Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa

Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing

(2012) Simon R Harris et al.   NATURE GENETICS

SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics

(2011) F. Bielejec et al.   BIOINFORMATICS

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

(2011) Ankur Mutreja et al.   NATURE

Immunodominance of HIV-1 Specific CD8+ T-Cell Responses Is Related to Disease Progression Rate in Vertically Infected Adolescents

(2011) Elizabeth R. Sharp et al.   PLoS One

Rapid Pneumococcal Evolution in Response to Clinical Interventions

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

Temporal Fluctuation of Multidrug Resistant Salmonella Typhi Haplotypes in the Mekong River Delta Region of Vietnam

(2011) Kathryn E. Holt et al.   PLoS Neglected Tropical Diseases

Clonal Differences between Non-Typhoidal Salmonella (NTS) Recovered from Children and Animals Living in Close Contact in The Gambia

(2011) Michel M. Dione et al.   PLoS Neglected Tropical Diseases

A Population Genetics-Based and Phylogenetic Approach to Understanding the Evolution of Virulence in the Genus Listeria

(2010) H. C. den Bakker et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Invasive Non‐typhoid Salmonellae Establish Systemic Intracellular Infection in HIV‐Infected Adults: An Emerging Disease Pathogenesis

(2010) Melita A. Gordon et al.   CLINICAL INFECTIOUS DISEASES

Nontyphoidal salmonellosis in Africa

(2010) Stephen M Graham   CURRENT OPINION IN INFECTIOUS DISEASES

Both Hemolytic Anemia and Malaria Parasite-Specific Factors Increase Susceptibility to Nontyphoidal Salmonella enterica Serovar Typhimurium Infection in Mice

(2010) C. M. Roux et al.   INFECTION AND IMMUNITY

Using genetic evidence to evaluate four palaeoanthropological hypotheses for the timing of Neanderthal and modern human origins

(2010) Phillip Endicott et al.   JOURNAL OF HUMAN EVOLUTION

Community-acquired bloodstream infections in Africa: a systematic review and meta-analysis

(2010) Elizabeth A Reddy et al.   LANCET INFECTIOUS DISEASES

Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity

(2010) Giovanna Morelli et al.   NATURE GENETICS

Evolutionary dynamics of Clostridium difficile over short and long time scales

(2010) M. He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dysregulated Humoral Immunity to Nontyphoidal Salmonella in HIV-Infected African Adults

(2010) C. A. MacLennan et al.   SCIENCE

Evolution of MRSA During Hospital Transmission and Intercontinental Spread

(2010) S. R. Harris et al.   SCIENCE

Spatial phylodynamics of HIV-1 epidemic emergence in east Africa

(2009) Rebecca R Gray et al.   AIDS

ABACAS: algorithm-based automatic contiguation of assembled sequences

(2009) S. Assefa et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi

(2009) Kathryn E Holt et al.   BMC GENOMICS

HIV Infection, Malnutrition, and Invasive Bacterial Infection among Children with Severe Malaria

(2009) James A. Berkley et al.   CLINICAL INFECTIOUS DISEASES

Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype

(2009) R. A. Kingsley et al.   GENOME RESEARCH

NontyphoidalSalmonellaSerovars Cause Different Degrees of Invasive Disease Globally

(2009) Gemma C. Langridge et al.   JOURNAL OF INFECTIOUS DISEASES

Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic

(2009) Gavin J. D. Smith et al.   NATURE

Dating the emergence of pandemic influenza viruses

(2009) Gavin J. D. Smith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Invasive non-typhoidalSalmonellain Mozambican children

(2009) Inácio Mandomando et al.   TROPICAL MEDICINE & INTERNATIONAL HEALTH

Salmonella Serovars and Antimicrobial Resistance Profiles in Beef Cattle, Slaughterhouse Personnel and Slaughterhouse Environment in Ethiopia

(2009) B. Sibhat et al.   Zoonoses and Public Health

Genotypic and demographic characterization of invasive isolates of Salmonella Typhimurium in HIV co-infected patients in South Africa

(2009) Karen H. Keddy et al.   Journal of Infection in Developing Countries

Bayesian Phylogeography Finds Its Roots

(2009) Philippe Lemey et al.   PLoS Computational Biology

Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database

(2008) Tim Carver et al.   BIOINFORMATICS

Epidemics of InvasiveSalmonella entericaSerovar Enteritidis andS. entericaSerovar Typhimurium Infection Associated with Multidrug Resistance among Adults and Children in Malawi

(2008) Melita A. Gordon et al.   CLINICAL INFECTIOUS DISEASES

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Characterization of the Genomes of a Diverse Collection of Salmonella enterica Serovar Typhimurium Definitive Phage Type 104

(2008) F. J. Cooke et al.   JOURNAL OF BACTERIOLOGY

Salmonella infections in immunocompromised adults

(2008) Melita A. Gordon   JOURNAL OF INFECTION

Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960

(2008) Michael Worobey et al.   NATURE

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi

(2008) Kathryn E Holt et al.   NATURE GENETICS

Simian immunodeficiency virus–induced mucosal interleukin-17 deficiency promotes Salmonella dissemination from the gut

(2008) Manuela Raffatellu et al.   NATURE MEDICINE