Select a year 2001 2002 2003    Select a researcher Alan G. Barbour, M.D. William Bishai, M.D., Ph.D. Martin J. Blaser, M.D. John C. Boothroyd, Ph.D. Jon Clardy, Ph.D. Peter Cresswell, Ph.D. Roy Curtiss, III, Ph.D. Ronald W. Davis, Ph.D. Jack E. Dixon, Ph.D. Stanley Falkow, Ph.D. Gerald R. Fink, Ph.D. Richard A. Flavell, Ph.D. Lee Gehrke, Ph.D. Laurie H. Glimcher, M.D. Jeffrey I Gordon, M.D. Daniel L. Hartl, Ph.D. William R. Jacobs, Jr., Ph.D. Keith A. Joiner, M.D., co-PI Karla Kirkegaard, Ph.D. Roberto G. Kolter, Ph.D. W. Ian Lipkin, M.D. Richard M. Locksley, M.D. Carl Nathan, M.D. Peter Palese, Ph.D. Pradipsinh K. Rathod, Ph.D. David A. Relman, M.D. Charles M. Rice, Ph.D. Alexander Rich, M.D. Lee W. Riley, M.D. David S. Roos, Ph.D. Abigail A. Salyers, Ph.D. Gary K. Schoolnik, M.D. Iwona Stroynowski, Ph.D. Ronald P. Taylor, Ph.D. Elisabetta Ullu, Ph.D. John Waitumbi, D.V.M., Ph.D Select a project A Gnotobiotic Zebrafish Model for Analyzing Symbiotic Host...Antiviral Effects of Interferon-Inducible Cytosolic ProteinsArming the Immune System against Pathogens with Selective ...Bacterial Pathogen Families that Function in Both the Anim...Cellular Genes and Viruses: Who Wins The War?Conditional Targeted Deletions in Plasmodium falciparum...Designing and Mining Pathogen Genome Databases: The Apicop...Development of Genetic Systems for Genetically Intractable...Development of New Genetic Tools to Identify Nutrient Upta...Ecological Influences on Pathogen Genome EvolutionEvolution of Virulence in Eukaryotic PathogensExploiting an Evolutionary Omission in Pathogenic RNA Viru...Exploring Novel Pathways of Immune Defenses Against Orally...Genomic Approach to Improved Immunogenicity of M. tuber...Genomic tools to characterize hypermutating Plasmodium fal...Investigation of Mechanisms Leading to Anemia at Low Paras...Molecular definition of the bacterial population of human ...Mycobacterium Tuberculosis Latency and Reactivation Tuberc...New Antibiotics from Environmental DNAOptimizing Immunity to Complex Pathogens In VivoPandora's Box ProjectProviding an Economic Benefit to Using a Vaccine to Enhanc...Resistance Gene Flow in the Human Colonic MicrofloraRole of Nucleotide Binding Domain-Leucine Rich Repeat Prot...Sexually Transmitted Disease Agents in the “Healthy” Human...Systematic Analysis of Positive-strand RNA Viral Transmiss...The Human Intestinal Microbiome: Community Analysis, Host ...The Molecular Ecology of Vibrio cholerae in the Gangetic D...The Natural History of Typhoid Infection in VietnamThe Role of Quorum Sensing in Fungal DiseaseTowards Broad-spectrum Antivirals: Functional Screens for ...Transmission Blocking Vaccines for TuberculosisTransmission-blocking Vaccines Against Arthropod VectorsViral Pathogenic Mechanisms Involving Z-DNA Binding Proteins Select an institution Albert Einstein College of Medicine of Yeshiva University Columbia University Harvard Medical School Harvard School of Public Health Harvard University Johns Hopkins School of Public Health Massachusetts Institute of Technology Mount Sinai School of Medicine New York University School of Medicine Rockefeller University Stanford University School of Medicine Stanford University School of Medicine, VA Palo Alto Health Care System University of California - Berkeley University of California - Irvine University of California - San Diego University of California - San Francisco University of Illinois - Urbana-Champaign University of Pennsylvania University of Texas Southwest Medical Center University of Virginia University of Washington Washington University Washington University School of Medicine Weill Medical College of Cornell University Whitehead Institute for Biomedical Research Yale University School of Medicine

David S. Roos, Ph.D. University of Pennsylvania

Genomics research is characterized by the production of large-scale datasets derived from DNA sequencing, RNA and protein _expression profiling, high-throughput structural data, global analysis of protein-protein interactions, metabolic pathway studies, journal publications, clinical outcomes data, etc. Successful exploitation of these resources requires access to the underlying datasets, databases designed to integrate this information, tools for data analysis, practical resources for querying the data, education of scientists in the use these tools, and new paradigms for providing credit to the numerous investigators contributing to large-scale projects.

The Plasmodium genome database -- PlasmoDB -- establishes a single location for storing, downloading, browsing and querying the data emerging from various projects focused on malaria parasites, including the complete genome of P. falciparum. A relational architecture allows researchers to form queries integrating genetic and physical maps, DNA sequence, gene and protein predictions, RNA and protein _expression data, taxonomic relationships with related parasite species, and comparisons with data from GenBank and other databases. Similar databases have been established for Toxoplasma and other parasites.

Success stories attributable to the Plasmodium genome project and the PlasmoDB database include the identification of novel secretory and surface antigens, and cataloging of all metabolic pathways associated with the apicoplast. Phylogenetic studies demonstrate that the apicoplast -- an essential organelle -- was acquired when an ancestral parasite 'ate' a eukaryotic alga, and retained the algal chloroplast. Integrated computational, genomic, genetic, biochemical, cell biological, and pharmacological studies have identified several hundred nuclear-encoded plastid genes (~15% of the parasite genome), providing a virtually complete picture of the apicoplast "metabolome", and several promising targets for parasiticidal drug design.

Similar strategies can be exploited to identify other targets for drug and vaccine design. For example, efforts to develop an anti-malaria vaccine would benefit from the identification of potential surface antigens that are predicted to be immunodominant and show evidence of (positive) immune selection. Drug development efforts would benefit from the identification of enzymes that are expressed in bloodstream parasites and differ significantly from their human counter-parts, providing a potential therapeutic window.

Contact Dr. Roos.