Literature DB >> 23332401

Database resources for the tuberculosis community.

Jocelyne M Lew1, Chunhong Mao, Maulik Shukla, Andrew Warren, Rebecca Will, Dmitry Kuznetsov, Ioannis Xenarios, Brian D Robertson, Stephen V Gordon, Dirk Schnappinger, Stewart T Cole, Bruno Sobral.   

Abstract

Access to online repositories for genomic and associated "-omics" datasets is now an essential part of everyday research activity. It is important therefore that the Tuberculosis community is aware of the databases and tools available to them online, as well as for the database hosts to know what the needs of the research community are. One of the goals of the Tuberculosis Annotation Jamboree, held in Washington DC on March 7th-8th 2012, was therefore to provide an overview of the current status of three key Tuberculosis resources, TubercuList (tuberculist.epfl.ch), TB Database (www.tbdb.org), and Pathosystems Resource Integration Center (PATRIC, www.patricbrc.org). Here we summarize some key updates and upcoming features in TubercuList, and provide an overview of the PATRIC site and its online tools for pathogen RNA-Seq analysis.
Copyright © 2012 Elsevier Ltd. All rights reserved.

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Year:  2013        PMID： 23332401      PMCID： PMC3592388          DOI： 10.1016/j.tube.2012.11.003

Source DB:  PubMed          Journal:  Tuberculosis (Edinb)        ISSN： 1472-9792            Impact factor:   3.131


  41 in total

1.  KEGG: kyoto encyclopedia of genes and genomes.

Authors:  M Kanehisa; S Goto
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

Review 2.  Proteogenomics.

Authors:  Santosh Renuse; Raghothama Chaerkady; Akhilesh Pandey
Journal:  Proteomics       Date:  2011-01-18       Impact factor: 3.984

3.  Integration and visualization of host-pathogen data related to infectious diseases.

Authors:  Timothy Driscoll; Joseph L Gabbard; Chunhong Mao; Oral Dalay; Maulik Shukla; Clark C Freifeld; Anne Gatewood Hoen; John S Brownstein; Bruno W Sobral
Journal:  Bioinformatics       Date:  2011-06-27       Impact factor: 6.937

4.  Extensive phosphorylation with overlapping specificity by Mycobacterium tuberculosis serine/threonine protein kinases.

Authors:  Sladjana Prisic; Selasi Dankwa; Daniel Schwartz; Michael F Chou; Jason W Locasale; Choong-Min Kang; Guy Bemis; George M Church; Hanno Steen; Robert N Husson
Journal:  Proc Natl Acad Sci U S A       Date:  2010-04-05       Impact factor: 11.205

5.  Identification of mycobacterial sigma factor binding sites by chromatin immunoprecipitation assays.

Authors:  Sébastien Rodrigue; Joëlle Brodeur; Pierre-Etienne Jacques; Alain L Gervais; Ryszard Brzezinski; Luc Gaudreau
Journal:  J Bacteriol       Date:  2006-12-08       Impact factor: 3.490

6.  Multiple small RNAs identified in Mycobacterium bovis BCG are also expressed in Mycobacterium tuberculosis and Mycobacterium smegmatis.

Authors:  Jeanne M DiChiara; Lydia M Contreras-Martinez; Jonathan Livny; Dorie Smith; Kathleen A McDonough; Marlene Belfort
Journal:  Nucleic Acids Res       Date:  2010-02-24       Impact factor: 16.971

7.  Characterization of two in vivo-expressed methyltransferases of the Mycobacterium tuberculosis complex: antigenicity and genetic regulation.

Authors:  Paul Golby; Javier Nunez; Paul J Cockle; Katie Ewer; Karen Logan; Philip Hogarth; H Martin Vordermeier; Jason Hinds; R Glyn Hewinson; Stephen V Gordon
Journal:  Microbiology       Date:  2008-04       Impact factor: 2.777

8.  Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence.

Authors:  S T Cole; R Brosch; J Parkhill; T Garnier; C Churcher; D Harris; S V Gordon; K Eiglmeier; S Gas; C E Barry; F Tekaia; K Badcock; D Basham; D Brown; T Chillingworth; R Connor; R Davies; K Devlin; T Feltwell; S Gentles; N Hamlin; S Holroyd; T Hornsby; K Jagels; A Krogh; J McLean; S Moule; L Murphy; K Oliver; J Osborne; M A Quail; M A Rajandream; J Rogers; S Rutter; K Seeger; J Skelton; R Squares; S Squares; J E Sulston; K Taylor; S Whitehead; B G Barrell
Journal:  Nature       Date:  1998-06-11       Impact factor: 49.962

9.  Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences.

Authors:  Jeremy Goecks; Anton Nekrutenko; James Taylor
Journal:  Genome Biol       Date:  2010-08-25       Impact factor: 13.583

10.  The RAST Server: rapid annotations using subsystems technology.

Authors:  Ramy K Aziz; Daniela Bartels; Aaron A Best; Matthew DeJongh; Terrence Disz; Robert A Edwards; Kevin Formsma; Svetlana Gerdes; Elizabeth M Glass; Michael Kubal; Folker Meyer; Gary J Olsen; Robert Olson; Andrei L Osterman; Ross A Overbeek; Leslie K McNeil; Daniel Paarmann; Tobias Paczian; Bruce Parrello; Gordon D Pusch; Claudia Reich; Rick Stevens; Olga Vassieva; Veronika Vonstein; Andreas Wilke; Olga Zagnitko
Journal:  BMC Genomics       Date:  2008-02-08       Impact factor: 3.969
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  15 in total

1.  Biochemical Characterization of Isoniazid-resistant Mycobacterium tuberculosis: Can the Analysis of Clonal Strains Reveal Novel Targetable Pathways?

Authors:  Luisa Maria Nieto R; Carolina Mehaffy; M Nurul Islam; Bryna Fitzgerald; John Belisle; Jessica Prenni; Karen Dobos
Journal:  Mol Cell Proteomics       Date:  2018-05-29       Impact factor: 5.911

Review 2.  Mycobacterium tuberculosis metabolism.

Authors:  Digby F Warner
Journal:  Cold Spring Harb Perspect Med       Date:  2014-12-11       Impact factor: 6.915

3.  REMap: Operon map of M. tuberculosis based on RNA sequence data.

Authors:  Shaaretha Pelly; Kathryn Winglee; Fang Fang Xia; Rick L Stevens; William R Bishai; Gyanu Lamichhane
Journal:  Tuberculosis (Edinb)       Date:  2016-04-29       Impact factor: 3.131

4.  Genome-scale analyses of Escherichia coli and Salmonella enterica AraC reveal noncanonical targets and an expanded core regulon.

Authors:  Anne M Stringer; Salvatore Currenti; Richard P Bonocora; Catherine Baranowski; Brianna L Petrone; Michael J Palumbo; Andrew A Reilly; Zhen Zhang; Ivan Erill; Joseph T Wade
Journal:  J Bacteriol       Date:  2013-11-22       Impact factor: 3.490

5.  TBDBT: A TB DataBase Template for collection of harmonized TB clinical research data in REDCap, facilitating data standardisation for inter-study comparison and meta-analyses.

Authors:  Taryn Allie; Amanda Jackson; Jon Ambler; Katherine Johnston; Elsa Du Bruyn; Charlotte Schultz; Linda Boloko; Sean Wasserman; Angharad Davis; Graeme Meintjes; Robert J Wilkinson; Nicki Tiffin
Journal:  PLoS One       Date:  2021-03-26       Impact factor: 3.240

6.  Association between intrinsic disorder and serine/threonine phosphorylation in Mycobacterium tuberculosis.

Authors:  Gajinder Pal Singh
Journal:  PeerJ       Date:  2015-01-08       Impact factor: 2.984

7.  RefSeq microbial genomes database: new representation and annotation strategy.

Authors:  Tatiana Tatusova; Stacy Ciufo; Boris Fedorov; Kathleen O'Neill; Igor Tolstoy
Journal:  Nucleic Acids Res       Date:  2013-12-06       Impact factor: 16.971

8.  PolyTB: a genomic variation map for Mycobacterium tuberculosis.

Authors:  Francesc Coll; Mark Preston; José Afonso Guerra-Assunção; Grant Hill-Cawthorn; David Harris; João Perdigão; Miguel Viveiros; Isabel Portugal; Francis Drobniewski; Sebastien Gagneux; Judith R Glynn; Arnab Pain; Julian Parkhill; Ruth McNerney; Nigel Martin; Taane G Clark
Journal:  Tuberculosis (Edinb)       Date:  2014-02-15       Impact factor: 3.131

9.  Population tailored modification of tuberculosis specific interferon-gamma release assay.

Authors:  Kata Horvati; Szilvia Bősze; Hannah P Gideon; Bernadett Bacsa; Tamás G Szabó; Rene Goliath; Molebogeng X Rangaka; Ferenc Hudecz; Robert J Wilkinson; Katalin A Wilkinson
Journal:  J Infect       Date:  2015-11-26       Impact factor: 6.072

10.  Structural characterization of CYP144A1 - a cytochrome P450 enzyme expressed from alternative transcripts in Mycobacterium tuberculosis.

Authors:  Jude Chenge; Madeline E Kavanagh; Max D Driscoll; Kirsty J McLean; Douglas B Young; Teresa Cortes; Dijana Matak-Vinkovic; Colin W Levy; Stephen E J Rigby; David Leys; Chris Abell; Andrew W Munro
Journal:  Sci Rep       Date:  2016-05-26       Impact factor: 4.379
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