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Keynote
Speakers Title: The Role Of Computation In Biomedical Research
And Health Care
Abstract The National Institutes of
Health sees that non-trivial computation is critical to every aspect of our
mission, from the most basic research to the efficient and effective delivery
of health care in all venues. We see the corollary: Inefficiencies, gaps, and
flaws in computation are limiting the pace and scope of all aspects of the
NIH mission. The Biomedical Information Science and Technology Initiative
(BISTI) at the NIH are devoted to implementing our understandings about
computation in programs and practices. The core of our immediate programmatic
initiative is the creation beginning this year of NIH National Centers for
Biomedical Computing around the country, followed by the establishment of a
network of collaborating projects. Our ten year goal is for every person
involved in the biomedical enterprise---basic researcher, clinical
researcher, practitioner, student, teacher, policy maker---to have at their
fingertips through their keyboard instant access to all the data sources,
analysis tools, modeling tools, visualization tools, and interpretative
materials necessary to do their jobs with no inefficiencies in computation or
information technology being a rate-limiting step. In twenty years, much of
the information retrieval, analysis, and modeling that people will be doing
in ten years should be done by intelligent agents, so that people will be
able to deal rapidly, effectively, and rigorously with biomedical issues at
the highest conceptual level. Biography of
Eric Jakobsson
Eric Jakobsson is a leader in the field of
computational biology, an area that joins biology with computer science,
engineering, mathematics and physics. His academic degrees are in chemical
engineering and physics. While a graduate student in physics, he was drawn to
the problem of the physical bases of electrical excitability in nerve. Since
1972 he has been on the faculty at the University of Illinois at
Urbana-Champaign, with a primary appointment in Physiology and other
appointments in The Beckman Institute for Advanced Science and Technology,
Biochemistry, Bioengineering, Biophysics and Computational Biology, the
National Center for Supercomputing Applications, and Neuroscience. He has
served as the Director of the Center of Biophysics and Computational Biology
and the Bioengineering Program. His research interests span many areas of
computational biology and include the use of computational technology in
education. In May 2003, Jakobsson came to NIH to serve as Director of the
Center for Bioinformatics and Computational Biology at the National Institute
of General Medical Sciences and the Chair of the NIH Biomedical Information
Science and Technology Initiative Consortium. He was the prime drafter of the
NIH Bioinformatics and Computational Biology Roadmap, an 8-10 year plan to
create an excellent national computational environment for biomedical
research. Jakobsson continues to do research at the University of Illinois by
weekly commuting. |
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Invited Speakers
Speaker:
Steven Benner University of Florida , V.
T. and Louise Jackson Distinguished Professor Departments of Chemistry
and Anatomy and Cell Biology Title: Evolutionary Analysis of Protein Sequence DataAbstract Computation has been important in
molecular studies for some time, but its role is especially critical
when the molecules being studied come from living systems. Many of the
most common tools used in systems biology, including DNA microarrays
and proteomics tools, are noisy to the point of requiring computational
tools to have any chance of molecular interpretation. Imaging methods
applied in biological systems can generate large volumes of data, often
not easily represented by conventional data structures. Data from whole
genome sequencing projects do fit into conventional data structures,
but the evolutionary analyses that place meaning on these sequences
must confront np hard computational tasks. Driving both the information
and molecular scientist to confront these problems is a rich set of
rewards that success will deliver. These include tools for identifying
genes and proteins involved in human disease, the ability to treat patients
as individuals through personalized care, and a model for the history
of life on Earth, extending from its origins to the modern day. This
talk will present examples to illustrate these points. Biography
of Steven Benner Steven Benner received BS and MS from Yale University
in Molecular Biophysics and Biochemistry and PhD from Harvard University in
Chemistry. He is Distinguished Professor, Department of Chemistry, University
of Florida. He is also Professor of Department of Anatomy and Cell Biology,
University of Florida. Before joining Florida, he was Professor of
Bio-organic Chemistry, Swiss Federal Institute of Technology. He received
several honors and fellowships, and delivered the Carl Sagan Lecture,
American Geophysical Union in 2002. His research areas include experimental
paleobiochemistry, protein Engineering, combinatorial chemistry, nucleic acid
chemistry, nucleic acids enzymology, molecular biology, bioinformatics,
planetary biology, phylogenomics, pharmacophylogenomics, and astrobiology. Speaker:
Joyce A. Mitchell Biomedical
and Health Informatics Research and Education Programs and Department
of Health Management and Informatics, School of Medicine, University
of Missouri Title: Ontologies in BioinformaticsAbstract
This talk will start with the basics of ontologies with
illustrations of several ontologies that are available in bioinformatics.
Examples will be used from (1) the Gene Ontology, used to index gene
functional information, (2) the Microarray Gene Expression Data (MGED)
Ontologies, used to index the information on microarray experiments,
(3) the Clinical Bioinformatics Ontology (CBO), used to create metadata
on genetic tests that will be part of electronic medical records, (4)
the Medical Subject Headings (MeSH), used to index the scientific literature,
and (5) the Unified Medical Language System (UMLS), used to tie together
various ontologies to draw inferences from multiple domains. Examples
of various ongoing research projects such as the Semantic Web, e-Science,
and the author's own collaborative work using ontologies for knowledge
discovery should help the audience acquire an understanding of the current
areas of research in bioinformatics ontologies. Biography
of Joyce A. Mitchell Joyce Mitchell is a professor in the School of Medicine,
Department of Health Management and Informatics at the University of
Missouri-Columbia, with joint appointments in the Division of Medical
Genetics and the School of Information Science and Learning Technologies.
She received her Ph.D. in population genetics from the University of
Wisconsin, Madison. Her postdoctoral research includes both medical
information sciences at the University of Missouri and clinical medical
genetics at the University of California, San Francisco. She is certified
by the American Board of Medical Genetics as a Ph.D. Medical Geneticist.
An elected Fellow of the American College of Medical Informatics, she
is also a Founding Fellow of the American College of Medical Genetics.
Dr. Mitchell fulfilled several roles for the University of Missouri. While progressing through the professorial ranks, she served as Director of the Medical Information Sciences Group which became the Medical Informatics Group. She further served as Associate Dean for Information Technology of the School of Medicine, and Chief Information Officer for MU Health System. She currently serves as Director of the MU Informatics Institute, with responsibility for graduate education and research programs in both bioinformatics and health informatics. Following a sabbatical at the NLM in 2001-2002, Dr. Mitchell's research is increasingly focused on bioinformatics, including bioinformatics tools in biomedical knowledge discovery, and the incorporation of bioinformatics data into electronic information resources in health care. This research ranges from consumer health website development to the creation of bioinformatics tools for researchers. She is the project co-leader of the NLM's Genetics Home Reference (http://ghr.nlm.nih.gov), a consumer health website dedicated to bringing to the public the health implications and specific genetic data of the Human Genome Project. She is involved with bioinformatics ontology research, including linking ontologies, investigating the use of ontologies in the clinical world, and organizing seminars on biomedical ontologies. Dr. Mitchell has been active in the American College of Medical Informatics (ACMI) and in the American Medical Informatics Association (AMIA), having served on the Board of Directors for both. She was a Chair of the NLM's grant review study section. She served as Chair of the Board of Scientific Counselors (BoSC), a panel that advises on internal NLM research for the Lister Hill National Center for Biomedical Communications. Speaker:
Wen-Hsiung Li Department of Ecology and Evolution University
of Chicago Title: Some Topics in Computational Genomicsabstract Biological (protein interaction and regulatory) networks are current topics in computational genomics. I shall first describe the properties of protein-protein interaction networks. I shall then present a study on the evolution of the yeast protein interaction network. I shall also give a description of regulatory networks. I shall then present a dynamic model of regulatory circuits of yeast genes. This modeling uses a cross-gene identification scheme and the model is shown to give good fit to the expression profiles of yeast genes. It also gives accurate predictions of the expression profiles of genes that have not been used in the construction of the model (in the estimation of the parameters of the model), validating the reliability of the model. Biography Wen-Hsiung Li is James
D. Watson Professor since 2004 of the Dept of Ecology & Evolution, University
of Chicago. He received Ph.D. from Brown University in Applied Math/Genetics,
1972. He was George Beadle Professor 1999-2004 of the Dept of Ecology
& Evolution, University of Chicago. He was Professor, 1984-1998, and
Betty Wheless Trotter Professor in Medical Sciences, 1996-1998, of the
Human Genetics Center, University of Texas Health Science Center-Houston.
He started to teach at the University of Texas Health Science Center-Houston
since 1973, after one year at Medical Genetics, Univ. of Wisconsin-Madison.
Dr. Li received the Balzan Prize 2003 for Genetics and Evolution and
Horace Mann Medal 2004. He is Member of the National Academy of Sciences
since 2003; Fellow, American Academy of Arts and Sciences 1999; Academician,
Academia Sinica, Taiwan 1998; and President, Society for Molecular Biology
and Evolution 2000. Among various professional responsibilities, he
is Editor, Molecular Phylogenetics and Evolution, 1991 - present; Associate
Editor, Journal of Molecular Evolution, 1998 -2004; Associate Editor,
Journal of Bioinformatics and Computational Biology, 2003-present; Area
Editor (Evolution & Comparative Genomics) Encycl. of Human Genome, Macmillian
1999-present; Editorial Board, Zoological Studies, 1993 -present; Editorial
Board, Botanical Bulletin of Academia Sinica, Taiwan, 1993 -present:
Scientific Advisory Board, the Max Planck Institute for Evolutionary
Anthropology, Leipzig, Germany, 2000-present; Overseers Committee, the
Department of Organismic & Evolutionary Biology, Harvard, 2000-present;
Academic Advisor, Institute of Zoology, Academia Sinica, Taiwan, 1997
-present; Academic Advisor, Institute of Botany, Academia Sinica, Taiwan,
1997 -present; Academic Advisor, Research Center for Biodiversity, Academia
Sinica, Taiwan, 2003 -present; Academic Advisor, Laboratory of Cellular
and Molecular Evolution, Kunming Institute of Zoology, The Chinese Academy
of Sciences, 1997 -2002; Editorial Board, Mathematical Biosciences,
1990 - 2003; Associate Editor, Theoretical Population Biology, 1981
-1986; Associate Editor, Genetics, 1986 - 1997; Editorial Board, Journal
of Molecular Evolution, 1984 - 1997; Editorial Board, Molecular Biology
and Evolution, 1983 - 1993; Editor, Gene, 1997 - 2001. His research
interests include: Evolutionary Genomics, Molecular Evolution, Bioinformatics
and Computational Biology, Population Genetics, Human Genetics. He has
published more than 200 papers. His books include: Li, W.-H. Ed. (1977)
Stochastic Models in Population Genetics. Dowden, Hutchinson Ross, Stroudsburg,
Pa; Li, W.-H. and D. Graur (1991) Fundamentals of Molecular Evolution,
Sinauer Associates, Sunderland, Massachusetts; Li, W.-H. (1997) Molecular
Evolution, Sinauer Associates, Sunderland, Massachusetts; Graur, D.
And W.-H. Li (1999) Fundamentals of Molecular Evolution, 2nd Edition,
Sinauer Associates, Sunderland, Massachusetts. Speaker:
Philip E. Bourne University
of California, San Diego, San Diego Supercomputer Center, Burnham Institute,
Keck Graduate Institute, and Protein Data Bank Title: Protein Folds as a Tool in Studying EvolutionAbstract It is
truly remarkable that all of Nature is comprised of a very limited set of
parts in the form of protein domain folds - taken here to mean independent
and stable folding units. While the exact number remains a point of some
conjecture, no one disputes that it is a small number in the 1000s. Some
folds are promiscuous, taking part in a variety of functions and some are
selective, perhaps having a sole function. At this time we can assign, with
reasonable reliability, the number and distribution of domain folds to all
fully sequenced genomes (over 150 from the three major kingdoms), achieving
30-60% coverage depending on the complexity of the genome. This presentation
will argue that, based on these assignments, we are at a very interesting
time in the study of structural bioinformatics, which classifies domain
folds, since a useful contribution can be made to the field of molecular
evolution. This statement is based on two underlying principles: 1. structure
can provide information on distant evolutionary relationships not seem by
current methods of sequence analysis; 2. since Nature is comprised of a very
limited parts list of protein domain folds, for a species to loose or gain a
fold is a major distinguishing event. Using these two principles we will describe
our recent efforts in structure-based phylogenetic analysis, including one
interpretation of the tree of life. Biography
of Philip E. Bourne Professor Philip Bourne received his Ph.D. in chemistry
from the Flinders University of South Australia in 1980 where he studied the
structural and electrophilic effects of substitution on fully saturated caged
hydrocarbon molecules. While a post-doctoral fellow at Sheffield University
UK he contributed to the understanding of the structural role of the protein
ferritin in iron storage. Later as a Senior Research Scientist at Columbia
University in New York he proposed mechanisms for the role of caracurines and
snake toxins that operate postsynaptically. During the 80's as first the
Director of the Cancer Center Computer Facility and later Director of the
Medical School Computer Facility at Columbia University he helped establish a
tumor registry and various applications and databases in support of patient
care. In the early 90's as a Senior Associate of the Howard Hughes Medical
Institute he worked on developing high performance hardware and software for
computational structural biology. He moved to UCSD in 1995, while
bioinformatics was still a bad word, to work on structural bioinformatics. He
is currently the Senior Advisor to the Life Sciences at the San Diego
Supercomputer Center (SDSC), a Professor in the Department of Pharmacology at
UCSD, an Adjunct Professor at the Burnham Institute and the Keck Graduate
Institute, Co-Director of the Protein Data Bank (PDB), an elected Fellow of
the American Medical Informatics Association and the immediate past President
of the International Society for Computational Biology. His current interests
are in structural genomics, proteomics, apoptosis, cell signaling, data
modeling and scientific visualization. He is the author of over 140
scientific papers and 4 books, one of which sold over 120,000 copies. He has
received two UCSD Connect Awards for new inventions in the areas of
comparative protein structure analysis and shared visualization. Most
recently he was the recipient of the 2002 Sun Microsystems Convergence Award
and the 2004 Convocation Medal for career achievement from his graduate
university. He has founded two companies, both of which will be successful
soon. National
Center for Genomics Research Title: Integrated Information Resources for Plant Biology Research CommunitiesAbstract Biography: Dr. Susan Baxter, Chief Operating
Officer at The National Center for Genome Resources (NCGR), leads and
directs software engineering, bioinformatics tool development and information
technology for NCGR's discovery platforms, based on data obtained from
high-throughput biotechnologies. Prior to joining NCGR, Dr. Baxter was
Vice President of Research and Genome Analysis at GeneFormatics, later
Cengent Therapeutics, a drug discovery company in San Diego. Her responsibilities
included managing programs in both target and lead discovery, along
with development of automated protein annotation and analysis pipelines.
Previously she was a tenured researcher at the New York State Department
of Health's Wadsworth Center, where she used nuclear magnetic resonance
spectroscopy to characterize DNA-binding proteins and their complexes.
Dr. Baxter received her M.S. and Ph.D. degrees in Chemistry from Northwestern
University in Evanston, Illinois. She holds a B.A. degree in Chemistry
from the University of Virginia in Charlottesville, Virginia. Following
doctoral work, Baxter was an NIH Postdoctoral Fellow at the Institute
of Molecular Biology at University of Oregon. Speaker: Ambuj K. Singh University
of California at Santa Barbara Title: Current challenges in biological database designAbstract
Recent spurt in high-throughput techniques has led to
phenomenal growth in the quantity and diversity of biological data. There is
an immediate need to utilize this data to speed up the progress of biomedical
research. Supporting access to such data requires fundamental advances in
databases: scalable querying of new data types, use of probabilistic and
interpreted data, encoding of complex domain knowledge, and integration of
information from multiple data sources. I will broadly discuss the above
points and then focus on a couple of applications from bio-image databases
and protein interaction networks. These applications illustrate how the
individual research thrusts combine to support biological discovery. Biography
of Ambuj K. Singh Ambuj K. Singh is a professor in the department of
computer science at the University of California at Santa Barbara. He
received his B.S. from Indian Institute of Technology Kharagpur in 1982, his
MS from Iowa State University in 1984, and his PhD from the University of
Texas at Austin in 1989. He has been on the faculty at UC Santa Barbara since
then. His research interests have been in formal methods, parallel and
distributed systems, and databases. More recently, he has been drawn to
biological databases, on account of the inherent complexity and novelty, and
the reliance on cross-disciplinary knowledge. Speaker: Weixiong Zhang Washington
University in St. Louis Title:A steganographic approach to motif finding that combines word counting and statistical modelingAbstract
It has been a challenge to discover
transcription factor (TF) binding motifs (TFBMs), which are short cis-regulatory
DNA sequences playing essential roles in transcriptional regulation.
We approach the problems of modeling genomic regulatory sequences and
discovering TFBMs from a steganographic perspective. In this talk, I
will describe an efficient, genome-wide motif finding algorithm, called
WordSpy, based on the new perspective. I will discuss the design of
WordSpy and its superb performance, comparing many existing algorithms,
on recovering the first ten chapters of novel Moby Dick from a stegoscript
and discovering all known cell-cycle related TFBM of S. cerevisiae.
This is a joint work with Guandong Wang. Biography
of Weixiong Zhang Dr.
Weixiong Zhang is Associate Professor in computer science and genetics at
Washington University in Saint Louis. He received his B.S. and M.S. in
computer engineering from Tsinghua University, Beijing, China, and his Ph.D.
in computer science from UCLA in 1994. From 1994 to 2000, he was Senior
Scientist at Information Sciences Institute of USC and research assistant
professor at USC. Dr. Zhang's research interests include computational
biology (e.g., multiple sequence alignment, RNA folding, targeted gene
finding, and gene regulatory networks), artificial intelligence (heuristic
search, distributed multiagent systems) and combinatorial optimization (TSP
and Boolean satisfiability). NicK Tsinoremas is currently a Senior
Director of Informatics at Scripps Florida . His department is responsible
for providing informatics and scientific computing support related to
Scripps Florida's biomedical research, drug discovery, and technology
development programs. Tsinoremas will oversee the development of scientific
applications, databases, and data analysis systems that are essential
in the drug discovery process, ranging from statistical genetics and
data mining to chemo-informatics and sequence-based analysis. Tsinoremas
received his B.A. in Chemistry from the University of Athens, Greece
and his Ph.D. in Molecular Biology from the University of Leeds, UK.
His subsequent postdoctoral work at Texas A & M University focused on
light-regulated gene expression and circadian rhythms. Before joining
Scripps Florida, he served as director of Computational Genomics and
Genomic Discovery at Rosetta/Merck. There he directed the project that
combined informatics and computational approaches with gene expression
profiling to discover, prioritize, and define drug target genes. Prior
to working for Merck/Rosetta, Tsinoremas was the Vice-President of Genomics
at DoubleTwist Inc., where he determined the scientific direction of
DoubleTwist's bioinformatics applications and databases and was responsible
for the creation of Prophecy, the first commercial database annotating
all human genes. He also held bioinformatics positions at Incyte Genomics
and Progenitor Inc. Tsinoremas' research at Scripps will focus on pattern
recognition in sequences, structures and processes, the studying of
systems ranging from single protein molecules through complex molecular
interactions, and the data analysis, interpretation, and reverse-engineering
of complex disease-genomic/genetic interactions in order to enhance
our understanding of complex diseases. Smith School of Business and Institute
for Advanced Computer Studies and Center for Bioinformatics and Computational
Biology and Department of Computer Science, University of Maryland Title:Enhancing the Semantics of Links and Paths in Life Science SourcesAbstract Web-accessible bio-molecular data sources contain data about scientific entities such as genes, sequences, proteins and citations. The sources are diverse in content and richly interconnected to each other. Data integration queries that are critical to scientific exploration explore multiple sources and must traverse both the links and the paths (informally concatenations of links) through these sources. Such navigational queries pose significant challenges because the links are poor with respect to both representation (structure) and meaning. These limitations make it difficult for links to be explored meaningfully when answering queries. In this research, we propose a methodology and tools to assist scientists in exploring and exploiting the knowledge captured in these sources and their interconnections. In order to do so we must accomplish the following: 1. We develop a data model that can represent sources, data objects and the enhanced e-links between data objects. The data model will be augmented with a semantics to compose e-links into meaningful paths, e-paths. 2. We develop a query language and query evaluation engine for scientists to meaningfully explore e-links and e-paths. 3. We develop a methodology to (semi) automatically generate and label links. |
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Last
Updated: May 30, 2004 |