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Appendix B Participant Biographies John C. Doyle (Workshop Chair) is professor of electrical engineering and control and dynamical systems at California Institute of Technology. His research interests are in integrating modeling, analysis, and design of uncer- tain nonlinear systems with applications throughout the aerospace and pro- cess-control industries and for complex networks in both engineering and biology. He received his BS and MS in electrical engineering from Massa- chusetts Institute of Technology in 1977 and his PhD in mathematics from the University of California, Berkeley in 1984. He has received the IEEE Centennial Outstanding Young Investigator Award (1984), the IEEE Hickernell Award (1976), the American Automatic Control Council Eckman Award (1983), and the Bernard Friedman Award (1984) and was an ONR Presidential Young Investigator and an NSF Presidential Young Investiga- tor. He was a coconvenor of the Second International Conference on Sys- tems Biology in Pasadena, California (20011. Patrick Dennis is program director of Genes and Genome Systems Cluster in the Division of Molecular and Cellular Biosciences at the National Science Foundation. His research interests have focused on aspects of biochemistry and molecular biology of ribosome synthesis and cell growth. In the last 15 years he has characterized the organization of rRNA and ribosomal pro- tein genes and the pathways for precursor rRNA processing and ribosome assembly and biogenesis in various halophilic and thermophilic archaeal species. Recently, he identified and biochemically characterized a novel class of small archaeal ribonucleoprotein machines that function in the assembly of ribosomal particles. In addition, he has continued a long-term interest in 31
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32 APPENDIX B the intimate relationship between ribosome synthesis and growth rate in Escherichia coli. Timothy Donobue is professor of bacteriology at the University of Wisconsin, Madison. His research interest is in deciphering the fundamental problem of biological energy generation. His laboratory analyzes the strat- egies that cells use to generate energy. Members of his laboratory are using the resulting information to dissect important metabolic activities of bacteria to identify new energy-generating pathways of agricultural, environmental, and medical importance and to design new types of microbial machines that can efficiently degrade toxic compounds, remove greenhouse gases, or synthesize biodegradable polymers. Frank Doyle is professor of chemical engineering at the University of California, Santa Barbara. His research focuses on nonlinear model-based control of complex nonlinear and distributed processes and the application of systems-engineering tools to problems in biology. The former topic is addressed with advanced simulation, optimization, and model-reduction methods, and the problems of interest span the chemical, pulp and paper, and pharmaceutical sectors. In systems biology, he uses traditional systems- engineering tools (such as mode! identification, parametric sensitivity, and closed-loop analysis) to analyze complex, hierarchic biological systems. Daniel Drell is biologist and program manager in the Human and Micro- bial Genome Program in the Life Sciences Division of the Department of Energy. He also manages the Ethical, Legal, and Social Issues Program and has spoken extensively on this topic. lames F. Fredrickson is Laboratory Fellow in the Environmental Microbiology Group at Pacific Northwest National Laboratory. Since joining Battelle- Northwest in 1985, he has focused his research efforts on the microbial ecology and biogeochemistry subsurface environments, using geochemical and molecular approaches. More recently, he has been investigating the geochemical and microbial factors that control the rate and extent of reduc- tion and dissolution of Fe oxides by Assimilatory iron-reducing bacteria. Integral to this research are investigations of the influence of the processes on the fate of inorganic contaminants, including uranium and technetium. Steven Gill is associate investigator at the Institute of Genomic Research. He is project leader of the Staphylococcus aureus genome project. His research interests include genomics of microbial pathogens, microbial patho- genesis and host interactions, gene regulation and protein networks, and cytoskeletal-based motility.
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APPENDIX B 33 Alan Hastings is professor in the Department of Environmental Science and Policy and a member of the Institute of Theoretical Dynamics and the Center for Population Biology at the University of California, Davis. His research interests include theoretical ecology (structure populations, and chaos) and theoretical population genetics (multilocus theory and quantitative genetic models). His current research projects focus on metapopulation dynamics, transients in ecological systems, fitting models to data in ecology, spatial dynamics in ecology (tussock moths and marine populations with mero- planktonic larvae), and hybrid zone dynamics. He received his PhD in applied mathematics from Cornell. He was president of the Society for Mathematical Biology in 1999-2001 and organizer of the NSF Workshop on Quantitative Environmental and Integrative Biology (20001. He also is managing editor of the Journal of Mathematical Biology, associate editor of Theoretical Population Biology, and a member of the editorial board of Mathematical Biosciences and served on the editorial board of Oecologia in 1997-2001. John C. Houghton directs programs in computational biology and selected aspects of the Genomes to Life research program and directs the Integrated Assessment of Global Climate Change research program in the Department of Energy (DOE) Office of Science. He is the point of contact in the Office of Science for the DOE hydrogen program. Matthew D. Kane is program director in the Division of Molecular and Cellular Biosciences at the National Science Foundation (NSF). His research interests range from specific study of the ecology and evolution of insect- microorganism to general aspects of the taxonomic, genomic, and physi- ological diversity of microorganisms. At NSF he manages or comanages a wide variety of programs that support microbial research, including Micro- bial Observatories and Microbial Interactions and Processes, the Interagency (NSF-US Department of Agriculture) Microbial Genome Sequencing Pro- gram, Biocomplexity in the Environment: Genome-Enabled Environmental Science and Engineering, and Assembling the Tree of Life. fared Leadbetter is assistant professor of environmental microbiology at the California Institute of Technology. His research seeks to clarify the form, function, and spatial distribution of diverse microorganisms in their environment. His studies have focused on the cultivation of microbial strains possessing unusual, atypical, or previously unrecognized properties and have sought to reveal the impact of these organisms on their environ- ment. He has applied a number of physiological, chemical, and molecular genetic techniques to his studies, underscoring the utility of both classical
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34 APPENDIX B and newly developed methods in the pursuit of fundamental questions in environmental microbiology. Derek R. Loviey is Distinguished University Professor and head of the Department of Microbiology at the University of Massachusetts, Amherst. He received his BA from the University of Connecticut and his MA from Clark University in biological sciences and his PhD from Michigan State University in microbiology. His research focuses on the physiology and ecology of novel anaerobic microorganisms. Current topics of investiga- tion include microbial metabolism and community structure in the deep subsurface and hydrothermal zones, evolution of anaerobic respiration, mechanisms of electron transport to Fe(III) and humic acids, anaerobic bioremediation of petroleum-contaminated subsurface and aquatic habitats, and bioremediation of metal contamination. These studies are being approached at the genetic, biochemical, and ecological levels. Michael Savageau is professor of bioengineering at the University of Cali- fornia, Davis. He received his PhD in cell physiology and systems science from Stanford University. His research interests are in quantitative theory of organizationally complex biological systems, generic nonlinear methods for mathematical and computer analysis, application of theory to specific classes of cellular and molecular networks, elucidation of biological design principles, and design and construction of novel gene circuits. He was a Guggenheim Fellow and Fulbright Senior Research Fellow at the Max- Planck Institut fur Biophysikalische Chemie in Gottingen and is a Fellow of the American Association for the Advancement of Science. He has served or serves in an editorial role for Mathematical Biosciences, Journal of Theo- retical Biology, Mathematical Ecology and Evolution Series, Biocomplexity, and Nonlinear World. Gary S. Sayler is professor of microbiology and ecology and evolutionary biology and director of the Center for Environmental Biotechnology at the University of Tennessee, Knoxville. His major research interests include ecological and toxicological impact of environmental contaminants on micro- bial communities, biodegradative mechanisms, plasmids and transposons, the application of molecular methods in analysis of biodegradative micro- bial community structure and function, and genetic-engineering strategies for biodegradative and biosensing organisms. Thomas M. Schmidt is associate professor of microbiology at Michigan State University. His interests and expertise are in microbial physiology and ecology, organization and activity of microbial communities, relation- ships between genes, genomes, and ecologic strategies of microorganisms.
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APPENDIX B 35 Research in his laboratory focuses on microbial physiology and ecology. Members of his laboratory routinely develop and apply techniques of molecular biology to explore the diversity of microbial communities with- out the bias potentially introduced by cultivation methods. Hal Smith is professor of mathematics at Arizona State University. His research interests include differential equations, dynamical systems, and mathematical biology. He is studying dynamical systems in biology. Eberhard O. Voit is professor in the Department of Biometry and Epidemi- ology and the Department of Biochemistry and Molecular Biology at the Medical University of South Carolina. He is in charge of bioinformatics and systems biology. His research interests focus on the analysis of organi- zationally complex biomedical systems, particularly metabolic pathways. He uses biochemical systems theory defined by highly structured sets of nonlinear ordinary differential equations to study complex systems that are characterized by numerous components that interact in a nonlinear fashion and can exhibit emerging responses not possible in smaller sub- systems. Their function and design can be fully understood only if they are represented and analyzed mathematically and computationally. Lyle Whyte is associate professor in the Department of Natural Resource Sciences at McGill University, Canada. Prior to joining McGill University, he was research officer at the National Research Council of Canada. He received his BSc from the University of Regina, Canada, and his PhD from the University of Waterloo, Canada. His research interests include genetics, physiology and ecology of cold-adapted microorganisms able to degrade a variety of pollutants at cold temperatures, polar microbial ecology and biodiversity, and development of genome-based tools and their applications for studying microbial ecology. lizbong Thou is distinguished scientist and director for the Environmental Microbial Genomics Program at Oak Ridge National Laboratory. He received a BS in plant pathology and entomology, MS in mathematical ecology, and PhD in molecular genetics and cell biology. His research focuses on microbial functional genomics, genomics technology, and mi- crobial ecology. He received the Presidential Early Career Award for Scien- fists and Engineers in 2001, and the Environmental Sciences Division Dis- tinguished Scientific Achievement Award in 2001. He has authored more than 80 publications on molecular biology, molecular evolution, microbial ecology, bioremediation, and theoretical ecology. He chaired the 7th, 9th and 11th International Conference on Microbial Genomes.
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36 Observer Karl Koehier, National Science Foundation Staff Evonne Tang Robin Schoen Fran Sharples Bridget Avila Danielle Greene Science writer Patricia McAdams APPENDIX B
Representative terms from entire chapter: