The paper submission deadline has passed, and the list of accepted papers has been selected by our referees.
The thirteenth Pacific Symposium on Biocomputing (PSB), will be held January 4-8, 2008 at the Fairmont Orchid on the Big Island of Hawaii. PSB will bring together top researchers from North America, the Asian Pacific nations, Europe and around the world to exchange research results and address open issues in all aspects of computational biology. PSB will provide 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. PSB intends to attract a balanced combination of computer scientists and biologists, presenting significant original research, demonstrating computer systems, and facilitating formal and informal discussions on topics of importance to computational biology.
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 2008 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://psb.stanford.edu/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.
An email confirmation will be sent to you once the paper has been checked for proper format. Please allow 2-3 business days for the confirmation. If you do not receive confirmation after 3 days, please contact the PSB Coordinator (email: psb @ helix.stanford.edu).
Contact Russ Altman (psb-submit @ helix.stanford.edu) for additional information about paper submission requirements.
This session focuses on multiple sequence alignment and phylogeny estimation under complex models of evolution. We invite papers that present and evaluate in some detail new models and methods for these two problems that go beyond the current limitations to indels and site substitutions, e.g., by handling location- or neighbor-dependencies, by modeling genomic scale events (duplication and loss, rearrangements, etc.), or by targeting noncoding regions.Contact: Tandy Warnow
In recent years, small regulatory RNAs -- particularly microRNAs and siRNAs -- have emerged as a major class of genetic regulators primarily
involved in post transcriptional gene silencing. Their function is central to many cellular processes and they are implicated in a number
of human diseases, including cancer pathogenesis. The molecular pathway of regulatory RNAs is also the basis for the powerful RNAi
technology that is used to selectively silence genes. Many of the advances in this field are facilitated by computational efforts
related to the discovery and functional characterization of these RNA genes.
This session will focus on new computational work in the area of small regulatory RNAs and RNAi technology. It is intended to cover the wide range of computational challenges in this field, including the discovery, functional characterization biogenesis and modeling of small regulatory RNAs.
This session will be focused on the computational methods, tools, and algorithms required for utilizing the staggering volumes of short sequence reads that the emerging next-generation sequencing platforms generate in several applications, including de novo genome sequencing, medical resequencing, gene expression, epigenomics, chromatin remodeling, and metagenomics.Contact:
The integration of diverse data types and the inclusion of a priori biological knowledge to address the curse of dimensionality problem common in high-throughput data are linked problems in data analysis. Data, such as from microarrays, SNP chips, mass spectrometry and metabolomic measurements, can have millions of measurements for a single system spanning genomic to phenotypic information. Methods for integration and analysis of such data are the focus of this session.Contact: Michael Ochs
We are seeking original research that aims to capitalize on novel computational methods and technological developments in addressing protein interactions in diseases or other bioinformatics approaches involving phenomic networks. The goal of this session is to bring together bioinformaticians, systems biologists, biomedical informaticians, physicians, pharmacologists, computer scientists, statisticians, members of the pharmaceutical industry and others to share their experience and scientific findings in these emerging fields.
Contact: Yves Lussier
Email: Lussier @ uchicago.edu
It is crucial to develop simulation systems that can operate at multiple scales to better understand human physiology for disease prevention and treatment. This session will address modeling focused on a particular system level such as proteins, cells, tissues, organs, up to organisms. It will also address modeling across scales from nanometers and nanoseconds for molecules to meters and minutes for human bodies.
Contact: Jung-Chi Liao
Email: liaojc @ stanford.edu
Genome-scale data are being gathered for gene expression, protein-protein and protein-ligand interactions, and protein-nucleic acid interactions, while efforts in structural biology are yielding structural data on proteins, protein complexes, and protein-ligand interactions. This session will focus on methods and studies that bridge structure, sequence, and function to infer previously undiscovered associations between these different aspects of protein-nucleic acid interactions.
Contact: Martha Bulyk
Email: mlbulyk @ receptor.med.harvard.edu
Tiling and other high density microarrays are becoming a standard for performing unbiased, genome-wide surveys of transcriptional regulation and chromosomal aberrations among others. High volumes of data generated by individual labs as well as the ENCODE consortium are being made publicly available. Analysis of these datasets present challenges - from computational efficiency to the need for effective algorithms for estimation and reduction of false discovery rates. This session will provide a forum for bioinformaticists and biostatisticians to discuss the present and future of the field.
Contact: Srinka Ghosh
Email: Srinka_Ghosh @ affymetrix.com
Biomedical science is now an information-intensive field, and this information must be accessible both to computers and to people. This requires translation between human-readable forms--e.g., text and figures--to computer-readable forms, such as databases and ontologies. Text mining has reached reasonable performance on some tasks, and we have seen several deployed systems. This raises new questions: Do these tools work? Are they robust? Are they usable, and if so, who uses them, and how? Are they cost-effective? Can they be adapted to new domains and maintained over time?
Contact: Kevin Bretonnel Cohen
Email: kevin.cohen @ gmail.com