Genome-Wide Association Study of HIV Whole Genome Sequences Validated using Drug Resistance

PANGEA-HIV: phylogenetics for generalised epidemics in Africa

(2015) Deenan Pillay et al.   LANCET INFECTIOUS DISEASES

Genetic architecture of artemisinin-resistant Plasmodium falciparum

(2015) Olivo Miotto et al.   NATURE GENETICS

The genetics of diabetic complications

(2015) Emma Ahlqvist et al.   Nature Reviews Nephrology

Second-generation PLINK: rising to the challenge of larger and richer datasets

(2015) Christopher C Chang et al.   GigaScience

Dissecting Vancomycin-Intermediate Resistance in Staphylococcus aureus Using Genome-Wide Association

(2014) Md Tauqeer Alam et al.   Genome Biology and Evolution

Defining the role of common variation in the genomic and biological architecture of adult human height

(2014) Andrew R Wood et al.   NATURE GENETICS

Large-scale genomics unveils the genetic architecture of psychiatric disorders

(2014) Jacob Gratten et al.   NATURE NEUROSCIENCE

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Southern African Treatment Resistance Network (SATuRN) RegaDB HIV drug resistance and clinical management database: supporting patient management, surveillance and research in southern Africa

(2014) J. Manasa et al.   Database-The Journal of Biological Databases and Curation

Characterizing the genetic basis of bacterial phenotypes using genome-wide association studies: a new direction for bacteriology

(2014) Timothy D Read et al.   Genome Medicine

Comprehensive Identification of Single Nucleotide Polymorphisms Associated with Beta-lactam Resistance within Pneumococcal Mosaic Genes

(2014) Claire Chewapreecha et al.   PLoS Genetics

Drug resistance in children at virological failure in a rural KwaZulu-Natal, South Africa, cohort

(2014) Sureshnee Pillay et al.   AIDS Research and Therapy

Searching for virus phylotypes

(2013) François Chevenet et al.   BIOINFORMATICS

Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis

(2013) Maha R Farhat et al.   NATURE GENETICS

Discovery and refinement of loci associated with lipid levels

(2013) Cristen J Willer et al.   NATURE GENETICS

Viral population analysis and minority-variant detection using short read next-generation sequencing

(2013) S. J. Watson et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

High-Levels of Acquired Drug Resistance in Adult Patients Failing First-Line Antiretroviral Therapy in a Rural HIV Treatment Programme in KwaZulu-Natal, South Africa

(2013) Justen Manasa et al.   PLoS One

High Coverage of ART Associated with Decline in Risk of HIV Acquisition in Rural KwaZulu-Natal, South Africa

(2013) F. Tanser et al.   SCIENCE

Increases in Adult Life Expectancy in Rural South Africa: Valuing the Scale-Up of HIV Treatment

(2013) J. Bor et al.   SCIENCE

A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control

(2013) István Bartha et al.   eLife

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease

(2012) Luke Jostins et al.   NATURE

Chapter 11: Genome-Wide Association Studies

(2012) William S. Bush et al.   PLoS Computational Biology

Prevention of HIV-1 Infection with Early Antiretroviral Therapy

(2011) Myron S. Cohen et al.   NEW ENGLAND JOURNAL OF MEDICINE

GCTA: A Tool for Genome-wide Complex Trait Analysis

(2010) Jian Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Impact of recombination on bacterial evolution

(2010) Xavier Didelot et al.   TRENDS IN MICROBIOLOGY

The A62V and S68G Mutations in HIV-1 Reverse Transcriptase Partially Restore the Replication Defect Associated With the K65R Mutation

(2009) Evguenia S Svarovskaia et al.   JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES

A global network for investigating the genomic epidemiology of malaria

(2008) Eric Akum Achidi et al.   NATURE

Genes mirror geography within Europe

(2008) John Novembre et al.   NATURE