To provide focus for the very broad area of biological computing, PSB is
organized into a series of specific sessions. Each session will involve
both formal research presentations and open discussion groups.
The PSB 2003 sessions are:
Each paper must be accompanied by a cover letter. The cover letter must state the following:
Submitted papers are limited to twelve (12) pages in our publication format. Please format your paper according to instructions found at http://www.smi.stanford.edu/projects/helix/psb-online/psb-submit/. If figures can not be easily resized and placed precisely in the text, then it should be clear that with appropriate modifications, the total manuscript length would be within the page limit.
Color pictures can be printed at the expense of the authors. The fee is $500 per page of color pictures, payable at the time of camera ready submission.
Contact Russ Altman (russ.altman@stanford.edu) for additional information about paper submission requirements.
The goal of structural genomics is to discover and characterize the three dimensional structure of all the proteins and other macromolecules found in nature. Presentations will focus on progress in solving the computational challenges in this field. Topic areas included in the discussions will be (1) Determination of all common scaffolds found in naturally evolved proteins, (2) Structure-based prediction and classification of function and (3) Elucidating structurally defined function.
Contact:
Sean Mooney
mooney@smi.stanford.edu
+1 (650) 723-2990
The sequencing of over 800 complete genomes presents unprecedented opportunities for biological discovery as well as new technical challenges for the computational sciences. This session calls for papers on novel computational algorithms and biological applications in genome-wide analysis and comparative genomics. The session will bring together researchers from the biological, computational and mathematical fields with the goal of sharing new research ideas and achieving a better understanding of the current issues and challenges.
Contact:
Liping Wei
wei@nexusgenomics.com
+1 (650) 960-0640
This session solicits papers on improving information access to the biomedical literature and databases by leveraging the complementary resources and techniques provided by the literature, databases, nomenclatures, and ontologies. We particularly wish to focus on problems of importance to the biology and biomedical research communities, where such techniques have been demonstrated to provide a quantifiable improvement in performance. The session will give preference to papers that leverage resources or techniques from several areas. We will also give preference to papers describing systems of demonstrated utility to end users
Contact:
Lynette Hirschman
lynette@mitre.org
+1 (781) 271-7789
Ontologies provide an organizational framework of the concepts involved in biological processes in a system that can be used computationally for reasoning about biomedical knowledge. Ontologies provide a conceptualization of the domain that can be shared among diverse groups of researchers and computational systems. This session will explore the theories, techniques, and applications of biomedical ontologies. The overall session goal is to share new research ideas and achieve a better understanding of current approaches, issues, and challenges in ontology research.
Contact:
Olivier Bodenreider
olivier@nlm.nih.gov
+1 (301) 435-3246
The session "Human Genome Variation: Haplotypes, Linkage Disequilibrium, and Populations" will be devoted to the computational and statistical challenges of building genome-wide haplotypes, defining haploytpe blocks and their variation across different populations, and their application for linking genotypes and phenotypes using the data generated by high-throughput SNP genotyping technologies.
Contact:
Francisco De La Vega
delavefm @ appliedbiosystems.com
+1 (650) 638-6989
This session is intended to be a continuing forum for addressing the advances and needs of computational tools for modeling and managing genomic, pathway and interaction information, including metabolic pathways, signal-transduction pathways, genetic regulatory circuits, protein-protein interactions, and other types of biological interactions.
Contact:
Pedro Romero
promero@ai.sri.com
+1 (650) 859-5669
This session is intended to bring together researchers who are developing or using bioinformatics tools for understanding gene regulation in prokaryotic and eukaryotic genomes. Such research includes, but is not limited to, methods for the computational prediction of promoters and other regulatory elements, comparative genomics approaches to gene regulation, prediction of regulatory motifs in genes with common expression patterns, local multiple alignment algorithms, gene expression analyses, and discovery of regulatory networks and pathways.
Contact:
Serafim Batzoglou
serafim@cs.stanford.edu
The theme of this PSB03 session is to address recently emerging issues that spring from our increasing technical
ability to easily and rapidly obtain DNA-based information for large numbers of individuals from throughout the world.
With the tremendous increase in DNA-based data, the nature and degree of human genetic variation is now becoming an
area of increasing scientific study. With this in mind, the general theme of this session will be on the real and
potential uses and abuses of knowledge regarding human genetic variation. Specific topics include:
1. What has science told us about genetic variation within our species? How does society reconcile that fact that
genetic variations can have functional effects and underlie or at least contribute to many differences in human
characteristics with the societal views about non-discrimination, equal opportunity, and fairness?
2. Current uses of human genetic variation data in DNA-based personal identification strategies (forensics and
criminal investigations, genealogical and population studies, medical studies; pharmacogenomics; military;
genetic testing, evolutionary studies, etc.).
3. What are known misuses of human genetic variation data (discrimination by employers, insurance companies;
racial/ethnic profiling, etc.)?
4. What are potential new uses and misuses of data on human genetic variation and DNA-based personal identification?
5. What policy protections need to be developed in order to prevent misuses while optimizing the beneficial
applications of DNA-based personal identification?
Moderated by:
James Sikela and Eric Juengst
Contact:
James Sikela
James.Sikela@UCHSC.edu
Bioinformatics education is an area of rapid expansion. There are
new programs at the Bachelor's, Master's, Doctoral, and Postdoctoral
levels, but still not enough graduates to satisfy the demands of
industry and academia. This panel will discuss different approaches
to bioinformatics education at all levels, and the different mixes
between the constituent fields. It will provide a forum for
panelists and participants to discuss the needs and solutions to
bioinformatics program development.
Contact:
Richard Hughey
rph@soe.ucsc.edu