2006 LSS Computational Systems Bioinformatics Conference Workshop on
Comparative Genome Analyses of Bacterial Genomes and Applications
Friday, August 18, 2006 Stanford, CA
Organized by: John C. Wooley, Hongwei Wu, Fenglou Mao & Heidi J. Sofia

SPEAKERS:

  • Robert Edwards, Fellowship for Interpretation of Genomes, and San Diego State University
  • Jonathan A. Eisen, The Institute for Genomic Research
  • Arthur Grossman (or Devaki Bhaya), Stanford University
    Lecture title: "Thermophilic, mat-dwelling cyanobacterial strains, Diversity and metabolism"
  • Kostas Mavrommatis, Joint Genome Institute
    Lecture title: "METAGENOMIC ANALYSIS: BENCHMARKING METHODS AND TOOLS"
  • Maria Poptsova, University of Connecticut
    Lecture title: "AUTOMATED ASSEMBLY OF GENE FAMILIES AND DETECTION OF HORIZONTALLY TRANSFERRED GENES"
  • Heidi J. Sofia, Pacific Northwest National Laboratory
  • John C. Wooley, University of California San Diego
  • Ying Xu, University of Georgia
    Lecture title: "Characterization of microbial genome structure and application to biological pathway prediction "
THEME AND SCOPE:

The world-wide genome sequencing efforts have produced ~400 complete bacterial genomes, and this number is expected to extend beyond 10,000 within the next few years. With the pool of complete bacterial genomes rapidly growing, which represents an increasingly richer source of information, comparative genomic analysis has clearly become one of the most important classes of tools for mining the genomes and for studying bacterial biology and evolution at a systems level. The community is clearly in an urgent need for more powerful methodologies, tools and application protocols to help address fundamental biological problems regarding, e.g., mechanisms of bacterial genome evolution.
Invited scientists from leading research centers/laboratories will present their work in the field of comparative genomic analysis, particularly for the studies of bacterial biology and evolution, which may cover but may not be limited to the following topics:
  • Metagenomics
  • Modeling of phylogenetic and environmental diversities of bacterial genomes, and its application to the design of comparative genomic analysis;
  • Prediction and analysis of homologous/orthologous genes with the presence of uncertainties and noise;
  • Prediction and analysis of cis-regulatory elements and their homologs/orthologs across bacterial genomes;
  • Prediction and analysis of high-level genomic structures (e.g., operons, uber-operons, and regulons) and their homologs/orthologs across different bacterial genomes;
  • Prediction and analysis of biological networks/pathways and their homologs/orthologs across different bacterial genomes;
  • Evolution and adaptation of bacterial genomes;
  • Computational issues.

The workshop is aimed to eliminating barriers and providing a platform for researchers from different disciplines to exchange visions, insights, ideas, and discoveries about the challenges and opportunities in the field, to share and appreciate research efforts that have been devoted to the field, provide and seek advice/suggestion/solutions to some problems in the field, and to establish face-to-face collaboration.