The molecular clock of Mycobacterium tuberculosis

Multiple Introductions of Mycobacterium tuberculosis Lineage 2–Beijing Into Africa Over Centuries

(2019) Liliana K. Rutaihwa et al.   Frontiers in Ecology and Evolution

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

(2018) Fabrizio Menardo et al.   BMC BIOINFORMATICS

A comparison of methods for estimating substitution rates from ancient DNA sequence data

(2018) K. Jun Tong et al.   BMC EVOLUTIONARY BIOLOGY

Inferring demographic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods

(2018) Sebastian Duchene et al.   BMC EVOLUTIONARY BIOLOGY

Impact of the tree prior on estimating clock rates during epidemic outbreaks

(2018) Simon Möller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tuberculosis outbreak investigation using phylodynamic analysis

(2018) Denise Kühnert et al.   Epidemics

Global variation in bacterial strains that cause tuberculosis disease: a systematic review and meta-analysis

(2018) Kirsten E Wiens et al.   BMC Medicine

Compensatory evolution drives multidrug-resistant tuberculosis in Central Asia

(2018) Matthias Merker et al.   eLife

A New Phylogenetic Framework for the Animal-Adapted Mycobacterium tuberculosis Complex

(2018) Daniela Brites et al.   Frontiers in Microbiology

Global expansion of Mycobacterium tuberculosis lineage 4 shaped by colonial migration and local adaptation

(2018) Ola B. Brynildsrud et al.   Science Advances

Beyond the SNP Threshold: Identifying Outbreak Clusters Using Inferred Transmissions

(2018) James Stimson et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic Epidemiology of a Major Mycobacterium tuberculosis Outbreak: Retrospective Cohort Study in a Low-Incidence Setting Using Sparse Time-Series Sampling

(2017) Dorte Bek Folkvardsen et al.   JOURNAL OF INFECTIOUS DISEASES

Interpreting whole genome sequencing for investigating tuberculosis transmission: a systematic review

(2016) Hollie-Ann Hatherell et al.   BMC Medicine

Inferences from tip-calibrated phylogenies: a review and a practical guide

(2016) Adrien Rieux et al.   MOLECULAR ECOLOGY

Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages

(2016) David Stucki et al.   NATURE GENETICS

Armed conflict and population displacement as drivers of the evolution and dispersal ofMycobacterium tuberculosis

(2016) Vegard Eldholm et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Use of bacterial whole-genome sequencing to investigate local persistence and spread in bovine tuberculosis

(2016) Hannah Trewby et al.   Epidemics

Co-evolution ofMycobacterium tuberculosisandHomo sapiens

(2015) Daniela Brites et al.   IMMUNOLOGICAL REVIEWS

The Performance of the Date-Randomization Test in Phylogenetic Analyses of Time-Structured Virus Data

(2015) Sebastián Duchêne et al.   MOLECULAR BIOLOGY AND EVOLUTION

Lack of support for the time-dependent molecular evolution hypothesis

(2015) Brent C. Emerson et al.   MOLECULAR ECOLOGY

Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage

(2015) Matthias Merker et al.   NATURE GENETICS

Population genomics ofMycobacterium tuberculosisin the Inuit

(2015) Robyn S. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast Dating Using Least-Squares Criteria and Algorithms

(2015) Thu-Hien To et al.   SYSTEMATIC BIOLOGY

Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe

(2015) Gemma L. Kay et al.   Nature Communications

Four decades of transmission of a multidrug-resistant Mycobacterium tuberculosis outbreak strain

(2015) Vegard Eldholm et al.   Nature Communications

Evolution of Extensively Drug-Resistant Tuberculosis over Four Decades: Whole Genome Sequencing and Dating Analysis of Mycobacterium tuberculosis Isolates from KwaZulu-Natal

(2015) Keira A. Cohen et al.   PLOS MEDICINE

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

KvarQ: targeted and direct variant calling from fastq reads of bacterial genomes

(2014) Andreas Steiner et al.   BMC GENOMICS

Improved Calibration of the Human Mitochondrial Clock Using Ancient Genomes

(2014) Adrien Rieux et al.   MOLECULAR BIOLOGY AND EVOLUTION

Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis

(2014) Kirsten I. Bos et al.   NATURE

Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates

(2014) S. Duchene et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A robust SNP barcode for typing Mycobacterium tuberculosis complex strains

(2014) Francesc Coll et al.   Nature Communications

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

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

Metagenomic Analysis of Tuberculosis in a Mummy

(2013) Jacqueline Z.-M. Chan et al.   NEW ENGLAND JOURNAL OF MEDICINE

The Role of Selection in Shaping Diversity of Natural M. tuberculosis Populations

(2013) Caitlin S. Pepperell et al.   PLoS Pathogens

Rib lesions in skeletons from early neolithic sites in Central Germany: On the trail of tuberculosis at the onset of agriculture

(2012) Nicole Nicklisch et al.   AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY

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

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

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

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

(2011) H. Li   BIOINFORMATICS

Time-dependent rates of molecular evolution

(2011) SIMON Y. W. HO et al.   MOLECULAR ECOLOGY

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

(2011) Christopher B Ford 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

Mycobacterium tuberculosis strains with the Beijing genotype demonstrate variability in virulence associated with transmission

(2010) D. Aguilar L et al.   TUBERCULOSIS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Deficiencies and challenges in the study of ancient tuberculosis DNA

(2009) Alicia K. Wilbur et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

Biomolecular archaeology of ancient tuberculosis: response to “Deficiencies and challenges in the study of ancient tuberculosis DNA” by Wilbur et al. (2009)

(2009) Helen D. Donoghue et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

High Rates of Molecular Evolution in Hantaviruses

(2008) C. Ramsden et al.   MOLECULAR BIOLOGY AND EVOLUTION

Detection and Molecular Characterization of 9000-Year-Old Mycobacterium tuberculosis from a Neolithic Settlement in the Eastern Mediterranean

(2008) Israel Hershkovitz et al.   PLoS One

Origin, Spread and Demography of the Mycobacterium tuberculosis Complex

(2008) Thierry Wirth et al.   PLoS Pathogens