NDEx Team Members
Dexter Pratt – Project Director
Prior to NDEX, Dexter served as VP of Knowledge and Innovation at Selventa Inc., where he led teams in algorithm development, curation, and drug discovery consulting engagements. His earlier career was in commercial artificial intelligence research and product development at Lisp Machine Inc. and at the CYC Project at the Microelectronics and Computer Consortium. He is the creator of BEL (the Biological Expression Language) and has the role of Founder and Evangelist in the OpenBEL Consortium.
Rudolf T. Pillich – Application Manager
Rudi is a research scientist with 10+ years of hands-on experience in Cell & Molecular Biology mainly focused on pancreas biology and diabetes. After completing his PhD at the University “La Sapienza” of Rome, Rudi joined the Dept. of Pediatrics at UC San Diego to pursue his postdoctoral training. He is the author of several peer reviewed scientific publications and is interested in project management and science communication. As a scientist with an international cultural background and academic training, Rudi is bridging the gap between biologists and software engineers and ensuring that the NDEx Project understands and satisfies the needs of our vibrant biomedical research community.
Jing Chen – Senior Software Engineer
Jing has many years of software development experience in biological sciences and his career has been mainly focused on integrating and managing genomic, ontological, RDF and graph data for life sciences. Before joining the NDEx Team, Jing worked as software architect for GeneticXchange Inc., a software product company that provides data integration middleware for the biotech and pharmaceutical industry. He also participated in the UCSD interdisciplinary Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA) project as a database architect.
Chris Churas – Software Engineer
Chris holds a BS in Computer Science and has 18+ years of experience working as a software developer. Chris has worked on various projects in the Schwartz lab at the University of Wisconsin - Madison and in the Ellisman lab at UC San Diego. Chris's work in the past has involved development of software to enable parallel processing of genomic and image data on large computer clusters.
Trey Ideker – Principal Investigator
Trey Ideker is Professor of Genetics in the Department of Medicine at the University of California at San Diego. He serves as Director of the National Resource for Network Biology and Director of the San Diego Center for Systems Biology, as well as being Adjunct Professor of Computer Science and Bioengineering and Member of the Moores UCSD Cancer Center. Trey received Bachelor’s and Master’s degrees from MIT in Electrical Engineering and Computer Science and his PhD from the University of Washington in Molecular Biology under the supervision of Dr. Leroy Hood. Trey has founded influential bioinformatic tools including Cytoscape, a popular network analysis platform which has been cited over 12,000 times. He serves on the Editorial Boards for Cell, Cell Reports, Nature Scientific Data, EMBO Molecular Systems Biology, and PLoS Computational Biology and is a Fellow of AAAS and AIMBE.
Former members
Sophie Liu – Software Developer
Sophie has a BS in Bioinformatics and experience in front-end development using Java and Python. Besides software development, Sophie is also interested in improving and optimizing the end-user experience.
David Otasek – Software Engineer
David has a BA in Computer science and over 15 years of experience developing, implementing and maintaining software projects. Before joining the Ideker lab, he led the team responsible for the development of NAViGaTOR, a visualization toolkit for graphs and built a text-mining system for the automated extraction of protein-protein interactions in online literature. This required research that culminated in a conference paper for the Society for Industrial and Applied Mathematics. Within the NDEx Team, David is responsible for the development of multiple software applications and services for the Ideker lab, including contributions to the Cytoscape Consortium, an open source platform for network analysis.
Vladimir Rynkov – Software Engineer
Vladimir holds an MS in Computer Sciences and has more than 10 years of experience working as a software developer and customer support engineer. Earlier in his career, Vladimir worked as an embedded systems and networking protocols developer and then as a software engineer for different companies including Cisco. Prior to joining the NDEx Project, Vladimir served as Programmer Analyst in the Business Application Development Group at the UC San Diego School of Medicine, where he developed and maintained programs for managing business processes and day-to-day operations.
Aaron Gary – Software Engineer
Aaron has been designing and developing multi-teir enterprise applications in the healthcare industry for over 12 years now. He holds a bachelors degree in Electrical Engineering and a masters in Computer Science. In addition to software development he also spent time as a volunteer web master for a non-profit health initiative based in Haiti.
David Welker – Software Engineer
David graduated with a BS in Information and Computer Science from UC Irvine in 2002 and is currently pursuing an MS in Computer Science from Georgia Tech. In his career, he has worked in a variety of capacities, including as a software engineer for defense contractors developing air command-and-control systems, as a software engineer developing applications to orchestrate scientific workflows, and as a software architect supervising developers and analysts designing and developing mobile-friendly web-applications. David joined the Department of Medicine at UC San Diego due to his interest in the vast possibilities opened up by applying the power of computation to analyze the human genome. Within the Department of Medicine, before working on the NDEx Project, David worked on Cytoscape, the world’s leading application for visualizing networks in the emerging field of network biology.