Transition bias influences the evolution of antibiotic resistance in Mycobacterium tuberculosis

Treemmer: a tool to reduce large phylogenetic datasets with minimal loss of diversity

(2018) Fabrizio Menardo et al.   BMC BIOINFORMATICS

Ecology and evolution of Mycobacterium tuberculosis

(2018) Sebastien Gagneux   NATURE REVIEWS MICROBIOLOGY

Isoniazid resistance levels of Mycobacterium tuberculosis can largely be predicted by high-confidence resistance-conferring mutations

(2018) Pauline Lempens et al.   Scientific Reports

Mutational Biases Influence Parallel Adaptation

(2017) Arlin Stoltzfus et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evidence for the Selective Basis of Transition-to-Transversion Substitution Bias in Two RNA Viruses

(2017) Daniel M Lyons et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mutation-Driven Parallel Evolution during Viral Adaptation

(2017) Andrew M Sackman et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance

(2017) Abigail L Manson et al.   NATURE GENETICS

A novel twelve class fluctuation test reveals higher than expected mutation rates for influenza A viruses

(2017) Matthew D Pauly et al.   eLife

Anti-tubercular Activity of Pyrazinamide is Independent of trans-Translation and RpsA

(2017) Nicholas A. Dillon et al.   Scientific Reports

The properties of spontaneous mutations in the opportunistic pathogen Pseudomonas aeruginosa

(2016) Jeremy R. Dettman et al.   BMC GENOMICS

The Effect of Local Sequence Context on Mutational Bias of Genes Encoded on the Leading and Lagging Strands

(2016) Jeremy W. Schroeder et al.   CURRENT BIOLOGY

Tuberculosis

(2016) Keertan Dheda et al.   LANCET

Genome-Wide Biases in the Rate and Molecular Spectrum of Spontaneous Mutations inVibrio choleraeandVibrio fischeri

(2016) Marcus M. Dillon et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic diversity in autopsy samples reveals within-host dissemination of HIV-associated Mycobacterium tuberculosis

(2016) Tami D Lieberman et al.   NATURE MEDICINE

The Rate and Spectrum of Spontaneous Mutations in Mycobacterium smegmatis , a Bacterium Naturally Devoid of the Postreplicative Mismatch Repair Pathway

(2016) Sibel Kucukyildirim et al.   G3-Genes Genomes Genetics

Virulence of Mycobacterium tuberculosis after Acquisition of Isoniazid Resistance: Individual Nature of katG Mutants and the Possible Role of AhpC

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The Spontaneous Mutation Rate in the Fission YeastSchizosaccharomyces pombe

(2015) Ashley Farlow et al.   GENETICS

The Rate and Molecular Spectrum of Spontaneous Mutations in the GC-Rich Multichromosome Genome of Burkholderia cenocepacia

(2015) Marcus M. Dillon et al.   GENETICS

Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study

(2015) Timothy M Walker et al.   LANCET INFECTIOUS DISEASES

On the Causes of Evolutionary Transition:Transversion Bias

(2015) Arlin Stoltzfus et al.   MOLECULAR BIOLOGY AND EVOLUTION

Contribution of a mutational hot spot to hemoglobin adaptation in high-altitude Andean house wrens

(2015) Spencer C. Galen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bypass of genetic constraints during mutator evolution to antibiotic resistance

(2015) A. Couce et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Spontaneous Mutation Rate in the Fission YeastSchizosaccharomyces pombe

(2015) Ashley Farlow et al.   GENETICS

The Rate and Molecular Spectrum of Spontaneous Mutations in the GC-Rich Multichromosome Genome of Burkholderia cenocepacia

(2015) Marcus M. Dillon et al.   GENETICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Precise estimates of mutation rate and spectrum in yeast

(2014) Y. O. Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modeling Evolution Using the Probability of Fixation: History and Implications

(2014) David M. McCandlish et al.   QUARTERLY REVIEW OF BIOLOGY

Accelerated gene evolution through replication–transcription conflicts

(2013) Sandip Paul et al.   NATURE

Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans

(2013) Iñaki Comas et al.   NATURE GENETICS

Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis

(2013) Christopher B Ford et al.   NATURE GENETICS

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Oxidative DNA damage is important to the evolution of antibiotic resistance: evidence of mutation bias and its medicinal implications

(2012) Zhong-Yi Wang et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Dynamic Population Changes in Mycobacterium tuberculosis During Acquisition and Fixation of Drug Resistance in Patients

(2012) Gang Sun et al.   JOURNAL OF INFECTIOUS DISEASES

New Insights into Fluoroquinolone Resistance in Mycobacterium tuberculosis: Functional Genetic Analysis of gyrA and gyrB Mutations

(2012) Seidu Malik et al.   PLoS One

General and inducible hypermutation facilitate parallel adaptation in Pseudomonas aeruginosa despite divergent mutation spectra

(2012) M. R. Weigand et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing

(2012) H. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantifying the Adaptive Potential of an Antibiotic Resistance Enzyme

(2012) Martijn F. Schenk et al.   PLoS Genetics

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection

(2011) Christopher B Ford 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

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Nature, Position, and Frequency of Mutations Made in a Single Cycle of HIV-1 Replication

(2010) M. E. Abram et al.   JOURNAL OF VIROLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

(2010) S. Ossowski et al.   SCIENCE

DNA double-strand break repair and the evolution of intron density

(2010) Ashley Farlow et al.   TRENDS IN GENETICS

Evidence That Mutation Is Universally Biased towards AT in Bacteria

(2010) Ruth Hershberg et al.   PLoS Genetics

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines

(2009) P. D. Keightley et al.   GENOME RESEARCH

Resistant mutants of Mycobacterium tuberculosis selected in vitro do not reflect the in vivo mechanism of isoniazid resistance

(2009) Indra L. Bergval et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

The role of DNA shape in protein–DNA recognition

(2009) Remo Rohs et al.   NATURE

The epidemiological fitness cost of drug resistance in Mycobacterium tuberculosis

(2009) F. Luciani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tuberculosis Drug Resistance Mutation Database

(2009) Andreas Sandgren et al.   PLOS MEDICINE