TB Database: an integrated platform for tb drug discovery
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News and Updates

  • Patients with inadequately treated multidrug resistant (MDR TB) are more infective than others. A study by Escombe et al. finds a small number of inadequately treated MDR TB patients coinfected with HIV were responsible for almost all TB transmission, and some patients were highly infectious. This study highlights the importance of rapid TB drug-susceptibility testing to allow prompt initiation of effective treatment, and environmental control measures to reduce ongoing TB transmission in crowded health care settings.
  • TB's return comes with high costs: You might think tuberculosis hasn't been a problem since your grandparents' era, but the illness is making a worldwide comeback. Its costs of treatment and lost productivity are estimated at almost $3 billion a year. Listen to Frank Browning reports on NPR's Market Place.
  • Aggressive TB treatment a success: Tuberculosis which is resistant to many current treatments can be overcome with aggressive therapy, research suggests.
  • The New England Journal of Medicine: More than 60 percent of patients diagnosed with extensively drug-resistant TB (XDR-TB), a type of tuberculosis that is very difficult to treat were cured with aggressive drug treatment by a team of Peruvian doctors.
  • Genome Research: Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis
  • Association calls on state to fund tb programs In recognition of World TB Day on March 24, the American Lung Association of California released troubling statewide tuberculosis (TB) statistics and called on the state to avert a resurgence of TB by funding prevention and control efforts.
  • Sequencing of XDR TB: Work of South Africa-US research team gives first look at genome of XDR TB from KZN outbreak. Initial analysis highlights small number of DNA differences among drug-resistant and -sensitive microbes.
  • PLos Pathogens: Mycobacterium tuberculosis nuoG Is a Virulence Gene That Inhibits Apoptosis of Infected Host Cells
  • Elsevier Tuberculosis Journal: Browse or search for articles in the current issue.
  • Search PubMed for articles related to Tuberculosis.
  • World Health Organization provides information about Tuberculosis for clinicians and public health workers.
  • US Centers for Disease Control and Prevention (CDC) provides news and updates about Tuberculosis.

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Announcements

October 2008:

We are delighted to announce the publication of a paper titled "TB database: an integrated platform for tuberculosis research" in Nucleic Acids Research.

September 2008:

We are pleased to announce that TBDB now holds data from a publication by Nuria Andreu and Isidre Gibert titled "Cell population heterogeneity in Mycobacterium tuberculosis H37Rv". Despite the apparent stability of the H37Rv laboratory strain, the authors report the existence of heterogeneity in terms of its virulent indicators: neutral red staining and content of phthiocerol dimycocerosates (PDIMs). Using transcriptional profiling the authors confirmed that a significant heterogeneity existed in strains isolated from H37Rv, in addition to the neutral red and PDIM phenotypes.

August 2008:

  • We are pleased to announce the integration of dozens of new data analysis tools that are available from GenePattern. Registered users click on the 'GP' icon in their repository.
  • We made enhancements to Publication Page and implemented Expression Connection, that provides users an easy access to explore the entire clustered datasets from a given publication in TBDB. For an example of the new Publication Detail page, visit Rustad et al. This enables a novice user to directly view clustered datasets, explore and interrogate TBDB without going through data analysis pipeline.
  • We have added two new genome browsing tools to TB Database: Circular Genome Viewer, and Genome Map. Using the Circular Genome Viewer, one can visualize user-selected genome annotations for all TB Database genomes in a circular chromosomal representation. Regions selected in the Circular Genome Viewer can then be exported or viewed in the new Genome Map browser. The Genome Map (right) allows more detailed comparative visualization of genomic regions between different genomes selected manually by the user, or through the Circular Genome Viewer.
    Genome Map Viewer

    • July 2008:

  • We are pleased to make available the annotated Mycobacterium marinum genome sequence as reported in Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis. M. marinum, a pathogen of fish and amphibians, is a close relative of M. tuberculosis, the etiologic agent of tuberculosis in humans. Analysis of the M. marinum genome reveals genome downsizing and lateral gene transfer in M. tuberculosis that allowed it to become a specialized pathogen of humans and primates, and facilitates better understanding of tuberculosis disease.
  • We recently made enhancements to the quick search function to find Rfam annotations, which allow identification of likely functional RNAs, for example riboswitches.
    Rfam Search results

    • June 2008: We are pleased to announce that TBDB now holds data from a publication by Rustad et al. titled "The enduring hypoxic response of Mycobacterium tuberculosis". The DosR regulon is known to play a primary role in survival of hypoxia induced bacteriostasis in Mycobacterium tuberculosis. Based on the results presented in this paper the authors suggest a reassessment of the role of DosR and the initial hypoxic response in MTB physiology.

    May 2008:
    TubercuList provides a complete dataset of DNA and protein sequences derived from the paradigm strain M. tuberculosis H37Rv, linked to the relevant annotations and functional assignments, using various criteria (gene names, location, keywords, etc.). Now TBDB provides direct links to TubercuList from 'External Links' section of a Gene Detail page. For an example of the new Gene Detail page with a link to TubercuList, visit     RV2429.

    February 2008: We are happy to announce that TBDB provides links from gene pages to the Tuberculosis Structural Genomics Consortium (TBSGC). Using this resource, you can find stuctural information as well as images for TB proteins.

    webtb

    Stanford School of Medicine
    Broad Institute

    About the TB Database Project

    Tuberculosis (TB) is a public health challenge of paramount importance. Control of TB will require a multifaceted approach integrating efficient public health interventions with the discovery and use of new vaccines and drugs. TBDatabase (TBDB) makes available the tools and resources available at the Stanford Microarray Database and the Broad Institute.

    Anyone is welcome to access the published data available on the TBDB site without signing in. Some data in TBDB are unpublished and can therefore only be accessed by the authors and their collaborators after they sign in. The "Access Polices" page provides more information about TBDB accounts.

    A grant from the Bill & Melinda Gates Foundation has enabled us to create an integrated software platform for tuberculosis drug discovery and research. Learn more >

    TB Resources

    Citing TBDB


    Please cite :
    Reddy TB, Riley R, Wymore F, Montgomery P, Decaprio D, Engels R, Gellesch M, Hubble J, Jen D, Jin H, Koehrsen M, Larson L, Mao M, Nitzberg M, Sisk P, Stolte C, Weiner B, White J, Zachariah ZK, Sherlock G, Galagan JE, Ball CA, Schoolnik GK. TB database: an integrated platform for tuberculosis research. Nucleic Acids Res doi: 10.1093/nar/gkn652

    Full text  |  PubMed