Pacific Symposium on Biocomputing 2013
January 3-7, 2013
The Big Island of Hawaii
Deadline extended to Wednesday, August 8, 2012
Scientists have known for a long time that the sequence of nucleotides that comprise the genome is not sufficient to explain the heritability of traits from one generation to the next, nor is that sequence sufficient to drive the myriad functions of a living cell. Recently, however, catalyzed by the rapid acquisition of a wide variety of genome-scale data sets from projects such as ENCODE, modENCODE, and the Epigenomics Roadmap, scientists have begun to recognize just how much information is encoded beyond the primary DNA sequence. Accordingly, many of the central questions facing biology today concern the interpretation and integration of epigenomic data with our existing knowledge of the molecular pathways within the cell, including DNA, RNA, proteins, and metabolites.
This session will focus on computational methods for the analysis and interpretation of various types of epigenomic data. We define the phenomena that fall under this heading fairly broadly, including histone modifications, DNA methylation, nucleosome positioning, chromatin structure and accessibility, and DNA-DNA interaction. The session will include papers that describe methods for building computational models of physical phenomena as well as methods for interpreting the functional significance of epigenomic data. Such papers may describe either the development and validation of novel analytical methods or the application of existing methods to novel data sets. Papers may describe methods for interpreting a single type of epigenomic data or methods for integrating heterogeneous data types. Overall, the session will emphasize techniques that are applicable on a genome-wide scale; however, recognizing the value in detailed analysis of small sets of well-studied loci, we welcome such submissions if the analysis yields broader insights, either methodological or biological.
- Michael Snyder is the Stanford Ascherman Professor and Chair of Genetics and the Director of the Center of Genomics and Personalized Medicine. Dr. Snyder received his Ph.D. training at the California Institute of Technology and carried out postdoctoral training at Stanford University. He is a leader in the field of functional genomics and proteomics. His laboratory study was the first to perform a large-scale functional genomics project in any organism, and currently carries out a variety of projects in the areas of genomics and proteomics both in yeast and humans. These include the large-scale analysis of proteins using protein microarrays and the global mapping of the binding sites of chromosomal proteins. His laboratory built the first proteome chip for any organism and the first high resolution tiling array for the entire human genome.
- Frank Pugh received his graduate training with Michael Cox from 1983-1987, studying the biochemistry of genetic recombination at the University of Wisconsin at Madison. He was then a Leukemia and Lymphoma Society postdoctoral fellow with Robert Tjian (from 1988-1991) at the University of California Berkeley, where he discovered the first set of eukaryotic transcriptional coactivators (TAFs in TFIID). Dr. Pugh joined the Penn State University faculty as a Searle Scholar in 1991. He is currently a professor and holder of the Willaman Chair in Molecular Biology in the department of Biochemistry and Molecular Biology. He is conducting biochemical and genomic research on molecular mechanisms that govern eukaryotic transcriptional regulation. He is an editor for Molecular and Cellular Biology, and the director of Penn States Center for Eukaryotic Gene Regulation.
- Paper submission deadline: August 8, 2012
- Notification of acceptance/rejection: September 10, 2012
- Camera-ready final paper deadline: October 1, 2012
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.
Please see the PSB paper format template and instructions at http://psb.stanford.edu/psb-online/psb-submit.
- Alexander J. Hartemink, Alexander F. Hehmeyer Associate Professor of Computer Science, Statistical Science, and Biology at Duke University
- Manolis Kellis, Associate Professor, Department of Computer Science and Engineering, Massachusetts Institute of Technology
- William Stafford Noble, Professor, Department of Genome Sciences and Department of Computer Science and Engineering, University of Washington
- Zhiping Weng, Professor, Program in Bioinformatics and Integrative Biology and Department of Molecular Pharmacology, University of Massachusetts Medical School
- Ferhat Ay, Postdoctoral Fellow, Department of Genome Sciences, University of Washington
Please direct questions to Ferhat Ay (firstname.lastname@example.org).