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About the Editors

Andreas D. Baxevanis, Ph.D. is the Deputy Director for Intramural Research and the Director of the Computational Genomics Program at the National Human Genome Research Institute, National Institutes of Health. He is currently the editor-in-chief of Current Protocols in Bioinformatics, senior editor of Molecular Cancer Therapeutics, and associate editor of Proteins: Structure, Function, and Bioinformatics. His involvement in educational activities include teaching bioinformatics at The Johns Hopkins University, serving as adjunct faculty at Boston University, lecturing in numerous courses, and developing materials intended to facilitate the use of genomic sequence data. He is the recipient of the Bodossaki Foundation's 2000 Academic Prize in Medicine and Biology.


B. F. Francis Ouellette, M.Sc. is Director of the University of British Columbia Bioinformatics Centre and Director for the Canadian Genetic Disease Network (CGDN) Bioinformatics Facility, where he coordinates the Canadian Bioinformatics Workshop series. His research includes work on the Biomolecular Interaction Network Database (BIND), development of gene prediction tools, and use of comparative genomics approaches to help identify human genes. Dr. Ouellette has worked on yeast genome sequencing and analysis, and has previously served as GenBank coordinator at the National Center for Biotechnology Information (NCBI), NIH.

About the Chapter Authors

Rolf Apweiler, Ph.D. is Head of the Sequence Database Group at the European Bioinformatics Institute. He is currently a member of the editorial boards of the European Journal of Biochemistry, Proteomics, and Biochimica et Biophysica Acta.

Gary D. Bader, Ph.D. is currently a post-doctoral fellow in the lab of Dr. Chris Sander at the Computational Biology Center at Memorial Sloan-Kettering Cancer Center in New York City. Previously, Dr. Bader completed a Ph.D. in the lab of Dr. Christopher Hogue in the Department of Biochemistry at the University of Toronto and the Program in Proteomics and Bioinformatics at the Samuel Lunenfeld Research Institute at Mount Sinai Hospital in Toronto. His thesis was the development and research use of the Biomolecular Interaction Network Database (BIND).

Geoff Barton, Ph.D. is Professor of Bioinformatics at the School of Life Sciences, University of Dundee, and Co-Director of the Post Genomics and Molecular Interactions Centre. Dr. Barton obtained his doctorate in the Department of Crystallography, Birkbeck College, University of London, and then spent two years as an ICRF Fellow working with Chris Rawlings at the Imperial Cancer Research Fund Labs in London. In 1989 he was awarded a Royal Society University Research Fellowship to work in the Lab of Molecular Biophysics, University of Oxford. Since that time Dr. Barton has held posts as Head of Genome Informatics at the Wellcome Trust Centre for Human Genetics (1995-1997), Research and Development Team Leader at the EMBL European Bioinformatics Institute (1997-2001), and Head of the European Macromolecular Structure Database at EBI (1998-2001) before taking up his present appointments in 2001. Dr. Barton has published over 50 papers about computational protein sequence and structure analysis in refereed journals as well as around 20 book chapters and other contributions. Software developed by his group is widely distributed and in daily use in many research laboratories worldwide.

Enrique Blanco is a computer engineer at Universitat Politècnica de Catalunya, Spain, finishing his Ph.D. thesis in the Genome Bioinformatics Laboratory from Institut Municipal d'Investigació Mèdica-Universitat Pompeu Fabra in Barcelona, Spain. He works in the design of new algorithms of sequence alignment for the detection and characterization of the gene promoter regions. He has been involved in many educational activities, including teaching bioinformatics in numerous courses, and developing materials to facilitate the understanding of bioinformatics for undergraduates, graduates, and Ph.D. students from other disciplines.

Gerard G. Bouffard, Ph.D. is the Director of the Bioinformatics Group of the National Institutes of Health Intramural Sequencing Center (NISC) where he oversees data generation, management and analysis for this high-throughput DNA sequencing facility. His graduate work in mapping and sequencing in the E. coli genome evolved into post-doctoral research in physical mapping of human chromosome 7 and interest in comparative genomics.

Fiona S. L. Brinkman, Ph.D. is an Assistant Professor in Molecular Biology and Biochemistry at Simon Fraser University. She is also Research Director of the Genome Canada Pathogenomics Project, Coordinator of the Pseudomonas Community Genome Annotation Project, and a Core Faculty for the Canadian Bioinformatics Workshops. She has won numerous career awards for her evolutionary infectious disease and bioinformatics research, including being the only Canadian professor listed as one of the "Top 100 of the World's Young Innovators in Technology" in 2002 by the Massachusetts Institute of Technology, the 2003 Science Council of BC Young Innovator award, and Canada's "Top 40 Under 40" for 2003-2004. She has a strong interest in bioinformatics education through development of both graduate and undergraduate curricula and she developed the first undergraduate bioinformatics joint major program (computing science and molecular biology and biochemistry) in Canada.

Anton J. Enright, Ph.D. is a Research Group Leader at the Wellcome Trust Sanger Institute in Cambridge, United Kingdom. Previously he worked at the Computational Biology Center at Memorial Sloan-Kettering Cancer Center, New York and completed his EMBL and Cambridge University predoctoral fellowship at the European Bioinformatics Institute (EBI) in Cambridge, United Kingdom.

Morgan C. Giddings, Ph.D. is an Assistant Professor in the Departments of Microbiology and Immunology and Biomedical Engineering at the University of North Carolina at Chapel Hill. He is a founding member of the UNC-CH training program in bioinformatics and computational biology, computational advisor to the Michael Hooker Proteomics Core at UNC, and a member of the Carolina Center for Genome Sciences. He is the recipient of an NIH/NHGRI Genome Scholar Career Development award. His research applies both computational and laboratory science to examine how genomes encode proteomic diversity.

Roderic Guigó i Serra, Ph.D. leads the Genome Bioinformatics Laboratory at the Institut Municipal d'Investigació Mèdica in Barcelona. He is also Professor at the Universitat Pompeu Fabra, and coordinates the Bioinformatics and Genomics program within the recently created Center for Genomic Regulation. His research focuses on computational gene prediction. He is author of one of the first general purpose gene finding programs, and he has contributed to the development of standards for the evaluation of the accuracy of gene prediction programs. He has also participated in the analysis consortiums of numerous eukaryotic genomes.

Nancy Fisher Hansen, Ph.D. is a Member of the Bioinformatics group at the National Institutes of Health Intramural Sequencing Center. She designs, implements, and modifies software tools to facilitate the generation and analysis of Ordered and Oriented sequence data. She received her doctorate in physical chemistry from Stanford University, and subsequently worked as a software developer at the Stanford Genome Technology Center.

Mark Holmes is a Bioinformatics Developer in the Department of Microbiology & Immunology at the School of Medicine, University of North Carolina at Chapel Hill. His professional computing experience began in 1974 and includes early work automating his own experimental protocols at the Clinical Center of the U.S. National Institutes of Health. A former art historian and museum registrar, he worked for many years in the private sector as a senior computing consultant before returning to academic life in 2000.

David H. Mathews, M.D., Ph.D. is an Assistant Professor of Biochemistry and Biophysics in the Center for Human Genetics and Molecular Pediatric Disease at the University of Rochester Medical Center. He is the author of RNAstructure, a software package for analyzing RNA secondary structure on Windows.

Tara C. Matise, Ph.D. is Associate Professor in the Department of Genetics at Rutgers University in New Jersey. She runs the Laboratory of Computational Genomics, serves on the editorial board of Genome Research, has previously served on the Board of Scientific Counselors for the National Institute of Biotechnology Information (NCBI), National Institutes of Health (NIH), and was previously a HUGO editor for human chromosome 1.

James C. Mullikin, Ph.D. is an Associate Investigator within the Genome Technology Branch of the National Human Genome Research Institute, National Institutes of Health. Prior to joining NHGRI, Dr. Mullikin served as the Head of production software development from 1988-2002 at the Sanger Institute, where he also served as Acting Director of Informatics in 2002. He has been involved in polymorphism discovery and analysis methods since the beginning of The SNP Consortium project in 1999 while at the Sanger Institute.

Yanay Ofran, Ph.D. is a Research Fellow at Columbia University Bioinformatics Center (CUBIC) in the Department of Molecular Biophysics and Biochemistry. He is the developer of several tools and web servers for sequence analysis and prediction. His educational activity includes teaching bioinformatics and computational biology at Columbia University. He is the recipient of the 2002 Freund Memorial Prize.

B. F. Francis Ouellette, Ph.D. is Director of the University of British Columbia (UBC) Bioinformatics Centre and Associate Professor in Medical Genetics and the Michael Smith Laboratories at UBC. He is also the Director for the Canadian Genetic Diseases Network (CGDN) Bioinformatics Core Facility, where he coordinates the Canadian Bioinformatics Workshop series. He works in comparative genomics and in building tools and databases for bioinformatics analyses. He has previously served as GenBank coordinator at the National Center for Biotechnology Information (NCBI), National Institutes of Health (NIH).

John Quackenbush, Ph.D. is an Investigator in Functional Genomics and Bioinformatics at The Institute for Genomic Research (TIGR) in Rockville, Maryland. He also holds appointments as Professor of Biochemistry at The George Washington University, as Adjunct Professor of Biostatistics at the Bloomberg School of Public Health at The Johns Hopkins University, and as Adjunct Professor of Chemical Engineering at the University of Maryland. Dr. Quackenbush has organized and taught many workshops and courses on DNA microarray analysis and has authored a book (with Helen Causton and Alvis Brazma) as well as numerous articles in the subject. Among other accomplishments, he and his group build the TIGR Gene Index databases, including RESOURCERER and are responsible for the freely-available, open-source TM4 software package for DNA microarray analysis. He is also actively involved in the Microarray Gene Expression Data society (MGED), which has been developing standards for microarray data reporting.

Kevin R. Ramkissoon, BSc. is a doctoral graduate student in the department of Microbiology & Immunology at the University of North Carolina at Chapel Hill. His current research interests include the development proteomic and bioinformatic methods to study viral and prokaryotic evolution with a focus on antimicrobial drug resistance, pathogenicity, and immune response evasion.

Burkhard Rost, Dr. rer. nat. is an Associate Professor in the Department of Biochemistry and Molecular Biophysics at Columbia University. Since obtaining his doctorate at the Institute of Theoretical Physics, Heidelberg, Dr. Rost held posts at EMBL Heidelberg (1990–1994), EBI Cambridge (1995), EMBL Heidelberg (1996–1998), and LION Biosciences (1998) before taking up his present appointment in 1999. His group focuses on methods for predicting protein structure and function from sequence, primarily in the context of entirely sequenced organisms. Dr. Rost has given 93 invited lectures in 16 countries, has had over 100 papers published that have been quoted over 5,000 times, and has been responsible for PredictProtein, one of the first web servers in molecular biology.

Stephen T. Sherry, Ph.D. is Staff Scientist at the National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), where he supervises the dbSNP database of genetic variation and directs the development of open-source software tools for quality assessment of DNA forensic data. He received the Library's Board of Regents Award for Scholarship or Technical Achievement in 2003 for his advisory role in applying computational forensic methods to help identify victims of the September 11, 2001 tragedy of the World Trade Center in New York City.

Lincoln D. Stein, M.D., Ph.D. is an Associate Professor at the Cold Spring Harbor Laboratory, where he works on genome databases. He teaches bioinformatics and genetics at the Watson School for Biomedical Sciences, and was recently awarded the Benjamin Franklin prize for service to bioinformatics.

Pamela Jacques Thomas, Ph.D. is a Member of the Bioinformatics Group at the National Institutes of Health Intramural Sequencing Center (NISC) where she focuses on the assembly and annotation of BAC-derived sequences from multiple vertebrates. She received her doctorate from Case Western Reserve University and previously worked as a GenBank Scientific Data Analyst at the National Center for Biotechnology Information (NCBI), National Institutes of Health (NIH).

Peter S. White, Ph.D. is a Research Assistant Professor in the Department of Pediatrics at the University of Pennsylvania, and in the Division of Oncology, Children¹s Hospital of Philadelphia (CHOP). Dr. White holds the David Lawrence Altschuler Endowed Chair in Genomics and Computational Biology at CHOP. He is a member of Penn’s Center for Bioinformatics and Penn¹s Genomics Institute, and he is the Faculty Director of CHOP¹s bioinformatics core facility.

David S. Wishart, Ph.D. is a Professor of Biological Sciences and Computing Science at the University of Alberta. He also holds the Bristol Myers Squibb Chair in protein chemistry and is a Senior Research Officer with the National Institute for Nanotechnology (NINT) in Edmonton. In addition to starting two bioinformatics companies (BioTools and Chenomx) in the 1990's, Dr. Wishart has been actively involved in teaching bioinformatics for nearly a decade, including several undergraduate and graduate courses at the University of Alberta. He has been a principal instructor for numerous week-long training workshops offered through the Canadian Bioinformatics Workshop series (CBW), the Canadian Proteomics Initiative (CPI) and Genome Canada (ACGC).

Tyra G. Wolfsberg, Ph.D. is an Associate Investigator and the Associate Director of the Bioinformatics and Scientific Programming Core at the National Human Genome Research Institute, National Institutes of Health. She lectures and publishes extensively on using bioinformatics tools, especially online genome browsers, to mine genomic sequence information.

Michael Zuker, Ph.D. is a Professor of Mathematical Sciences and Biology at Rensselaer Polytechnic Institute. He works on the development of algorithms to predict folding, hybridization and melting profiles in nucleic acids. His educational activities include developing and teaching his own bioinformatics course at Rensselaer, and participating in both a Chautauqua short course in bioinformatics for college teachers and an intensive bioinformatics course at the University of Michigan.