RECOMB-SEQ: THIRD ANNUAL RECOMB SATELLITE WORKSHOP ON MASSIVELY PARALLEL SEQUENCING

April 11-12, 2013
Beijing, China

About the Workshop

RECOMB-seq is a workshop held immediately after the main RECOMB conference, with a distinct paper submission process and program. Our goal is to bring together the community of scientists working on methods for massively parallel sequencing.

Scope

The recent revolution in sequencing technology has opened the door for myriads of new applications and bio-medical discoveries. Projects are under way to sequence thousands of individuals (the 1000 Genome project), tens of thousands of vertebrate species (the Genome10K project), and the whole microbial ecosystem that live in our bodies (the Human Microbiome project). Simultaneously, the novelty and complexity of the data has highlighted the challenges and limitations of current methods. As the technology continues to evolve and approaches its third generation, the challenges facing the community are becoming increasingly computational.

We would like to invite contributions describing new methodology to deal with all aspects of massively parallel sequencing data, including, but not limited to:

• Bio-medical applications, including cancer genomics
• Discovery and genotyping of genomic variants; including SNPs, indels, and structural variants
• Local and de novo sequence assembly
• RNA sequencing, including the analysis of RNA expression and novel transcript assembly
• Epigenetics, including ChIP-SEQ analysis, methylation profiling, and histone modifications
• Metagenomics
• Read mapping
• Methods for emerging sequencing technologies, such as single-cell or single molecule real time sequencing

Paper Submission

We are soliciting high-quality contributions that will go through a rigorous peer-review process. Selected papers will be presented at the workshop and published in a special proceedings issue of BMC Bioinformatics. You may also specify that you do not wish your paper to be published in the proceedings, if accepted. In this case, you will be asked to provide a one-page abstract to be included in the conference program booklet.

The cover page should contain the title, author(s) names and affiliations, an abstract, the keywords, and the contact author e-mail. The manuscript should start with a succinct statement of the problem, the results achieved, their significance, and a comparison with previous work. This material should be understandable to non-specialists. A technical exposition directed to the specialist should follow. The length, excluding cover page and bibliography, should not exceed 10 pages. The manuscript should be easy to read, using at least 11 point font size on U.S. standard 8 1/2 by 11 inch paper with no less than one inch margin all around. If the authors believe that more details are absolutely necessary to substantiate the claims of the paper, they may include a clearly marked appendix, which might be read at the discretion of the reviewers. Manuscripts that deviate significantly from these guidelines risk rejection without consideration of their merits.

Speicial Note for Papers Submitted to RECOMB'2013

If you would like to consider submitting a paper rejected by RECOMB'2013 to the satellite workshop, you have the option of including, with your submission, the RECOMB'2013 reviews together with an explanation of how you have addressed the issues raised in the reviews. This will help enable a more thorough and accurate review for your paper. If you would like to use this option, please send an email to recombseq2013@easychair.org prior to the submission deadline and include your RECOMB'2013 reviews and your response to reviewers. Please note that your reviews will be treated confidentially and will only be visible to the PC members evaluating your paper.

Poster Submission

RECOMB-seq invites the submission of abstracts for the poster track. Please submit a one-page abstract (about 200 words, plain justified text in at least 10pt character size, formatted to fit A4: 21 x 29.7 cm) of your poster including title, author(s), affiliation, e-mail and abstract text, via the easychair system. The actual poster space will be 90 x 120 cm (width x height), which corresponds to A0 format (or 16 pages in A4 format). The accepted poster abstracts will be published in the workshop book of abstracts. Simultaneous submissions of the same poster to both RECOMB'2013 and RECOMB-Seq'2013 are permitted.

EasyChair Submission Site

Manuscript submission is closed. Poster abstracts should be submitted through the easyChair conference system, following this link: http://www.easychair.org/conferences/?conf=recombseq2013

Important Dates

Keynote Speakers

• Inna Dubchak (http://www.jgi.doe.gov/whoweare/dubchak.html), DOE Joint Genome Institute and LBNL, USA
• Bing Ren (http://bioinformatics-renlab.ucsd.edu/rentrac/), UCSD and Ludwig Institute for Cancer Research, USA
• Colin Collins (http://www.prostatecentre.com/about-us/people/clinical-research-scientists/dr-colin-collins), Vancouver Prostate Centre, Canada

Accepted Papers

After careful review, the program committee decided to accept these papers.

Program

Please visit this page to see the tentative program.

Steering Committee

• S. Cenk Şahinalp, Simon Fraser University, Canada
• Michael Brudno, University of Toronto, Canada
• Inanc Birol, BC Genome Sciences Centre, Canada
• Eran Halperin, Tel-Aviv University, Israel
• Ben Raphael, Brown University, USA

Program Committee

• Haixu Tang, Indiana University, Bloomington, USA (chair)
• Tao Jiang, University of California, Riverside, USA (chair)
• Max Alekseyev, University of South Carolina, USA
• Can Alkan, Bilkent University, Turkey
• Vikas Bansal, Scripps Translational Science Institute, USA
• C. Titus Brown, Michigan State University, USA
• Xin Chen, Nanyang Technological University, Singapore
• Francis Chin, University of Hong Kong, China
• Jason Ernst, UCLA, USA
• Peilin Jia, Vanderbilt University, USA
• Rui Jiang, Tsinghua University, China
• Sun Kim, Seoul National University, Korea
• Ben Langmead, John Hopkins University, USA
• Jingchu Luo, Peking University, China
• Paul Medvedev, Pennsylvania State University, USA
• Satoru Miyano, The University of Tokyo, Japan
• Adam Phillippy, National Biodefense Analysis and Countermeasures Center, USA
• Mina Rho, Rosewell Park Cancer Institute, USA
• Jared Simpson, Wellcome Trust Sanger Institute, UK
• Jens Stoye, Bielefeld University, Germany
• Xiao Sun, Southeast University, China
• Glenn Tesler, University of California, San Diego, USA
• Todd Treangen, BNBI/NBACC, USA
• Chaochun Wei, Shanghai Jiao Tong University, China
• Shibu Yooseph, J. Craig Venter Institute, USA
• Alex Zelikovsky, Georgia State University, USA
• Daniel Zerbino, UC Santa Cruz, USA
• Shaojie Zhang, University of Central Florida, USA
• Xuegong Zhang, Tsinghua University, China
• Fangqing Zhao, Beijing Institute of Life Sciences, China
• Zhongming Zhao, Vanderbilt University, USA

Local Organization Committee Chairs

• Xuegong Zhang, Tsinghua University, China
• Rui Jiang, Tsinghua University, China