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Appendix—
Chapter Authors

Craig J. Benham
Professor and Chair, Biomathematical Sciences Department
Mount Sinai School of Medicine
New York, New York

Dr. Benham was trained as a pure mathematician, his thesis being in the field of complex manifold theory. He received his Ph.D. degree in mathematics from Princeton University in 1972. During his first academic appointment at Notre Dame University, he became interested in problems involving biomolecular structure. In order to educate himself in this new area, he took a postdoctoral position in 1976 with Max Delbrueck in the Biology Division at California Institute of Technology. At that time he began his work on superhelical DNA.

Dr. Benham initiated the theoretical analysis of superhelical DNA conformational equilibria. Over the years he has developed both elastomechanical and statistical approaches to the analysis of the large-scale structure of supercoiled DNAs. He also has developed theoretical methods to predict changes in the secondary structure of DNA in response to imposed stresses, the subject of Chapter 7 in this volume.

Fred E. Cohen
Professor of Pharmaceutical Chemistry, Medicine,
Pharmacology, Biochemistry, and Biophysics
University of California
San Francisco, California

Dr. Cohen's research on computational approaches to the protein folding problem began as an undergraduate at Yale University and was the subject of his doctoral work at Oxford University, where he studied as a Rhodes Scholar. Upon completing graduate school, he came to the University of California, San Francisco (UCSF) as a postdoctoral fellow



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Page 272 Appendix— Chapter Authors Craig J. Benham Professor and Chair, Biomathematical Sciences Department Mount Sinai School of Medicine New York, New York Dr. Benham was trained as a pure mathematician, his thesis being in the field of complex manifold theory. He received his Ph.D. degree in mathematics from Princeton University in 1972. During his first academic appointment at Notre Dame University, he became interested in problems involving biomolecular structure. In order to educate himself in this new area, he took a postdoctoral position in 1976 with Max Delbrueck in the Biology Division at California Institute of Technology. At that time he began his work on superhelical DNA. Dr. Benham initiated the theoretical analysis of superhelical DNA conformational equilibria. Over the years he has developed both elastomechanical and statistical approaches to the analysis of the large-scale structure of supercoiled DNAs. He also has developed theoretical methods to predict changes in the secondary structure of DNA in response to imposed stresses, the subject of Chapter 7 in this volume. Fred E. Cohen Professor of Pharmaceutical Chemistry, Medicine, Pharmacology, Biochemistry, and Biophysics University of California San Francisco, California Dr. Cohen's research on computational approaches to the protein folding problem began as an undergraduate at Yale University and was the subject of his doctoral work at Oxford University, where he studied as a Rhodes Scholar. Upon completing graduate school, he came to the University of California, San Francisco (UCSF) as a postdoctoral fellow

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Page 273 and simultaneously began medical school at Stanford University. He subsequently completed a medical residency and subspecialty training at UCSF before joining the full-time research faculty in 1988. Dr. Cohen's research interests center around computational models for protein folding, structure, and function. Applications of this work have led to advances in drug design and discovery with a particular emphasis on parasitic disease. More recent work has attempted to understand the structural underpinnings of the neurodegenerative diseases caused by prions. Dr. Cohen has received a Searle Scholars Award, the Richard E. Weitzmann Young Investigator Award from the Endocrine Society, and the Young Investigator Award of the Western Society of Clinical Investigation. Dr. Cohen serves on the Molecular and Cellular Biophysics Study Section of the National Institutes of Health, as an editor of the Journal of Molecular Biology, and as a member of the editorial boards of Protein Engineering, Perspectives in Drug Discovery and Design, Computational Biology, and Molecular Medicine. Eric S. Lander Director, Whitehead Institute for Biomedical Research and Professor, Massachusetts Institute of Technology Cambridge, Massachusetts Dr. Lander is a member of the Whitehead Institute for Biomedical Research, director of the Center for Genome Research, and professor of biology at the Massachusetts Institute of Technology. His background includes both pure mathematics and laboratory molecular genetics. He also taught managerial economics at the Harvard Business School from 1981 to 1989. Early in this period, he became interested in biology and acquired laboratory training in fruit fly, nematode, and human genetics. Dr. Lander's theoretical work includes the development of mathematical methods for the genetic dissection of complex inherited traits; algorithms for genetic mapping; analytical approaches to physical map construction; and population genetic methods for finding human disease genes. His laboratory work includes the construction of genetic linkage maps of the mouse and rat genomes; construction of physical maps of the human genome; genetic dissection of traits, including colon cancer susceptibility in the mouse and diabetes susceptibility in the rat;

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Page 274 and cloning of human disease genes. He receive a MacArthur Fellowship in 1987 for his work at the interface of molecular biology and mathematics. He received a Ph.D. in pure mathematics from Oxford University in 1981, where he studied algebraic combinatorics. Eugene W. Myers Professor, Department of Computer Science University of Arizona Tucson, Arizona Dr. Myers specializes in algorithm designs, an area of computer science focusing on the creation of computer methods to solve problems efficiently and accurately. He first entered the area of computational molecular biology in 1986 when he began to focus on algorithms for searching biosequence databases, discovering DNA sequence patterns, comparing sequences, sequencing DNA, and displaying molecular images. He is an editor for Computer Applications in the Biosciences and the Journal of Computational Biology. His algorithm designs are at the heart of the software tools BLAST, Inheret, ANREP, and MacMolecule. Dr. Myers received a bachelors degree in mathematics from the California Institute of Technology in 1975 and a Ph.D. in computer science from the University of Colorado in 1981. Immediately thereafter he joined the faculty of the Department of Computer Science at the University of Arizona, where he became a full professor in 1991 and where he works today. De Witt Sumners Distinguished Research Professor Florida State University Tallahassee, Florida Dr. Sumner's professional interests are knot theory and scientific applications of topology, and his research activity includes knotting in random chains and topological models in molecular biology. Dr. Sumners initiated the development of the tangle model to analyze the

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Page 275 binding and mechanism of enzymes which alter the goemetry and topology of DNA. He has been a visiting professor at Kwansei Gakuin University in Japan and at the University of Geneva in Switzerland. He is a member of the Program in Mathematics and Molecular Biology at the University of California at Berkeley and has been a member of the Mathematical Sciences Research Institute, Berkeley and the Institute for Advanced Study, Princeton. Dr. Sumners received the B.Sc. degree in physics from Louisiana State University, Baton Rouge, in 1963 and the Ph.D. in mathematics (specializing in topology) from the University of Cambridge in 1967, where he was a Marshall Scholar. Dr. Sumners is a member of the editorial boards of the Journal of Knot Theory and Its Ramifications, Nonlinear World, and the Journal of Computational Biology. Simon Tavaré Professor of Mathematics and Biological Sciences University of Southern California Los Angeles, California Dr. Tavaré's scientific interests are in the application of probability and statistics to problems in population genetics, human genetics, and molecular evolution. He has held positions at the University of Utah and Colorado State University. Dr. Tavaré is a Fellow of the Institute of Mathematical Statistics. He received a Ph.D. in probability and statistics in 1979 from the University of Sheffield in England. Michael S. Waterman Professor of Mathematics and Biological Sciences University of Southern California Los Angeles, California Dr. Waterman's main scientific interests are in the application of mathematics, statistics, and computer science to molecular sequence data. He holds a USC Associates Endowed Chair and is a Fellow of the Institute of Mathematical Statistics and a Fellow of the American Association for the Advancement of Science. Dr. Waterman has held

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Page 276 positions at Idaho State University and Los Alamos National Laboratory. He received a Ph.D. in probability and statistics from Michigan State University in 1969. James H. White Professor, Department of Mathematics University of California Los Angeles, California Professor White's work involves the study of the geometric properties of curves and surfaces in three-space. It was in his thesis that he gave the first complete mathematical proof (outlined in the first part of Chapter 6 in this volume) that the linking number of the backbone strands of a closed circular DNA is equal to the twist of one of the backbone strands about the axis plus the writhing number of the axis. Because of this work, he was contacted in 1977 by Francis Crick at the Salk Institute to explain how the supercoiling of the axis of a DNA affected its topology. The answer to Crick's question is included in the second part of Chapter 6, having evolved over the years not only to applications to DNA but also to DNA-protein interactions. Professor White has been involved with mathematical applications to DNA for almost 18 years, assisting molecular biologists in many laboratories throughout the United States and Europe, including William Bauer at SUNY, Stony Brook and Nicholas Cozzarelli at the University of California, Berkeley. These collaborations have led to the development of the surface linking theory outlined in Chapter 6 and the applications of knot polynomial theory to recombination. Professor White is a founding member of the Program in Mathematics and Molecular Biology, a National Science Foundation project that has been established to further the advancement of the mathematical sciences in the field of molecular biology. As a member of this group, he has written many articles and has organized several conferences on the applications of geometry and topology to DNA and protein work. He is at the forefront of those encouraging young researchers to work in this new interdisciplinary field. He received a Ph.D. from the University of Minnesota in 1968 in the field of differential geometry.