Press Releases [2005]
TNO EXPANDS RELATIONSHIP WITH GENEGO TO COVER ALL MAJOR EUROPEAN NUTRIGENOMICS INITIATIVES St. Joseph, Michigan, November 14th, 2005 - GeneGo, Inc., a leading provider of software and databases for systems biology, announced today the expansion of their partnership with TNO (the worlds largest independent nutrition research institute, www.tno.nl), the Dutch Nutrigenomics Consortium and the European Nutrigenomics Organization (NUGO, www.nugo.org), together forming a group of 23 Universities and Research Institutes active in the area of nutrigenomics. TNO and the NuGO consortium members will be using MetaCore™ version 3.0 in multiple research areas on nutrition, metabolism and related diseases. The latest version of MetaCore™ will allow them to build combined metabolic/signaling networks from virtually any kind of experimental data. They will be able to share experiments and results between any other NuGO consortium member and TNO's employees using a novel information management module in MetaCore™. "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 are very excited about this expanded agreement as there will now be 23 academic institutes in Europe using MetaCore™ under this agreement", said Julie Bryant, VP of business development at GeneGo. "Our collaboration with TNO researchers helped us to adjust MetaCore™ for the needs of nutritional science which requires comprehensive coverage of human metabolism and understanding the connectivity between metabolic and signaling pathways. We have also developed the first metabolic parser which enables import of metabolomics data, its visualization and analysis along with molecular data in the framework of pathways and networks."
VELCURA THERAPEUTICS AND GENEGO ENTER MULTI YEAR AGREEMENT St. Joseph, Michigan, November 9th, 2005 - GeneGo, Inc., a leading provider of software and databases for systems biology, today announced that Velcura Therapeutics, Inc. has licensed MetaCore™, GeneGo's manually curated pathways database and data mining suite. All Velcura employees will have access to the MetaCore™ database and suite of software tools for three years to focus on bone related disease research. Velcura researchers will be using MetaCore™ for analysis of gene expression, proteomic, and other data related to human bone formation. "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 have Velcura as a new GeneGo customer," said Julie Bryant, Vice President of Business Development at GeneGo. "High-throughput experimentation matures fast, and nowadays researchers deal not only with gene expression, but also individual DNA variability, protein abundance and isoforms content, changes in body liquid metabolic profiles and high content drug screening data. To be able to visualize and analyze such diverse datasets, we have built a comprehensive database of direct interactions between genes, proteins, enzymes, metabolic by-products and cell-regulators in human and other mammals. Velcura researchers will be able to directly access this content and use it in projects via their MetaCore™ license."
FOR THE FIRST TIME, SIGNALING AND METABOLIC NETWORKS CAN NOW BE MERGED WITH GENEGO'S METACORE™ VERSION 3.0 St. Joseph, Michigan, October 31st, 2005 - GeneGo, Inc., a leading provider of software and databases for systems biology, announced today the major new release of its flagship data mining platform MetaCore™ 3.0. In the new version, scientists can for the first time build combined signaling/metabolic networks from virtually any kind of experimental data. This breakthrough may provide a quantum leap in the resolution of functional analysis of gene expression, proteomics, metabolomics, high content screening (HCS), siRNA and other types of experimental data. MetaCore™ 3.0 also features a unique parser for visualizing metabolomics data in the context of pathways with seamless connectivity between networks, canonical pathways, cellular processes and human diseases. The new version also adds a sophisticated enterprise-wide data management and user access system and disease specific networks. "We believe that in this new version, we solved a major problem in functional data analysis - namely the uncoupling between signaling and effector networks in complex systems," said Dr. Tatiana Nikolskaya, Chief Scientific Officer, President and Founder of GeneGo. "A living cell reacts to stimuli largely by changing its core biochemistry, and many metabolites serve as signaling molecules and mediators. Genome-wide formalization of the whole process from receptor-ligand interactions to activation of certain metabolic pathways is key in the understanding of complex conditions such as diseases or drug effects. Yet, signaling and metabolic pathways so far were largely not connectible even for the best studied yeast. Now, we have completed this project for human and other mammals. With integration of metabolic and signaling networks, as well as receptor-ligand interactions, the spectrum of resolution in MetaCore™ covers all levels from cellular processes to individual proteins small molecules interactions." "In practical terms, this means that our customers can now analyze in one system multiple datasets which would be incompatible in any other environment, for instance mass spec metabolic data from human blood generated in clinical trials with pre-clinical rat expression arrays and cell culture siRNA experiments", said Julie Bryant, VP of business development at GeneGo. "Think about cross-validation of metabolic biomarkers and drug mode of action studied in animal systems and screening data. MetaCore™ 3.0 is a common environment for both biologists and chemists throughout the whole drug discovery pipeline. We have also addressed sharing of experiments, knowledge and analysis with a sophisticated enterprise account and experiment management system with hierarchical access to shared accounts, data and results exchange and annotation through e-notes."
THE U.S. FOOD AND DRUG ADMINISTRATION WILL USE GENEGO'S METACORE™ FOR "OMIC'S" RESEARCH AND REVIEWING OF GENOMICS DATA St. Joseph, Michigan, October 10th, 2005 - GeneGo, Inc., a leading provider of software and databases for systems biology, today announced that the U.S. Food and Drug Administration (FDA) have licensed MetaCore™ for "OMIC's" research and reviewing of genomics data. GeneGo and the FDA will also integrate MetaCore™ with ArrayTrack and make it available for FDA researchers, http://www.fda.gov/nctr/science/centers/toxicoinformatics/ArrayTrack/ The MetaCore™ platform allows scientists to concurrently visualize, map and network multiple types of data including gene expression, SiRNAi, proteomic, metabolomic, SAGE and SNP data, both from pre-clinical discovery and clinical studies. "High throughput (HT) experimentation is increasingly important for life science research, and HT data is now included in many new drug applications submissions. The analysis of such complex datasets requires novel systems biology tools, such as MetaCore™," said Dr Tatiana Nikolskaya, founder and CSO of GeneGo Inc. "One important issue in FDA submissions is compatibility and cross-referencing of multiple types of pre-clinical and clinical data, which are collected at different times by different research groups. MetaCore™ offers both a functional framework and analytical engine for this." "Working with the FDA is very important for GeneGo and we are very pleased to announce this relationship," said Julie Bryant, Vice President of Business Development at GeneGo. "Since MetaCore™ is already being applied in drug discovery by our pharmaceutical customers for a couple of years now, it is logical that it will be also used on the regulatory side as well." GeneGo has assembled the world largest manually curated database of human biology and medicinal chemistry, which includes genes, proteins, natural ligands, metabolites, drugs and diseasesfrom millions of literature findings. About Array Track ArrayTrack provides an integrated solution for managing, analyzing, and interpreting microarray gene expression data. Specifically, ArrayTrack is MIAME (Minimum Information About A Microarray Experiment) supportive for storing both microarray data and experiment parameters associated with a pharmaco- or toxico- genomics study. Many statistical and visualization tools are available with ArrayTrack. ArrayTrack also provides a rich collection of functional information about genes, proteins and pathways for biological interpretation. The primary emphasis of ArrayTrack is the direct linking of analysis results with functional information for facilitating the interaction between the choice of analysis methods and the biological relevance of analysis results. Using ArrayTrack, user can easily select a statistical method applied to a stored microarray data to determine a list of differentially expressed genes and the gene list can be directly linked to pathways and gene ontology for functional analysis.
GENEGO'S METACORE™ SOFTWARE APPLICATION ACHIEVES GENECHIP-COMPATIBLE™ STATUS WITH AFFYMETRIX' GENECHIP® MICROARRAY PLATFORM MetaCore for easy, intuitive visualization and analysis of expression data on pathways and networks St Joseph, MI, September 19th , 2005 - GeneGo today announced that its MetaCore software application has achieved GeneChip-compatible™ status with the Affymetrix Inc. (Nasdaq: AFFX) GeneChip® microarray platform and that it has joined the Affymetrix GeneChip-compatible™ Applications Program, which provides customers with a broad spectrum of software solutions for biomedical research and development. As a GeneChip-compatible software provider, GeneGo is committed to seamlessly integrating its MetaCore platform with the Affymetrix GeneChip platform. MetaCore has worked with Affymetrix probe IDs since the product's launch in March 2004, alongside with a number of other conventional identifiers. Upon parsing, microarray expression data is visualized and analyzed in the context of pathways, biological networks and cellular processes, using the manually curated knowledge base of over 4.5 million findings. MetaCore supports parsing species specific arrays for human, rat, mouse, yeast, worm, fly and chicken, as well as specialty arrays such as Affymetrix tox chips. MetaCore also has the unique ability to visualize multiple gene expression, genetic and proteomic data sets concurrently. "Affymetrix is a clear market leader in microarray technology and we make it a priority that our products work seamlessly with the content of their GeneChip microarrays. Currently, we map more Affymetrix probes on pathways and networks than any other data mining platform" said Julie Bryant Vice President of Business Development. "We work in close contact with the Affymetrix team to keep on top of their development and new products". "Pathway analysis and annotation represents a critical link between microarray data and biomedical utility." Said Steve Lincoln, Vice President of Informatics at Affymetrix. "We are pleased to be working with GeneGo in integrating our platforms, allowing our mutual customers to get the most from their GeneChip data."
GENEGO IS AWARDED A PHASE II NIH GRANT FOR IN SILICO ASSESSMENT OF DRUG METABOLISM AND TOXICITY St Joseph, Michigan, August 8th, 2005 - GeneGo Inc., a leading provider of databases, software and services in systems biology, announced today that they have received a Phase II SBIR grant from the National Institute of General Medical Science. The grant enables the further development of a computational tool MetaDrug™ to improve the prediction of ADME and Toxicology properties of novel small molecule compounds. "MetaDrug™ is the very first systems pharmacology platform in the market, designed primarily for small molecule discovery programs at drug companies and academic centers. Building this benchmark platform, we relied on customer feedback and our own vision for the field. Now, we are very glad that NIH agrees with our development goals," said Julie Bryant, Vice President, business development. "Our customers particularly like the flexibility of the system which makes their version of MetaDrug™ specific to their chemistry space and informatics environment. We will continue working in this direction. New funding will also allow us to expand applicability of MetaDrug™ in other areas of biological effects of drug action such as pharmacogenomics, prediction of side effects and new therapeutic indications." "This funding will enable us to expand the scope of MetaDrug™ integrating predictive algorithms for ADME/Tox properties, and add a database of ligand-protein interactions from other species, in addition to humans," said Dr. Sean Ekins, Vice President of Computational Biology, GeneGo. "We will develop large in vitro datasets for drug interactions with key human cytochrome P450s that will be used to build predictive algorithms to complement those currently in MetaDrug™. We also intend to integrate a novel algorithm for metabolite prediction that will allow us to highlight the important metabolites. Our approach to understanding the potential for interactions using predictive algorithms and our core strength of database generation and gene network algorithms represents a novel system for in silico assessment of drug metabolism and toxicity."
UCSD EXPANDS LICENSES OF METACORE™ FROM GENEGO TO MORE DEPARTMENTS St. Joseph, Michigan, July 25th, 2005 - GeneGo, Inc., a leading provider of software and databases for systems biology, today announced that UCSD has expanded licenses of MetaCore™, GeneGo's platform for mining and visualization of high-throughput experimental data in the context of biological networks, pathways and diseases. MetaCore™ will be utilized in Schizophrenia, bipolar disorder, HIV associated neurodegeneration and Hep C infection projects as well as in the core micro array facility to explore gene expression profiles of psychotropics. MetaCore™ enables concurrent visualization and analysis of gene expression, proteomics and metabolomics data in multiple formats including LocusLink, Genbank, RefSeq, All Affymetrix arrays tags, OMIM, Unigene, SwissProt as well as other approved gene symbol IDs. MetaCore™'s content is manually curated and species specific. MetaCore™ is an easy to use program that can be accessed at the map level or by building networks on the fly choosing from one of our 8 network building algorithms. 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 have had a great relationship with UCSD over the past few years and are happy to expand on it", said Julie Bryant, VP of Business Development. "We are hoping that the added visibility, especially at the core facility, will give more scientists a chance to utilize MetaCore™ in their research. We plan to continue to work closely with UCSD on these and several other projects."
ROSETTA BIOSOFTWARE AND GENEGO TO OFFER INTEROPERABILITY BETWEEN THE ROSETTA RESOLVER® SYSTEM AND METACORE™ SEATTLE, Wash., and ST. JOSEPH, Mich., July 18, 2005 - Rosetta Biosoftware and GeneGo, Inc. today announced a collaboration to establish interoperability between Rosetta Biosoftware's Resolver system and GeneGo's MetaCore™ system. Researchers will be able to easily exchange data between the MetaCore™ and Resolver systems to leverage both systems' ability to analyze gene expression data and perform sophisticated pathway analysis. The Rosetta Resolver system is a versatile and robust comprehensive gene expression data analysis system that enables research organizations to efficiently and effectively conduct life-saving discoveries and develop drugs. The MetaCore™ system is an integrated platform that includes a software suite for functional analysis of microarrays, Serial Analysis of Gene Expression (SAGE), proteomics, metabolomics and other high throughput experimental data. The platform is based on a unique, manually-curated database of human protein-protein and protein-DNA interactions, transcriptional factors, signaling, metabolism, and bioactive molecules. "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." "GeneGo is pleased to be working with Rosetta Biosoftware in response to customers asking for the two companies to smoothly integrate their platforms so they can follow a daily workflow from expression analysis through to pathway analysis and visualization in an iterative easy to use manner," said Julie Bryant, vice president of business development. The Rosetta Resolver system is developed and supported by Rosetta Biosoftware, and is distributed exclusively by Agilent Technologies.
SIENABIOTECH LICENSES METACORE™ FROM GENEGO St. Joseph, Michigan, July 6th, 2005 - GeneGo, Inc., a leading provider of software and databases for systems biology, today announced that Siena Biotech has licensed MetaCore™ version 2.5, GeneGo's platform for mining and visualization of high-throughput experimental data in the context of biological networks, pathways and diseases. MetaCore™ enables concurrent visualization and analysis of gene expression, proteomics and metabolomics data in multiple formats including LocusLink, Genbank, RefSeq, All Affymetrix arrays tags, OMIM, Unigene, SwissProt as well as other approved gene symbol IDs. MetaCore™'s content is manually assembled from full text experimental articles by qualified curators. The latest release, MetaCore™ version 2.5, features multiple functions for statistical analysis of biological networks, inter-experimental comparisons, and new algorithms for pathways prioritization based on tissue specificity, sub-cellular localization, interaction types, and relevance to cellular processes. "We tested several platforms in the systems biology marketplace and felt that MetaCore™ best suited our current needs," said Dr. Georg C. Terstappen, Vice President Discovery Research at Sienabiotech SpA. "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," included Dr. Andreas Kremer, Head of Bioinformatics. "We are happy to welcome Sienabiotech as the first Italian company on our rapidly growing list of new customers", said Julie Bryant VP of Business Development. "With fast evolution of OMICs technologies, and concurrent analysis and cross-validation of multiple data types becoming increasingly important, we emphasize such features in the new version of MetaCore™. Sienabiotech will be able to visualize and directly compare gene expression and proteomic data on the same networks and pathways maps. Our new version features over 400 static maps of canonical signaling and metabolic pathways and eight network building algorithms."
GENEGO IS AWARDED DOD GRANT FOR SYSTEMS BIOLOGY PROTEOMICS PLATFORM St. Joseph, Michigan, June 27th, 2005 - GeneGo, Inc., a leading provider of databases, software and services in systems biology, announced today they have been awarded a SBIR grant from Department of Defense (DARPA) for the development of a systems biology suite of tools for visualization and analysis of proteomics data. In Phase I, GeneGo will adapt its data-mining platform MetaCore™ for handling a broad range of proteomics data types; connectivity of these data with other OMICs datasets; and will develop new algorithms for reconstruction of protein-state specific biological networks and pathways. "Proteomics enables experimental analysis of protein complexes and protein-protein interactions, which carry out most cellular processes. Therefore, proteomics data is destined to play a central role among OMICs datasets characteristic for a condition," said Dr. Tatiana Nikolskaya, Chief Scientific Officer and President of GeneGo. "However, proteomics data is more complex and ambiguous than, for instance, microarray gene expression or DNA sequences. We know how to work with processed proteomics datasets, but it is the details such as fold, post-translational modification, sequence variation, local abundance in compartments, which define the cellular state in normal and disease. In our proposal, we emphasized these specifics as well as systemic approach to the understanding of proteomics and other OMICs datasets." In the scope of the grant, GeneGo will work in collaboration with Associate Professor Austin Yang's group from the University of Southern California. "Because of rapid advance of proteomic technologies and improved of mass spectrometry user interface, most laboratories can generate a very large amount of data in a rather short period of time. Thus, one of the major issues facing most proteomics laboratories now is how to establish a proper bioinformatics workflow and how to adequately validate and interpret their proteomic results. Unfortunately, like most "omics" analyses, because hundreds or thousands of proteins are examined in a single experiment, it is very difficult to evaluate the biological significance or resolution of any given proteomics analysis. Two years ago, we decided to incorporate Metacore™ into our proteomics data analysis workflow. By integrating the conventional proteomic analysis with a well-annotated network or pathway analysis program such as Metacore™, we are able to quickly and objectively evaluate our proteomic results with high confidence. Recently, we have used this combination of bioinformatics and mass spectrometric approaches to address the roles of amyloid in altering synaptic signaling pathways in Alzheimer's disease," said Professor Yang.
INVITROGEN CREATES UNIQUE SYSTEMS BIOLOGY CONCEPT THROUGH INTRODUCTION OF I-PATH 225 original maps identifying and visualizing biologic pathways, available free to researchers Carlsbad, CA. and Philadelphia, PA., June 20, 2005 - Invitrogen Corporation (NASDAQ - IVGN), a leading life sciences company with a broad portfolio of technologies to improve and accelerate biomedical research, drug discovery and commercial bioproduction, unveiled its latest concept in bioinformatics and systems biology with the launch of i-Path at the BIO 2005 international conference. A new resource for scientists worldwide, i-Path consists of 225 high-level, annotated, validated original maps of human cell signaling and metabolic pathways compiled by GeneGo Inc, a leading provider of databases and software for systems biology. Invitrogen scientists have further identified the specific antibodies, siRNA, full-length DNA clones and other biological molecules involved in cell function and disease on these maps. The system enables researchers to visualize molecular interactions in a highly graphical, user-friendly, interactive format and will be available to scientists free of charge on Invitrogen's Web site. "i-Path continues our tradition of providing enabling, Web-based technologies to support researchers throughout their experiments," said Michael Stapleton, Vice President & General Manager eCommerce and Bioinformatics for Invitrogen. "Building on a rich history that includes the acquisition of InforMax, Invitrogen has moved powerful design and analytic capabilities into the mainstream of science by coupling these systems with familiar research tools and making them freely available through our Web site." i-Path includes maps of pathways that cover more than 2,500 genes - all of them human -of interest to biotech and pharmaceutical researchers. These include 171 signal transduction pathways representing the majority of known proteins involved in these processes and 54 metabolic pathways representing a significant number of genes involved in drug metabolism. The maps were created and annotated by a team of more than 40 scientists using information from thousands of scientific papers and validated with the accuracy and authenticity of pathways based on the latest scientific consensus. i-Path will also provide a time-saving link to reagents, kits and other Invitrogen research products related to the study of each molecule detailed in the pathway maps. "With Invitrogen's deep portfolio of research capabilities we are in a unique position to support systems biology as a driver of life science research and drug discovery," said Gregory T. Lucier, Chairman and CEO of Invitrogen Corporation. "With our latest offerings we are solidifying our Website as the center of scientific conversation about the nature, structure and utility of biologic pathways." Details about Invitrogen's new bioinformatics initiative will be made available at a news conference at the BIO 2005 conference, 2pm, Monday, June 20th in room 203B Demonstrations will also be available the Invitrogen booth in the exhibit hall. i-Path will be accessible at www.invitrogen.com/ipath beginning June 20, 2005. About Invitrogen Invitrogen Corporation (Nasdaq:IVGN) provides products and services that support academic and government research institutions and pharmaceutical and biotech companies worldwide in their efforts to improve the human condition. The company provides essential life science technologies for disease research, drug discovery and commercial bio-production. Invitrogen's own research and development efforts are focused on breakthrough innovation in all major areas of biological discovery, including functional genomics, proteomics, bio-informatics and cell biology, placing Invitrogen's products in nearly every major laboratory in the world. Founded in 1987, Invitrogen is headquartered in Carlsbad, Calif., and conducts business in more than 70 countries around the world. The company globally employs approximately 4,500 scientists and other professionals, and had revenues in excess of $1 billion in 2004. Information about Invitrogen is available on the Web at www.invitrogen.com. Forward-Looking Statements Certain statements contained in this press release are considered "forward-looking statements" within the meaning of the Private Securities Litigation Reform Act of 1995, and it is Invitrogen's intent that such statements be protected by the safe harbor created thereby. Forward-looking statements include, but are not limited to: 1) Invitrogen's intent to provide i-Path content free of charge on its Web site; 2) Researchers' ability to visualize their pathway of interest; 3) Invitrogen's intent to link its technology portfolio to molecules identified in i-Path's maps; 4) Invitrogen's Web site becoming the center of scientific conversation around the nature, structure and utility of biologic pathways. Potential risks and uncertainties include, but are not limited to, the risks: a) Changing market conditions and restrictions on providing scientific content b) Availability and range of pathway content; c) Access to matching Invitrogen products from its catalog; d) Industry adoption and use of i-Path and Invitrogen's Web site, as well as other risks and uncertainties detailed from time to time in Invitrogen's Securities and Exchange Commission filings.
GENEGO IS AWARDED NIH GRANT FOR DISEASE NETWORK ALGORITHMS St Joseph, Michigan, June 13th, 2005 - GeneGo Inc., a leading provider of databases, software and services in systems biology, announced today that they have received a Phase I SBIR grant from the National Institute of General Medical Science for development of methodologies intended for reconstruction of functional networks affected in common human diseases. In Phase I, GeneGo will generate and test novel algorithms enabling comparison of disease related OMICs datasets of different origin, based on networks topology and content. "Analysis of human biological networks is an exciting new area of systems biology, and we are glad that our efforts are appreciated by the NIH", said Dr. Tatiana Nikolskaya, Chief Scientific Officer and President of GeneGo. "Common diseases have profound effects on both signaling and metabolic machinery, usually in more than one cell type. Because of this, the result detected by ?genome scale" technologies such as microarray gene expression, proteomics and genotyping, is complex and multi-level. Each data type provides only one level of information, and total reconstruction of the ?big picture" of molecular pathology is a major challenge. We will study conditional perturbations of the human interactome assembled from manually curated physical protein interactions and develop algorithms for assembly of complete functional networks, from membrane receptors to transcriptional factors and ?core effector" metabolic pathways. We will test the approach on disease datasets in collaboration with the Van Andel Research Institute". "We are truly excited at this opportunity to collaborate with the GeneGo team. We believe that the integrated approach offered through GeneGo?s advanced computational systems will be critical in deciphering the key molecular mechanisms of disease progression, and offer new diagnostic and therapeutic strategies for the future advancement of molecular-based medicine"; said Dr. Craig Webb, a lab head at Van Andel and an advisor on the grant.
GENEGO INC. INTEGRATES ACCELRYS ACCORD TECHNOLOGY IN METADRUG™ St. Joseph, Michigan, June 6th, 2005-GeneGo Inc., a leading provider of databases and software for systems biology, announced today that they have integrated Accelrys' Accord technology in MetaDrug™, their Systems-ADME/Tox and medicinal chemistry platform. MetaDrug™ features maps, pathways and networks for human proteins related to ADME/TOX; a database of small molecules with kinetic data for human drug metabolizing enzymes, Proprietary algorithms for rule-based metabolite prediction, highlighting of reactive metabolites, >40 QSAR models for ADME/TOX properties, descriptors relevant to ADME parsers for importing data from all major microarray platforms, SAGE, proteomics and metabolomics data; two proprietary network building algorithms; flexible visualization and data exchange tools. MetaCore™ features a comprehensive set of maps, pathways and networks for almost all known human proteins; parsers for importing data from all major microarray platforms, SAGE, aCGH, RNAi proteomics and metabolomics data; seven proprietary network building algorithms; flexible visualization and data exchange tools. "Integrating Accelrys' Accord technology with GeneGo's MetaDrug™, is another example of how Accelrys is looking to expand access to best-of-breed technologies to scientists in the Pharmaceutical and Biotech sector," commented Dr. Eric Jamois, Director of Business Development at Accelrys. "Combining the power of the Accord Chemistry engine with MetaDrug™'s algorithms will ultimately help enhance the data visualization and database searching capabilities of MetaDrug™." "We are thrilled to be working with Accelrys and excited about the capabilities of our combined software for the field of Systems-ADME/Tox." said Dr. Sean Ekins, Vice President, Computational Biology at GeneGo. "It took our team several years to build tools and pathway content, proprietary algorithms for metabolite prediction and ADME/Tox QSAR models. We can now apply the Accord tools for molecule visualization and database searching capabilities within MetaDrug™." About Accelrys, Inc Accelrys, Inc. is a leading provider of software for computation, simulation, and the management and mining of scientific data used by biologists, chemists and materials scientists, including nanotechnology researchers for product design as well as drug discovery and development. Accelrys technology and services are designed to meet the needs of today's leading research organizations. The company is headquartered in San Diego, California.
NATIONAL CANCER INSTITUTE LICENSES METACORE™ SITE WIDE FROM GENEGO St. Joseph, Michigan, May 31st, 2005 - GeneGo, Inc., a leading provider of software and databases for systems biology, today announced that the National Cancer Institute has licensed MetaCore 2.5™, GeneGo's platform for mining of high-throughput experimental data in the context of biological networks, pathways and diseases. All NCI researchers will now have access to MetaCore™ in house through their web browser and will be able to analyze multiple types of small to "genome scale" experimental datasets from their workstations. Based on the largest curated database of mammalian biology and physical protein interactions, the latest version, MetaCore 2.5™ was released in May 2005. Among other features, it offers multiple network building algorithms and filters; maps with established metabolic and signaling pathways; advanced network comparison option; statistical cross-referencing and scoring between networks, pathways and functional processes; custom pathway editor. "We welcome NCI as a new customer", said Julie Bryant VP of Business Development. "Cancer datasets are inherently complex for interpretation because multiple pathways and cell types are affected. Therefore, the requirements for data mining techniques and tools in oncology are high. We are very pleased that NCI scientists chose MetaCore™ as an enterprise, institution-wide system".
GENEGO IS AWARDED NIEHS GRANT IN TOXICOGENOMICS St. Joseph, Michigan, May 24th, 2005 - GeneGo, Inc., a leading provider of databases, software and services in systems biology, announced today they have received a Phase I SBIR grant from the National Institute of Environmental Health Sciences for the elucidation and analysis of signaling and metabolic networks implicated in cellular response to drugs and toxins. In the first phase of research, publicly available data will be re-analyzed by GeneGo scientists using the company's flagship systems biology platform, MetaCore™. "Over the past few years, we have witnessed an unprecedented accumulation of gene expression and other high throughput data in toxicity research", said Dr. Tatiana Nikolskaya, Chief Scientific Officer and President of GeneGo. "This has been mainly rat and mouse microarray data that has been interrogated with then currently available tools, but some important biological mechanisms and patterns were missed, as they can be only accessed via analysis of biological networks. Now we intend to re-examine the data from different microarray platforms and identify specific modules, "signature networks", characteristic for toxic effects and conserved cross-platform". "MetaCore gene network analysis will address a critical need in drug safety evaluation by the identification of novel diagnostic biomarkers for adverse responses to drugs or chemicals", said Professor Craig Giroux from Wayne State University, a consultant on the grant. "In addition, these unique Gene Network Signature motifs will provide a valuable resource in support of biomarker development programs for comparative toxicogenomics and predictive risk assessment of environmentally responsive disease in my and other labs."
TGEN LICENSES METACORE™ FROM GENEGO St. Joseph, Michigan, May 16th, 2005 - GeneGo, Inc., a leading provider of software and databases for systems biology, today announced that the Translational Genomics Research Institute (TGen) has licensed MetaCore™, GeneGo's platform for mining of high-throughput experimental data in the context of human and mammalian "interactome" and common diseases. MetaCore™ is designed to process "genome scale" data files including microarrays and SAGE gene expression, proteomics and metabolomics. MetaCore™ applies multiple algorithms for generation, comparison and functional interpretation of biological networks and pathways. "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 are very pleased to be working with TGen in aiding their mission to make and translate genomic discoveries into advances in human health that will that have a direct impact on patients", said Julie Bryant, VP of business development at GeneGo. "TGen has amassed an impressive group of experts in pre-clinical research and clinical trials that we plan to collaborate with." About TGen The Translational Genomics Research Institute (TGen) is a not-for-profit organization whose primary mission is to make and translate genomic discoveries into advances in human health. Translational genomics research is a relatively new field employing innovative advances arising from the Human Genome Project to apply to the development of diagnostics, prognostics and therapies for cancer, neurological disorders, diabetes and other complex diseases.
GENEGO LICENSES METACORE™ TO EXELIXIS St. Joseph, Michigan, May 13th, 2005 - GeneGo, Inc., a leading provider of software and databases for systems biology, today announced that Exelixis has licensed MetaCore™, GeneGo's platform for mining of high-throughput experimental data in the context of biological networks, pathways and human diseases. Among other features, MetaCore™ has built manually curated proprietary database of transcriptional factors and receptors supported by unique network algorithms enabling reconstruction of full length regulatory pathways. This allows users to investigate all the genes that regulate a specific gene or a group of genes at the transcription level or build transcriptional regulation networks characteristic for particular diseases and other conditions. "Exelixis is renowned for its powerful, fully integrated discovery platform that is capable of high-throughput target identification and validation. This has been applied to develop high-quality, differentiated pharmaceutical compounds for the potential treatment of cancer and metabolic diseases in collaborations with top pharmaceutical companies", said Julie Bryant, VP of business development at GeneGo. "We are very pleased that Exelixis chose MetaCore™ to assist their discovery endeavors."
PROCTER & GAMBLE LICENSES METACORE™ AND METABASE™ FROM GENEGO St. Joseph, Michigan, May 9th, 2005 - GeneGo, Inc., a leading provider of software and databases for systems biology, today announced that Procter & Gamble Pharmaceuticals, Inc., a subsidiary of The Procter & Gamble Company (NYSE - PG), has licensed MetaCore™ and MetaBase™ from GeneGo. MetaCore™ is a manually curated, proprietary human database with the ability to work with rat, mouse, fly, yeast and worm orthologs. MetaCore™ also includes a suite of software tools for analysis in the context of pathways. MetaBase™ provides researchers with direct access to MetaCore™ content and the ability to add their own algorithms and data to the MetaCore™ schema. GeneGo's MetaCore™ platform has unique interoperability by allowing users to examine multiple types of data concurrently such as gene expression, proteomics and metabolomics in the context of biological networks and pathways. MetaCore™ also allows users to edit pathways, add their own knowledge and annotations. MetaBase™ is an open-architecture, manually curated content database with information on mammalian signaling, metabolism, transcription factors, receptors, drug targets and bioactive chemistry. "We are glad to see Procter & Gamble choosing our products to support their R&D efforts", said Julie Bryant, VP Business development of GeneGo. "We are pleased that a company of the caliber of P&G recognizes the potential value that our manually curated databases and analytical tools can add to their already strong R&D programs."
GENEGO RELEASES METACORE™ VERSION 2.5 St. Joseph, Michigan, May 2nd, 2005 - GeneGo Inc., a leading provider of databases, software and services in systems biology, announced today the release of a major new version of its flagship data mining suite MetaCore™ 2.5. The new version features fine mapping of human metabolism, transcription regulation and signaling; novel network building algorithms, filters and statistical procedures for multi-variant interpretation of human networks in terms of canonical pathways and functional processes. Primarily a human system, these tools are also applied for analysis of rat, mouse, fly, worm and yeast data. "Over the past five years of development, we have undertaken for MetaCore™, we have always focused on the quality of the manually curated content and its utility for laboratory research; and these principles are emphasized in the new version," said Dr. Tatiana Nikolskaya, Chief Scientific Officer, President and Founder of GeneGo. "First, we have completed the first fine mapping of human metabolism at the "sub-EC number" level of individual proteins (isozymes) and substrates. Second, we have resolved and networked virtually all human transcription factors and known receptors. Third, we have added novel network building algorithms and refined the existing ones. We have also developed a comprehensive toolkit for the statistical analysis of networks generated on the fly; including the evaluation and scoring of the relevance of networks to the experimental data, subcellular localization, canonical pathways and GO functional processes. Finally, we have added a large curated database of drugs, drug targets and diseases." "Over the last two years, MetaCore™ has become the platform of choice for functional analysis of genome scale experimental datasets in human and model organisms," said Julie Bryant, GeneGo's VP of business development. "In version 2.5, we have substantially expanded its content and capabilities in interpretation of mammalian "interactome". The current version is a mature third generation tool, whose features reflect numerous suggestions by our customers and collaborators in academy and industry. We also continue to maintain flexibility by integrating MetaCore™ with in house and third party algorithms as well as providing flexible business models for licensing."
ORGANON LICENSES METACORE™ FROM GENEGO St. Joseph, Michigan, April 19th, 2005 - GeneGo, Inc., a leading provider of software and databases for systems biology, today announced that N.V. Organon has licensed MetaCore™, GeneGo's platform for mining of high-throughput experimental data in the context of biological networks and human diseases. MetaCore™ is an enterprise platform being installed in the majority of the top Pharmaceutical companies internationally. The suite includes a comprehensive, manually curated database which covers all levels of human cellular functionality, as well as rat, mouse, fly, worm and yeast orthologs, and functional information on over 3,000 human diseases and thousands of drugs connected with pathway targets Organon plans to use MetaCore™ in pre-clinical research across various therapeutic areas and departments. "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 are happy that Organon decided to choose MetaCore™ as their systems biology solution", said Julie Bryant, VP of business development at GeneGo. "In addition to extensive content and data mining tools, we emphasize flexible open architecture compatible with different informatics environments and third-party software. We are glad that this strategy is appreciated by researchers in different areas of drug discovery. Organon is one of the leading companies focused on hormone therapy, fertility and mental health and we look forward to working closely with them on making advances in these areas using systems biology tools." About Organon Organon - with shared head offices in Roseland, NJ, USA and Oss, The Netherlands - creates, manufactures and markets prescription medicines that improve the health and quality of human life. Through a combination of independent growth and business partnerships, Organon strives to remain or become one of the leading pharmaceutical companies in each of its core therapeutic fields: reproductive medicine, psychiatry and anesthesia. Organon products are sold in over 100 countries, of which more than 60 have an Organon subsidiary. Organon is the human health care business unit of Akzo Nobel.
GENEGO INC. IS AWARDED NCI GRANT FOR ANALYSIS OF CANCER NETWORKS St. Joseph, Michigan, February 7th, 2005 - GeneGo Inc., a leading provider of databases and software for systems biology, announced today that they will be receiving a Phase I SBIR grant from the National Cancer Institute for elucidation and analysis of cellular networks implicated in breast cancer. GeneGo's MetaCore™, an integrated systems biology platform for mining of high-throughput experimental data will be utilized for advanced analysis. "We are pleased to win this competitive grant from a premier cancer research institution," said Dr. Tatiana Nikolskaya, Chief Scientific Officer and President of GeneGo. "It took our team many years to build tools and pathway content that is comprehensive enough for the analysis of complex human diseases. We will now apply these tools to identify network models and additional patterns in public OMICs cancer data that have been missed by other methods."
GLAXOSMITHKLINE LICENSES METABASE™ FROM GENEGO Company licenses MetaBase™ systems biology database St. Joseph, Michigan, January 31st, 2005 - GeneGo, Inc., a leading provider of software and databases for systems biology, today announced that GlaxoSmithKline (GSK) has licensed MetaBase™, GeneGo's database of human biology and medicinal chemistry. MetaBase™ represents a comprehensive, manually curated database which covers all levels of human cellular functionality, from GPCRs and other receptors to signal transduction cascades, transcriptional factors, core effector networks, endogenous and xenobiotics metabolism and the relevant bioactive compounds (metabolites and xenobiotics). GSK intends to apply MetaBase™ towards a broad range of applications in pre-clinical drug discovery, and to integrate MetaBase™ content with their internal informatics systems. "We are happy that GSK decided to in-license MetaBase™ based on its comprehensive coverage and its flexible architecture that will allow them to integrate MetaBase™ in to their current environment" said Tatiana Nikolskaya, Ph.D., President and CSO of GeneGo. "GSK is known for its strong research record in the areas of molecular modeling and systems biology, and we are pleased that their experts find MetaBase™ useful for the internal programs."
RNAI CO., LTD. (RCL) LICENSES METACORE™ FROM GENEGO AND COLLABORATES IN PLATFORM DEVELOPMENT St. Joseph, Michigan, January 24th, 2005 - GeneGo, Inc., a leading provider of software and databases for systems biology, today announced that RCL has licensed MetaCore™ for its RNA interference drug discovery efforts. MetaCore™ is an integrated platform for the analysis of different types of experimental data in drug discovery. MetaCore™ applies a proprietary, manually curated, human protein interaction and pathway database to drug discovery. The flexible database architecture enables straightforward integration of in house and third party software and databases. MetaCore™ also has easy to use software for building, visualization and analysis of tissue specific biological networks with and without experimental data. "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 welcome RCL as our first Japanese customer." said Tatiana Nikolskaya, Ph.D., President and CSO of GeneGo. "RCL has built an impressive and unique technology portfolio in the RNA interference area. Their findings are very synergistic with pathway analysis of complex diseases we are working on. We consider this agreement as the first step in long term collaboration in the intersection of these two exciting technologies." About RNAi RCL (www.rnai.co.jp) is a biotechnology company in the field of functional genomics based on RNA interference. RCL conducts two types of business. One is research support business for life science and the other is drug discovery business. RCL's unparallel RNA interference science and technology achieves high specificity of gene knock-down while minimizing unwanted off-target effects. RCL has already identified and applied the patent about 820,000 kinds of siRNA/shRNA/Oligo interference for all of human and mice genes known publicly. RCL's licensees can access to the most comprehensive RNAi design system, siDirect™ with usage of 820,000 sequences and get high-quality chemically synthetic siRNA manufactured by Proligo, siPerfect™ at the most attractive price in the market. RCL currently has two business offices and a wet lab and a dry lab in Japan with 20 employees and plans to enhance GMP functionality for preclinical study this year.
ALTANA PHARMA AG LICENSES METACORE™ FROM GENEGO St. Joseph, Michigan, January 21th, 2005 - GeneGo, Inc., a leading provider of software and databases for systems biology, today announced that Altana Pharma AG has licensed MetaCore™. MetaCore™ is a comprehensive platform that contains proprietary, manually curated, human data that is curated by GeneGo's staff of PhD's following strict quality control guidelines. The database architecture is flexible, which allows changes to be made quickly and makes integration straight forward. This was a key component to Altana when choosing a systems biology platform. MetaCore™ also has a software component that allows for concurrent visualization of multiple types of data. GeneGo has led the way in systems biology to allow more than just microarray data to be visualized in the context of pathways. "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 are pleased to have more international companies using MetaCore™ based on its comprehensive coverage and its flexible architecture that will allow them to integrate MetaCore™ in to their current environment" said Tatiana Nikolskaya, Ph.D., President and CSO of GeneGo. "Altana is known for its research in the areas of gastrointestinal and respiratory indications and we are pleased that they are using MetaCore™ to provide more insight to their drug discovery effort in these areas." About ALTANA Pharma ALTANA Pharma AG is the pharmaceutical division of ALTANA AG, headquartered in Konstanz, Germany. The international pharmaceutical group employs more than 8,200 people in 30 subsidiaries and is present in markets in Europe, North and South America, Asia, South Africa and Australia. In 2003, the company achieved sales of about €2 billion, up 6% from 2002. ALTANA Pharma concentrates on innovative pharmaceutical products in therapeutics, imaging (contrast media) and OTC medication. Therapeutics, the most important business area, is based on prescription drugs for gastrointestinal and respiratory diseases. Research focuses on gastroenterology, respiratory/inflammation and oncology.
GENEGO LAUNCHES METADRUG™ FOR SYSTEMS - ADME/TOX St. Joseph, MI. - January 14th, 2005, GeneGo, Inc., A leading systems biology company, today announced the official launch of MetaDrug™ V1.0. MetaDrug™ is a pioneering Systems-ADME/TOX platform which combines software for predicting metabolites and over 40 ADME/Tox properties with visualization and analysis of toxicogenomics and metabolomics data. MetaDrug™ can be used as a stand alone product or together with MetaCore™, GeneGo's flagship analytical platform. "MetaDrug™ is the first commercial product that merges ADME/TOX predictions in human with systems biology", said Dr. Sean Ekins, Vice President, Computational Biology. MetaDrug™ contains an extensive, expert curated database of small molecule content related to human drug metabolism, algorithms for predicting and prioritization of metabolites, the ability to highlight reactive metabolites and the most extensive set of predictive ADME/TOX models available. MetaDrug™ also enables analysis of toxicogeneomics data that can be visualized on networks and on static pathways maps. The user can therefore interpret both chemical and biological data in the context of the whole organism, merging predictions with empirical data when available. MetaDrug™ will be useful for preclinical assessment of molecules and their predicted properties. MetaDrug™ is also complimentary with MetaCore™ enabling researchers to build and analyze protein-protein, protein-ligand and genetic interaction networks using GeneGo's comprehensive databases of human biology and active chemistry. Ultimately both products enable the prediction of interactions of a small molecule with both xenobiotic and endogenous metabolism, regulation and cellular signaling.
TNO LICENSES GENEGO'S METACORE™ St Joseph, MI and Zeist, Netherlands - January 3rd 2005, GeneGo Inc., a leading systems biology company, announced today that TNO of the Netherlands has licensed its analytical tool MetaCore™. The product will be used internally by TNO's nutritional division, as well as in collaboration with the NuGO consortium of 21 universities throughout Europe (www.nugo.org). MetaCore™ is an integrated systems biology platform which includes a proprietary, manually curated database of eukaryotic biology and bioactive chemistry, network analysis software and a toolkit for visualization and management of high-throughput experimental data. "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." "We are very happy with TNO's decision to apply MetaCore™ in nutrigenomics studies", said Dr. Tatiana Nikolskaya, Chief Scientific Officer and President of GeneGo. "Although MetaCore™ is broadly used for drug discovery in industry and academy, this is its first non-pharmaceutical application. We consider the collaboration with TNO as an important step forward in adaptation of systems biology technology for everyday use." About TNO TNO is one of the leading research and technology organizations in Europe. It was established by the Dutch Government in 1932. TNO has a workforce of 5,500 employees, working in areas such as life sciences, industrial research, infrastructure, ICT and defense and safety. Within the life sciences area, focus is on nutrition and toxicology (including systems biology), analysis, working environment, microbiology and product innovation. The main markets for life sciences contract research are the food, chemical and pharmaceutical industries.
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