Call for Papers and Posters

Computational Challenges in the Study of Small Regulatory RNAs

A session at the Pacific Symposium on Biocomputing 2008

January 4-8, 2008

The Big Island of Hawaii

Motivation and Significance

Small regulatory RNAs such as microRNAs and small interfering RNAs (siRNAs) are a class of non-coding RNAs that are primarily involved in post-transcriptional gene silencing. microRNAs are single-stranded ~21 nucleotide RNAs that guide a gene silencing complex to an mRNA by complementary base pairing at the 3’ untranslated region (3’UTR). The association of the silencing complex to the conjugate mRNA results in silencing the gene either by translational repression or by degradation of the mRNA.

In recent years, microRNAs have emerged as a major class of regulatory genes central to a wide range of cellular activities, including stem cell maintenance, developmental timing, cell proliferation, metabolism, host-viral interaction, apoptosis and neuronal gene expression. Because of their central role, changes in the expression, sequence or target sites of microRNAs are associated with a number of human genetic diseases including the pathogenesis of cancer. The importance of microRNAs is further underscored by their ubiquitous expression in almost all cell types as well as their evolutionary conservation in most of the metazoan and plant species.

The molecular pathway of gene silencing by microRNAs is also the basis for the powerful RNA interference (RNAi) experimental technique that is used to selectively silence genes. This technique is currently employed in a high throughput manner to investigate the effects of gene repression and is being adopted for therapeutic purposes.

In addition to microRNAs and siRNAs, new types of regulatory small RNA have been identified, including rasiRNAs, PIWI-interacting RNAs (piRNAs) and more recently 21U-RNAs. Collectively, the discovery of these sequences and their regulatory roles has had a profound impact on our understanding on the post-transcriptional regulation of genes, suppression of transposable elements, heterochromatin formation and programmed gene rearrangement.

Computational Problems and Session Scope

Recent work on the biochemical and functional characterization of microRNAs and other small regulatory RNAs has been facilitated by computational efforts, such as microRNA target predictions, conservation and phylogenetic analysis, microRNA gene predictions and microRNA expression profiling. Many of these computational problems are the subject of ongoing research. Moreover, new computational challenges continue to emerge as new types of regulatory RNAs are discovered, new datasets published and new mechanistic details revealed.

The scope of this session is intended to encompass the wide range of computational challenges related to this field; suggested topics include:

• microRNA target prediction, using novel algorithms and new methods that integrate other sources of experimental data (e.g. mRNA expression and proteomics data)
• Elucidating the mechanism of microRNA post-transcriptional regulation, including mode of regulation (translational arrest vs. mRNA degradation) and interaction with the silencing complex
• Incorporating microRNA regulation into pathway models and regulatory networks
• Analysis of transcriptional regulation of microRNAs and microRNA expression studies
• Design of RNAi screening libraries and minimizing off-target effects
• Functional prediction for new classes of small regulatory RNAs (e.g. piRNA, 21U-RNA)
• Discovery of new microRNAs and other non-coding RNA genes
• The role of microRNAs in human diseases
• Computational study of the evolution and conservation of microRNAs

General Information on Papers and Presentations

The scientific core of the conference consists of rigorously peer-reviewed full-length papers reporting on original work. Accepted papers will be published in an archival proceedings volume (fully indexed in PubMed), and a number of the papers will be selected for presentation during the conference. Researchers wishing to present their research without official publication are encouraged to submit a one-page abstract, and present their work in a poster session.

Paper Formatting and Submission

All papers must be submitted to psb-submit @ helix.stanford.edu in electronic format with PSB in the subject line. The only acceptable file formats are Adobe Acrobat (*.pdf) and postscript (*.ps). Attached files should be named with the last name of the first author (e.g., altman.pdf or altman.ps). 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:

• The email address of the corresponding author
• The specific PSB session that should review the paper or abstract
• The submitted paper contains original, unpublished results, and is not currently under consideration elsewhere
• All co-authors concur with the contents of the paper

Submitted papers are limited to twelve (12) pages in the official PSB publication format. Please format your paper according to these instructions, which can be found at http://psb.stanford.edu/psb-online/psb-submit/. If figures cannot 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.

Important Dates

• Paper submission deadline: July 16, 2007

• Notification of paper acceptance: September 5, 2007
• Final paper deadline: September 24, 2007
• Poster abstract deadline: November 9, 2007
• Meeting: January 4-8, 2008

Session Co-Chairs

Doron Betel,

Memorial Sloan-Kettering Cancer Center, New York

betel@cbio.mskcc.org

Christina Leslie

Columbia University, New York

cleslie@cs.columbia.edu

Nikolaus Rajewsky

Max Delbrück Centrum for Molecular Medicine, Berlin

rajewsky@mdc-berlin.de