Genome-scale Pattern Analysis in the Post-ENCODE Era

Call for Abstracts

“With the genome sequence now established, the next challenge is to discover how the cell actually uses it as an instruction manual.” ¹

“The aim of the ENCODE (encyclopedia of DNA elements) project is exactly that — to identify every sequence with functional properties in the human genome. The results of the pilot phase of this project, which involved an analysis of 1% (30 megabases) of the human genome, are not good news for genes, which will no longer be able to hog the limelight. Even this preliminary study reveals that the genome is much more than a mere vehicle for genes, and sheds light on the extensive molecular decision-making that takes place before a gene is expressed.” ²

According to the above statements, which refer to findings of the ENCODE project, the meaning of most of the human genome remains a mystery! A recent editorial³ by the SIG Chairs discusses four startling outcomes of the ENCODE project:

much functional information is not “conserved” across organisms;
epigenetic marks predict the presence and activity of functional regions;
remarkably, up to 93% of bases in the ENCODE regions are transcribed; and
regulatory binding sites (motifs) extend upstream and downstream of transcription start sites.

An important implication of these outcomes is that the existing models for computational genomics are insufficient to handle the shifting paradigms of biological interpretation. Thus, the SIG will focus on specific research challenges that must be addressed to utilize computational genomics approaches to assimilate ENCODE’s findings into research and technology. The SIG will consist of a mix of presentations and discussions. The prevailing objectives are to engage participants in discussion, to raise awareness of computational approaches that are likely to benefit current research projects, and to foster a collaborative research environment. We are planning 4 technical sessions, each consisting of 1 plenary talk, 3 research presentations, and group discussion. Individuals who would like to make a research presentation at the SIG are invited to submit a 300 word abstract to the SIG Chairs by April 23, 2008. Topics of interest include the following:

The Post-ENCODE Paradigm
Identification of Novel Functional Elements
Genome-scale Pattern Analysis
Personalized medicine

Important Dates

Abstracts due: April 23, 2008
Acceptance notification: May 15, 2008
SIG Meeting at ISMB: July 21, 2008

SIG Chairs

Dr. Laura Elnitski, National Human Genome Research Institute, elnitski@mail.nih.gov
Prof. Lonnie R. Welch, Ohio University , welch@ohio.edu

References:

1. Decoding the blueprint (editor's summary), Nature 447 (14 June 2007).
2. John M. Greally, Genomics: Encyclopaedia of humble DNA, Nature 447, 782-783 (14 June 2007).
3. New Frontiers in Computational Genomics: Identification of Novel Functional Elements and Genome-scale Pattern Analysis, Laura Elnitski and Lonnie R. Welch, Scalable Computing: Practice and Experience, Volume 8, no. 3, pages i–vii (September 2007).



• Home • Call for Abstracts • Organizers • Program • Post-ENCODE book • ENCODE Project • Post-ENCODE Editorial • ISMB 2008	Genome-scale Pattern Analysis in the Post-ENCODE Era Special Interest Group (SIG) at ISMB 2008 21 July 2008, Toronto, Ontario

	Call for Abstracts “With the genome sequence now established, the next challenge is to discover how the cell actually uses it as an instruction manual.” ¹ “The aim of the ENCODE (encyclopedia of DNA elements) project is exactly that — to identify every sequence with functional properties in the human genome. The results of the pilot phase of this project, which involved an analysis of 1% (30 megabases) of the human genome, are not good news for genes, which will no longer be able to hog the limelight. Even this preliminary study reveals that the genome is much more than a mere vehicle for genes, and sheds light on the extensive molecular decision-making that takes place before a gene is expressed.” ² According to the above statements, which refer to findings of the ENCODE project, the meaning of most of the human genome remains a mystery! A recent editorial³ by the SIG Chairs discusses four startling outcomes of the ENCODE project: much functional information is not “conserved” across organisms; epigenetic marks predict the presence and activity of functional regions; remarkably, up to 93% of bases in the ENCODE regions are transcribed; and regulatory binding sites (motifs) extend upstream and downstream of transcription start sites. An important implication of these outcomes is that the existing models for computational genomics are insufficient to handle the shifting paradigms of biological interpretation. Thus, the SIG will focus on specific research challenges that must be addressed to utilize computational genomics approaches to assimilate ENCODE’s findings into research and technology. The SIG will consist of a mix of presentations and discussions. The prevailing objectives are to engage participants in discussion, to raise awareness of computational approaches that are likely to benefit current research projects, and to foster a collaborative research environment. We are planning 4 technical sessions, each consisting of 1 plenary talk, 3 research presentations, and group discussion. Individuals who would like to make a research presentation at the SIG are invited to submit a 300 word abstract to the SIG Chairs by April 23, 2008. Topics of interest include the following: The Post-ENCODE Paradigm Identification of Novel Functional Elements Genome-scale Pattern Analysis Personalized medicine Important Dates Abstracts due: April 23, 2008 Acceptance notification: May 15, 2008 SIG Meeting at ISMB: July 21, 2008 SIG Chairs Dr. Laura Elnitski, National Human Genome Research Institute, elnitski@mail.nih.gov Prof. Lonnie R. Welch, Ohio University , welch@ohio.edu References: 1. Decoding the blueprint (editor's summary), Nature 447 (14 June 2007). 2. John M. Greally, Genomics: Encyclopaedia of humble DNA, Nature 447, 782-783 (14 June 2007). 3. New Frontiers in Computational Genomics: Identification of Novel Functional Elements and Genome-scale Pattern Analysis, Laura Elnitski and Lonnie R. Welch, Scalable Computing: Practice and Experience, Volume 8, no. 3, pages i–vii (September 2007).	Important dates April 23, 2008 Abstracts due May 15, 2008 Acceptance Notification June 1, 2008 Final Abstracts Due July 21, 2008 SIG Meeting 8:30am-6:30pm

Call for Abstracts

Important dates