s experimental system, is of tremendous benefit to me. The addition of STKE signaling pathways curated by leading authorities in the field will reinforce tremendously what we can do with PathwayAssist. I’m looking forward to seeing more and more curated pathways incorporated within the software.” - Aura Perez, M.D., Ph.D., Department of Pediatrics, Case Western Reserve University, Cleveland, Ohio.

“We have customized Pathway Studio’s natural language processing capability to extend the data set provided by Ariadne with alternative splicing information retrieved from literature sources.  Pathway Studio is a valuable tool in our standard research process." - Dr. John Jaskowiak, Executive VP of Business Development at ExonHit.