BioCompute Leadership

Dr. Vahan Simonyan has a diverse academic background, with an MS in Physical Organic Chemistry, a Ph.D. in Quantum Physics and Mathematics, and post-doctoral training in Nanotechnology and Quantum Statistical Thermodynamics. He’s authored over 60 publications on topics ranging from chemistry and genetics to physics and quantum mechanics, and served as a principal investigator on large national and international grants. In 2001, Dr. Simonyan began to focus his career on biotechnology and biomedical informatics. He has served as Lead Scientist, Principal Investigator, and the R&D Director of Bioinformatics for the U.S. Food and Drug Administration (FDA). As the Director, Dr. Simonyan developed and donated the codebase for the High-performance Integrated Virtual Environment (HIVE) as a mechanism to accept high throughput sequencing data at the FDA. It was in this capacity that he co-developed BioCompute. Currently, Dr. Simonyan is the Senior Director of Bioinformatics at CRISPR Therapeutics, where he establishes data and process infrastructures for analysis of healthcare and biomedical information from diverse data-sources, in order to discover new genetic targets through the understanding of underlying molecular machinery in cells and control networks. He also serves as adjunct faculty at George Washington University, and has served as the Organizer and Chairman of international conferences on high throughput sequencing standardization. Dr. Simonyan is a Co-author of the first BioCompute publication.

Dr. Dennis A. Dean, II is a Director at Seven Bridges where he leads the Scientific Team in the Cambridge office and leads several national-scale genomic analysis projects. Dr. Dean’s oversight responsibilities includes system architects, engagement managers bioinformatics scientists and genomic data scientists. In this capacity, he is responsible for the success of his team members across commercial, government, and internal projects. He leads collaboration outreach with the US Food and Drug Administration (FDA), the US Department of Veteran Affairs Million Veteran Program (MVP), and oversee several projects with large pharmaceutical companies. Dr. Dean trained as a research fellow in medicine at the Harvard Medical School and Brigham and Women’s Hospital in the Program for Sleep Epidemiology and the Program for Sleep and Cardiovascular Medicine. He earned his PhD in biomedical engineering and biotechnology and M.S. in computer science from the University of Massachusetts. He earned his B.S. in computer science from SUNY, Empire State College.

Jeremy is an expert in computational biomedicine and has made contributions in many areas of bioinformatics and computational science, including genome and proteome analysis methods, cancer informatics, scientific computing infrastructure, machine learning, and user interfaces and visualization. He has more than 15 years of computational science experience and has spent the last 10 years developing algorithms, software, and infrastructure for biomedical data science. Jeremy is a lead investigator for the Galaxy platform (http://galaxyproject.org), a Web-based system for analyzing biomedical data that is used by thousands of scientists throughout the world. As a lead Galaxy investigator, he participates in Galaxy at all levels: strategic planning, architecting scalable systems for large analysis projects, leading the development of new software components, and implementing and benchmarking best-practice analysis pipelines. Jeremy directs informatics for precision oncology at Oregon Health and Science University (OHSU). In this work, he leads a team developing computational systems for processing, storing, modeling, and visualizing clinical, imaging, and omics data for (1) treating cancer using combination therapies adapted over time; and (2) discovering and understanding mechanisms of resistance and priming in cancer. He is PI/co-PI on several resource and research grants for NCI, NHGRI, and NSF focused on genome informatics, cancer informatics, and precision oncology. Dr. Goecks is a co-author of the first BioCompute publication.

Dr. Keeney’s academic experience is cross disciplinary at the intersection of neuroscience and genomics. Work with Jim Sikela at the University of Colorado investigated the functional role of copy number genomics in the evolutionary expansion of the primate brain, where he was a Coleman Institute for Cognitive Disability Fellow, and a student at Woods Hole Marine Biological Laboratory. He has experience in functional genomics and designing bioinformatic analyses, including novel experimental design for bioinformatic data collection. Dr. Keeney has also worked in the private sector as a Technical Specialist for a patent law firm in Denver, Colorado, as a startup cofounder, and as Director of Complex Visualization for a medical device company. He has been an invited author to a live discussion with Digg Dialog, and a judge for a startup pitch competition. During this time, he maintained strong connections to academia, and assisted with the establishment and development of three different public private partnerships. He brings experience in both the academic and private sectors in his current role, in which he leads multiple initiatives. Most notably, Dr. Keeney currently drives the creation of a public-private partnership around BioCompute, leads the development of the BioCompute project into a formal IEEE standard, and serves as the Managing Director for the Executive Steering Committee of the BioCompute Partnership. In this role, he leads project outreach, coordinates workshops with the high throughput sequencing and broader communities, and moderates discussion in both the public and private spaces to make BioCompute meet the needs of all stakeholders.