• Conference program

    11th October

    17:00 - 18:00

    Registration and poster setup

    18:20 - 18:30

    Welcome address
    Matthew Cockerill, BioMed Central

    18:30 - 19:15

    Keynote: Between a chicken and a grape: estimating the number of human genes
    Steven Salzberg, University of Maryland, College Park, USA

    19.30 - 20:00

    Keynote: Reading and writing genomes
    George Church, Harvard Medical School, Boston, USA

    20:15 - 21:30

    Poster viewing

    21:30

    End of Day 1

    12th October

    08:00 - 08:30

    Registration

    Session 1: Sequencing Cancer and Complex Disease Genomes
                     Chair: Elaine Mardis, Washington University School of Medicine, St Louis, USA

    08:30 - 09:15

    Keynote: Next-generation cancer genomics
    Elaine Mardis, Washington University School of Medicine, St Louis, USA

    09:15 - 09:45

    Gene discovery for complex diseases using exomic sequencing: identifying pancreatic cancer susceptibility genes
    Alison Klein, Johns Hopkins University, Baltimore, USA

    09:45 - 10:15

    Personalized oncogenomics
    Steven Jones, Genome Science Centre, Vancouver, Canada

    10:15 - 10:45

    TBA
    Craig Thompson, University of Pennsylvania, Philadelphia, USA

    10:45 - 11:15

    Coffee break

    11:15 - 11:45

    Large-scale identification of tissue-specific enhancers in vivo
    Len Pennacchio, Lawrence Berkeley University National Laboratory, USA

    11:45 - 12:15

    Deciphering the genetic basis of common diseases by integrated functional annotation of common and rare variants
    Olivier Harismendy, The Scripps Research Institute, La Jolla, USA

    Selected talks

    12:15 - 12:30

    BIC-seq: a fast algorithm for detection of copy number alterations based on high-throughput sequencing data
    Peter Park, Harvard Medical School, Boston, USA

    12:30 - 12:45

    Candidate genes and biological processes from autism de novo CNVs
    Hyun Noh, University of Oxford, UK

    12:45 - 13:00

    A genomewide ordered-subset linkage analysis for alcohol dependence in African-Americans
    Shizhong Han, Yale University, New Haven, USA

     

    13:00 - 13:15

    Session sponsor: Avadis NGS – Next-Gen Sequencing analysis for the rest of us
    Thon de Boer, Strand Life Sciences

    13:15 - 14:00

    Lunch

    Session 2: The true gene count. How much of the genome is functional?
                     Chair: Michele Clamp, Bioteam, Boston, USA

    14:00 - 14:30

    TBA
    Michele Clamp, Bioteam, Boston, USA

    14:30 - 15:00

    Most of the 6.5% - 10% of human DNA bases that are functional now will soon be turned over
    Chris Ponting, University of Oxford, UK

    15:00 - 15:30

    The developmental transcriptome of Drosophila melanogaster
    Brenton Graveley, University of Connecticut Health Center, Farmington, USA

    15:30 - 16:00

    Transcriptomics in a high-throughput world
    Chad Nusbaum, Broad Institute, Cambridge, USA

    16:00 - 16:30

    Coffee break

    16:30 - 17:00

    Synthetic and sequencing-based approaches to high-throughput genetic analysis
    Jay Shendure, University of Washington, Seattle, USA

    17:00 - 17:15

    Session sponsor: From Sample to Sequence: Caliper Solutions for Next Generation Sequencing
    Isaac Meek, Caliper Life Sciences

    17:15 - 17:30

    Helicos single molecule sequencing: unique capabilities and corresponding importance for molecular diagnostics
    Patrice Milos, Helicos BioSciences, Cambridge, USA

    Selected talks

    17:30 - 17:45

    Defining the human reference protein-coding gene set
    Suganthi Balasubramanian, Yale University, New Haven, USA

    17:45 - 18:00

    From identification to validation to gene count
    Clara Amid, The Wellcome Trust Sanger Institute, Hinxton, UK

    18:00 - 18:15

    Beyond the FANTOM4
    Harukazu Suzuki, RIKEN Omics Science Center, Yokohama, Japan

     

    18:30 - 19:30

    Poster viewing

    20:00 - 23:00

    Conference dinner - Elements at Harvard Medical School

    23:00

    End of Day 2

    13th October

    Session 3: Microbiomes in human and other environments
                     Chair: Rob Knight, University of Colorado, Boulder, USA

    08:30 - 09:00

    Translational medicine and the human microbiome
    Rob Knight, University of Colorado, Boulder, USA

    09:00 - 09:30

    TBA
    Stephan Schuster, Pennsylvania State University, University Park, USA

    09:30 - 10:00

    Exploring the human gut microbiome
    Jun Wang, Beijing Genomics Institute, Shenzhen, China

    10:00 - 10:30

    Skin microbiome in health and disease
    Julie Segre, National Human Genome Research Institute, NIH, Bethesda, USA

    10:30 - 11:00

    Coffee break

    11:00 - 11:30

    The rare biosphere: sorting out fact from fiction
    Mitchell Sogin, Josephine Bay Paul Center, Woods Hole, USA

    Selected talks

    11:30 - 11:45

    A data analysis and coordination center for the Human Microbiome Project
    Jennifer Wortman, University of Maryland School of Medicine, Baltimore, USA

    11:45 - 12:00

    Statistical methods for comparing the abundances of metabolic pathways in metagenomics
    Bo Liu, University of Maryland Institute for Advanced Computer Studies, College Park, Baltimore, USA

    12:00 - 12:15

    Beyond the genome (BTG) is a (PGDB) pathway genome database: HumanCyc
    Miles Trupp, SRI International, Menlo Park, USA

     

    12:15 - 13:00

    Lunch

    Session 4: Insights from genomic analyses into evolution
                     Chair: Sarah Tishkoff, University of Pennsylvania, Philadelphia, USA

    13:00 - 13:30

    Genomic variation and adaptation in Africa: implications for human evolutionary history and disease
    Sarah Tishkoff, University of Pennsylvania, Philadelphia, USA

    13:30 - 14:00

    Reconstructing sex chromosome evolution
    David Page, Whitehead Institute for Biomedical Research, Cambridge, USA

    14:00 - 14:30

    Mining 1000 Genomes data to identify the causal variant in regions under positive selection
    Shari Grossman, Broad Institute, Cambridge, USA

    14:30 - 15:00

    Tracking for Genes and Finding Mutations: Finding Genes for Complex Traits in the Domestic Dog (Canis familiaris)
    Elaine Ostrander, National Human Genome Research Institute, NIH, Bethesda, USA

    15:00 - 15:30

    Coffee break

    Selected talks

    15:30 - 15:45

    Genome sequencing and analysis of admixed genomes of African and Mexican ancestry: implications for personal ancestry reconstruction and multi-ethnic medical genomics
    Francisco De La Vega, Life Technologies, Foster City, USA

    15:45 - 16:00

    Genome wide association study SNPs in the human genome diversity project samples: Does selection affect unlinked SNPs with shared trait associations?
    Amanda Casto, Stanford University, USA

    16:00 - 16:15

    The genetic structure of South Asian populations as revealed by 650 000 SNPs
    Mait Metspalu, University of Tartu, Estonia

    16:15 - 16:30

    Next-generation sequencing and the era of personal Y genomes
    Qasim Ayub, The Wellcome Trust Sanger Centre, Hinxton, UK

    Session 5: Workshop: Cloud computing in genomics and bioinformatics
                     Chair: Folker Meyer, Argonne National Lab, University of Chicago, USA

    16:45 - 17:00

    Welcome and Overview
    Folker Meyer, Argonne National Lab, University of Chicago, and Vivien Bonazzi, National Human Genome Institute, Bethesda, USA

    The novel cloud platform

    17:00 -17:20

    The cloud platform - a purely technical perspective. Paradigm, security, data transfer, limitations
    Narayan Desai, Argonne National Laboratory, University of Chicago, USA

    17:20 - 17:40

    Using commercial clouds for bioinformatics
    Chris Dagdigian, Bioteam, Boston, USA

    17:40 - 18:00

    Private clouds
    Bob Grossmann, Open Cloud Consortium / Bionimbus, USA

    18:00 - 18:20

    Coffee break

    Three parallel sessions with different foci

    18:20 - 19:20

    Session I: Getting on to the cloud and sequence analysis in the cloud
    Titus Brown, Michigan State University, USA

    18:20 - 19:20

    Session II: Using CLOVR for bioinformatics purposes
    Florian Fricke and Sam Angiuoli, University of Maryland School of Medicine,
    Antonio González Peña and Nigel Cook, University of Colorado, USA

    18:20 - 19:20

    Session III: Real technical challenges and limitations of the cloud platform
    Narayan Desai, Argonne National Laboratory, and Michael Schatz, Cold Spring Harbor Laboratory, USA

    Real-world examples

    19:20 - 19:40

    Assembly in the cloud
    Michael Schatz, Cold Spring Harbor Laboratory, USA

    19:40 - 20:00

    The Galaxy workflow system
    James Taylor, Galaxy, Emory University, USA

    20:00 - 20:20

    The Argonne Workflow Engine (AWE): scaling applications inside the cloud
    Narayan Desai, Argonne National Laboratory, USA

    20:20 - 20:40

    Applying Cloud Computing to Community Genome Analysis & Distribution
    Lincoln Stein, Cold Spring Harbor Laboratory, USA

    20:20 - 20:40

    Closing remarks

    20:50

    End of Day 3

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