{ C O N T E N T S }
Volume 7, Issue 2

President's Letter


Special Interest Groups

ISCB Student Council

2004 Call for Nominations

PSB 2004


Introducing ASBCB

ISCB as Member of FASEB

Events and Opportunities of Interest


Pacific Symposium on Biocomputing 2004

Once again, ISCB was proud to be affiliated with the Pacific Symposium on Biocomputing (PSB) 2004, an international, multidisciplinary conference focused on the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. Through ISCB’s ongoing student travel fellowship program, four young scientist members were able to attend PSB 2004 to present their work in the form of papers and posters. The conference was held January 6-10, 2004 at the beautiful Fairmont Orchid Hotel on the Big Island of Hawaii.

PSB 2004 brought together over 300 top researchers from the US, the Asian Pacific nations, and around the world to exchange research results and address open issues in all aspects of computational biology. PSB is a forum for the presentation of work in databases, algorithms, interfaces, visualization, modeling and other computational methods, as applied to biological problems, with emphasis on applications in data-rich areas of molecular biology. Papers and presentations were rigorously peer reviewed and published in an archival electronic proceedings volume available at http://psb.stanford.edu/psb-online/ or from World Scientific Press as a complete set of bound proceedings.

PSB 2004 sessions included:

  • Computational and Symbolic Systems Biology – Ten talks were given on the nascent field of Systems Biology. In its current form Systems Biology relies on a variety of novel computational approaches, including, dynamics modeling, multivariate analysis, and Bayesian networks. Yet it is also highly dependent on experimental design, such as how one perturbs a particular system under investigation. Therefore, a key aspect of this field is that the computational side is very closely tied to the experimental wet-lab side, and focus on one without regard for the other will be inadequate. What differentiated this session from other computational biology programs was that it relied on the inclusion of experimental design models to show its full potential.

  • Joint Learning from Multiple Types of Genomic Data - This session featured nine talks focused on novel methods that use more than one type of data in their analysis and do so jointly. As an example, rather than obtaining clusters of genes with similar expression profiles and then trying to identify common DNA-binding sequence motifs in promoter regions of the genes in each cluster, methods are expected to combine the gene expression levels and sequences of promoter regions in a single framework or algorithm. Since there are many largely equivalent ways to cluster genes according to their expression profiles, the advantage of a combined approach is that it may refine the clustering so that it is also supported by the presence of sequence motifs, potentially increasing the signal-to-noise ratio critical to achieving meaningful results.

  • Alternative Splicing – Seven talks made up this session, the first for PSB, which brought together researchers from the biological, computational and statistical fields with the goal of sharing efforts in alternative splicing research. Alternative splicing is an essential yet complicated biological process, often controlled by developmental or tissue-specific factors. More than one alternatively spliced mRNA from the same gene may be expressed in the same tissue, sometimes simultaneously yielding an extensive set of proteins with distinct functions. In humans, it is estimated that approximately 30-60% of genes undergo alternative splicing, and many human diseases are associated with aberrant splicing. However, until recent times, the complexity of alternative splicing has eluded detailed analysis. Bolstered by genomic data and new experimental approaches, bioinformatics is emerging as an important tool for studying this phenomenon.

  • Computational Tools for Complex Trait Gene Mapping - This session presented six talks on the novel computational and statistical strategies required for planning, executing, and analyzing the data of large association studies aimed to elucidate the basis of complex-traits, either common disease, response to environmental impact, or adverse drug response. This session was the presentation and discussion of new research, methods, algorithms, and tools, that promise to facilitate the elucidation of the connections between genotypes and complex-traits using the data generated by high-throughput SNP genotyping technologies.

  • Biomedical Ontologies - As we celebrate the 50th anniversary of the description of the structure of DNA, biology is evolving from a science of organisms and molecules to a science of information. Eight talks featured ontologies providing a conceptualization of a domain that can be shared among diverse groups of researchers and health care professionals and used computationally for multiple purposes. Promoting the creation and use of ontologies for the field and linking to other ontologies in related domains holds the promise of assisting those working in biomedical disciplines and thus making more rapid scientific progress.

  • Informatics Approaches in Structural Genomics - The goal of structural genomics is to discover and characterize the three dimensional structure of all proteins and other macromolecules found in nature. Currently there are ongoing efforts to develop high-throughput methods for protein structure determination both in industry and in academia. This session presented eight talks on the progress and achievements in the field through the use of computational techniques. Topic areas included in the discussions were (1) Progress in projects aimed at high throughput structure determination, (2) Structure-based functional prediction and classification and (3) Determining, using and analyzing large datasets of experimental and modeled proteins and nucleic acid structures.

In addition to the 48 presentations that made up the above six sessions of PSB 2004, a keynote address was delivered by Henry (Hank) Greely, the C. Wendell and Edith M. Carlsmith Professor of Law and a professor, by courtesy, of genetics at Stanford University. His riveting lecture, entitled Social Constraints on Acquiring and Using Human Biodata - Is Privacy Dead? focused on the difficult legal and ethical ramifications of biodata collection, use and storage.

A selection of tutorials was also presented immediately preceding the conference. They included (1) Systems Biology Host/Pathogen and Other ‘Community’ Interactions, (2) Creating Web Services for Bioinformatics, (3) Network (Reticulated) Evolution: Biology, Models, and Algorithms, and (4) Modeling Genetic and Metabolic Networks: Design of High Throughput Experiments.

In addition, ISCB hosted an open members meeting with a presentation on the state of the Society by Michael Gribskov, ISCB President. He discussed the 2003 year in review, looking back on the many accomplishments of the past year, and outlined goals and plans for 2004.

For more information on the past or future PSB conferences, please see http://psb.stanford.edu/ or contact Tiffany Jung, PSB Coordinator, at psb@smi.stanford.edu