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Call for Papers and Posters Protein-Nucleic Acid Interactions: Integrating Structure, Sequence, and Function Session at the Pacific Symposium on Biocomputing 2008 |
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This session will focus on novel research employing a combination of structure, sequence, and function to analyze the regulation of all stages of gene expression from transcription to splicing. Transcription of genes into RNA is in large measure regulated by proteins that bind DNA. These interactions include the basal transcription apparatus recognizing the core promoter and its associated general transcription factors; a host of other more specialized transcription factors that combinatorially regulate the transcription of specific subsets of genes through DNA-binding events; nucleosome-forming histones that regulate the structure of chromatin fibers; and factors like DNA methylases that mark the genome epigenetically, in some cases completely silencing gene expression. RNA sequence elements and RNA binding proteins also play a significant role in gene regulation by affecting mRNA stability and degradation. In addition to regulation of mRNA levels, regulatory complexity and protein diversity are further controlled at the level of splicing, which involves many RNA binding proteins that act in a combinatorial manner. There is now an opportunity to integrate functional and structural data, to understand how the biophysical aspects of protein-nucleic acid interactions affect their functions. Until recently protein-nucleic acid interactions have largely been studied either through structural approaches (for example, structure determination of the polymerase holoenzyme) or through computational approaches based on sequence data (for example, de novo motif finding algorithms, or phylogenetic footprinting) or functional expression data (for example, using gene expression data to infer genetic regulatory networks). Recent technological advances have enabled many different types of data to be gathered at a genome-wide and proteome-wide scale, including: genomic sequences, tissue-specific ESTs and mRNA expression data, the abundance of various RNA populations, protein-protein and protein-ligand interactions, chromosomal interactions, and protein-nucleic acid binding data. In addition, efforts in structural biology are yielding structural data on proteins, protein complexes, and protein-ligand interactions. These new data provide new opportunities for an integrative approach. Combining the previously distinct perspectives of structural, functional, and genomic analyses should improve our ability to identify essential biological associations, and ultimately to model and predict these interactions. Studies combining these different types of analysis and data may also spur new collaborations between researchers in these historically distinct fields. Session Focus: The session will focus on methods and studies that bridge structure, sequence, and function to infer previously undiscovered associations between these different aspects of protein-nucleic acid interactions. For example, can available experimental data on genome-wide protein-nucleic acid interactions allow one to infer structure-related features of these interactions; or vice versa? How does knowledge of structure allow one to find regulatory sequence motifs with greater sensitivity and specificity? Do certain types of domains of nucleic acid-binding proteins confer particular biophysical properties, either in terms of kinetics or ligand specificity, that would better explain their use in regulation of certain classes of genes? What DNA or RNA secondary structure sequence elements appear to be important for interactions with DNA or RNA binding proteins and what are the regulatory consequences? Priority will be given to manuscripts that combine all three perspectives, namely structure, sequence, and function. There will be a preference towards papers on protein-DNA and/or protein-RNA (including protein-coding and/or small noncoding RNA) interactions that combine the following types of data: protein-nucleic acid interaction data (such as from ChIP-chip, protein binding microarrays, etc.), protein or nucleic acid 3D structure data (or protein-nucleic acid 3D structure data), phylogenetic conservation from comparative genomic sequencing efforts, and gene expression data (including but not limited to splicing isoform-specific microarrays). Information from functional annotation databases, literature mining, or data regarding protein-protein interactions will also be of interest if the studies are otherwise connected with an integrative analysis of protein-nucleic acid interactions. Individuals who cannot submit to this session but are willing to help referee submissions are kindly requested to contact one of the session co-chairs before the paper submission deadline. General Information on PSB 2008: The Pacific Symposium on Biocomputing (PSB) 2008 is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. Papers and presentations are rigorously peer reviewed and are published in an archival proceedings volume. PSB 2008 will be held January 4-8, 2008 at the Fairmont Orchid on the Big Island of Hawaii. Tutorials will be offered prior to the start of the conference. PSB
2008 will bring together top researchers from the The PSB has been designed to be responsive to the need for critical mass in sub-disciplines within biocomputing. For that reason, it is the only meeting whose sessions are defined dynamically each year in response to specific proposals. PSB sessions are organized by leaders in the emerging areas and targeted to provide a forum for publication and discussion of research in biocomputing's "hot topics." In this way, PSB provides an early forum for serious examination of emerging methods and approaches in this rapidly changing field. More information on the conference can be obtained from the conference web page: http://psb.stanford.edu/. General Information on Papers, Abstracts, and Demonstrations: The scientific core of the conference consists of rigorously peer-reviewed full-length papers reporting on original work. Accepted papers will be published in a hard-bound archival proceedings volume (which is fully indexed in Medline), and the best of these will be presented orally to the entire 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: All
papers must be submitted to psb-submit @ helix.stanford.edu
in electronic format with PSB in the subject line. The only acceptable file formats are Adobe Acrobat (*.pdf). Attached files should be
named with the last name of the first author (e.g., altman.pdf). Hardcopy submissions or unprocessed Each paper must be accompanied by a cover letter. The cover letter must state the following:
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:
Session Co-chairs:
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