Call for Papers and Posters Microbiome studies: Understanding how the dominant form of life affects us Pacific Symposium on Biocomputing January 3-7, 2011 Fairmont Orchid Resort The Big Island of Hawaii, U.S.A.

Motivation

Microbes, including eubacteria, archaea, and single celled eukaryotes, are the dominant forms of life on earth. They dominate "large" organisms like us in absolute numbers, biomass, habitat dominance, and phylogenetic diversity. During more than half of the Earth's history, only microbes existed. It has been known for over thirty years that, in the human body there are ten times more microbial cells than human cells. Microbial genes outnumber human genes in each of us by at least two orders of magnitude. Microbial physiology is a dominant factor in carbon cycling, greenhouse gas emission and oxygen production. Microbes live deep in the earth's crust, in the deep ocean, in frozen and boiling waters, and in both highly acidic and highly basic environments. However, over 97% of all microbes cannot be cultivated, which has significantly biased existing model systems and microbial genome sequencing projects. Consequently, we have until recently it has been difficult to appreciate the complexity and function of some of the most important ecological players on earth.

Fortunately, new sequencing and bioinformatics technologies such as tagged barcoding, community genomics, pyrosequencing and metagenomics, large scale genotyping, and large scale genome sequencing have made it possible to study the structure, function and dynamics of microbial communities in natural microbiomes. Surveys of the human microbiome are emerging, including the microbiomes of the gastrointestinal tract, skin, reproductive tracts, and oral cavities, along with their affects on obesity, women's health, peradontal disease, and other human health concerns. Ecological surveys of soil, air, and water are emerging in order to understand the consequences of climate change, pollution, deforrestation, and agricultural practices. Studies of microbial consortia in extreme environments are shedding light on the origins of life, and on possible mechanisms for bioremediation of severely poluted sites. At the same time, new bioinformatics tools and community resources for storing and analyzing community genomic data are coming online.

Nonetheless, microbiome studies are scarcely in their infancy. Most natural ecosystems remain uncharacterized. Many human microbiome sites have not been studied at all, and even fewer comparative studies of microbiomes in healthy versus diseased patients exist. Mechanisms for microbial adaption and ecological engineering are far from systematic. And the computational tools to enable us to meet these needs are in their infancy, at best.

Session Topics

We invite contributions to microbiome studies that expand our understanding of the composition, structure, and function of microbial ecosystems and their impact on human health and well being. We particularly encourage studies that apply "next generation" sequencing technologies, and reports of tools that support the analysis and sharing of data from such studies. Problems of specific interest may include, but are not limited to:

• Algorithm, tool, and database development for analyzing data from shotgun metagenomics, 16S hypervariable region surveys, and microbial transcriptomics.
• Association studies of microbial consortia with human health, agriculture, bioremediation, climate change, and engineering.
• Theoretical and simulation studies of microbial ecology, function, and evolution.
• The role of microbial consortia in natural ecosystems.

Other topics within the subject area are welcome. Note that all submitted papers should make clear their relevance for the study of Microbiome Studies. If unsure whether your paper fits the session theme, please contact one of the co-chairs.

Session Co-Chairs

James A. Foster, Ph.D. University of Idaho foster _AT uidaho _DOT edu

Jason Moore, Ph.D. Dartmouth Medical School Jason.H.Moore _AT Dartmouth _DOT edu

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: July 18, 2010 (EXTENDED!)
• Notification of paper acceptance: September 10, 2010
• Camera-ready final paper deadline: September 20, 2010 at 11:59pm PT
• Abstract deadline for non-reviewed posters: November 29, 2010 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.

Please note that, unlike many biology conferences, the PSB proceedings is an archival, peer-reviewed publication. PSB publications are indexed in Medline, and should be thought of as short journal articles. Submissions which do not reach this level of publication quality can be disseminated at the meeting through a separate booklet of unrefereed abstracts, and/or by poster presentations.

Contact Russ Altman at psb.hawaii at gmail.com for additional information about paper submission requirements.