Bios for CDD Town Hall: Human vs. Machine-Enhanced Scientific Discovery
Dr. Musen is Professor of Biomedical Informatics and of Biomedical Data Science at Stanford University, where he is Director of the Stanford Center for Biomedical Informatics Research. Dr. Musen conducts research related to intelligent systems, reusable ontologies, metadata for publication of scientific data sets, and biomedical decision support. His group developed Protégé, the world’s most widely used technology for building and managing terminologies and ontologies. He is principal investigator of the National Center for Biomedical Ontology, one of the original National Centers for Biomedical Computing created by the U.S. National Institutes of Heath (NIH). He is principal investigator of the Center for Expanded Data Annotation and Retrieval (CEDAR). CEDAR is a center of excellence supported by the NIH Big Data to Knowledge Initiative, with the goal of developing new technology to ease the authoring and management of biomedical experimental metadata. Dr. Musen directs the World Health Organization Collaborating Center for Classification, Terminology, and Standards at Stanford University, which has developed much of the information infrastructure for the authoring and management of the 11th edition of the International Classification of Diseases (ICD-11).
Dr. Musen was the recipient of the Donald A. B. Lindberg Award for Innovation in Informatics from the American Medical Informatics Association in 2006. He has been elected to the American College of Medical Informatics and the Association of American Physicians. He is founding co-editor-in-chief of the journal Applied Ontology.
Jan holds a BS in Chemistry from the University of Illinois at Champaign-Urbana, and a PhD in Biology from Harvard University. For the last 4 years, she has been an independent consultant helping small drug discovery companies with project and grant strategy, management, and writing. She has over 20 years’ experience in companies and non-profits, in both ‘bench research’ and bioinformatics, and in managing large projects in both of those arenas.
Jan’s career path has given her both breadth and depth of experience in drug discovery: First, a foundation in rational target-based drug discovery from 5 years at Cubist Pharmaceuticals, which she joined in 1993 when it was a startup, where she worked on target identification, validation and assay development for antimicrobials. Second, immersion in bioinformatics, including work at both a non-profit disease- and patient-centric research institute (ALS-Therapy Development Institute) and at Proteome/ BioBase, where she led projects curating biological information from the literature into a database of biological knowledge, and then using this database content in a proprietary curation method to apply Gene Ontology terms to the then-new human genome sequence. Third, Jan had the opportunity to work directly for Dr. Edward Scolnick (who was President of Merck Research for 17 years), from whom she learned both the essential rigor and potential pitfalls of drug discovery, over the time (2007-2012) they established and built the Stanley Center for Psychiatric Research at the Broad Institute.
Most recently, Jan has been working with CDD’s Alex Clark and Barry Bunin in creating and developing BioAssay Express (BAE), a software tool enabling scientists to quickly annotate assay protocols with semantic terms from the BioAssay Ontology.
Dr Stephan Schürer is Associate Professor in the Department of Pharmacology and Director of Drug Discovery at the Center for Computational Science at the University of Miami.He is also adjunct Associate Professor at the at the Scripps Research Institute Florida where he was previously heading the HTS- and drug discovery chemoinformatics development. In prior industry positions Dr. Schürer was Sr. Director at Eidogen-Sertanty, a developer of life science information technology and scientific content products. At Libraria Inc. he was directing the content operations to develop chemistry and SAR knowledge bases.
The core research theme at the Schürer group is systems drug discovery. We integrate and model small molecule-protein interaction, systems biology ‘omics’, and chemistry data to improve translation of disease models into novel functional small molecules. Using distributed and parallelized big data analytics, bio- and chemoinformatics tools we build sophisticated modeling pipelines to understand and predict drug mechanism of action, promiscuity and polypharmacology with a particular focus on kinases and epigenetic bromodomain reader proteins. I n several focused as well as larger-scale projects, we develop formal ontologies (e.g. BioAssay Ontology, Drug Target Ontology), data standards, and end-user multi-tier software applications. We have several drug discovery collaborations ranging from cancer to neurological disorders.
To generate and test the most promising small molecules, we are developing computationally-optimized synthetic routes and we use parallel synthesis technologies to make small compound libraries.
Dr Schürer is a PI in two national Consortia, the Library of Integrated Network-based Cellular Signatures (LINCS) project (http://bd2k-lincs.org/), which is also part of the Big Data to Knowledge (BD2K) program (https://datascience.nih.gov/bd2k), and the Illuminating the Druggable Genome (IDG) project (http://targetcentral.org/).
Stephan Schürer received his Ph.D. in synthetic organic chemistry from the Technical University of Berlin and studied chemistry at Humboldt University-Berlin and University of California Berkeley.
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