PSB 2008

Call For Papers, Abstracts and Demonstrations

Pacific Symposium on Biocomputing

Big Island of Hawaii -- January 4-8, 2008

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:

Papers and posters

The core of the conference consists of rigorously peer-reviewed full-length papers reporting on original work. Accepted papers will be published in a hard-bound archival proceedings, and the best of these will be presented orally to the entire conference. Researchers wishing to present their research without official publication are encouraged to submit a one page abstract by November 9, 2007 to present their work in the poster sessions.

Important dates

Paper submissions due: July 16, 2007
Notification of paper acceptance: September 5, 2007
Final paper deadline: September 24, 2007 midnight PT
Abstract deadline: November 9, 2007
Meeting: January 4-8, 2008

Paper format

All papers must be submitted to psb-submit @ in electronic format with PSB in the subject line. The file formats we accept are: postscript (*.ps) and Adobe Acrobat (*.pdf). Attached files should be named with the last name of the first author (e.g. or altman.pdf). Hardcopy submissions or unprocessed TEX or LATEX files will be rejected without review.

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 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 @

Contact Russ Altman (psb-submit @ for additional information about paper submission requirements.

Travel support

We have been able to offer partial travel support to many PSB attendees in the past. However, please note that no one is guaranteed travel support. Travel support applications will be available on the website soon.

PSB 2008 Sessions:

Each session has a chair who is responsible for organizing submissions. Please contact the specific session chair relevant to your interests for further information. Links on each of the session titles below lead to more detailed calls for participation for each session.

Beyond Gap Models: Reconstructing Alignments and Phylogenies Under Genomic-Scale Events

Chair: Michael Brudno, Randy Linder, Bernard Moret, and Tandy Warnow

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
Email: tandy @

Computational Challenges in the Study of Small Regulatory RNAs

Cochairs: Doron Betel, Christina Leslie, and Nikolaus Rajewsky

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.

Contact: Doron Betel
Email: betel @

Computational tools for next-generation sequencing applications

Cochairs: Francisco De La Vega, Gabor Marth, and Granger Sutton

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.

Francisco M. De La Vega
E-mail: delavefm @

Knowledge-Driven Analysis and Data Integration for High-Throughput Biological Data

Cochairs: Michael Ochs, John Quackenbush, and Ramana Davuluri

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
Email: mfo @

Molecular Bioinformatics for Diseases: Protein Interactions and Phenomics

Cochairs: Atul Butte, Maricel Kann, Yves Lussier, Yanay Ofran, Marco Punta, and Predrag Radivojac

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 @

Multiscale Modeling and Simulation: from Molecules to Cells to Organisms

Cochairs: Jung-Chi Liao, Peter Arzberger, Roy Kerckhoffs, Anushka Michailova, and Jeff Reinbolt

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 @

Protein-Nucleic Acid Interactions: Integrating Structure, Sequence, and Function

Cochairs: Martha Bulyk, Ernest Fraenkel, Alexander Hartemink, and Yael Mandel-Gutfreund

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 @

Tiling Microarray Data Analysis Methods and Algorithms

Cochairs: Antonio Piccolboni and Srinka Ghosh

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 @

Translating Biology: Text Mining Tools that Work

Cochairs: Kevin Bretonnel Cohen, Philip Bourne, Lynette Hirschman, and Hong Yu

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 @

Back to the main PSB page