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Motivation
Biological functions are often explained in terms of networks and pathways. Innumerable college students have memorized canonical metabolic pathways, and signal transduction pathways such as MAPK, JAK/STAT and WNT have entered the biological lexicon.
Inasmuch as these pathways provide a useful abstraction of biology, they can be used as a framework for understanding how mutations affect life processes and potentially cause disease. While much work has been invested in mapping these and other pathways in human and simpler model organisms, our knowledge remains incomplete and efforts to infer how pathways are perturbed in disease are limited by current scientific understanding of the full spectrum of inter-molecular interactions within cells and organisms.
A promising approach to discovery of pathways and their disease relevance is to develop network models, based on measurements of the individual interactions between proteins, genes, metabolites, drugs, and other species. In model organisms these networks can be perturbed by directed experiments. Directed perturbations of human networks in vivo are not possible, but genotype and phenotype data sets from individuals present a rich spectrum of information for network modeling and analysis.
High-dimensional data sets potentially useful for network modeling and analysis have been generated by GWAS, proteomic and metabolomic studies, cancer genome projects (Cancer Genome Atlas, International Cancer Genomics Consortium), pharmacogenomic studies of cancer cell lines (NCI-60, CCLE), and genome-wide functional element studies (ENCODE). These very large data sets characterize genome-wide RNA transcript abundance, DNA methylation, copy number variation, inherited and somatic DNA sequence variation, structural rearrangements, transcription factor binding sites, histone marks, chromatin accessibility, RNA binding and cellular abundance of peptides and metabolites.
Interpretation of this data urgently requires new analysis methods, algorithms, and visualization tools, presenting a significant challenge to the computational biology and bioinformatics community.
This year we are particularly interested in papers whose primary focus is not using network models as a basis for gene ranking but rather papers that focus on novel approaches to network algorithms and analysis.
Session Topics
— Top-down and bottom-up approaches to infer altered pathway activities.
— Algorithms/analysis targeted at high-dimensional data sets in model organisms.
— Issues in applying methods developed in model organisms to human data sets.
— Network modeling of the effects of mutations in cancer.
— Network modeling of genomic alterations underlying complex disease phenotypes.
— Network models and algorithms to identify epistatic and synthetic lethal relationships in high-dimensional data sets.
— Identifying large macromolecular complexes from high-throughput interaction data.
Session Co-Chairs
Rachel Karchin
Johns Hopkins University
karchin at jhu dot edu
Michael Ochs
Johns Hopkins University
mfo at jhu dot edu
Josh Stuart
University of California, Santa Cruz
jstuart at ucsc at soe dot ucsc dot edu
Joel Bader
Johns Hopkins University
joel dot bader at jhu dot edu
Trey Ideker
University of California, San Diego
trey dot ideker at gmail dot com
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.
Submission Information
Please note that the submitted papers are reviewed and accepted on a competitive basis. At least three reviewers will be assigned to each submitted manuscript.
Important Dates
— Paper submissions due: August 5, 2012 extended deadline for this session
— Notification of paper acceptance: September 10, 2012
— Camera-ready final paper deadline: October 1, 2012 at 11:59pm PT
— Abstract deadline for non-reviewed posters: November 28, 2012 at noon PT
Paper Format
Please see the PSB paper format template and instructions at http://psb.stanford.edu/psb-online/psb-submit/.
The file formats we accept are: postscript (*.ps) and Adobe Acrobat (*.pdf)). Attached files should be named with the last name of the first author (e.g. altman.ps or altman.pdf). 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 our publication format. Please format your paper according to instructions 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.
Contact PSB at psb.hawaii @ gmail.com for additional information about paper submission requirements.
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