Tuberculosis drug resistance mutation database.
Andreas Sandgren,Michael J. Strong,Preetika Muthukrishnan,Brian Weiner,George M. Church,Megan Murray +5 more
TLDR
Sandgren et al. as mentioned in this paper described a new comprehensive resource on drug resistance mutations in M. tuberculosis, which they used to study drug-resistant mutations in drug-free tuberculosis.Abstract:
Andreas Sandgren and colleagues describe a new comprehensive resource on drug resistance mutations inM. tuberculosis.read more
Citations
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Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study.
Timothy M Walker,Thomas Kohl,Shaheed V. Omar,Jessica Hedge,Carlos del Ojo Elias,Phelim Bradley,Zamin Iqbal,Silke Feuerriegel,Katherine E. Niehaus,Daniel J. Wilson,David A. Clifton,Georgia Kapatai,Camilla L. C. Ip,Rory Bowden,Francis Drobniewski,Francis Drobniewski,Caroline Allix-Béguec,Cyril Gaudin,Julian Parkhill,Roland Diel,Philip Supply,Philip Supply,Derrick W. Crook,E. Grace Smith,A. Sarah Walker,Nazir Ahmed Ismail,Stefan Niemann,Tim E. A. Peto +27 more
TL;DR: A broad catalogue of genetic mutations enable data from whole-genome sequencing to be used clinically to predict drug resistance, drug susceptibility, or to identify drug phenotypes that cannot yet be genetically predicted.
Journal ArticleDOI
Molecular spandrels: tests of adaptation at the genetic level.
TL;DR: Experiments to test targets and agents of natural selection within a genomic context are necessary for identifying the adaptive consequences of individual alleles and may lead to incorrect conclusions about the relationships between gene function and fitness.
Journal ArticleDOI
The epidemiology, pathogenesis, transmission, diagnosis, and management of multidrug-resistant, extensively drug-resistant, and incurable tuberculosis
Keertan Dheda,Tawanda Gumbo,Gary Maartens,Kelly E. Dooley,Ruth McNerney,Megan Murray,Jennifer Furin,Edward A. Nardell,Leslie London,Erica Lessem,Grant Theron,Paul D. van Helden,Stefan Niemann,Matthias Merker,David W. Dowdy,Annelies Van Rie,Annelies Van Rie,Gilman Kit Hang Siu,Jotam G. Pasipanodya,Camilla Rodrigues,Taane G. Clark,F. A. Sirgel,Aliasgar Esmail,Hsien-Ho Lin,Sachin R Atre,H. Simon Schaaf,Kwok Chiu Chang,Christoph Lange,Payam Nahid,Zarir F Udwadia,C. Robert Horsburgh,Gavin J. Churchyard,Gavin J. Churchyard,Dick Menzies,Anneke C. Hesseling,Eric L. Nuermberger,Helen McIlleron,Kevin P. Fennelly,Eric Goemaere,Ernesto Jaramillo,Marcus Low,Carolina Morán Jara,Nesri Padayatchi,Robin M. Warren +43 more
TL;DR: Several lines of evidence suggest that alternative mechanisms-including pharmacokinetic variability, induction of efflux pumps that transport the drug out of cells, and suboptimal drug penetration into tuberculosis lesions-are likely crucial to the pathogenesis of drug-resistant tuberculosis.
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Drug tolerance in replicating mycobacteria mediated by a macrophage-induced efflux mechanism.
Kristin N. Adams,Kevin K. Takaki,Lynn E. Connolly,Heather Wiedenhoft,Kathryn Winglee,Olivier Humbert,Paul H. Edelstein,Christine L. Cosma,Lalita Ramakrishnan +8 more
TL;DR: The existence of multidrug-tolerant organisms that arise within days of infection, are enriched in the replicating intracellular population, and are amplified and disseminated by the tuberculous granuloma are described.
Journal ArticleDOI
Biomarkers and diagnostics for tuberculosis: progress, needs, and translation into practice
Robert S. Wallis,Madhukar Pai,Madhukar Pai,Dick Menzies,Dick Menzies,T. Mark Doherty,Gerhard Walzl,Mark D. Perkins,Alimuddin Zumla +8 more
TL;DR: Investments have yielded some progress in development of new diagnostics, although the existing pipeline is limited for tests for sputum-smear-negative cases, childhood tuberculosis, and accurate prediction of reactivation of latent tuberculosis.
References
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Database resources of the National Center for Biotechnology Information
David L. Wheeler,Deanna M. Church,Ron Edgar,Scott Federhen,Wolfgang Helmberg,Thomas L. Madden,Joan Pontius,Gregory D. Schuler,Lynn M. Schriml,Edwin Sequeira,Tugba O. Suzek,Tatiana Tatusova,Lukas Wagner +12 more
TL;DR: In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s website.
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A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae
Peter Uetz,Loic Giot,Gerard Cagney,Traci A. Mansfield,Richard S. Judson,James R. Knight,Daniel Lockshon,Vaibhav A. Narayan,Maithreyan Srinivasan,Pascale Pochart,Alia Qureshi-Emili,Ying Li,Brian C. Godwin,Diana Conover,Theodore S. Kalbfleisch,Govindan Vijayadamodar,Meijia Yang,Mark Johnston,Stanley Fields,Jonathan M. Rothberg +19 more
TL;DR: Examination of large-scale yeast two-hybrid screens reveals interactions that place functionally unclassified proteins in a biological context, interactions between proteins involved in the same biological function, and interactions that link biological functions together into larger cellular processes.
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Towards a proteome-scale map of the human protein–protein interaction network
Jean François Rual,Kavitha Venkatesan,Tong Hao,Tomoko Hirozane-Kishikawa,Amélie Dricot,Ning Li,Gabriel F. Berriz,Francis D. Gibbons,Matija Dreze,Nono Ayivi-Guedehoussou,Niels Klitgord,Christophe Simon,Mike Boxem,Stuart Milstein,Jennifer Rosenberg,Debra S. Goldberg,Lan V. Zhang,Sharyl L. Wong,Giovanni Franklin,Siming Li,Joanna S. Albala,Joanna S. Albala,Janghoo Lim,Carlene Fraughton,Estelle Llamosas,Sebiha Cevik,Camille Bex,Philippe Lamesch,Robert S. Sikorski,Jean Vandenhaute,Huda Y. Zoghbi,Alex Smolyar,Stephanie Bosak,Reynaldo Sequerra,Lynn Doucette-Stamm,Michael E. Cusick,David E. Hill,Frederick P. Roth,Marc Vidal +38 more
TL;DR: An initial version of a proteome-scale map of human binary protein–protein interactions is described, which increases by ∼70% the set of available binary interactions within the tested space and reveals more than 300 new connections to over 100 disease-associated proteins.
Journal ArticleDOI
DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions
Ioannis Xenarios,Lukasz Salwinski,Xiaoqun Joyce Duan,Patrick Higney,Sul-Min Kim,David Eisenberg +5 more
TL;DR: The Database of Interacting Proteins (DIP) is a database that documents experimentally determined protein-protein interactions and provides the scientific community with an integrated set of tools for browsing and extracting information about protein interaction networks.
Journal ArticleDOI
NCBI GEO: mining tens of millions of expression profiles--database and tools update.
Tanya Barrett,Dennis B. Troup,Stephen E. Wilhite,Pierre Ledoux,Dmitry Rudnev,Carlos Evangelista,Irene F. Kim,Alexandra Soboleva,Maxim Tomashevsky,Ron Edgar +9 more
TL;DR: A summary of the GEO database structure and user facilities is provided, and recent enhancements to database design, performance, submission format options, data query and retrieval utilities are described.
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