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Kevin Becker, Ph.D.
"Integrating gene expression and proteomic
data with other biological data types:
High throughput gene expression and proteomic studies demand equally matched systems for biological analysis of large quantities of data. We have developed three publicly accessible web based tools, which are useful for the integration of high throughput gene expression and proteomic data. These include: PubMatrix for high throughput semi-automated literature searching; The Genetic Association Database for the integration of human genetic data and BBID-The Biological Biochemical Image Database.
I will present the challenges in developing these tools; novel features which aid high throughput data analysis, and applications of these tools in microarray and proteomic data analysis.
"Digital Biology: The Emerging
Organized by the NIH
Biomedical Information Science and Technology Initiative (BISTI)
The symposium will offer a broad look at the convergence of biomedical and computational research. Key issues to be addressed include: (1) the mounting scientific imperative to study biological systems at multiple levels of organization, (2) the growing need to use quantitative approaches to analyze biomedical data on a large scale, and (3) the potential impact of extensive computer networks on the nature and conduct of biomedical research.
Keynote Speakers and Program Highlights Dr. Sydney Brenner, a recipient of the 2002 Nobel Prize in Physiology or Medicine, and Distinguished Professor at the Salk Institute, will present the Biology keynote address. Dr. Nathan Myhrvold, a co-founder and managing director of the private entrepreneurial firm Intellectual Ventures and formerly Chief Technology Officer at Microsoft Corporation will present the Technology keynote address.
Other program features include scientific poster presentations, demonstrations, a grant writing information session, and concurrent sessions addressing scientific data integration, networked science, and quantitative biology.
This talk will focus on the design of various sensor architectures constructed on gold, gold/silicon oxide and plastic substrates for monitoring DNA-DNA and Peptide Nucleic Acid (PNA)-DNA interactions. Self-assembly techniques were used to construct two and three dimensional sensor architectures on gold while plasma polymerization was used on plastic substrates. Using the newly developed surface plasmon enhanced fluorescence (SPFS) technique, the kinetics of nucleic acid interactions was monitored in real-time on the gold substrates by varying numerous experimental parameters (sensor architectures, effect of probe/target length, concentration, temperature, flow, etc.). On plastic substrates, conventional fluorescent scanners were used (since SPFS is applicable only for metallic substrates). Very high signal-to-noise ratios could be obtained on gold based sensors while the results were satisfactory (with room for improvement) on plastic substrates.
The above mentioned studies can be useful in avoiding certain pitfalls of commercially available DNA microarrays such as spot heterogeneity, cross-talk, microarray smearing, poor biocompatibility, high background and false hybridization interactions.
Dr. May Berenbaum
Dr. May Berenbaum
"Catepillars, Coumarins and Coevolution"
Dr. May Berenbaum graduated summa cum laude,
with a B.S. degree and honors in biology, from Yale University in 1975;
she attended graduate school at Cornell University and received a Ph.D.
in ecology and evolutionary biology in 1980. Since 1980, she has been
a member of the faculty of the Department of Entomology at the University
of Illinois at Urbana-Champaign; she has served as head of the department
since 1992. Among other accolades, she received the George Mercer award
from the Ecological Society of America in recognition of her research
on plant/insect interactions and the Founder's Award from the Entomological
Society of America in acknowledgment of her contributions to the science
of entomology. She is a fellow of the American Association for the Advancement
of Science and a member of the National Academy of Sciences. In addition
to her research, she is devoted to teaching and to fostering scientific
literacy; she is the recipient of the 1996 Entomological Society of America
North Central Branch Distinguished Teaching Award and has authored numerous
magazine articles, as well as three books, about insects for the general
public. She has also gained some measure of fame as the organizer of the
Insect Fear Film Festival at the University of Illinois, an annual celebration
of Hollywood's entomological excesses, entering its 20th year.
Keynote Speakers: Gary
Dorfman, M.D. & Kirby Vosburgh, Ph.D.
Gary Dorfman, M.D.
"Cancer Imaging for the Operating Room of 2020"
For further information and directions, visit
www.wabme.org or call
the workshop organizer, Kenneth H. Wong, Ph.D., at 202-784-1521.
J. Bartholomew, Ph.D.
Mary J. Bartholomew, Ph.D.
"Risk Assessment in the Federal Government "
Risk analysis is a process of assessing and communicating information about risks involved in various courses of actions in a way that facilitates appropriate management of factors that control risk. It has proven to be useful in business, and the federal government has also embraced it as a way for agencies to improve their decision making. This talk gives a general overview of risk analysis and then focuses on risk assessment, the most quantitative component of the risk analysis process. Risk assessment requires the synthesis of data of disparate types and quality. We will walk through an example of a food safety risk assessment completed at the Center for Veterinary Medicine. From the example, the opportunity for participation of statisticians in the highly multi-disciplinary activity of risk assessment will become apparent.
Ricardo Pietrobon, M.D.
Ricardo Pietrobon, M.D.
This presentation will describe the theoretical bases as well as the application of the Ultimate Research (UR) system and web application suite in the design of complex clinical research projects. The presentation is divided into the following topics:
Challenges in the field Clinical research as an interdisciplinary field involving clinical and biostatistics expertise. Individual researchers can hardly master both fields. Although interdisciplinary teams are frequently seen as an alternative, they tend to fail since there is no common language between the two groups. Clinical Research presents with multiple logistical challenges regarding project management. These challenges are usually responsible for the lack of completion, delay for completion, poor methodological quality, or lack of significance of individual projects. To our knowledge, no previous system or application has attempted to approach all the above-mentioned challenges.
Theoretical basis for the UR system Efficiency of current clinical research systems. This section will present some initial results of an ongoing study evaluating the economic impact of the lack of a structured clinical research system. Data is based on a historical study conducted to evaluate all clinical research protocols performed at Duke University in 1999 and followed until 2003. Rates of completion, time to completion, rates of publication, and estimated costs for each project will be presented. The presenter will argue that current systems are not efficient, with important economical and ethical consequences.
UR application suite - QUESTFORM application. QUESTFORM allows clinical researchers to navigate through the content (data dictionaries) of over 25 databases available in the Center for Excellence in Surgical Outcomes. Researchers are guided toward the formulation of methodologically sound questions, also having the opportunity to take previously formulated research questions as an example. Final questions are saved in a graphical format (Question Diagrams) and transferred to biostatisticians for immediate statistical coding.
Future directions - Our group is currently focusing on the widespread implementation of XML and UMLS to achieve the integration of all five pplications. This includes the use of recent standards from W3C including Xlinks (http://www.w3.org/TR/xlink), XPointers (http://www.w3.org/TR/xptr), XQuery (http://www.w3.org/XML/Query- full-text- requirements), XPath (http://www.w3.org/TR/xpath), as well as Topic maps (http://www.topicmaps.org). - Web mirrors are planned for Switzerland and Brazil. - A grant proposal to the Information Grant Systems grant (NLM) will be submitted on June 1st, 2003.a
Dr. Pietrobon is an Assistant Professor in the Division of Orthopaedic Surgery at Duke┬ University, Durham, NC. Dr. Pietrobon trained as an orthopedic surgeon and obtained a PhD degree in Epidemiology from the University of North Carolina at Chapel Hill. He currently holds the position of Research Director of the Center for Excellence in Surgical Outcomes at Duke University.
Refreshments will be served.
More information: www.nih-bcig.org.
Dr. John M. Frazier, PhD,
Dr. John M. Frazier, PhD, ST
"Cell-Like Entities - The Biological Equivalent of the Transistor"
Scientific Lead - John M. Frazier, Ph.D.
Objective: Living cells are robust autonomous nano-scale agents that possess amazing capabilities to self-organize, self-repair, and evolve new functionalities. From a systems engineering point of view, cells consist of a complex set of nested, nonlinear control systems that, taken together, can ensure survival in the face of large perturbations from “normal” conditions in a chaotic environment. To this end, cells are constantly monitoring their environment utilizing a multitude of sensor strategies. The inputs from these sensors are integrated into an overall control strategy to survive adverse perturbations and maintain essential functions. The objective of the CLE Project is to understand these integrated control systems and their underlying biomolecular components for the purpose of engineering these biological processes for incorporation into novel and revolutionary Air Force technologies, including toxicity detection and autonomous control of microsystems. The resulting product of this project will be a multifunctional, robust, self organizing, bioengineered entity (the biological equivalent of a transistor) that can be integrated into a wide range of systems and at the same time be affordable, self repairing, and sustainable.
R&D Plan: The CLE program is founded on the recent breakthroughs in automated DNA sequencing and synthesis, development of the gene chip microarray technology and is strongly supported by recent investments in bioinformatics. The research program is envisioned to examine, through the emerging disciplines of “functional genomics, proteomics and metabolomics", the dynamics of living cells as they respond to chemical and physical perturbations. The concept is to use the principles and processes inherent in cellular systems to engineer a unique entity that possess the functionalities required for autonomous control of physical devices. The program will demonstrate feasibility, prototype functionality and demonstrate control capability. Key components of the research effort include:
"Mid Atlantic Microbial
Sponsored by: East Carolina
University, Center for the Study of Biological Complexity, United States
Army Medical Research and Materiel Command,
"Mid Atlantic Microbial Pathogenesis Meeting"