The Merck Computational Biology and Chemistry Program

Seminar Series

Dr. Kearsley has twenty years of experience in computational chemistry, molecular modeling, and in particular, expertise in development of new modeling methods. He received a B.A. in natural science and Ph.D. in physical-organic chemistry at Cambridge University. During postdoctoral years at Yale University, he advanced his computational skills, having established that "wet" scientific experimentation was not for him. In particular, he become familiar with graphics programming and super-computing. He focused on molecular mechanics theory, crystal packing theory and surface walking algorithms. His main accomplishment was modeling zero-field splitting tensors of trapped bi-radicals in organic crystals. At Merck he started out as a scientific programmer for the modeling group. He accrued responsibility for all software development devoted to molecular modeling at Merck. The issues that faced modeling in industry, and modeling software and algorithm development in particular, were practicality, robustness and scale. His main focus was on chemical database mining methods. His group clearly changed the way chemical leads were identified. Later, he also became responsible for High Performance Computing, and systems infrastructure. High Throughput Screening and Combinatorial Chemistry were opportunities for further methods development which required his group to invent algorithms that dealt with even larger number of entities. Currently, he directs all aspects of molecular modeling at the main research sites at Merck. This now includes the Application of our modeling tools to drug discovery projects. His most significant strategic directions are associated with formalizing knowledge transfer between drug discovery projects.

Professor Shamir is Professor of Computer Science at Tel Aviv University. His research interests focus on Computational Biology/Bioinformatics, Graph Algorithms, and Optimization. He received his BsC in Mathematics and Physics from Hebrew University, Jerusalem (1977) and his PhD in Operations Research from the University of California, Berkeley (1984). He is currently serving as an ISMB 04 Program Committee member and on the SIAM Conference on Discrete Mathematics 04 Organizing Committee. He is also on the Program Committee of RECOMB 04 and the Steering Committee on RECOMB (International Conference on Computational Molecular Biology). He is a member of ACM and SIGACT, the Human Genome Organization (HUGO) and the International Society for Computational Biology (ISCB). He is also the author of numerous publications.

Dr. Pevzner is Ronald R. Taylor Professor of Computer Science at the University of California, San Diego and is a pioneer in computational biology. His interests are in algorithmic apporaches to bioinformatics and he co-founded the international RECOMB Conference. In addition to his many research accomplishments, he wrote the textbook "Computational Molecular Biology: An Algorithmic Approach" which is widely used in courses across the country. He is Executive Editor of the Journal of Computational Biology and is on the Editorial Board of Discrete Applied Mathematics, Bioinformatics, the Journal of Computer and Systems Sciences, and the Journal of Bioinformatics and Computational Biology.

Dr. Dill is Professor of Pharmaceutical Chemistry and Associate Dean of Research in the School of Pharmacy at the University of California, San Francisco. He has received a number of honors recognizing his pioneering work on protein folding, including receiving the Hans Neurath Award from the Protein Society and being named a Fellow of the American Association for the Advancement of Science and the American Physical Society. His group is interested in the physical bases for protein structure, stability, kinetics, and conformational change. He uses methods of polymer statistical mechanics, computer simulation, combinatorics, and inference methods to explore the accessible conformations and the energetics of chain molecules, in order to learn about the relationship between amino acid sequence and native structures of globular proteins.

Dr. Gusfield is Professor and Chair of Computer Science at the University of California, Davis. His primary interests involve the efficiency of algorithms, particularly for problems in combinatorial optimization and graph theory. These algorithms have been applied to study data and computer security, stable matching, network flow, matroid optimization, and string/pattern matching problems. Currently, Professor Gusfield is focused on string and combinatorial problems that arise in computational biology, particularly from the Human Genome Project, bioinformatics, and genomics.

Dr. Edelsbrunner is Arts and Sciences Professor of Computer Science and Mathematics at Duke University. His research focuses on developing algorithms to model proteins as geometric shapes to determine how protein structure affects the function of an enzyme. In a recent research milestone, Dr. Edelsbrunner, one of the founders of computational geometry, discovered how to express and compute mathematically the area derivatives of a protein in motion. Although there are thousands of researchers who focus on the study of protein structure, Dr. Edelsbrunner is one of a handful of computer scientists devoted to this field. In 2000, Dr. Edelsbrunner received a $7.2 million grant from the National Science Foundation to collaborate with Stanford University, the University of North Carolina at Chapel Hill, and North Carolina A&T University on research into bioinformatics, applying information technology to solve the riddles of protein structure. In 1996, he and his wife Ping Fu founded Raindrop Geomagic Inc. The start-up provides software that automatically converts data scanned from a physical object, such as a cylinder head or a molded hearing aid, to production quality 3D digital models. Dr. Edelsbrunner received his M.S. and Ph.D. from the Graz University of Technology in Austria. He is the only computer scientist to have won the National Science Foundation Waterman Award, which honors one researcher per year in science, engineering, math, or economics.

Dr. Honig is Professor of Biochemistry and Molecular Biophysics at Columbia University. His group uses computational and theoretical methods to study the structure and function of proteins, nucleic acids and membranes. A current focus involves the combined use of physical and chemical methods, amino acid sequence analysis, three dimensional structure analysis and data mining as tools in bioinformatics and genome analysis. Specific research areas include: The development of accurate computational methods to predict protein structure from amino acid sequence; the use of three-dimensional structural information to identify relationships between remote sequence homologs and the use of these relationships in the analysis of genomic information; the study of the physical chemical principles that underlie protein and RNA folding, protein-protein, protein-nucleic acid and protein-membrane interactions; the development of computational methods to identify protein function based on protein structure; the application of computational tools to the understanding of problems of biological importance such as subcellular localization in protein/membrane systems and the specificity of protein-protein interactions in signaling pathways.

Dr. Car is Professor of Chemistry at Princeton University with a joint appointment in the Princeton Materials Institute. He received a doctorate in nuclear engineering from the Milan Institute of Technology in 1971. Since then he has worked at the University of Milan, the Swiss Federal Institute of Technology, the IBM T. J. Watson Research Center, the International School for Advanced Studies in Trieste, and the University of Geneva. He has directed the Institute for Numerical Research in the Physics of Materials in Lausanne. He joined the Princeton faculty in 1999. His research has been focused on understanding physical and chemical properties of materials at the atomistic scale using computational methods based on first-principles microscopic quantum theory. Systems of interest include liquid and amorphous materials, surfaces and interfaces, defects, clusters, and molecular materials. He has received the Hewlett-Packard Prize of the European Physical Society, the Rahman Prize of the American Physical Society and was elected a Fellow of the American Physical Society.

Dr. Bryant is Senior Investigator in the Computational Biology Branch, National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health.

Dr. Nachbar earned his doctorate in 1979 in organic chemistry from Brown University under David Cane elucidating the regio- and stereochemical details of the biosynthesis of fomannosin. As a postdoctoral fellow at MIT under William Rastetter, he pursued the synthesis of dihydrodiol epoxides of polyaromatic hydrocarbons. It was during his subsequent postdoctoral appointment at Princeton University under Kurt Mislow that he embarked on his career in computational chemistry. Since 1982 he has been at Merck Research Laboratories, first in the Molecular Systems department where he has been involved with molecular modeling, drug design, statistics, software design and implementation, and methodology development, and more recently in Information Sciences Research where he has tackled problems in pharmacokinetics, proteomics, and computational biology.

Dr. Dunker is Professor of Biochemistry at Washington State University. He is a member of the Board of the International Society for Computational Biology and has been Co-Chair of the Pacific Symposium on Biocomputing since 1997.

Dr. Waterman is Professor of Mathematics, Biological Sciences and Computer Science at the University of Southern California. He was named a Guggenheim Fellow in 1995 and was elected to the American Academy of Art and Sciences in 1995. He is also a Fellow of the American Association for the Advancement of Science and Fellow of the Institute of Mathematical Statistics.