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

A “Copernican” Reassessment of the Human Mitochondrial DNA Tree from its Root

(2012) Doron M. Behar et al.   AMERICAN JOURNAL OF HUMAN GENETICS

After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection

(2012) A. Namouchi et al.   GENOME RESEARCH

A calibrated human Y-chromosomal phylogeny based on resequencing

(2012) W. Wei et al.   GENOME RESEARCH

Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study

(2012) Timothy M Walker et al.   LANCET INFECTIOUS DISEASES

Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe

(2012) Kathryn E Holt et al.   NATURE GENETICS

The great human expansion

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

Human Evolution Out of Africa: The Role of Refugia and Climate Change

(2012) J. R. Stewart et al.   SCIENCE

Role of the Commensal Microbiota in Normal and Pathogenic Host Immune Responses

(2011) Dan R. Littman et al.   Cell Host & Microbe

Palaeogenomics of Mycobacterium tuberculosis: epidemic bursts with a degrading genome

(2011) Zoheira Djelouadji et al.   LANCET INFECTIOUS DISEASES

The Expansion of mtDNA Haplogroup L3 within and out of Africa

(2011) P. Soares et al.   MOLECULAR BIOLOGY AND EVOLUTION

Time-dependent rates of molecular evolution

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

Evidence for several waves of global transmission in the seventh cholera pandemic

(2011) Ankur Mutreja et al.   NATURE

A draft genome of Yersinia pestis from victims of the Black Death

(2011) Kirsten I. Bos et al.   NATURE

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

(2011) Christopher B Ford et al.   NATURE GENETICS

Reciprocal seasonal variation in vitamin D status and tuberculosis notifications in Cape Town, South Africa

(2011) A. R. Martineau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid, global demographic expansions after the origins of agriculture

(2011) C. R. Gignoux et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia

(2011) M. Rasmussen et al.   SCIENCE

Rapid Pneumococcal Evolution in Response to Clinical Interventions

(2011) N. J. Croucher et al.   SCIENCE

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

ANCIENT URBANIZATION PREDICTS GENETIC RESISTANCE TO TUBERCULOSIS

(2010) Ian Barnes et al.   EVOLUTION

Possible underlying mechanisms for successful emergence of the Mycobacterium tuberculosis Beijing genotype strains

(2010) Ida Parwati et al.   LANCET INFECTIOUS DISEASES

S-DIVA (Statistical Dispersal-Vicariance Analysis): A tool for inferring biogeographic histories

(2010) Yan Yu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved

(2010) Iñaki Comas et al.   NATURE GENETICS

Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity

(2010) Giovanna Morelli et al.   NATURE GENETICS

Infection with Helicobacter pylori Is Associated with Protection against Tuberculosis

(2010) Sharon Perry et al.   PLoS One

Evolution of MRSA During Hospital Transmission and Intercontinental Spread

(2010) S. R. Harris et al.   SCIENCE

Microevolution of Helicobacter pylori during Prolonged Infection of Single Hosts and within Families

(2010) Giovanna Morelli et al.   PLoS Genetics

Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock

(2009) Pedro Soares et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Agricultural origins and the isotopic identity of domestication in northern China

(2009) L. Barton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bayesian Phylogeography Finds Its Roots

(2009) Philippe Lemey et al.   PLoS Computational Biology

The Past and Future of Tuberculosis Research

(2009) Iñaki Comas et al.   PLoS Pathogens

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Progression to Active Tuberculosis, but Not Transmission, Varies byMycobacterium tuberculosisLineage in The Gambia

(2008) Bouke C. de Jong et al.   JOURNAL OF INFECTIOUS DISEASES

A large genome center's improvements to the Illumina sequencing system

(2008) Michael A Quail et al.   NATURE METHODS

High Functional Diversity in Mycobacterium tuberculosis Driven by Genetic Drift and Human Demography

(2008) Ruth Hershberg et al.   PLOS BIOLOGY

Origin, Spread and Demography of the Mycobacterium tuberculosis Complex

(2008) Thierry Wirth et al.   PLoS Pathogens

Correlating viral phenotypes with phylogeny: Accounting for phylogenetic uncertainty

(2007) Joe Parker et al.   INFECTION GENETICS AND EVOLUTION

mtDNA Variation Predicts Population Size in Humans and Reveals a Major Southern Asian Chapter in Human Prehistory

(2007) Q. D. Atkinson et al.   MOLECULAR BIOLOGY AND EVOLUTION