Post-transcriptional gene regulation: RNA-protein interactions, RNA processing, mRNA stability and localization


Co-chairs:  Benjamin Blencowe, Steven Brenner, Timothy Hughes, Quaid Morris

Contact: Quaid Morris (


Schedule new!

Background and Scope


Regulation of gene expression at the post-transcriptional level is widespread in eukaryotes. As in the case of transcriptional regulation, differential regulation of gene expression at the levels of mRNA splicing, stability and localization is known to control networks of functionally-related genes.


The goal of our 3 hour workshop is to introduce some recent work in the area of post-transcriptional regulation to a wider computational community, discuss some of the unique computational problems faced in this area, and to present some preliminary solutions to these problems.


In particular, we will focus on emerging computational and large-scale experimental strategies (e.g. microarray and deep sequencing) for investigating aspects of gene regulation at the post-transcriptional level, with an emphasis on the identification and characterization of the cis- and trans-acting RNA and protein components involved.  We will also be exploring new developments in computational methods to detect and characterize cis-regulatory signals encoded in mRNAs.


Some proposed topics:


·        Alternative splicing

- Identifying and quantifying alternative splicing events using microarrays and deep sequencing (i.e. mRNA-Seq).

- Alternative splicing networks and the splicing code.

- Associating SNPs and other sources of genetic variation with changes in splicing


·        RNA-protein interactions

- Motif models for RNA-binding proteins (RBP) and algorithms for fitting those models to data.


·        Evolutionary models

- Models of the evolution of PTR mechanisms

- Detecting conservation and change of RNA-binding protein sites

- Evolutionary models of miRNA target site or RBP target site accessibility.


·        Regulatory Networks

- Methods for inferring networks of post-transcriptional regulation, or networks that combine both transcriptional and post-transcriptional regulatory networks.


·        MicroRNAs

- Methods for predicting microRNA targets based on sequence, expression, and/or secondary structure


Call for Abstracts


Our workshop will include talks selected from submitted abstracts as well as talks from invited speakers.  We also encourage abstract submissions from those wishing to present a poster.  Submitted abstracts will not be published in the PubMed-indexed PSB conference proceedings but we will self-publish an informal abstract book for the workshop attendees.

Submission instructions


Please submit your abstracts in Word, RTF, PDF, or Postscript format to  

  1. The abstract should be one page long in a 12 point font.
  2. Please leave at least a 1” margin between the text and the side of the page, and use the “letter” page size (i.e. 8.5” x 11”).
  3. The abstract title should appear at the top of the first page, and please list authors and affiliations directly under the title
  4. Underline the name of the presenter.
  5. Please indicate in your email whether or not we can publish a version of your abstract online before the workshop.


The co-chairs will determine which abstracts will be invited for oral presentations.


If your abstract is selected for an oral or poster presentation, you will be given an opportunity to submit a revised version of your abstract in early November.


Please also note if you are invited to speak at our workshop or wish to present a poster, you must register for PSB by September 19th, 2008.

Important Dates
Abstract submission deadline: August 31st, 2008
Notification of abstract decisions: September 16, 2008

•       Deadline for speaker registration: September 19, 2008
Meeting: January 5-9, 2008