Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance

In silico functional dissection of saturation mutagenesis: Interpreting the relationship between phenotypes and changes in protein stability, interactions and activity

(2016) Douglas E. V. Pires et al.   Scientific Reports

Twelve novel HGD gene variants identified in 99 alkaptonuria patients: focus on ‘black bone disease’ in Italy

(2015) Martina Nemethova et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Clinical Application of Whole-Genome Sequencing To Inform Treatment for Multidrug-Resistant Tuberculosis Cases

(2015) Adam A. Witney et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Rapid Whole-Genome Sequencing of Mycobacterium tuberculosis Isolates Directly from Clinical Samples

(2015) Amanda C. Brown et al.   JOURNAL OF CLINICAL MICROBIOLOGY

PDBe: improved accessibility of macromolecular structure data from PDB and EMDB

(2015) Sameer Velankar et al.   NUCLEIC ACIDS RESEARCH

Germline Mutations in the CDKN2B Tumor Suppressor Gene Predispose to Renal Cell Carcinoma

(2015) M. Jafri et al.   Cancer Discovery

Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences

(2015) Francesc Coll et al.   Genome Medicine

Toward better understanding of artifacts in variant calling from high-coverage samples

(2014) Heng Li   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Dissecting Vancomycin-Intermediate Resistance in Staphylococcus aureus Using Genome-Wide Association

(2014) Md Tauqeer Alam et al.   Genome Biology and Evolution

Revisiting susceptibility testing in MDR-TB by a standardized quantitative phenotypic assessment in a European multicentre study

(2014) E. Cambau et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Profiling of rpoB Mutations and MICs for Rifampin and Rifabutin in Mycobacterium tuberculosis

(2014) F. B. Jamieson et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Genomic insights into tuberculosis

(2014) James E. Galagan   NATURE REVIEWS GENETICS

DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach

(2014) D. E. V. Pires et al.   NUCLEIC ACIDS RESEARCH

Screening for Streptomycin Resistance-Conferring Mutations in Mycobacterium tuberculosis Clinical Isolates from Poland

(2014) Tomasz Jagielski et al.   PLoS One

A robust SNP barcode for typing Mycobacterium tuberculosis complex strains

(2014) Francesc Coll et al.   Nature Communications

The impact of drug resistance on Mycobacterium tuberculosis physiology: what can we learn from rifampicin?

(2014) Anastasia Koch et al.   Emerging Microbes & Infections

mCSM: predicting the effects of mutations in proteins using graph-based signatures

(2013) Douglas E. V. Pires et al.   BIOINFORMATICS

Systematic review of allelic exchange experiments aimed at identifying mutations that confer drug resistance in Mycobacterium tuberculosis

(2013) H. Nebenzahl-Guimaraes et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Genetic characterization of compensatory evolution in strains carrying rpoB Ser531Leu, the rifampicin resistance mutation most frequently found in clinical isolates

(2013) G. Brandis et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis

(2013) Maha R Farhat et al.   NATURE GENETICS

Evolution of high-level ethambutol-resistant tuberculosis through interacting mutations in decaprenylphosphoryl-β-D-arabinose biosynthetic and utilization pathway genes

(2013) Hassan Safi et al.   NATURE GENETICS

The Rationale for Using Rifabutin in the Treatment of MDR and XDR Tuberculosis Outbreaks

(2013) Frederick A. Sirgel et al.   PLoS One

Elucidating Emergence and Transmission of Multidrug-Resistant Tuberculosis in Treatment Experienced Patients by Whole Genome Sequencing

(2013) Taane G. Clark et al.   PLoS One

Correcting for Population Structure and Kinship Using the Linear Mixed Model: Theory and Extensions

(2013) Gabriel E. Hoffman   PLoS One

Putative Compensatory Mutations in the rpoC Gene of Rifampin-Resistant Mycobacterium tuberculosis Are Associated with Ongoing Transmission

(2012) M. de Vos et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences

(2012) Francesc Coll et al.   BIOINFORMATICS

Host-pathogen coevolution in human tuberculosis

(2012) S. Gagneux   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Fast Computation and Applications of Genome Mappability

(2012) Thomas Derrien et al.   PLoS One

Mutations ingidBConfer Low-Level Streptomycin Resistance in Mycobacterium tuberculosis

(2011) Sharon Y. Wong et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Genome-wide association studies and susceptibility to infectious diseases

(2011) M. J. Newport et al.   Briefings in Functional Genomics

Treatment Outcomes of Isoniazid-Resistant Tuberculosis Patients, Western Cape Province, South Africa

(2011) K. R. Jacobson et al.   CLINICAL INFECTIOUS DISEASES

The TDR Tuberculosis Strain Bank: a resource for basic science, tool development and diagnostic services

(2011) V. Vincent et al.   INTERNATIONAL JOURNAL OF TUBERCULOSIS AND LUNG DISEASE

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes

(2011) Iñaki Comas et al.   NATURE GENETICS

Characterization of mutations in streptomycin-resistant Mycobacterium tuberculosis clinical isolates in the area of Barcelona

(2010) G. Tudo et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

TubercuList – 10 years after

(2010) Jocelyne M. Lew et al.   TUBERCULOSIS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Efficient Control of Population Structure in Model Organism Association Mapping

(2008) H. M. Kang et al.   GENETICS

Elucidating Isoniazid Resistance Using Molecular Modeling

(2008) Habibah A. Wahab et al.   Journal of Chemical Information and Modeling

TB database: an integrated platform for tuberculosis research

(2008) T. B. K. Reddy et al.   NUCLEIC ACIDS RESEARCH

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY