C O N T E N T S }
Volume 7, Issue 2
Call for Nominations
as Member of FASEB
and Opportunities of Interest
Symposium on Biocomputing 2004
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 ISCBs 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.
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.
2004 sessions included:
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.
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.
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.
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.
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.
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.
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.
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
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 email@example.com