Stephen F. Altschul, PhD
Stephen Altschul is a Senior Investigator at the National Center for Biotechnology Information, which is part of the National Library of Medicine at the National Institutes of Health. He received his AB summa cum laude in mathematics from Harvard College and a PhD in mathematics from the Massachusetts Institute of Technology.
Figure 1.
Dr. Altschul held an IRTA postdoctoral fellowship at the Mathematics Research Branch of the National Institute of Diabetes and Digestive and Kidney Diseases before moving to the NCBI, where he has been for the past 12 years. His research has focused on developing measures, algorithms, and statistics for the comparison and analysis of DNA and protein sequences. He played a central role in developing the blast and psi-blast sequence database search programs, and his articles describing these programs have become, respectively, the most cited scientific papers published since 1990 and 1995.
Dr. Altschul has served on grants committees for the National Human Genome Research Institute of the NIH and for the Medical Research Council of Canada. He has been a member of the editorial boards of Protein Sequences & Data Analysis, Gene-combis, and Genome Biology and is invited to be a keynote speaker at the Tenth Annual Conference on Intelligent Systems for Molecular Biology.
Dennis Benson, PhD
Dennis Benson is Chief of the Information Resources Branch at the National Center for Biotechnology, National Library of Medicine. Dr. Benson received his undergraduate and graduate degrees in the neuroscience program at the University of Florida.
Prior to his current position, Dr. Benson was a postdoctoral fellow in the Department of Biomedical Engineering, Johns Hopkins School of Medicine, where his research focused on the neurophysiology of the auditory cortex. He came to the Lister Hill Center for Biomedical Communications at the NLM in 1980 and worked on knowledge-based retrieval systems in the area of hepatitis and toxicology.
Figure 2.
He developed a test bed for evaluating statistical-based text retrieval algorithms, which evolved into an operational text retrieval system known as IRX. Early applications of IRX included the McKusick Mendelian Inheritance in Man database and a seminal integrated genetics data resource known as GenInfo. With the creation of the NCBI in 1988, he has had responsibility for designing and managing the computing and network infrastructure for research and public access to the information resources NCBI produces—in particular, the Gen Bank, Entrez, and PubMed databases.
Mark S. Boguski, MD, PhD
Mark Boguski is Senior Vice President for Research and Development at Rosetta Inpharmatics, Inc. He received his BA in natural sciences from Johns Hopkins University and his MD and PhD in molecular biology from the University of Washington. He was a resident in anatomic pathology at Barnes, Children's and Jewish Hospitals and a medical staff fellow at the Mathematical Research Branch of the National Institute of Diabetes and Digestive and Kidney Diseases at the National Institutes of Health.
Dr. Boguski spent 11 years at the National Center for Biotechnology Information at the National Library of Medicine, rising from Senior Staff Fellow to Senior Investigator. Early in his career, he studied the organization and biological importance of repeated sequences in nucleic acids and proteins. He developed analytic methods to trace the molecular evolution of proteins from related species. At NCBI, he was instrumental in the design and implementation of a database system for representing expressed sequence tags. More recently, he led the development of several prototype database systems for storing and analyzing microarray-derived gene expression data.
Dr. Boguski has served as Editor of Genomics and is a member of the Board of Reviewing Editors of Science. He is recipient of the Regents Award of the NLM and the NIH Director's Award.
Douglas L. Brutlag PhD
Douglas Brutlag is Professor of Biochemistry and Biomedical Informatics (by courtesy) at Stanford University. He also serves as Honorary Professor of Bioinformatics at Keio University, Japan. He received a BS from the California Institute of Technology with honors and his PhD in biochemistry from Stanford University with great distinction.
Figure 3.
Dr. Brutlag was a cofounder of the first bioinformatics firm, IntelliGenetics, and one of the first artificial intelligence firms, IntelliCorp, in 1980. Dr. Brutlag has served as coinvestigator on the Bionet National Computer Resource (1982–87), funded by the National Institutes of Health, and the NIH Genbank Resource (1987–92), which first brought molecular biology databases to the Internet. His primary interest is deciphering the information encoded in the genome. His group has developed methods to discover DNA motifs that encode regulatory signals controlling gene expression (http://bioprospector.stanford.edu). These motifs can be used to help understand the control of regulation of genes both during development, disease, and aging. His group has also developed methods that discover functional sites in protein sequences (http://motif.stanford.edu/emotif/ and http://motif.stanford.edu/ematrix/). These protein motifs can be used to discover the function of new genes and also to identify and validate potential drug targets for the pharmaceutical industry. These protein motifs have been successful at predicting the function of over 70 percent of the genes in the human genome.
Dr. Brutlag serves on the editorial board of the Journal of Computational Molecular Biology. He was a cofounder of the International Society of Computational Biology and has co-organized two of their annual meetings (Intelligent Systems for Molecular Biology). He was awarded the ComputerWorld-Smithsonian Award in Science for his contributions to the NIH Genbank Resource.
Stephen H. Bryant, PhD
Stephen Bryant is a Senior Investigator at the Computational Biology Branch of the National Center for Biotechnology Information at the National Library of Medicine. He received his BA in chemistry and English from the University of Virginia and a PhD in biophysics from Johns Hopkins University.
Figure 4.
Dr. Bryant's previous positions include research officer in the Department of Crystallography at Birkbeck College at the University of London; senior research associate, protein databank at Brookhaven National Laboratory; and research scientist, Wadsworth Center for Laboratories and Research, New York State Department of Health.
At NCBI, he leads the structural biology group, one of the leading research teams in development of comparative analysis algorithms for three-dimensional structure data. Some of the team's accomplishments include development of sequence-structure threading methods, which use structural data to improve recognition of distant homology relationships. Their success was demonstrated by prediction of the Leptin structure in 1995, and in the 1998 CASP structure prediction competition, the Bryant team was awarded first place in the prestigious fold-recognition category. They have developed novel methods for structure–structure comparison. Their algorithms employ rigorous statistical tests and are fast enough to allow all-against-all “neighboring” of the structural database. These data, available through NCBI's Entrez service, allow biologists to identify conserved structural features in protein families. In addition, the team designs and maintains the database and software systems that incorporate structure data and comparative analysis results into NCBI's information retrieval systems. The Cn3D molecular graphics viewer, distributed with Entrez, allows biologists to view simultaneously structures, sequences, and sequence–structure alignments.
Lisa Cannon Albright, PhD
Dr. Albright is Director of Genetic Epidemiology, a division of the Medical Informatics Department at the University of Utah. Professor Albright also founded the Genetic Research Group at Intermountain Healthcare, Inc. in 1995, and has served as its director since its inception. She received an MS in biostatistics and a PhD in medical informatics from the University of Utah, Salt Lake City, Utah, where she has served since 1988.
Figure 5.
Dr. Albright is an excellent contributor to the field of bioinformatics. She has made major contributions to the use of clinical information systems along with computerized genealogical records to detect family relationships to diseases. Using these family relationships, she has been able to contact families and obtained permission to use blood samples to search for specific disease entities. She works as the leader of a team, initially started by Mark H. Skolnick, PhD, which has found two breast cancer genes, BRCA1 and BRCA2, and a prostate cancer gene.
Dr. Albright was involved in the studies that identified the first melanoma gene, the first two breast cancer genes, and the first prostate cancer gene. She is a genetic epidemiologist whose primary research concentration is in the analysis of common disorders that appear to have a genetic component. Her research utilizes computerized medical/health records that are record-linked to a genealogical database. The analysis of the linked medical diagnoses to genealogical records can allow clarification of the genetic component of disease. These data are analyzed to identify a genetic component for a particular disease or subset of individuals with particular disease characteristics. The data are also used to ascertain the high-risk families, to study record linkages being expanded to include clinical data, to allow further characterization of cases, and to pursue analysis of drug response.
Dr. Albright is a member of the American Association for the Advancement of Science, the American Association for Cancer Research, the American Society for Bone and Mineral Research, the American Society of Human Genetics, and the International Genetic Epidemiology Society. She serves on the Scientific Advisory Board for Intermountain Heart Study at LDS Hospital, the LDS Hospital Research and Administration Committee, the Intermountain Health Care Family Health Database Oversight Committee, and the International Consortium on Prostate Cancer Genetics. She also served on the Myriad Genetics, Inc. Scientific Advisory Board from 1997 through 2000.
Homer L. Chin, MD, MS
Homer Chin is the Medical Director for Clinical Information Systems at Kaiser Permanente Northwest and Assistant Professor in Medical Informatics and Outcomes Research at the Oregon Health and Sciences University. Dr. Chin received his BS degree with highest honors in bioengineering from the University of California, Berkeley, and his MD from Dartmouth Medical School. He completed residency training in internal medicine at the Santa Clara Valley Medical Center in San Jose, California, and a postdoctoral fellowship in medical informatics at Stanford University.
Figure 6.
In 1988, he joined Kaiser Permanente in Northern California, where he worked on strategic planning for information systems and was the clinician leader in the development of a centralized clinical data repository for the Kaiser Permanente Northern California Region. In 1992, he was recruited to his present position to lead the clinical information systems effort in Kaiser Permanente Northwest. He is board-certified in internal medicine and continues to maintain an active part-time medical practice.
His areas of interests include the development, implementation, and evaluation of clinical information systems, confidentiality of electronic patient information, optimization of the computer–clinician user interface, and the development and use of data repositories in health care. His fundamental interest is in the development and implementation of information systems that, by improving the efficiency and quality of health care delivery, support the overall clinical and business needs of a health care organization.
Kaiser Permanente Northwest embarked on the implementation of a comprehensive outpatient computer-based patient record in 1993 and completed their implementation in 1997. Kaiser Permanente won the 1998 Nicholas E. Davies CPR Recognition Award of Excellence, the 1999 Voh's Award for Quality Innovation, and the 2000 American Medical Group Association Acclaim Award, for work done in implementing the computer-based patient record.
Dr. Chin was a board member of Intel's Internet Initiative, a board member of the Oregon HIMSS Chapter, and the Program Chair for the CPRI Davies Recognition Award in 2001.
Fred E. Cohen, MD, DPhil
Fred Cohen is a Professor of Cellular and Molecular Pharmacology, Medicine, and Biochemistry and Biophysics at the University of California, San Francisco, and a partner at Texas Pacific Group. Dr. Cohen received his BS in molecular biochemistry and biophysics from Yale University, DPhil in molecular biophysics from Oxford University, and MD from Stanford Medical School. He completed a postdoctoral fellowship, medical residency and endocrinology fellowship at the University of California, San Francisco. In addition, he served as Chief of the Division of Endocrinology and Metabolism at UCSF for four years.
Figure 7.
Dr. Cohen is best known for his work in computational biology. He has used the computer as an experimental tool to explore the relationships between protein sequence and structure and gone on to use these relationships as a starting point for drug design efforts. The hallmark of these efforts has been the close connection between computation and experiment. More recently, Dr. Cohen and Dr. Stanley Prusiner have collaborated to investigate the molecular basis of prion replication. This work has led to our understanding of the prion diseases as diseases of protein folding. In the last few years, this insight has catalyzed their work on the development of novel diagnostic tests and therapeutic interventions for prion disease.
Dr. Cohen has been the recipient of many awards, including a Rhodes Scholarship, a Searle Scholars Junior Faculty Award, the Richard E. Weitzman Young Investigator Award from the Endocrine Society, the Young Investigators Award from the Western Society for Clinical Investigation, the Louis Vuitton-Moet Hennessey Prix d'Honneur Award, shared with Stanley Prusiner, for their work on prion diseases, recognition as one of 40 Under-40 in the Bay Area by San Francisco Focus Magazine, and the Burroughs Wellcome New Initiatives in Malaria Award, shared with Joe DeRisi. He has served on many committees, including the Rhodes Scholarship Selection Committee, a National Science Foundation Committee on Computational Biology, NIH Study Sections including service as a permanent member, vice-chair, and chair of the Molecular and Cellular Biophysics Study Section, the Advisory Committee of the Structural Biology Program of the Academia Sinica, and the nominating committee of the Protein Society.
Dr. Cohen has played significant roles with several journals, as an editor of the Journal of Molecular Biology and Folding and Design and as an editorial board member for Protein Engineering, Perspectives in Drug Discovery and Design, Journal of Computational Biology, and Molecular Medicine. He has given several eponymous lectures, including the Genetics Institute Lecture at the Dana Farber Cancer Institute, the Ninth and Tenth Annual Roland D. Pinkham, MD, Basic Science Lectures at the University of Washington, the Frederic M. Richards Lecture in Molecular Biophysics and Biochemistry at Yale University, and the J. Lawrence Oncley Lecture in Biophysics at the University of Michigan. Dr. Cohen has been elected as a Fellow of the American College of Physicians and as a member of the American Society for Clinical Investigation, the Western Association of Physicians, and the Association of American Physicians.
Ted Cooper, MD
Ted Cooper is the National Director of Confidentiality and Security at Kaiser Permanente. He is also an Associate Clinical Professor of Ophthalmology at the Stanford University School of Medicine. He received a BA and MD from George Washington University and completed a residency in ophthalmology there. He is a Fellow of the American Academy of Ophthalmology.
Figure 8.
Previously, Dr. Cooper served as the Associate Director for Medical Information Systems for Kaiser Permanente Northern California, where he sponsored the development and implementation of numerous large-scale clinical information systems.
Dr. Cooper's primary interest in medical informatics is privacy and security. He has worked to advance standards in this area as the chairperson of the American Society for Testing and Materials Subcommittee E31.20, Data and Systems Security for Health Information, and as a leader of Work Group 4 on Security of the U.S. Technical Advisory Group to the International Organization for Standardization Technical Committee 215 Health Informatics. At AMIA he has supported privacy and security as a member of its Internet Working Group and Public Policy Committee. He participated in the development of the AMIA guidelines for e-mail and has presented several AMIA tutorials on privacy and security.
Dr. Cooper has been active in the Computer-based Patient Record Institute since it was founded. He was its Board of Directors Chairperson in 1998, has chaired its Work Group on Privacy and Security, and led the development the “CPRI Toolkit: Managing Information Security in Health Care.” He is a commissioner of The Electronic Healthcare Network Accreditation Commission. He serves on the editorial advisory boards for the Report on Patient Privacy and the American Health Information Managers Association publication In Confidence.
Joachim W. Dudeck, PhD
Joachim W. Dudeck is Professor and Head of the Department of Medical Statistics, University Hospital Giessen, Germany. He received his MD from University of Heidelberg. He received additional training in physiology, internal medicine, medical statistics, and informatics at the Universities of Erlangen and Mainz and a habilitation in medical statistics and documentation at the University of Mainz.
Figure 9.
Dr. Dudeck's early work involved recognition process of positions of sounds and noises by the ear. He applied statistical methods in medicine, in particular to the multivariate analysis of variance in classification. In the late 1970s, he developed an automatic ECG program based on the Pipberger Program, a spelling checker as powerful as the system now used in Word, and a fault-tolerant network of minicomputers at Giessen University hospital.
Dr. Dudeck's research on the application of knowledge-based functions in hospital systems included implementation and adaptation of the HELP system to the environment of German hospitals; development of the comprehensive, knowledge-based hospital information system WING (knowledge-based information network at Giessen); development of a clinical workstation for oncology and cancer registries (Giessener Tumor Dokumentationssystem, CTDS), which is now in use in nearly 40 cancer registries and comprehensive cancer centers in Germany; and structuring of clinical guidelines using XML.
He served as member of the Commission on Computer Systems of the German Research Council between 1989 and 1995; as Chairman of the Section of Medical Informatics of the German Association for Medical Informatics, Biometry and Epidemiology 1995 to 1998; Founder and Chairman of the HL7 User Group in Germany since 1993; Member of the Board of Directors of HL7 USA as representative of the international affiliates, 1997 to 1999; and Chairman of the CEN TC 251 Task Force on XML Application in Healthcare.
Andrew Friede, MD, MPH
Andrew Friede joined Cerner Corporation in 1997 and serves as a Physician Executive. He completed his medical training at Johns Hopkins (MD, 1981), an internship in pediatrics at the Children's Hospital of Pittsburgh, and a residency in preventive medicine at Harvard School of Public Health (MPH, 1984).
Figure 10.
Cerner is a worldwide provider of clinical and management information systems and services to healthcare. Dr. Friede's current focus is on developing research products, often in collaboration with Cerner clients, to evaluate the impact of information systems in transforming health care. In particular, he is interested in the development of new database systems for genomics, the design of expert systems for pneumonia, heart failure, anti-retroviral drugs, and pressure ulcers; and using clinical data to study outcomes and improve safety. He also helps health care organizations strategize about their future information system needs, and collaborated on the installation and custom configuration of Cerner's products. His particular area of consulting interest is in developing information systems for research.
In 1984, he joined the Epidemic Intelligence Service at the Centers for Disease Control and Prevention, and stayed on as a medical epidemiologist. In 1987, he joined CDC's Information Resources Management Office, where he led a large group in the development of CDC Wonder, an integrated information and communications system that provides access to some 30 databases for 20,000 users and provides specialized features used by many CDC surveillance programs. CDC Wonder, uses a novel systems architecture that was specifically developed for public health information systems by the CDC Wonder team and includes specialized end-user communication and graphing software. Dr. Friede also served as a principal participant in the CDC INPHO (Information Network for Public Health Officials) project, which aims to develop a national information network for public health. The first stage of INPHO was the development of a statewide network in Georgia, funded by a $5.2 million grant from the Woodruff Foundation.
Dr. Friede has served as a consultant to the United Nations for family planning and clinical information systems in Madagascar and to the World Bank on statistical and information systems for China; he was the chief editor of the CDC Prevention Guidelines and has served on innumerable CDC and National Library of Medicine special emphasis panels. From 1998 to 2000, he served on the National Academy of Sciences/IOM workgroup, which produced the report “Networking Health: Prescriptions for the Internet.”
Peter Haug, MD
Peter Haug is the Director of Medical Informatics for the Urban Central Region, a three-hospital group of Intermountain Health Care. He is currently housed at the LDS Hospital in Salt Lake City, Utah. He is also an Associate Professor of Medical Informatics at the University of Utah and serves as adjunct faculty for the School of Nursing Informatics Program. He received a BA in mathematics and MD degree from the University of Wisconsin. Subsequently, he completed a residency in internal medicine at the LDS Hospital and a fellowship in medical informatics at the University of Utah.
Figure 11.
Dr. Haug's principal interests lie in the areas of medical information systems, medical decision support, and natural language processing. During his career, he has contributed to the development of the HELP system, a pioneering hospital information system, and has worked for a number of years in the area of applied decision support. He has been a participant in the development of the Arden Syntax for representing medical logic, first during its formulation as a produce of the American Society for Testing and Materials and, subsequently, within the responsible Health Level 7 committees. He remains an active member of the HL7 committees seeking to extend Arden and is a participant in HL7 committees seeking to develop a standard for authoring and exchanged medical guidelines. In addition, Dr. Haug has integrated a research interest in statistical decision making into his natural language research. The result has been a novel NLP approach, featuring a semantic component based in Bayesian statistics. Dr. Haug continues to focus a large segment of his time and effort on training new informaticians. He directs the Health Information Systems track in the University of Utah's informatics program and has contributed to a number ofinformatics training efforts, including the National Library of Medicine's informatics course at the Marine Biological Laboratory, Woods Hole, Massachusetts, from 1992 through 1995.
William T. Hole, MD
William Hole is Research Medical Officer for the Unified Medical Language System Metathesaurus at the National Library of Medicine. He received his BA in chemistry from Earlham College in Indiana and his MD from Ohio State University. He completed a residency in pediatrics at Mount Zion Hospital and Medical Center in San Francisco and a postdoctoral fellowship in child psychiatry and academic pediatrics at Stanford University.
Figure 12.
Dr. Brown was Assistant Professor in Pediatrics at Brown University and Director of Information Science at Bradley Hospital. His early work included direct computer recording of the physiology and behavior of premature infants in the neonatal intensive care unit. Since his arrival at the National Library of Medicine, Dr. Hole has been deeply involved in the UMLS. He has been responsible for the design, creation, and release of 13 annual editions of the Metathesaurus, the largest of the three UMLS Knowledge Sources. Since the initial 1990 experimental release, the Metathesaurus has grown to contain and relate more than 800,000 concepts containing terms from more than 60 biomedical vocabularies, including the current and proposed HIPAA standard terminologies.
Lawrence Hunter, PhD
Lawrence Hunter is the Director of the Center for Computational Pharmacology at the University of Colorado School of Medicine, and an Associate Professor in the Departments of Pharmacology, Computer Science, and Preventive Medicine and Biometrics. He is also a Founder and Director of Molecular Mining Corporation. He received his BA degree cum laude in psychiatry and a PhD in computer science from Yale University.
Dr. Hunter spent more than 10 years at the National Institutes of Health, beginning in the machine learning project at the National Library of Medicine and ending as the Chief of the Molecular Statistics and Bioinformatics Section at the National Cancer Institute. Dr. Hunter's research interests span a wide range of areas, from cognitive science to rational drug design. His primary focus recently has been the application of machine learning techniques to data generated by high-throughput molecular biology. He has also developed techniques for automated processing of biomedical texts, anatomically realistic models of neural computation, and neurobiologically and evolutionarily informed computational models of cognition. Dr. Hunter inaugurated two of the most important academic bioinformatics conferences, Intelligent Systems in Molecular Biology and Pacific Symposium on Biocomputing, and was Founding President of the International Society for Computational Biology.
Figure 13.
Ilias Iakovidis
Ilias Iakovidis is a Scientific Officer of the Health Telematics Unit of the European Commission General Directorate Information Society. He received a BSc in mathematics from Aristotle University of Thessaloniki and a PhD magna cum laude in applied mathematics from the Texas Tech University. He is currently serving as visiting faculty at three universities in Europe, teaching post graduate classes in medical informatics.
Figure 14.
Prior to his current position, Dr. Iakovidis was awarded a postdoctoral fellowship at the Biomedical Engineering Institute, University of Montreal, followed by an appointment as Research Associate at the Montreal Heart Institute, McGill University. His main responsibilities in his current position include preparation of the research policies and directions of the European Union in the area of medical informatics as well as monitoring of research projects on systems for health professionals and on personal health support systems. He is actively involved in promotion of international collaboration in medical informatics, in particular between the European Union and North America.
Dr. Iakovidis' primary interest has been electronic health records, user acceptance, and strategies for successful and beneficial application of health telematics systems. He has been supporting and driving research on the personal health record since 1993 and promoting the set-up of EHR centers in European countries. Particular focus has been on improving user acceptance by examining and promoting the uptake of human–computer interaction issues, such as universal access and design for all. He has also been gaining experience in the applicability and benefits of health telematics systems and has been invited by several European countries to contribute to implementation strategies. His current interest is promoting research between medical informatics and bioinfomatics and the effects on the personal health record.
Dr. Iakovidis has received honors from Hellenic Professional Society of Texas. He is member of the editorial boards of IEEE-Transactions on Information Technology in Biomedicine and the IOS Press series Health Technology and Informatics. He has been an invited keynote speaker at major international events (e.g., MedInfo 98, MIE 97, MIE 99) and lecturer at seminars and courses at European and U.S. universities, including the Short Course at Stanford University. He has initiated and chaired a series of conferences on user acceptance and has participated in the committees of conferences organized by the European Federation for Medical Informatics, IEEE, and the European Research Consortium for Informatics and Mathematics. He is a founding member of the international scientific forum Information Society for All.
Teri E. Klein, PhD
Teri Klein is a Senior Research Scientist at Stanford University and Project Director of the PharmGKB, a national resource for pharmacogenetics and pharmacogenomics data funded by the National Institutes of Health. She is also an Associate Adjunct Pro-fessor in the Department of Pharmaceutical Chemistry at the University of California, San Francisco. She received a BA degree with honors in chemistry/biology from the University of California, Santa Cruz, and a PhD in medical information sciences from the University of California, San Francisco.
Figure 15.
Dr. Klein moved to Stanford University in 2000 after 14 years on the faculty at University of California, San Francisco in the Department of Pharmaceutical Chemistry and at the Computer Graphics Laboratory. Her interests include bioinformatics for support of pharmacogenomics as well as molecular modeling to affect clinical disease syndromes with a structural basis, such as collagen-based diseases like Ehlers-Danlos and osteogenesis imperfecta. She is also interested in modeling the three-dimensional effects of human genetic polymorphisms, particularly those with implications for pharmacogenomics. She is now directing an informatics effort to construct a comprehensive knowledge base linking genomic, laboratory, and clinical data for the purposes of understanding how variation in human genes is correlated with variation in response to medications. As such, this knowledge base poses problems in both clinical informatics and bioinformatics, at their intersection.
Dr. Klein is a founding organizer of the Pacific Symposium on Biocomputing, an annual meeting for biocomputation that is now in its seventh year and attracts roughly 400 attendees each year. This meeting is one of three important meetings in bioinformatics and has hosted sessions designed to bridge clinical informatics and bioinformatics, including sessions on physiologic modeling, visualization and interfaces, and human genetic variation. Dr. Klein is also the Treasurer of the International Society for Computational Biology, an organization devoted to bioinformatics and one whose mission is closely related to that of AMIA. Finally, Dr. Klein recently served on a special panel convened by NIH/National Center for Research Resources to advise the NCRR on ways in which it could participate in the new informatics initiatives being developed at NIH in response to the Biomedical Information Science and Technology Initiative report.
Eugene V. Koonin, PhD
Eugene Koonin is Senior Investigator at the National Center for Biotechnology Information at the National Library of Medicine. He has a Biology diploma (equivalent to MSc ) summa cum laude and his PhD in biology from Moscow State University.
Prior to coming to NCBI, Dr. Koonin was Senior Research Scientist at the Laboratory of Virus Biochemistry, Institute of Poliomyelitis, Senior Research Scientist at the Laboratory of Bacterial Genetics and Head of the Laboratory of Gene Systematics and Bacterial Evolution, Institute of Microbiology, all of the USSR Academy of Sciences. Based on his research in computational biology analyzing the complete genome sequences of several cellular life forms, he has predicted the function of many families of proteins. Furthermore, he has delineated clusters of orthologous and paralogous protein groups, compared the gene organization in different organisms, determined a minimal gene set for cellular life, and reconstructed biochemical pathways in a variety of completely sequenced bacterial and archeal genomes. He also has done leading-edge research in the field of sequence analysis by developing a technique for analysis of protein motifs. Dr. Koonin is Editor of Archaea and of the “Genome Analysis” section in Trends in Genetics. He is a member of the editorial boards of Nucleic Acids Research, Bioinformatics, and In Silico Biology. He has received the National Library of Medicine's Regents Award.
Stephen H. Koslow, PhD
Stephen Koslow is Director, Office on Neuroinformatics, and Associate Director, National Institute of Mental Health, National Institutes of Health. He also coordinates the Human Brain Project, a multi-government agency informatics initiative. He earned his PhD from the Division of Biological Sciences, Department of Pharmacology, University of Chicago.
Figure 16.
Prior to his current position, Dr. Koslow was Director of the Division of Basic and Clinical Neuroscience at NIMH. His work focused on increasing the support and quality of neuroscience and behavioral research at NIMH to further an understanding of brain function and mental illness. While in this position, he initiated the Human Brain Project, a neuroinformatics initiative aimed at creating Web-based databases, analytic tools, and biological models of the brainDr. Koslow serves as the Chair of the Global Science Forum Neuroinformatics Working Group of the Organization of Economic Cooperation and Development, and Co-chair of the United States/European Commission Committee on Neuroinformatics. He serves on the editorial boards of Biomednet and the journals NeuroImage, CNS Drug Reviews, and Human Brain Mapping.
Dr. Koslow is a Fellow of the American Association for the Advancement of Science and the American College of Neuropsychopharmacology. He has been awarded the NIH Directors Award for his leadership efforts, and the International Neural Network Society President's Award for outstanding leadership fostering international collaboration of Human Brain Projects through modern neuroinformatics
Gilad J. Kuperman, MD, PhD
Gilad J. (Gil) Kuperman is the Director of Clinical Information Systems Research and Development at Partners HealthCare System, and an Instructor in medicine at Harvard Medical School. Dr. Kuperman has an MD from the Albert Einstein College of Medicine in New York, and a PhD in medical informatics from the University of Utah.
Figure 17.
Dr. Kuperman has worked in the Information Systems Department of Brigham and Women's Hospital and Partners HealthCare System since 1992. He has been involved in the development and evaluation of several clinical decision support systems, including an automated alerting system for critical laboratory results, reminders in physician order entry to improve the quality and efficiency of care, reminders in the ambulatory setting to improve compliance with guidelines, dosing decision support for patients with renal failure, and drug–drug interactions. Dr. Kuperman also has worked on important infrastructural components, such as coded problem lists and clinical medication dictionaries.
Dr. Kuperman won the 1996 CHIM Award at the AMIA Fall Symposium for his paper “Detecting Alerts, Notifying Physicians, and Offering Action Items: A Comprehensive Alerting System” for the application most likely to change the hospital information systems industry. He serves on the editorial board of the Joint Commission Journal for Quality Improvement and is on the American College of Physicians' Patient Safety Task Force. Dr. Kuperman speaks and has published widely on the effects of physician order entry and other information technologies on clinical care. He has served twice as a judge at AMIA's Student Paper Competition and has served as a Program Member at the Spring and Fall AMIA Symposia.
Leslie A. Lenert, MD, MSc
Dr. Lenert is Associate Professor of Medicine at the University of California, San Diego, and Staff Physician and Researcher at the Veterans Administration San Diego Healthcare System. His educational background includes a BS degree in biomedical sciences from the University of California, Riverside, an MD from the University of California, Los Angeles, and an MSc degree in medical information sciences from Stanford University. His clinical training includes a residency in internal medicine at the University of Texas Southwestern School of Medicine and a post-doctoral fellowship in clinical pharmacology at Stanford University School of Medicine.
Figure 18.
Prior to moving to his current position, Dr. Lenert was an Assistant Professor of Medicine in the Division of Clinical Pharmacology of the Department of Medicine at the Stanford University. Dr. Lenert's research has focused on the development and use of computer software to measure patients' health values and preferences. An important facet of this work are studies exploring differences in the values of stakeholders of medical decisions, such as patients, health care providers, and others. When values differ greatly, medical decisions on every level, from individual to societal, can be impaired. Other work includes development of computer methods for characterizing the “validity” of elicitations of preferences and for repair of apparent errors in elicitations.
Dr. Lenert has received awards that include second prize in the postdoctoral division of the AMIA Student Paper Competition, a National Research Service Award, a Henry Christian Award for Excellence in Clinical Research, and a Faculty Development Award from the Pharmaceutical Manufacturer's Association Research Foundation. An active member of AMIA since the late 1980s, Dr. Lenert served on the Program Committee for the 1998 and 2001 meetings and is currently the Chair of the Publications Committee. He is a member of the editorial boards of JAMIA, the Journal of Biomedical Informatics, and Medical Decision Making and a member of the AHRQ Health Care Quality and Effectiveness Research Study Section.
David J. Lipman, MD
David Lipman serves as the Director of the National Center for Biotechnology Information, a division of the National Library of Medicine, at the National Institutes of Health. Dr. Lipman received his BA from Brown University and his MD from the State University of New York at Buffalo. Following the completion of his internal medicine internship at the University of Arizona at Tucson, Dr. Lipman joined the National Institutes of Diabetes and Digestive and Kidney Diseases, NIH, as a Medical Staff Fellow in the Mathematical Research Branch. He has served as a member of the United States Public Health Service Commissioned Corps since 1984.
Figure 19.
Comparative studies are a powerful tool used by computational biologists to detect important nucleotide or protein fragments that may be hidden in a raw sequence, to identify novel genes and proteins and to gain insight into the structure and function of a protein. Dr. Lipman's research efforts have made a significant contribution toward advancing this field of study, beginning with the first algorithm for rapid database searching, which was used for the critical discovery that the viral oncogene v-sis and a platelet-derived growth factor are derived from closely related cellular genes.
Dr. Lipman's ongoing research includes the development of the most widely used tools for sequence database searching, including FASTA and BLAST. Dr. Lipman has also been instrumental in an effort to design and implement a platform for integrating the diverse data stored in the public databases. The NCBI Entrez Data Retrieval System was designed to allow users to search vast quantities of data with a technique that is both fast and sensitive yet easy to use. The ability to traverse both the literature and molecular databases via Entrez provides a very powerful method for accessing and analyzing data.
Dr. Lipman has received many honors and awards for his achievements and contributions to the field of computational biology, including his recent election the National Academy of Science's Institute of Medicine. Additional honors and awards include his recent appointment as a member of the Association of American Physicians, the Public Health Service Outstanding Service Medal, and the Public Health Service Meritorious Service Medal.
Prakash Nadkarni, MD
Prakash Nadkarni is an Associate Professor at the Center for Medical Informatics, Yale University School of Medicine. Dr. Nadkarni received his undergraduate medical degree from Bombay University, India, and subsequently obtained a specialty degree in pharmacology, a diploma in computer management, and a diploma in radiation medicine from Bombay University.
Dr. Nadkarni's research interests focused originally on parallel computation in biomedicine and later on representation approaches and algorithms concerned with chromosomal maps generated by a variety of experimental methodologies. He is now involved in creating applications that use databases and database-related technology to address a variety of biomedical problems.
An active area of recent research is the development of a generic (entity-attribute-value, or EAV) Web-accessible database for management of clinical studies. TrialDB, the database package resulting from these efforts, is available to informatics investigators as open source; it continues to be enhanced to better meet the needs of investigators and study management personnel.
Dr. Nadkarni also studies the application of EAV database design to represent highly heterogeneous scientific data, and the EAV/CR framework is being employed for a neuroscience database at Yale that is focused on the olfactory system. Both TrialDB and EAV/CR have been developed from a common basis —the use of metadata stored in the database to automate various tasks related to the creation of robust Web-based applications, notably the automatic generation of user interfaces for browsing as well as editing data. An offshoot of the focus on clinical databases has been research in the processing of textual medical data, such as discharge summaries and surgical notes.
Prior to joining Yale University, Dr. Nadkarni was lecturer in pharmacology at GS Medical College and King Edward VII Memorial Hospital, Bombay, India; a consultant with Tata Unisys (an affiliate of Unisys Corp.) for computer applications in medicine, and a contributing editor to Science Today (now renamed 2001), India's leading science magazine. He is a member of the editorial boards of JAMIA, the Pharmacogenomics Journal (published by the Nature group), and the Journal of Postgraduate Medicine, Bombay.
Stuart J. Nelson, MD
Stuart J. Nelson is the Head of Medical Subject Headings at the National Library of Medicine. He has an AB degree in Mathematics from the University of California at Berkeley, and an MD from State University of New York at Brooklyn. He completed a residency in internal medicine at the Philadelphia General Hospital and Metropolitan Hospital of New York City. He is board certified in internal medicine. Dr. Nelson is a Fellow of the American College of Physicians.
Dr. Nelson moved to NLM in 1996. Prior to that he served on the medical faculties of SUNY at Stony Brook (1978 to 1991) and of the Medical College of Georgia (1991 to 1996). While practicing and teaching clinical medicine, he collaborated with Marsden S. Blois on a clinical evaluation of the reconsider project and served as a consultant to the NLM on the UMLS project. He served for five years on the Medical Informatics Subcommittee of the American College of Physicians.
Figure 20.
Since coming to the Library, Dr. Nelson has successfully converted MeSH into a concept-oriented vocabulary, developed the widely used graphical interface MeSH browser, contributed to the reinvention of the indexing process at the Library, and designed several methods for finding previously unrecognized synonymy in the UMLS.
James Ostell, PhD
James Ostell has been Chief of the Information Engineering Branch of the National Center for Biotechnology Information since NCBI was created within the National Library of Medicine in 1988. He received his BS and MS degrees in zoology from the University of Massachusetts. His earned his PhD in cellular and developmental biology from Harvard University.
Figure 21.
Prior to coming to NCBI, Dr. Ostell was the author of a successful commercial software package for molecular biologists, now called MacVector, which is still on the market today. Moving to the public sector, Dr. Ostell came to NCBI on its founding. As Chief of the Information Engineering Branch, Dr. Ostell has been responsible for all major production resources at NCBI. These resources include such familiar names as GenBank, Entrez, PubMed, BLAST, RefSeq, and many others. Dr. Ostell has taken many roles in the different projects, from original designer in some to top level manager in others, and everything between. He has had to balance the freedom of the many talented and creative people behind each of these projects with the institutional needs for stability, standardization, and unification of effort, while attempting to respond to the rapidly changing science, politics, and user needs of the last decade. The growth of NCBI public resources from zero to more than two million unique users a month in ten years is the measure of his success in this endeavor.
Dr. Ostell is a member of the Senior Biomedical Research Service at NIH. He has received the NIH Award of Merit, the NLM Director's Honor Award, and the “Hammer” Award for Reinventing Government.
Thomas H. Payne, MD
Thomas Payne is Medical Director of Academic Medical Center Information Systems at the University of Washington. He has appointments as Clinical Associate Professor in the Departments of Medicine, Health Services, and Medical Education at the University of Washington, and is Attending Physician at the University of Washington Medical Center. He received a BS degree from Stanford University and a medical doctorate at the University of Washington. He completed an internal medicine residency at the University of Colorado Affiliated Hospitals. Following residency, he completed a fellowship in medical information science at Massachusetts General Hospital and Harvard School of Public Health.
Figure 22.
Dr. Payne's informatics activity has focused on the introduction of large-scale clinical computing systems into health care organizations and on the use of clinical computing systems to measure and improve care quality. Following his fellowship, he joined Group Health Cooperative of Puget Sound, where for eight years he combined clinical practice with work in the Clinical Computing Project. He served for six months as Chief Medical Information Officer for the Saudi/Universities Project at King Faisal Specialist Hospital and Research Centre in Riyadh. Between 1997 and 2001, he served as the first Associate Chief Medical Officer for Clinical Information Management at VA Puget Sound Health Care System in Seattle. In that role he led the Computerized Patient Record System (CPRS) project at VA Puget Sound, including the testing (as the third national test site) and implementation of an electronic medical record and practitioner order entry. VA Puget Sound received a 2000 Nicholas E. Davies CPR Recognition Award of excellence for work in implementing a computer-based medical record system.
Dr. Payne has served as a member of the National Veterans Administration CPRS Clinical Workgroup Advisory Committee, the National VA Workgroup on Warning Alerts and Order Checks, as a member of the Clinical Review Committee for the Government Computerized Patient Record (G-CPR) and has served as Chair of ASTM Division Two on Health Records of the E 31 Committee on Healthcare Informatics. He was a member of the AMIA Task Force on Guidelines for the Use of Clinic–Patient Electronic Mail and the 2001 Davies Review Committee for CPRI-HOST. He is a Fellow of the American College of Physicians–American Society of Internal Medicine. He has received numerous awards, including election to Phi Beta Kappa at Stanford and Alpha Omega Alpha.
Richard N. Shiffman, MD, MCIS
Richard Shiffman is Associate Director of the Center for Medical Informatics and Associate Professor of Pediatrics at Yale University School of Medicine. Dr. Shiffman received BA and MD degrees from the University of Pennsylvania and served as pediatric resident at Children's Hospital of Philadelphia and the James Whitcomb Riley Hospital for Children. He was Chief Resident at the University of Colorado Medical Center and completed a fellowship there in developmental pediatrics. Dr. Shiffman practiced primary care pediatrics in Colorado for 12 years and earned a Masters in Computer Information Systems from the University of Denver. He completed a fellowship in medical informatics at the Decision Systems Group, Brigham and Women's Hospital, before joining the faculty at Yale.
Figure 23.
Dr. Shiffman's primary research activities have been directed toward the use of guideline knowledge in computer-based decision support systems. He pioneered the use of decision tables for guideline knowledge representation and verification of completeness and consistency. The model was extended to create “augmented” tables that can store and manipulate information about evidence quality, test parameters, costs, and patient preferences. This work served as a basis for the Guideline Elements Model (GEM), an XML-based hierarchic document model for guidelines. Dr. Shiffman studied the effectiveness of an asthma decision support system on handheld computers in private practice and led a group that developed a computer-based system to support pediatric health maintenance activities at Yale, using a variety of scanning technologies for structured recording, storage, and manipulation of data.
.Dr. Shiffman served as Chair of an Expert Meeting on Information Technology in Children's Healthcare sponsored by AHRQ. He is a Fellow of the American Academy of Pediatrics (AAP) and served two terms as chairman of its Section on Computers and Other Technology. In addition, he serves on the AAP Task Force on Medical Informatics and the Steering Committee on Quality Improvement and Management. Dr. Shiffman won a Generalist Physician Faculty Scholars Award from the Robert Wood Johnson Foundation and served on an Institute of Medicine Committee to advise the AHCPR.
David Johnson States, MD, PhD
David States is Professor of Human Genetics and Director of Bioinformatics at the University of Michigan. He received his BA in biochemistry magna cum laude, and his MD and PhD in biophysics, all from Harvard University. He completed his internship and residency in internal medicine at University of California at San Diego Medical Center, and his pulmonary fellowship at National Heart Lung and Blood Institute, National Institutes of Health.
Figure 24.
Dr. States was senior staff fellow at the National Center for Biotechnology Information before going to Washington University as Associate Professor of Biomedical Computing and Associate Professor of Biochemistry and Molecular Biophysics. At Washington University, he served as Director of the Biomedical Engineering Program in the School of Engineering and Applied Science, Director of the Institute for Biomedical Computing, and Director of the Center for Genetics in Medicine. In these capacities, he integrated the institute into the broader array of genomics and biomedical engineering efforts at the university. His own research has focused on the development of tools for sequence analysis and on annotation of those analyses.
Dr. States is Associate Editor for North America of Bioinformatics, is a member of the editorial board of the Journal of Computational Biology, and has served on the editorial board of GENE-COMBIS and as Treasurer of the International Society for Computational Biology.
Mario Stefanelli, PhD, Engineer
Mario Stefanelli is Full Professor of Biomedical Engineering and Chief of the Laboratory of Medical Informatics of the Department of Computer and System Sciences at the University of Pavia, Italy. He is the coordinator of the PhD course on Bioengineering and Bioinformatics of the University of Pavia. He received a degree in Electrical Engineering from the University of Pavia in 1969. Since 1995, he has been the head of the Research and Development Unit of the Consortium of Bioengineering and Med-ical Informatics in Pavia, which involves several research organizations, hospitals, and IT companies. Since 2001, he is also Scientific Consultant of ITC-Irst in Trento, Italy, a large public research institution promoting technologic innovation in many different fields.
Figure 25.
Prior to his current position, Prof. Stefanelli served from 1971 to 2000 as an Assistant, Associate, and Full Professor of Control Engineering at the University of Pavia, where he was also Head of the Department of Computer and System Sciences from 1985 to 1990.
Professor Stefanelli has influenced developments in three main areas of medical informatics—models of biological systems to advance pathophysiologic knowledge and estimate clinically relevant parameters that could not be measured directly; medical decision support systems, by integrating methodologies derived from artificial intelligence, decision theory, and computer science; and health care information systems supporting collaborative work among health care professionals and patients. He was the manager or principal investigator of several international, large national, and European projects, such as GAMES (General Architecture for Medical Expert Systems) I and II, HC-ReMa (Health Care Resource Management), T-IDDM (Telemanagement of Insulin Dependent Diabetic Mellitus patients), ProGuide (building and disseminating of medical guidelines), patman (patient management), M2DM (Multi-access System for the Management of Diabetic Mellitus Patients), and HOMEY (Home Monitoring through Intelligent Dialog System).
Professor Stefanelli has presented invited lectures at several international conferences. The most recent ones have been given at Medinfo ‘98, nnesmed ‘98, the 1999 Joint European Conference on Artificial Intelligence in Medicine and Medical Decision Making, the First European Workshop on Computer-based Support for Clinical Guidelines and Protocols (2000), the 2001 Workshop on Challenges in Medical Informatics, and MedNet (2001).
Professor Stefanelli is currently a member of the editorial boards of American Modeling Physiology: Modelling Forum, Artificial Intelligence in Medicine, International Journal of Biomedical Informatics, International Journal of Medical Informatics, and Methods of Information in Medicine. He is also member of several scientific associations, such as the Italian Association for Artificial Intelligence, American Association for Artificial Intelligence, AMIA, Association for Computing Machinery, European Association of Artificial Intelligence in Medicine, Institute of Electrical and Electronic Engineers, and Italian Group of Biomedical Engineering.
Gary D. Stormo, PhD
Gary Stormo is Professor in the Department of Genetics at Washington University School of Medicine, where he is also the Director of the Graduate Program in Computational Biology. He received his BS degree in biology from Caltech and MA and PhD degrees in molecular, cellular and developmental biology from the University of Colorado. He remained at the University of Colorado for postdoctoral research and was then hired as an Assistant Professor. He attained the rank of Professor before moving to his current position at Washington University in 1999.
Figure 26.
Dr. Stormo's research includes both experimental and computational studies. The experimental work is focused primarily on DNA–protein interactions and their role in regulating gene expression. His computational research also involves analysis of DNA–protein intearctions, including the development of pattern recognition algorithms for discovering DNA sites required for gene regulation. He has also developed methods for predicting RNA structure and identifying RNA motifs involved in protein interactions. Another area of computational research has been new methods for predicting protein coding genes in genomic DNA sequences.
Dr. Stormo was Executive Editor of Bioinformatics from 1994 to 1999. He is currently on the editorial board for Bioinformatics and Nucleic Acids Research. He is on the board of directors of the International Society for Computational Biology and serves as Chair of the Publications Committee.
Arthur W. Toga, PhD
Arthur W. Toga is a Professor of Neurology at UCLA, founder and Director of the Laboratory of Neuro Imaging, Co-Director of the UCLA Brain Mapping Center, and the founding editor of the journal NeuroImage.
Dr. Toga received his MS degree and PhD in neuroscience from St. Louis University and did a postdoctoral fellowship at Washington University in the Department of Neurology. He has formal training in neuroscience and great of depth of knowledge and expertise in computer science and informatics. Dr. Toga has a career-long funding and publication record in the analysis, registration, and modeling of structural and functional images obtained from many species, including humans. He has developed unique mathematical techniques for global and local warping of images and visualization of composite brain image sets. Dr. Toga's laboratory coordinates neuroimage analysis activities throughout the UCLA campus and with collaborators around the world.
Figure 27.
All his activities continue to focus on the relationship between brain structure and function, primarily emphasizing structure utilizing three-dimensional atlasing and analyses of morphometric variability in populations and individuals, both in health and disease, including children and aged populations. The work that he has pioneered continues to focus on the creation, testing, and validation of mathematical strategies for computational neuroanatomy and the development of algorithmic approaches resulting in the characterization and measurement of anatomy.
Dr. Toga's interests in visualization and data immersion stem from research in mapping, deformation correction, graphics, and database. He serves on several relevant national and international boards and commissions including the United States–European Community MegaScience Forum and is a U.S. representative for the Office of Economic and Cooperative Development Committee on Neuroinformatics. He has worked with industry and entertainment leaders including Silicon Graphics Inc., IBM, Paramount Pictures, MGM, and Digital Light and Magic. He is the recipient of many awards and recently received the SPIE image-processing “cum laude” award, the Di Chiro Award for Outstanding Scientific Researcher, and a Smithsonian Award for Innovation in 1999.
W. John Wilbur, MD, PhD
John Wilbur is a Senior Scientist in the Computational Biology Branch of the National Center for Biotechnology Information. He is a principal investigator leading a research group in the study and development of statistical text processing algorithms. He obtained a PhD in pure mathematics from the University of California at Davis and an MD from Loma Linda University. He completed residency training in internal medicine at UCD-Sacramento and a fellowship in computational biology at the National Institute National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health. He is board certified in internal medicine.
Figure 28.
While both were fellows at the Mathematical Research Branch of NIADDK, Dr. Wilbur and Dr. Lipman developed the first rapid search technique for discovering similarities between DNA sequences and sequence homologies between proteins. On completion of his fellowship, Dr. Wilbur practiced medicine for five years, during which time he developed software to produce discharge instructions for patients. Shortly after the founding of NCBI, he joined NCBI as a research scientist.
While at NCBI, Dr. Wilbur has developed the algorithm that produces PubMed related documents and the algorithm that in PubMed allows fuzzy phrase matching. Most recently, he is the author of algorithms for phrase identification in natural language text that are used in NCBI's electronic textbook project and allow for easy reference from medline documents to related textbook material.
Dr. Wilbur attended the University of California at Davis on a University Fellowship and is a full member of Sigma Xi. He received the President's Award and the Student Investigator of the Year Award from Loma Linda University. He is a member of Alpha Omega Alpha. He is also the author of more than 50 papers in pure and applied mathematics.