Biotechnology Innovation and Computation
Faculty and Advisors



Faculty


John Vu, Program Director


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John Vu is the Director of the M.S. in Biotechnology Innovation and Computation program as well as Distinguished Career Professor in the School of Computer Science. John was a Chief Engineer and Technical Fellow (retired) at The Boeing Company where he led several successful programs including the integration of computer design systems for the 777, IT integration into Lean Manufacturing and various company wide software improvement initiatives. John has over 35 years of experience in software and systems development and has managed several large-scale integration programs in which the final products required the integration of in-house components with commercial off-the shelf products and outsourced suppliers.


John has participated in the development of several Capability Maturity Models (CMMIs) at the Software Engineering Institute (SEI) and authored the software e-commerce model and the procurement model. He was a member of the IEEE Software Industry Advisory Board and has written many books and articles on software project and program management.


John received master's degrees from Carnegie Mellon University and the University of Nevada in addition to undergraduate degrees from Ohio University and Seattle Pacific University. He is also a lecturer at Carnegie Mellon Silicon Valley, Seattle University, the Korean Advanced Institute of Science and Technology and Tsinghua University.

Eric Nyberg, Co-Director


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Eric Nyberg is a Professor in the Language Technologies Institute. He is the co-Director for the M.S. Program in Biotechnology, Innovation, and Computation as well as the MSIT Program in Very Large Information Systems. Dr. Nyberg has made significant research contributions to the fields of automatic text translation, information retrieval and automatic question answering. His research has been funded by global corporations (including IBM, Caterpillar, Daimler-Benz, Hewlett-Packard, Hitachi and Denso), and a variety of U.S. government agencies. Dr. Nyberg received his Ph.D. from Carnegie Mellon University and his BA from Boston University. In 2012, Dr. Nyberg received the Allen Newell Award for Research Excellence for his scientific contributions to the field of question answering and his work on IBM's Watson project.

Jaime Carbonell


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Jaime Carbonell is the Allen Newell Professor in the School of Computer Science. He is the Director of the Language Technologies Institute. Overall, he has published over 250 articles and books. His research includes text and data mining, machine translation, reasoning under uncertainty, and computational proteomics where he investigates machine learning and language technologies to predict proteomic 3D structure (a.k.a. "the folding problem") and function. Dr. Carbonell has served on various advisory committees including the NIH Human Genome Advisory Committee and the National German AI Lab (DFKI) Scientific Advisory Board. He has also served as an advisor for numerous technology startups and companies, and has consulted to large financial institutions such as Citigroup. He received his MS and Ph.D. from Yale University and his BS in Physics from MIT.

Robert Murphy


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Robert Murphy is the Ray and Stephanie Lane Professor of Computational Biology. He co-founded the Computational Biology Ph.D. Program which is jointly administered with the University of Pittsburgh. He helped developed the first formal undergraduate program in computational biology in 1987 and founded the Merck Computational Biology and Chemistry program at Carnegie Mellon in 1999. His research group does both experimental and computational cell biology, with a particular emphasis on developing fully-automated methods to understand the subcellular locations of proteins and how they change during development or disease (location proteomics). Dr. Murphy received his Ph.D. from the California Institute of Technology and his BA from Columbia College.

Karen Thickman


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Dr. Karen Thickman received her PhD from the Johns Hopkins School of Medicine in Molecular Biophysics. There she studied the structure of spliceosomal proteins and the thermodynamics of protein-protein interactions involved in recruiting the spliceosome to the pre-mRNA. During her postdoctoral fellowship at the University of Pittsburgh, she studied the biochemical properties and DNA structure specificity of a gram-positive bacterial helicase, PcrA. Dr. Thickman's teaching focuses on laboratory courses in computational biology and biological sciences. Her interests include automation of biology, protein interaction studies, teaching laboratory and research skills, and science policy.

Kai-min Kevin Chang


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Dr. Kevin Kai-Min Chang received his Ph.D. and M.S. from Carnegie Mellon University. His research interests include using mathematical methodologies and machine learning techniques to investigate and model various human cognitive processes in the brain. In particular, He has studied semantic presentation of concepts and multi-words phrases using functional Magnetic Resonance Imaging and knowledge representation in the context of an intelligent tutoring system. His current research projects use consumer EEG devices to help improve intelligent tutoring systems and automatic speech recognizers in dialog systems by monitoring and recording users' mental state, such as affection, engagement, etc.

Industry Advisors


Mark Ahn


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Mark J. Ahn, Ph.D. is President & Chief Executive Officer, and Director of Galena Biopharma (Nasdaq: GALE) and Professor (adjunct), Biosciences, Creighton University. Prior to Galena , Dr. Ahn was Principal at Pukana Partners, Ltd. that provides strategic consulting to life science companies; and Associate Professor, Global Management at Atkinson Graduate School of Management, Willamette University. He previously served as Chair, Science & Technology Management, Victoria University at Wellington, New Zealand. Dr. Ahn was also founder, President, and Chief Executive Officer of Hana Biosciences. Prior to Hana, he served as Vice President, Hematology and corporate officer at Genentech, Inc., as well as held positions of increasing responsibility at Amgen and Bristol-Myers Squibb Company; and served in the US Army. Dr. Ahn also serves on public and venture capital-backed Board of Directors for Access Pharmaceuticals, Mesynthes and Scribes STAT. Dr. Ahn is the author of over 50 peer reviewed journal articles and books including Making the Case for Biotechnology (Logos Press).

Dr. Ahn received a BA and MBA from Chaminade University; and MA from Victoria University. He was a graduate fellow in Economics at Essex University, and obtained a Ph.D. from the University of South Australia. Dr. Ahn is a Henry Crown Fellow at the Aspen Institute.

James Cai


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Dr. James Cai is the Head of Disease and Translational Informatics at Roche Pharmaceuticals in Nutley, New Jersey. He leads a group of informatics scientists that provide a wide array of support to scientists in the areas of data capture, management, analysis and sharing/collaboration. Prior to his current role, James was Head of Research Statistics and Data Mining, and later Head of the Biomedical Informatics group, both within the Pharma Research and Early Development (pRED) Informatics organization at Roche. Dr. Cai has worked in a wide range of informatics areas including genomic data analysis, algorithm development, enterprise system development, text analytics and data mining. He played leading roles in several global initiatives that helped to shape the Informatics strategies at Roche. He and his team are also responsible for a number of scientific applications widely used within the company. Dr. Cai received his Ph.D. in Molecular Biology from Cornell University and a Master's degree in Biomedical Informatics from Columbia University. He was a National Library of Medicine postdoctoral fellow in Biomedical Informatics, with broad training in informatics practices from basic biological research to clinical medicine.

Richard Chin


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Richard Chin is currently the CEO of One World Health. He has overseen over 40 Investigational New Drug (IND) Applications for new molecular entities and new indications, as well as eight New Drug Applications (NDAs)/Biologic License Applications (BLAs). Dr. Chin joined One World Health from OXiGENE, where he served as President and CEO. Previously, Dr. Chin served as Senior VP and Head of Global Development for Elan Corporation, where he had worldwide responsibility for Clinical Development, Regulatory, Biostatistics, CMC, QA/Compliance, Safety and Medical Affairs. Dr. Chin has also held various clinical and scientific roles for Genentech, Inc. including Head of Clinical Research for the Biotherapeutics Unit, overseeing approximately half of the drugs at Genentech, and began his career at Procter and Gamble Pharmaceuticals, where he served as Associate Medical Director. He received a B.A. in Biology from Harvard University and the equivalent of a J.D. with honors from Oxford University in England under a Rhodes scholarship. Dr. Chin received his MD from Harvard Medical School.

Madhavi Ganapathiraju


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Madhavi Ganapathiraju, Ph.D., is Assistant Professor at Department of Biomedical Informatics and Intelligent Systems Program at University of Pittsburgh and Molecular and Cellular Cancer Biology Program of University of Pittsburgh Cancer Institute. She is also Faculty of Language Technologies Institute of Carnegie Mellon University and Joint Carnegie Mellon University of Pittsburgh Ph.D. Program in Computational Biology. She has a Ph.D. from School of Computer Science of Carnegie Mellon University and a Masters in Engineering from Department of Electrical Communications Engineering from Indian Institute of Science. She is the recipient of the Biobehavioral Research Awards for Innovative New Scientists (BRAINS) from National Institute of Mental Health of the National Institutes of Health of USA. In this award-funded project, her group is discovering the Mental Health and Inflammation Interactome of Protein-Protein Interactions, by applying machine learning and graph mining methods.

Xuong Nguyen-Huu


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Dr. Xuong Nguyen-Huu is an Emeritus Professor of Physics, Biology, Chemistry & Biochemistry at the University of California San Diego (UCSD). He is also a Research Professor of Chemistry & Biochemistry at UCSD. His field of research is on the High Resolution Structure of Biological Macromolecules using Protein Crystallography. He has also been working in the field of detectors for 50 years, first with particle detectors (both electronics and Bubble Chambers) for High Energy Particles Physics, then with X ray detectors for Protein Crystallography ( using Multi-wire Proportional Chambers and then Silicon detectors). Last but not least he is one of the pioneers of the field of Direct Detection Device (DDD) that will be used in Electron Microscopy. He has received an MS and Ph D (Physics) from the University of California Berkeley, an MS in Mathematics from the University of Paris and an MS in Electronic Engineering from the Ecole Superieure d’Electricite de Paris.

John Shon


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John Shon is the Director of Disease and Translational Informatics at Johnson & Johnson Pharmaceuticals, where he leads an informatics group that supports and develops systems to enable the discovery and development of new medicines. He is particularly interested in systems that leverage high-dimensional genetics, genomics, pathways, and text data in the context of clinical therapeutics for personalized medicine. Dr. Shon has multidisciplinary background in clinical medicine, biomedical informatics, molecular biology, and drug discovery and development. He received his degree in medicine at Stanford, completed his internship and residency in internal medicine at the University of Chicago, and completed a masters degree and National Library of Medicine post-doctoral fellowship in biomedical informatics at Stanford. He subsequently worked in industry in several biotech and informatics consulting firms prior to joining Johnson & Johnson.
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