Bioinformatics Activities

Briographical sketches of contributors to this project.

Douglas Brutlag received his B.S. in chemistry from the California Institute of Technology and his Ph.D. in biochemistry from Stanford University in 1972, where he has remained as professor. He is the co-founder of IntelliGenetics, Inc. and IntelliCorp, and is currently the Chief Scientific Officer of DoubleTwist, Inc. Brutlag has been the Director of the Bioinformatics Resource at Stanford and he was cofounder of the International Society for Computational Biology. Brutlag states that his primary research objective is to understand the flow of genetic information from the genome to the phenotype of an organism. This includes understanding the sequence-structure dependencies and the structure-function dependencies of macromolecules. These goals represent the bioinformatic and functional-genomic approach to predicting structure and function from sequence. Specifically, we develop computer representations that can discover structural and functional properties of DNA, RNA and protein from sequences and from first principles. We spend much of our time learning the first principles of molecular and structural biology from known examples. We are also interested in predicting the interactions between ligands and proteins and between two interacting proteins. Given the structure, function and interactions of the proteins in a cell, we will eventually be able to simulate the metabolism of the organism. We attack these critical problems using a variety of different representations of sequences, structures and functions. Multiple representations of sequences include simple consensus sequence patterns, parametric representations, probabilistic techniques, graph theoretic approaches as well as computer simulations. Much of our work consists of developing a new representation of a structure or a function of a macromolecule, applying the methods of machine learning to this representation, and then evaluating the accuracy of the method. We have developed novel representations of sequence correlations that have predicted amino acid side chain interactions that stabilize protein strands and helices. We have developed novel algorithms for aligning sequences that give insight into the secondary structure of proteins. We have developed novel methods for discovering both sequence and structural motifs in proteins that help establish semantics of protein structure and function.

Peter Friedland received undergraduate degrees in chemistry and electrical engineering from Princeton University in 1974, and a Ph.D. in computer science from Stanford University in 1979. In 1994, he was awarded the Feigenbaum Medal, an international award given biannually for outstanding success in expert systems technology development and practical application. As a graduate student he worked on MOLGEN with Mark Stefik and Edward Feigenbaum. He was a cofounder of IntelliGenetics. Peter is known for his breakthrough work in the application of intelligent planning methods to practical problems in science and engineering. He co-founded two now-public companies - IntelliCorp and Teknowledge - that built hundreds of successful commercial applications of expert systems technology.
Before founding Intraspect, Friedland created and led the Artificial Intelligence Research Laboratory at NASA Ames Research Center, which grew to become the nation's largest governmental/industrial artificial intelligence research, development, and application center. During this time he managed a staff of over 60 professionals and a budget of greater than $10M, and co-managed a NASA-wide program involving eight Centers and over a $25M budget.

Joshua Lederberg was born in Montclair, New Jersey on May 23, 1925, the son of a rabbi. Lederberg's interest in a scientific career began quite early. His family moved to New York City when Lederberg was a child, and Lederberg was able to attend Stuyvesant High School, which concentrated in the sciences. In New York Lederberg was also able to take advantage of facilities such as the American Institute, which made laboratory space and equipment available to talented high school science students. Upon graduating from high school at 16, Lederberg took advantage of a local scholarship to attend Columbia University. After his experiments with Edward L. Tatum that demonstrated sexual recombination in bacteria, Lederberg decided to leave medical school to pursue a Ph.D., which he received from Yale in 1948. He then joined the Genetics Department at the University of Wisconsin, which at the time was part of the University's School of Agriculture. He eventually helped form and served as chair of the Department of Medical Genetics.

Lederberg received the Nobel Prize in 1958. Shortly afterward he joined the new Department of Genetics at Stanford University's School of Medicine, where he remained until 1978, when he left Stanford to become President of Rockefeller University.

Computer science and molecular biology caught Lederberg's scientific imagination during the mid-1960s at Stanford. In collaboration with computer scientists Edward A. Feigenbaum and Bruce Buchanan and chemist Carl Djerassi, Lederberg developed DENDRAL (DENDRitic ALgorithm), one of the first "expert" or "knowledge-based" systems. DENDRAL was designed to further two goals. The first was to aid scientists by determining the molecular structure of a chemical compound of known composition. The second was to investigate the combination of acquired knowledge and experience and inductive reasoning that a human would use to solve similar problems. Lederberg was involved in other early computer science, artificial intelligence, and cooperative communications projects, like SUMEX-AIM (Stanford University Medical EXperimental-Artificial Intelligence in Medicine). In a very early realization of the Internet, remote users could connect to a mainframe at Stanford to collaborate on problems that applied the methods and theories of artificial intelligence-the use of computers in complex decision making-to questions of medical science and medical diagnosis.

He became a professor emeritus in 1990, and he continues to research, lecture, and serve on a number of advisory panels.

Edward Feigenbaum received his B.S. and Ph.D. degrees at Carnegie Mellon University. He is a Professor of Computer Science and Co-Scientific Director of the Knowledge Systems Laboratory at Stanford University. Until 1992 Dr. Feigenbaum was Co-Principal Investigator of the national computer facility for applications of Artificial Intelligence to Medicine and Biology known as the SUMEX-AIM facility, established by NIH at Stanford University. He was Co-Principal Investigator of the DENDRAL Project, and Principal Investigator of the MOLGEN Project. Dr. Feigenbaum served as Principal Investigator Chief Scientist of the United States Air Force from 1994 to 1997. Professor Feigenbaum was Chairman of the Computer Science Department and Director of the Computer Center at Stanford University. He is the Past President of the American Association for Artificial Intelligence. He has served on the National Science Foundation Computer Science Advisory Board, an ARPA study committee for Information Science and Technology; and on the National Research Council's Computer Science and Technology Board. He has been a member of the Board of Regents of the National Library of Medicine.

Feigenbaum is the author and editor of numerous volumes, including the co-editor of the encyclopedia, The Handbook of Artificial Intelligence, and of the early book, Computers and Thought, published by McGraw-Hill. He is co-author of the McGraw-Hill book, Applications of Artificial Intelligence in Organic Chemistry: The DENDRAL Program and was the founding editor of the McGraw-Hill Computer Science Series. He is co-author with Pamela McCorduck of the book The Fifth Generation: Artificial Intelligence and Japan's Computer Challenge to the World, published by Addison-Wesley (1983) and by New American Library (1984). He is also co-author with Penny Nii and Pamela McCorduck of the book, The Rise of the Expert Company, on corporate successes in the use of expert systems, published by Times Books in New York and Macmillan in London (1988).

Edward Feigenbaum is a co-founder of several start-up firms in applied artificial intelligence, including IntelliGenetics, IntelliCorp, Teknowledge and Design Power Inc. and served as a member of the Board of Directors of IntelliCorp and Design Power Inc. He also was a member of the Board of Directors of Sperry Corporation prior to its merger with Burroughs. He is a member of the Advisory Council of the Kansai Silicon Valley Venture Forum.