Testimonials on GeneGo’s Bioinformatics Tools

“GeneGo has demonstrated the capability to develop a good pharma oriented bioinformatics tool in the past years” said Peter Groenen, project manager for pharmacogenetics at Organon. “We have now started to use their software for more advanced projects to support our translational medicine efforts”.

“Biologist see the importance of looking at the circuitry rather than just simple wiring. That is why MetaCore™ interactions are so much more powerful as they have directionality, show effect and mechanism of interaction all validated with papers one click away”.

“During the past year, we have used MetaCore™ in analyzing our quantitative proteomic data on ischemic rodent brains,” said Dr. An Zhou, a scientist at the RSDNL. “MetaCore™ allows us to efficiently handle multiple sets of high throughput proteomic data with statistics and visual presentation, as well as to identify pathways and networks that are unique to different ischemic conditions of the brain”.

“GeneGo’s MetaCore™ and MapEditor™ is one of the integrated bioinformatics platforms installed in the Chang Gung Bioinformatics Center for analysis of data generated from research projects of different disciplines. Current and ongoing projects include the identification of biomarkers that can reveal the presence of nasopharyngeal carcinoma (NPC) in a blood test; the Trichomonas vaginalis Systems Biology Project and the Acanthamoeba Expressed Sequence Tag Project. These powerful tools will highly improve our research stretch” said Professor Tang

“We compared several platforms before we finally decided on GeneGo. MetaCore™ has broad and deep, high quality content coverage, which was important to us. Furthermore its ability to work with mixed ID's is critical for our internal R&D work and service offerings based on our unique DSA™ (patent pending) research tools” said Dr Vitali Proutski, Bioinformatics Manager at Almac Diagnostics. “We were also very impressed by GeneGo's responsiveness and strong customer support which we feel is vital in relationships with our partners.”

“We are pleased to have acquired this excellent research tool from GeneGO. MetaCore™ will increase our ability to translate research discoveries into clinical applications that will improve the quality of life for patients with infertility,” said Dr. Nathan Treff, Principle Investigator of Molecular Biology at RMA of New Jersey.

“We appreciate MetaCore’s flexibility and GeneGo’s ability to quickly implement customer feedback,” said Dr. Georg C. Terstappen, Vice President Discovery Research, of the Italian Company. “GeneGo and Siena Biotech in their respective fields are leading the way in pathway proteomics: we expect advantages for both companies form this collaboration.”

Nicholas Schork, Professor of Psychiatry and Co-Director of the new UCSD Center for Human Genetics and Genomics says, “We and others within the UCSD Medical School are developing integrative approaches to understanding the pathophysiology of human diseases that will include, among other things, emphases on DNA sequence variation, altered gene expression, and protein perturbations, so having a tool like MetaCore™ to help synthesize information about pathways and genetic networks is absolutely crucial.”

“My group evaluated MetaCore™ to better understand neuropathological changes associated with Schizophrenia using our high throughput data. We felt that this software can help us understand the details of cellular changes in these disorders so we decided to license it, along with several other groups at UCSD,” said Dr. Ian Everall, Professor of Psychiatry, Department of Psychiatry, UCSD School of Medicine.

“We will be using MetaCore™ for a number of projects investigating the mechanisms of signal transduction downstream of GPCR and tyrosine kinase receptors. This software will help us to understand the complex physiological regulation of reproduction and glucose metabolism,” said Dr. Nicholas Webster, Professor of Medicine and Director of the Genechip Miicroarray Core Facility.

“We tested several platforms in the systems biology marketplace and felt that MetaCore™ best suited our current needs,” said Dr Andreas Kramer, Head of Bioinformatics for Siena Biotech. “We felt that the content was broad, deep with a high level of quality control and we can access information without having experimental data as a starting point.”

“We evaluated MetaCore™ and decided that it was a good fit for TGen,” said Dr. Edward Suh, TGen’s Chief Information Officer. “GeneGo enables our scientists to generate global pathways and smaller targeted networks, and in addition, extending pathways and networks with GeneGo was a very attractive feature for gaining information.”

“We evaluated several platforms and decided that MetaCore™ was the best fit for our current needs at Organon. We are very much looking forward to working closely with GeneGo,” said Dr. Peter Groenen, senior research scientist at Organon.

“We will use MetaCore™ for biological interpretation of genomics data and hypothesis generation” said Timo Wittenberger, Ph.D., leader of the bioinformatics group at ALTANA Pharma. “Our aim is a more profound understanding of patho-mechanisms which will allow us to develop more innovative drugs. MetaCore™ helps us here by representing our data in the context of public knowledge.”

“We looked at several systems biology packages and found that MetaCore™ suited our needs the best.” said Mr.Yukikazu Natori, Chairman of RNAi. “The system is flexible for customization, and the GeneGo team is open minded for collaborative development. We needed a flexible partner that was willing to integrate with our current siRNA technology.”

“We chose MetaCore™ as it has the most comprehensive, detailed database of human metabolism and signaling, and is also a one-stop shop for our systems analysis needs” said Dr Ben van Ommen, Senior Research Fellow in Nutritional Systems Biology of TNO. “Experimental data in nutrition are inherently complex, as the diet-influenced changes in disease onset and progression are subtle and multi-factorial. We also have the data from both human and model animals. In MetaCore™, we can upload and compare all these data on the same networks and pathways and then analyze the networks with a variety of tools.”

“I was personally impressed to hear that the “annotation/curation” team is constituted by 45 full time Ph.D. scientists reading the full articles. I can confirm that in a given case, I checked an interaction between two proteins, and that this binding interaction was only described in a figure (an immunoprecipitation) of the paper referenced, and not at all in the title or in the abstract.”

“Rosetta Biosoftware’s collaboration with GeneGo supports our customers’ desire to analyze data in the Rosetta Resolver system in conjunction with pathway information from MetaCore™,” said Yelena Shevelenko, vice president and general manager of Rosetta Biosoftware. “Our mutual customers will now be able to combine the Resolver system’s powerful analysis tools with the MetaCore™ system’s comprehensive pathways to determine on- and off-target effects and to enrich gene expression data with biological context.”

“We spent quite some time evaluating systems biology platforms and were impressed by the depth and breadth of the MetaCore™ knowledge base.” said Dr. Daniel Chagnovich, Director of Research Operations for Velcura. “MetaCore™ has impressive coverage of signaling and metabolic pathways and in-depth disease and tissue-specific data that is invaluable for our research. In addition, MetaCore™ has a flexible and powerful front-end that allows our bench scientists to integrate multiple data streams and algorithms to fully mine our bone therapy data.”

“We are very pleased to bring MetaCore™ into our research,” said Hugh Salamon, senior computational biologist, Berlex. “It is essential to exploit curation of scientific findings given the large body of knowledge relevant to therapeutic research. GeneGo is providing us with an important view of current knowledge of mammalian signaling, metabolism, drugs and diseases through the MetaCore™ platform.”

“MetaCore™ has grown to become a key component in the research toolbox in the life sciences, particularly within the pharmaceutical industry, and we are pleased to have the opportunity to work with GeneGo,” commented Dr. Jonathan Sheldon, Chief Scientific Officer, InforSense. “The integration of pathway analysis with InforSense KDE is a key component of our multidisciplinary analytics platform for Systems Biology.”

“We were impressed by the quality of the content and unique capabilities of the visualization and analysis software in MetaCore™,” said Dr Koen Kas, CSO of Peakadilly.

“The integration of MDL databases with GeneGo’s pathways information systems enables scientists to bridge the gap between cell biology and organic chemistry,” comments Steve Young, Director of MDL Content Strategy. “For the first time, biologists will be able to quickly review cheminformatics data of small molecules involved in biological pathways and chemists will be able to view molecular pathway information related to their lead compounds.”

“The use of informatics to enable life science research has changed dramatically in the last 18 months,” said Jordan Stockton, Agilent Informatics marketing manager. “Today, researchers demand applications that allow them to pool evidence from as many sources as possible. The integration of GeneSpring and MetaCore™ allows leading scientists to rapidly synthesize information about pathways and molecular interactions with those from microarray technologies.”

“Genedata’s open and scalable architecture provides a strong basis for integration with client and third party content”, says Dr. Daniel Keesman, CEO of Genedata AG. Expressionist enables omics data and associated information to be imported, processed and analyzed in an automated and repeatable workflow. Phylosopher has been integrated closely with MetaCore’s visualization tools to identify and prioritize pathways affected by disease. The integrated solution achieves unrivaled standards in research information management and decision support. Dr. Keesman added, “This integration has been customer-led and helps scientists place their results in biological context, thus deriving maximum benefit from experimental data”.

“We were satisfied with the demonstrated capabilities and quality of data obtained through MetaCore™,” commented Dr. Graham Dixon, Senior Vice President of Drug Discovery at Galapagos. “We have already identified and validated novel, proprietary targets using our adenoviral technology platform in bone and joint diseases; applying MetaCore™ to this target set could allow us to gain valuable insights at the system level thereby improving our understanding of the underlying disease biology and increasing our speed and success in finding new drugs against these targets.”

“At TNO, we have worked with MetaCore™ for one year now; both the tool and the interaction with GeneGo were highly satisfactory,” said Dr Ben van Ommen, responsible for the nutrigenomics activities at TNO and director of NuGO. “In the area of nutrigenomics, the interaction between the transcriptome and metabolome are crucial. Upon our request, GeneGo has extended its software with a metabolomics parser, allowing simultaneous visualization of gene expression and metabolite concentration in the same pathways. Nutrition science experiences a rebirth now that we can combine physiology with molecular details in the new area of nutrigenomics and nutritional systems biology, and adequate bioinformatics is one of the main limiting factors to success.”

“We see MetaCore as a further step into systems biology, a novel discipline which holds much promise for pharmaceutical research,” said Dr Friedrich Rippmann, Director of Bio- and Chemoinformatics.

“We have been loyal MetaCore users for quite some time now and we have been able to make significant progress in our projects supported by the Department of Energy’s Low Dose Radiation Research Program. The software helped us to interpret proteomic data from irradiated cells and to identify pathways responsible for cytokine release following radiation exposure. Understanding these pathways is important for both radiation protection standards and effective use of radiation therapy to treat cancer,” said Dr. John Miller, Associate Professor, Washington State University Tri-Cities, and Emeritus staff member at Pacific Northwest National Labs. “We like the openness of MetaCore that allows us to understand our data in terms of biological processes, not just lists of identified proteins.” Dr. Miller focuses on biological and environmental research including radiation induced protein release.

“We outsourced prioritization of three compounds to GeneGo. While we understood the effect of these drugs, we needed to prioritize them with respect to biologic potency and possible toxicity. GeneGo’s software was able to confirm the biologic activity that we expected and highlighted functional processes and key drug targets that allowed us to focus our testing by suggesting biological activities that could be critical to the success of the candidates, saving us time and money.”

“When we designed our Computational Toxicology course a few years ago we anticipated a shift in the future toward ‘systems biology’ that is, looking at the complex interactions of metabolic, genetic, protein, and cellular elements with the goal of modeling entire systems in relation to chemical stresses,” said Dale Johnson, Pharm.D., Ph.D., Adjunct Professor, who designed and teaches the Computational Toxicology course. “The complexity of these chemical/biological interactions resulting from environmental exposures, food sources, or pharmaceutical compounds, highlights our thinking that an overall systems approach will be necessary if relevant advances are to be made in applying computational solutions. GeneGo has presented us with an outstanding platform that continues to grow in functionality each year. We are extremely pleased to be able to utilize MetaCore/MetaDrug as the core part of our coursework.”

Harris Lewin, Principal Investigator and Director of the Institute for Genomic Biology at UIUC had this to say “We were very pleased to work with the team at GeneGo on the identification of cattle orthologs. My group feels that MetaCore is currently the premier product for data mining and pathway analysis. The addition of bovine orthologs of human, mouse and rat genes to MetaCore will make the recently sequenced cattle genome more accessible for functional genomics and systems biology.”

“The manually curated content available from GeneGo is exceptional and will allow us to advance our projects,” said Dr Nat Goodman, a Senior Research Scientist at ISB. “We are initiating several research projects together that will hopefully result in publications.”

“The entrepreneur knowledgebase behind the merged platform is impressive in the areas of cell adhesion and immunology, which is essential in blood transfusion field,” said docent Jukka Partanen, research director at the FRC Blood Service R&D.

“In the market, we have not found any other manually curated platform where multiple parallel omics data could be submitted in a batch mode in such a systems medicine fashion. We are delighted that the curation does not ignore the non-English journals and reviews patent literature as well. The principle of taking only causality and not mere association into account is critical in the era of NLP text mining servers and HTS data flood,” said Jukka Partanen.

“TNO is routinely applying omics technologies to better understand the activities of nutrients and toxicants. A strong focus is on statistically and biologically driven bioinformatics towards drawing of relevant biological conclusions. We are coordinating the bioinformatics for the consortia mentioned above. MetaCore is a valuable add on to this portfolio and allows us to better understand omics data in the context of mechanisms of action. Within NuGO and NGC, Metacore is used by researchers in the fields of nutritional systems biology. Within NTC, it is used in the context of a variety of toxicological problems. Through interaction with these scientists, TNO is capable of further strengthen its scientific systems biology backbone in these areas.” said Dr Rob Stierum Head Toxicogenomics

“Our research students of drug innovation should learn to see the big picture as soon as possible, in order to become effective drug researchers. MetaDrug is state-of-the-art, but still very accessible to the novice user,” said Dr Ed Moret. “We really like the support and training they have offered to our students.”

“We joined the MetaTox Consortium because of the proposed deliverables and the cost effective access to resources to develop tools and content we need for toxicogenomics at Elan,” said Dan Ness, Director of Research, Toxicology. “This approach is novel and we believe will be a successful ROI for our experimental data.”

“We hope this collaboration will better help us to understand the disease and potential therapies at the molecular level,” said Robert J. Beall, Ph.D., president and CEO of the Foundation. “Using computational platforms adds to our arsenal of already existing strategies.”

“Expression Analysis is committed to being a full-service genomics provider,” said Steve McPhail, CEO and President of Expression Analysis, Inc. “Our standard microarray service includes statistical analyses to identify differentially expressed genes. However, some investigators request help translating the gene list into functional relationships. The GeneGo service will provide this assistance using an established software product. We see it as a natural partnership for both companies and a definite value for our clients.”

“Chenomx’s partnership with GeneGo offers several significant advantages to our shared customers,” explains Jack Newton, Director of Product Development for Chenomx. “First, our customers will now be able to combine Chenomx NMR Suite’s powerful metabolite identification and quantification capabilities with GeneGo’s pathway analysis tools, thereby improving their interpretation and understanding of the underlying biology. This integration also allows our customers to integrate genomic and proteomic data sources with their Chenomx metabolomics data.”

“We are happy to work with GeneGo on functional analysis of toxin-induced effects”, said Jennifer Fostel from NIEHS. “Their tools are well suited for datamining of large omics datasets, and their knowledge base on human pathways, networks and ontologies will be helpful for elucidation of mechanistic toxicity.”

Professor Jos Kleinjans, Director of the NTC said “Having GeneGo as a partner in the project, and having access to their leading systems biology data visualization and analysis tools and expertise, will help us to derive the best value from the data we are generating and make progress in the application of an integrated systems toxicology approach to risk assessment.”

“The strength in MetaCore, however, is in its super-rich annotation on which to discern these effects, and the organization by which the effects are tracked. There are over 2 million individual curated interactions within the database, most from peer-reviewed journals. Each interaction is highly annotated and connected back to the literature as well with other interactions. For those of you who have been using MetaCore to do analyses of high-dimensional data, you know how powerful the package can be, which often shows up in how busy the software is on some days.”

“One last thing I wanted to add is that (as you know) John really saved me before the trip to France! He has always been great about answering my questions and promptly helping me, but this time he topped it all! Thank you very much!” - Rosane

“There are many “generic” pathway tools on the market, helpful to some extent in cancer data analysis. However, none of them is centered around cancer biology, which is essential,” said Kornelia Polyak, an Associate Professor at Dana-Farber Cancer Institute and a consultant on the grant. “Another focus will be on the development of pathway-based tools for integration of different types of OMICs data - somatic mutations, high copy number genes, epigenetics, gene expression, proteomics and metabolomics.”

“KineMed’s biological pathway insights and GeneGo’s database for systems biology link network complexity to physiologic phenotypes and disease genotypes which is one of the primary goals for personalized medicine. These insights will answer the challenge of determining the right medicine for the right patient at the right time,” said Gregory Hayes, Ph.D., Director of Oncology Research at KineMed.

“We are looking forward to working with GeneGo as the company provides the kind of forward-looking bioinformatics software that we are excited to use,” said Sawsan Khuri, Ph.D., assistant research professor at the Center for Computational Science at the University of Miami Miller School of Medicine. “The technology will be extremely useful for researchers here, especially those at the Miami Project to Cure Paralysis and the Miami Institute for Human Genomics, both of which will benefit greatly from the collaboration with GeneGo as we work toward new scientific breakthroughs.”

“MetaCore’s extensive information content allows us to perform detailed data analysis of high throughput assay results that is currently not possible with any other tool. MetaCore has been adopted as a favorite tool by our users from day one.” Burak Kutlu, PhD Research Scientist, ISB

Mary E. Edgerton, a pathologist performing cancer research at MD Anderson and a long-term client, says “I have been using Metacore for many years in my research into pathways and networks that control aggressive behavior in cancers. I am currently using it to infer networks from analysis of gene expression array data for pathways in lung, brain, and breast cancer. I also use the curated pathways to formulate mathematical models of molecular networks that predict tumor behavior using multiscale modeling. Not only do I find the product to be very useful, but I also appreciate the responsiveness of the staff at Genego to my technical questions and suggestions.”

“After trying it out, I am completely sold. I have not seen any other commercial software that matches it for flexibility, content, and ease of use. Finding answers in these datasets can be difficult without a tool like GeneGo.” Jerry Glenn, Cardiovascular Genomics Laboratory, Southwest Foundation for Biomedical Research

“MetaBase is, arguably, the most comprehensive manually curated database of mammalian biology and medicinal chemistry data available. Overall, it contains over 6 million experimental findings on protein-protein, protein-DNA, and protein-compound interactions. MetaBase also includes thousands of established signaling and metabolic pathways, ligand-receptor information for known drugs, drug targets and diseases, kinetic information on drug-metabolizing enzymes and relevant signaling proteins, ontologies for diseaes, functional processes, toxicites, proteins, and drugs.”

“MetaCore integration with Array Studio will have an immediate impact for some of our mutual clients, taking the analysis results generated by Array Studio and moving it to the next level with GeneGo’s pathway analysis tools.” said Jack Liu, President at OmicSoft. “GeneGo’s flexibility and collaborative thinking has made this a smooth integration, and we look forward to working more with them in the future.”

“We will be using MetaCore to support a range of researchers across Cardiff University who are using our transcriptomics core facility, including major programs in cancer research, infection and immunity, and neuropsychiatric disease,” said Professor David Kipling, Director of Operations of Central Biotechnology Services.

“We feel that it is important to support such an initiative as there is a lot of stem cell information in the literature but no one has brought it all together in a set of comprehensive pathway maps,” said Professor Marcelo Bento Soares, Director, Cancer Biology and Epigenomics Program. “This initiative will allow researchers to have more of a global perspective and allows newcomers to the field to get up to speed quickly.”

“We feel that it is important to support such an initiative. There is an increasing amount of information in the cancer literature but no one has brought it all together in a set of comprehensive pathway maps that can be further explored,” said Craig Webb “This initiative will allow researchers to have more of a global perspective and allows newcomers to the field to get up to speed quickly.”

Professor Simon Lovestone said: “This is an important initiative as it will give researchers a global perspective of CNS pathways and enable those new to the field to get up to speed quickly. Currently there is a huge amount of CNS data available but until now no one has brought it all together in a comprehensive form.”

Dr Breen, BRC-MH Genetics Coordinator, adds “Accurate and comprehensive pathway annotation is necessary for us to discern the biological mechanisms revealed by large scale omics approaches to CNS disorders, such as genomewide association and expression array studies.”

“We are very pleased to be working with GeneGo and participating in their MetaTox projects,” said Alan Roter, VP of Informatics at Entelos. “GeneGo’s unique approach of generating functional descriptors is a great complement to the classifiers and predictive models in DrugMatrix, and we see great benefit to the scientific community using predictive toxicogenomics.”

“In many cases, discovering the mechanisms of disease and uncovering new drug targets requires an understanding of not just individual biological events, but key biological pathways,” said Siamak Baharloo, PhD, Director of eBusiness at Millipore. “This tool provides a relevant new interface to assist scientists in planning and executing their research within the context of the biological systems in which they are interested.”

Jeremy Barker, QFAB’s Chief Executive Officer said, “We are currently using MetaCore for an in-house project and have seen the power that it provides in a systems biology framework. In partnering with GeneGo we aim to help researchers in our part of the world realize the benefits that can come from using this software.”

“We feel that it is important to support such an initiative as there is a lot of stem cell information in the literature but no one has brought it all together in a set of comprehensive pathway maps,” said Nicol Keith, Professor of Molecular Oncology. “This initiative will allow researchers to have more of a global perspective and allows newcomers to the field to get up to speed quickly.”

“We are looking forward to working with GeneGo as the company provides the kind of forward-looking bioinformatics software that we are excited to use,” said Sawsan Khuri, Ph.D., assistant research professor at the Center for Computational Science at the University of Miami Miller School of Medicine. “The technology will be extremely useful for researchers here, especially those at the Miami Project to Cure Paralysis and the Miami Institute for Human Genomics, both of which will benefit greatly from the collaboration with GeneGo as we work toward new scientific breakthroughs.”

“MetaCore is being heavily used by our users and we find it to be very intuitive, easy to use and powerful tool for performing pathway analysis of the microarray data,” said Dr Shrikant Mane, Director of Keck Microarray Resource.

“KineMed’s biological pathway insights and GeneGo’s database for systems biology link network complexity to physiologic phenotypes and disease genotypes which is one of the primary goals for personalized medicine. These insights will answer the challenge of determining the right medicine for the right patient at the right time,” said Gregory Hayes, Ph.D., Director of Oncology Research at KineMed.

“MetaCore is helpful to interpret the translational relevance of the genes we found in our glaucoma research,” said Thomas J. Lukas, professor of Molecular Pharmacology & Biological Chemistry.

“GeneGo provides unique, innovative reconstructions of disease pathways that are fundamentally important and required for the understanding of disease processes so we can find cures”, said Milka Sokolovic, PhD, Medical Biochemistry, Academic Medical Center, Amsterdam. “We want to be a part of this innovation to have access to high quality resources to build pathways we need for our research programs that we will use to publish.”

“It’s critical that Sigma Aldrich has a presence through out all stages of an experiment’s life cycle,” said Nathan Allen, Market Segment Manager, Sigma Aldrich. “By incorporating our products into MetaCore, MetaDrug, and Eureka! we ensure that researchers have easy access to Sigma Aldrich products presented in the appropriate context during the initial stages of experiment preparation.”

“We prefer the coverage and quality of disease annotation, as well as the rodent specific pathway analysis, which is critical to seeing species differences. I am not aware of another platform that has this capability,” said Susan Dorsey, Director, UMB Center for Pain Studies.

“GeneGo provides unique, innovative reconstructions of disease pathways that are fundamentally important and required for the understanding of disease processes so we can find cures,” said Milka Sokolovic, PhD, Medical Biochemistry, Academic Medical Center, Amsterdam. “We want to be a part of this innovation to have access to high quality resources to build pathways we need for our research programs that we will use to publish.”

“A primary goal of the Indiana CTSI Translational Technologies Program (TTR) is to build an infrastructure that enhances the opportunity for our researchers to utilize state-of-the-art technologies. GeneGo’s agreement to provide access to their software tools to all investigators across our partner institutions at a cost equivalent to that for a few researchers to purchase their own agreements significantly contributes to this goal and offers an expanded opportunity for inter-campus collaborations,” said Lilith Reeves, Chief Scientific Officer, Indiana CTSI, IUSM