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 OctoberSession 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 |
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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