4.7 Article

The molecular clock of Mycobacterium tuberculosis

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

Beyond the SNP Threshold: Identifying Outbreak Clusters Using Inferred Transmissions

James Stimson et al.

MOLECULAR BIOLOGY AND EVOLUTION (2019)

Article Ecology

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

Liliana K. Rutaihwa et al.

FRONTIERS IN ECOLOGY AND EVOLUTION (2019)

Article Biochemical Research Methods

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

Fabrizio Menardo et al.

BMC BIOINFORMATICS (2018)

Article Evolutionary Biology

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

K. Jun Tong et al.

BMC EVOLUTIONARY BIOLOGY (2018)

Article Evolutionary Biology

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

Sebastian Duchene et al.

BMC EVOLUTIONARY BIOLOGY (2018)

Article Multidisciplinary Sciences

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

Simon Moller et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Article Infectious Diseases

Tuberculosis outbreak investigation using phylodynamic analysis

Denise Kuhnert et al.

EPIDEMICS (2018)

Article Microbiology

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

Daniela Brites et al.

FRONTIERS IN MICROBIOLOGY (2018)

Article Multidisciplinary Sciences

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

Ola B. Brynildsrud et al.

SCIENCE ADVANCES (2018)

Review Biology

Bayesian molecular dating: opening up the black box

Lindell Bromham et al.

BIOLOGICAL REVIEWS (2018)

Article Evolutionary Biology

Fast Dating Using Least-Squares Criteria and Algorithms

Thu-Hien To et al.

SYSTEMATIC BIOLOGY (2016)

Review Medicine, General & Internal

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

Hollie-Ann Hatherell et al.

BMC MEDICINE (2016)

Review Biochemistry & Molecular Biology

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

Adrien Rieux et al.

MOLECULAR ECOLOGY (2016)

Article Multidisciplinary Sciences

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

Vegard Eldholm et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Article Genetics & Heredity

Genome-scale rates of evolutionary change in bacteria

Sebastian Duchene et al.

MICROBIAL GENOMICS (2016)

Review Immunology

Co-evolution of Mycobacterium tuberculosis and Homo sapiens

Daniela Brites et al.

IMMUNOLOGICAL REVIEWS (2015)

Article Biochemistry & Molecular Biology

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

Sebastian Duchene et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

Article Biochemistry & Molecular Biology

Lack of support for the time-dependent molecular evolution hypothesis

Brent C. Emerson et al.

MOLECULAR ECOLOGY (2015)

Article Genetics & Heredity

Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage

Matthias Merker et al.

NATURE GENETICS (2015)

Article Multidisciplinary Sciences

Population genomics of Mycobacterium tuberculosis in the Inuit

Robyn S. Lee et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Multidisciplinary Sciences

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

Gemma L. Kay et al.

NATURE COMMUNICATIONS (2015)

Article Multidisciplinary Sciences

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

Vegard Eldholm et al.

NATURE COMMUNICATIONS (2015)

Article Biochemical Research Methods

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

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

Alexandros Stamatakis

BIOINFORMATICS (2014)

Article Biotechnology & Applied Microbiology

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

Andreas Steiner et al.

BMC GENOMICS (2014)

Article Biochemistry & Molecular Biology

Improved Calibration of the Human Mitochondrial Clock Using Ancient Genomes

Adrien Rieux et al.

MOLECULAR BIOLOGY AND EVOLUTION (2014)

Article Biology

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

Sebastian Duchene et al.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2014)

Article Multidisciplinary Sciences

A robust SNP barcode for typing Mycobacterium tuberculosis complex strains

Francesc Coll et al.

NATURE COMMUNICATIONS (2014)

Article Biochemical Research Methods

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

Remco Bouckaert et al.

PLOS COMPUTATIONAL BIOLOGY (2014)

Letter Medicine, General & Internal

Metagenomic Analysis of Tuberculosis in a Mummy

Jacqueline Z. -M. Chan et al.

NEW ENGLAND JOURNAL OF MEDICINE (2013)

Article Microbiology

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

Caitlin S. Pepperell et al.

PLOS PATHOGENS (2013)

Article Biochemistry & Molecular Biology

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

Daniel C. Koboldt et al.

GENOME RESEARCH (2012)

Letter Biochemical Research Methods

jModelTest 2: more models, new heuristics and parallel computing

Diego Darriba et al.

NATURE METHODS (2012)

Article Immunology

Drug Susceptibility of Mycobacterium tuberculosis Beijing Genotype and Association with MDR TB

Jurriaan E. M. de Steenwinkel et al.

EMERGING INFECTIOUS DISEASES (2012)

Review Biochemistry & Molecular Biology

Time-dependent rates of molecular evolution

Simon Y. W. Ho et al.

MOLECULAR ECOLOGY (2011)

Article Biochemistry & Molecular Biology

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

Aaron McKenna et al.

GENOME RESEARCH (2010)

Article Biochemical Research Methods

Fast and accurate short read alignment with Burrows-Wheeler transform

Heng Li et al.

BIOINFORMATICS (2009)

Article Anthropology

Deficiencies and challenges in the study of ancient tuberculosis DNA

Alicia K. Wilbur et al.

JOURNAL OF ARCHAEOLOGICAL SCIENCE (2009)

Article Biochemistry & Molecular Biology

High rates of molecular evolution in hantaviruses

Cadhla Ramsden et al.

MOLECULAR BIOLOGY AND EVOLUTION (2008)

Article Microbiology

Origin, spread and demography of the Mycobacterium tuberculosis complex

Thierry Wirth et al.

PLOS PATHOGENS (2008)

Article Microbiology

First report of Mycobacterium bovis DNA in human remains from the Iron Age

G. Michael Taylor et al.

MICROBIOLOGY-SGM (2007)

Article Biochemistry & Molecular Biology

Relaxed phylogenetics and dating with confidence

Alexei J. Drummond et al.

PLOS BIOLOGY (2006)

Article Biochemistry & Molecular Biology

Time dependency of molecular rate estimates and systematic overestimation of recent divergence times

SYW Ho et al.

MOLECULAR BIOLOGY AND EVOLUTION (2005)

Review Ecology

Measurably evolving populations

AJ Drummond et al.

TRENDS IN ECOLOGY & EVOLUTION (2003)

Review Genetics & Heredity

The modern molecular clock

L Bromham et al.

NATURE REVIEWS GENETICS (2003)

Article Immunology

Genomic deletions suggest a phylogeny for the Mycobacterium tuberculosis complex

S Mostowy et al.

JOURNAL OF INFECTIOUS DISEASES (2002)

Article Multidisciplinary Sciences

A new evolutionary scenario for the Mycobacterium tuberculosis complex

R Brosch et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)