Call for Papers and Posters

Computational Studies of non-coding RNAs

A session at the Pacific Symposium on Biocomputing 2010

January 4-8, 2010

The Big Island of Hawaii

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Background and Motivation

Until recently, RNA has been viewed as a simple ``working copy'' of the genomic DNA, simply transporting information from the genome into the proteins. In the 1980s, this picture changed, to certain extent, with the discovery of ribozymes and the realization that the ribosome is essentially an ``RNA machine''. Since the turn of the millenium, however, RNA has moved from a fringe topic to a central research topic following the discovery of RNA interference (RNAi), the post transcriptional silencing of gene expression via interactions between mRNAs and their regulatory RNAs.

More recent studies have revealed that a large fraction of the genome sequences give rise to RNA transcripts that do not code for proteins. Those RNAs that do not code for proteins are called non-coding RNAs (ncRNAs). A recent computational screen estimated the number of small regulatory RNAs (srRNAs), which form an important class of non-coding RNAs, in Arabidopsis thaliana to be in the order of 1.5 million. Among srRNAs two subclasses form the bulk of all regulatory RNAs: microRNAs (miRNAs) and small interfering RNAs (siRNAs) - which are of similar length (21 to 25 nt) and composition but different by origin. It is predicted that these two subclasses regulate at least one-third of all human genes. There are many other classes of non-coding RNAs with functionalities beyond simple regulation of gene expression: examples include snoRNAs, snRNAs, gRNAs, and stRNAs, which respectively perform ribosomal RNA (rRNA) modification, RNA editing, mRNA splicing and developmental regulation. The functionality of many such non-coding RNAs are only scarcely known.

In addition to such endogenous ncRNAs, antisense oligonucleotides have been used as exogenous inhibitors of gene expression; antisense technology is now commonly used for therapeutic purposes and as a research tool. The therapeutic objective of antisense technology is to block the production of disease-causing proteins. In principle, these artificial regulatory RNA molecules could be employed as drugs for the treatment of a variety of human diseases such as several types of cancer, rheumatoid arthritis, brain diseases, and viral infections. As a research tool, antisense nucleic acids may be utilized as inputs to the metabolic network of a cell to control or interfere with the dynamics and function of various modules in the network. Furthermore, synthetic nucleic acid systems have been engineered to self assemble into complex structures performing various dynamic mechanical motions. Despite advances in computational studies of non-coding RNA, there are still many open areas and unresolved issues particularly for high-throughput applications based on the new genome sequencing technologies.

Session Objective and Scope

The main objective of this session is to discuss new algorithms, software tools and their applications in non-coding RNA bioinformatics. Recent improvements in sequencing methods introduced high-throughput, low-cost, and cloning-free (thus less labor-intensive) technologies. The revolution in DNA sequencing will shortly result in an enormous collection of sequence data pertaining to the genomes and transcriptomes of various human individuals from different populations and also various species. Exact and approximation, possibly high-throughput, algorithms and tools are therefore needed for non-coding RNA studies. Specific topics include:

• Algorithms for modelling interactions between RNAs and other molecules, particularly RNA-RNA and RNA-protein interactions
• Learning thermodynamic parameters that are involved in the prediction of secondary and tertiary structure of non-coding RNAs
• Novel approaches to single or joint RNA structure prediction and determination
• Algorithms for exploring RNA folding pathways and kinetic traps on the energy landscape
• Alignment and comparative analysis of multiple non-coding RNA sequences
• RNA evolution
• Functional classification of non-coding RNAs
• Modelling classes of single or joint non-coding RNAs through stochastic context free grammars and their variations
• Tools that detect structural motifs in a genome sequence, especially those that could be potentially involved in the regulation of target mRNAs
• Combinatorial and heuristic tools for de novo non-coding RNA identification in a genome sequence
• Efficient algorithms for searching RNAs in a data collection with specific sequence and structural motifs

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

Please see the PSB paper format template and instructions at http://psb.stanford.edu/psb-online/psb-submit.

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 20, 2009--updated deadline for this session only
• Notification of paper acceptance: September 10, 2009
• Final paper deadline: September 21, 2009 at 11:59pm PT
• Poster abstract deadline: November 9, 2009 at noon PT
• Meeting: January 4-8, 2010

Session Co-Chairs

Rolf Backofen

Institute of Computer Science, Albert-Ludwigs-University Freiburg, Germany

backofen@informatik.uni-freiburg.de

Hamidreza Chitsaz

School of Computing Science, Simon Fraser University, Canada

hrc4@cs.sfu.ca

Ivo Hofacker

Institute for Theoretical Chemistry, University of Vienna, Austria

ivo@tbi.univie.ac.at

S. Cenk Sahinalp

School of Computing Science, Simon Fraser University, Canada

cenk@cs.sfu.ca

Peter F. Stadler

University of Leipzig, Germany

studla@bioinf.uni-leipzig.de