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List of works by Taane G Clark

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Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing

scientific article (publication date: 19 July 2012)
Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice

scientific article
Independent emergence of artemisinin resistance mutations among Plasmodium falciparum in Southeast Asia

scientific article
Genome-wide and fine-resolution association analysis of malaria in West Africa

scientific article
A robust SNP barcode for typing Mycobacterium tuberculosis complex strains

scientific article
A transcriptional switch underlies commitment to sexual development in malaria parasites

scientific article (publication date: 13 March 2014)
Genetic loci associated with delayed clearance of Plasmodium falciparum following artemisinin treatment in Southeast Asia

scientific article published on 17 December 2012
A genotype calling algorithm for the Illumina BeadArray platform

scientific article published on 10 September 2007
Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences

scientific article published on 27 May 2015
Distinct phases of blood gene expression pattern through tuberculosis treatment reflect modulation of the humoral immune response

scientific article published on 7 August 2012
The epidemiology, pathogenesis, transmission, diagnosis, and management of multidrug-resistant, extensively drug-resistant, and incurable tuberculosis

scientific article
Genome-wide significance for dense SNP and resequencing data

scientific article
Allelic heterogeneity of G6PD deficiency in West Africa and severe malaria susceptibility

scientific article
Large-scale whole genome sequencing of M. tuberculosis provides insights into transmission in a high prevalence area

scientific article
Sequence-level population simulations over large genomic regions

scientific article published on 18 October 2007
Recurrence due to relapse or reinfection with Mycobacterium tuberculosis: a whole-genome sequencing approach in a large, population-based cohort with a high HIV infection prevalence and active follow-up

scientific article
Use of purified Clostridium difficile spores to facilitate evaluation of health care disinfection regimens

scientific article published on 27 August 2010
Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis

scientific article
SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences

scientific article published on 26 September 2012
Imputation-based meta-analysis of severe malaria in three African populations

scientific article
Characterization of Within-Host Plasmodium falciparum Diversity Using Next-Generation Sequence Data

scientific article (publication date: 29 February 2012)
Genome-wide analysis of selection on the malaria parasite Plasmodium falciparum in West African populations of differing infection endemicity

scientific article
A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains

scientific article
Directional selection at the pfmdr1, pfcrt, pfubp1, and pfap2mu loci of Plasmodium falciparum in Kenyan children treated with ACT.

scientific article
Genome-wide comparisons of variation in linkage disequilibrium

scientific article published on 18 June 2009
Whole Genome Sequencing Shows a Low Proportion of Tuberculosis Disease Is Attributable to Known Close Contacts in Rural Malawi

scientific article published on 16 July 2015
Outcomes, infectiousness, and transmission dynamics of patients with extensively drug-resistant tuberculosis and home-discharged patients with programmatically incurable tuberculosis: a prospective cohort study

scientific article
Contrasting Transmission Dynamics of Co-endemic Plasmodium vivax and P. falciparum: Implications for Malaria Control and Elimination

scientific article (publication date: May 2015)
PolyTB: a genomic variation map for Mycobacterium tuberculosis

scientific article
Population genomic structure and adaptation in the zoonotic malaria parasite Plasmodium knowlesi

scientific article
Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance

scientific article
Detecting and characterizing genomic signatures of positive selection in global populations

scientific article published on 23 May 2013
Association of sub-microscopic malaria parasite carriage with transmission intensity in north-eastern Tanzania

scientific article published on 16 December 2011
Elucidating emergence and transmission of multidrug-resistant tuberculosis in treatment experienced patients by whole genome sequencing

scientific article (publication date: 2013)
Genome-scale comparison of expanded gene families in Plasmodium ovale wallikeri and Plasmodium ovale curtisi with Plasmodium malariae and with other Plasmodium species

scientific article published on 5 July 2016
Genome-wide saturation mutagenesis of Burkholderia pseudomallei K96243 predicts essential genes and novel targets for antimicrobial development

scientific article
Positive selection of a CD36 nonsense variant in sub-saharan Africa, but no association with severe malaria phenotypes

scientific article published on 29 April 2009
High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta.

scientific article
Tumor necrosis factor and lymphotoxin-alpha polymorphisms and severe malaria in African populations

scientific article published on February 2009
Drug-resistant genotypes and multi-clonality in Plasmodium falciparum analysed by direct genome sequencing from peripheral blood of malaria patients

scientific article published in 2011
An effective method to purify Plasmodium falciparum DNA directly from clinical blood samples for whole genome high-throughput sequencing

scientific article
Polymorphisms in leucine-rich repeat genes are associated with autism spectrum disorder susceptibility in populations of European ancestry

scientific article published on March 25, 2010
African glucose-6-phosphate dehydrogenase alleles associated with protection from severe malaria in heterozygous females in Tanzania

scientific article
Genome-wide screen identifies new candidate genes associated with artemisinin susceptibility in Plasmodium falciparum in Kenya

scientific article
Population genetic analysis of Plasmodium falciparum parasites using a customized Illumina GoldenGate genotyping assay

scientific article
estMOI: estimating multiplicity of infection using parasite deep sequencing data

scientific article
Genomic expression catalogue of a global collection of BCG vaccine strains show evidence for highly diverged metabolic and cell-wall adaptations

scientific article
Unraveling Mycobacterium tuberculosis genomic diversity and evolution in Lisbon, Portugal, a highly drug resistant setting

scientific article
On the usage of HWE for identifying genotyping errors

scientific article published on 27 March 2007
Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages

scientific article

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