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List of works by Taane G Clark

A Bayesian approach using covariance of single nucleotide polymorphism data to detect differences in linkage disequilibrium patterns between groups of individuals

scientific article

A Poisson hierarchical modelling approach to detecting copy number variation in sequence coverage data

scientific article

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

scientific article

A forward genetic screen reveals a primary role for Plasmodium falciparum Reticulocyte Binding Protein Homologue 2a and 2b in determining alternative erythrocyte invasion pathways ⬇️

scientific article published on 29 November 2018

A genetic association study in the Gambia using tagging polymorphisms in the major histocompatibility complex class III region implicates a HLA-B associated transcript 2 polymorphism in severe malaria susceptibility

scientific article

A genotype calling algorithm for the Illumina BeadArray platform

scientific article published on 10 September 2007

A novel Ancestral Beijing sublineage of Mycobacterium tuberculosis suggests the transition site to Modern Beijing sublineages

scientific article published on 23 September 2019

A phylogenomic approach for the analysis of colistin resistance-associated genes in Klebsiella pneumoniae, its mutational diversity and implications for phenotypic resistance

scientific article published in 2022

A proportion of mutations fixed in the genomes of in vitro selected isogenic drug-resistant Mycobacterium tuberculosis mutants can be detected as minority variants in the parent culture

scientific article

A reference genome and methylome for the Plasmodium knowlesi A1-H.1 line

scientific article published on 16 December 2017

A robust SNP barcode for typing Mycobacterium tuberculosis complex strains.

scientific article

A snapshot of translation in Mycobacterium tuberculosis during exponential growth and nutrient starvation revealed by ribosome profiling

scientific article published on 01 February 2021

A transcriptional switch underlies commitment to sexual development in malaria parasites

scientific article (publication date: 13 March 2014)

African glucose-6-phosphate dehydrogenase alleles associated with protection from severe malaria in heterozygous females in Tanzania

scientific article

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

scientific article

Alternate efflux pump mechanism may contribute to drug resistance in extensively drug-resistant isolates of Mycobacterium tuberculosis

scientific article published on 22 November 2016

An In-Solution Hybridisation Method for the Isolation of Pathogen DNA from Human DNA-rich Clinical Samples for Analysis by NGS

scientific article

An analysis of large structural variation in global Plasmodium falciparum isolates identifies a novel duplication of the chloroquine resistance associated gene.

scientific article published on 4 June 2019

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

scientific article

An integrated whole genome analysis of Mycobacterium tuberculosis reveals insights into relationship between its genome, transcriptome and methylome

scholarly article by Paula J Gomez-Gonzalez et al published 26 March 2019 in Scientific Reports

An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities

scientific article published on 19 May 2021

Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing

scientific article (publication date: 19 July 2012)

Analysis of nuclear and organellar genomes of Plasmodium knowlesi in humans reveals ancient population structure and recent recombination among host-specific subpopulations

scientific article published on 18 September 2017

Artemisinin resistance-associated markers in Plasmodium falciparum parasites from the China-Myanmar border: predicted structural stability of K13 propeller variants detected in a low-prevalence area

article

Assessing genuine parents-offspring trios for genetic association studies

scientific article

Association of candidate gene polymorphisms and TGF-beta/IL-10 levels with malaria in three regions of Cameroon: a case-control study

scientific article

Association of cytokine and Toll-like receptor gene polymorphisms with severe malaria in three regions of Cameroon

scientific article

Association of sub-microscopic malaria parasite carriage with transmission intensity in north-eastern Tanzania

scientific article published on 16 December 2011

Author Correction: Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis.

scientific article published on 19 April 2018

Bacterial and host determinants of cough aerosol culture positivity in patients with drug-resistant versus drug-susceptible tuberculosis

scientific article published on 29 June 2020

COVID-profiler: a webserver for the analysis of SARS-CoV-2 sequencing data

scientific article published on 15 April 2022

Candidate human genetic polymorphisms and severe malaria in a Tanzanian population

scientific article

Candidate polymorphisms and severe malaria in a Malian population

scientific article

Changes in malaria parasite drug resistance in an endemic population over a 25-year period with resulting genomic evidence of selection

scientific article

Characterisation of drug-resistant Mycobacterium tuberculosis mutations and transmission in Pakistan

scientific article published on 11 May 2022

Characterisation of the opposing effects of G6PD deficiency on cerebral malaria and severe malarial anaemia

scientific article published on 09 January 2017

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

scientific article (publication date: 29 February 2012)

Characterization of genomic variations in SNPs of PE_PGRS genes reveals deletions and insertions in extensively drug resistant (XDR) M. tuberculosis strains from Pakistan

scientific article published on 21 January 2015

Characterization of rifampicin-resistant Mycobacterium tuberculosis in Khyber Pakhtunkhwa, Pakistan

scientific article published on 09 July 2021

Characterizing the genomic variation and population dynamics of Plasmodium falciparum malaria parasites in and around Lake Victoria, Kenya

scientific article published on 06 October 2021

Characterizing the impact of sustained sulfadoxine/pyrimethamine use upon the Plasmodium falciparum population in Malawi

scientific article

Clonal expansion across the seas as seen through CPLP-TB database: A joint effort in cataloguing Mycobacterium tuberculosis genetic diversity in Portuguese-speaking countries

article

Clusters of Drug-Resistant Mycobacterium tuberculosis Detected by Whole-Genome Sequence Analysis of Nationwide Sample, Thailand, 2014-2017

scientific article published on 01 March 2021

Conjunctival fibrosis and the innate barriers to Chlamydia trachomatis intracellular infection: a genome wide association 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)

Correction: Imputation-Based Meta-Analysis of Severe Malaria in Three African Populations.

scientific article published on 27 June 2013

Detecting and characterizing genomic signatures of positive selection in global populations

scientific article published on 23 May 2013

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

scientific article

Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: an inter-laboratory study

scientific article published on 12 February 2020

Diverticulosis and nine connective tissue disorders: epidemiological support for an association

scientific article published on 5 February 2019

Drug resistance profile and clonality of Plasmodium falciparum parasites in Cape Verde: the 2017 malaria outbreak

scientific article published on 31 March 2021

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

Effective preparation of Plasmodium vivax field isolates for high-throughput whole genome sequencing

scientific article

Elucidating emergence and transmission of multidrug-resistant tuberculosis in treatment experienced patients by whole genome sequencing

scientific article (publication date: 2013)

Emergence of multidrug-resistant Mycobacterium tuberculosis of the Beijing lineage in Portugal and Guinea-Bissau: a snapshot of moving clones by whole-genome sequencing

scientific article published on 01 December 2020

Enrichment of clinically relevant organisms in spontaneous preterm delivered placenta and reagent contamination across all clinical groups in a large UK pregnancy cohort.

scientific article

Evidence for Host-Bacterial Co-evolution via Genome Sequence Analysis of 480 Thai Mycobacterium tuberculosis Lineage 1 Isolates

scientific article published in Scientific Reports

Evidence of Clinical Pathology Abnormalities in People with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) from an Analytic Cross-Sectional Study

scientific article published on 10 April 2019

Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus

scientific article published on 26 June 2021

Further Evidence of Increasing Diversity of Plasmodium vivax in the Republic of Korea in Recent Years

scientific article

Further evidence supporting a role for gs signal transduction in severe malaria pathogenesis

scientific article

G6PD deficiency alleles in a malaria-endemic region in the Western Brazilian Amazon

scientific article

Genetic determinants of anti-malarial acquired immunity in a large multi-centre study

scientific article

Genetic diversity and population structure of Plasmodium vivax in Central China

scientific article

Genetic diversity of next generation antimalarial targets: A baseline for drug resistance surveillance programmes

scientific article published on 09 March 2017

Genetic diversity of the Plasmodium falciparum GTP-cyclohydrolase 1, dihydrofolate reductase and dihydropteroate synthetase genes reveals new insights into sulfadoxine-pyrimethamine antimalarial drug resistance

scientific article published on 31 December 2020

Genetic loci associated with delayed clearance of Plasmodium falciparum following artemisinin treatment in Southeast Asia

scientific article published on 17 December 2012

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 analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance

article

Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis

scientific article

Genome-wide analysis of selection on the malaria parasite Plasmodium falciparum in West African populations of differing infection endemicity

scientific article

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

scientific article

Genome-wide comparisons of variation in linkage disequilibrium

scientific article published on 18 June 2009

Genome-wide mutagenesis and multi-drug resistance in American trypanosomes induced by the front-line drug benznidazole

scientific article published on 31 October 2017

Genome-wide saturation mutagenesis of Burkholderia pseudomallei K96243 predicts essential genes and novel targets for antimicrobial development

scientific article

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

scientific article

Genome-wide significance for dense SNP and resequencing data

scientific article

Genomic analysis of a pre-elimination Malaysian Plasmodium vivax population reveals selective pressures and changing transmission dynamics.

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

Genomic variation in Plasmodium vivax malaria reveals regions under selective pressure

scientific article

Genomic variation in two gametocyte non-producing Plasmodium falciparum clonal lines

scientific article published on 21 April 2016

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

article

Global genetic diversity of var2csa in Plasmodium falciparum with implications for malaria in pregnancy and vaccine development

scientific article published in Scientific Reports

Glucose-6-phosphate dehydrogenase polymorphisms and susceptibility to mild malaria in Dogon and Fulani, Mali

scientific article

Haplotype analyses of haemoglobin C and haemoglobin S and the dynamics of the evolutionary response to malaria in Kassena-Nankana district of Ghana

scientific article

High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta.

scientific article

Human candidate gene polymorphisms and risk of severe malaria in children in Kilifi, Kenya: a case-control association study

article

Human candidate polymorphisms in sympatric ethnic groups differing in malaria susceptibility in Mali

scientific article (publication date: 2013)

Imputation-based meta-analysis of severe malaria in three African populations

scientific article

Imputation-based population genetics analysis of Plasmodium falciparum malaria parasites

scientific article (publication date: April 2015)

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

scientific article

Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs

scientific article published on 24 June 2019

Investigation of host candidate malaria-associated risk/protective SNPs in a Brazilian Amazonian population

scientific article

Know Your Heart: Rationale, design and conduct of a cross-sectional study of cardiovascular structure, function and risk factors in 4500 men and women aged 35-69 years from two Russian cities, 2015-18

scientific article published on 03 December 2018

Know Your Heart: Rationale, design and conduct of a cross-sectional study of cardiovascular structure, function and risk factors in 4500 men and women aged 35-69 years from two Russian cities, 2015-18

scientific article published in 2018

Lack of association of interferon regulatory factor 1 with severe malaria in affected child-parental trio studies across three African populations

scientific article

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

scientific article

Malaria Host Candidate Genes Validated by Association With Current, Recent, and Historical Measures of Transmission Intensity

scientific article

Methylation in Mycobacterium tuberculosis is lineage specific with associated mutations present globally

scientific article published on 9 January 2018

Modest heterologous protection after Plasmodium falciparum sporozoite immunization: a double-blind randomized controlled clinical trial

scientific article published on 13 September 2017

Multidrug-Resistant Mycobacterium tuberculosis of the Latin American Mediterranean Lineage, Wrongly Identified as Mycobacterium pinnipedii (Spoligotype International Type 863 [SIT863]), Causing Active Tuberculosis in South Brazil

scientific article

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

scientific article

Mycobacterium tuberculosis whole genome sequencing provides insights into the Manila strain and drug-resistance mutations in the Philippines

scientific article published on 26 June 2019

Novel genetic polymorphisms associated with severe malaria and under selective pressure in North-eastern Tanzania

scientific article published on 30 January 2018

Ocular chlamydial genomic variants and disease severity in trachoma: a cross-sectional population-based genome-wide association study

scientific article published in The Lancet

On the performance of multiple imputation based on chained equations in tackling missing data of the African α3.7 -globin deletion in a malaria association study

scientific article

On the usage of HWE for identifying genotyping errors

scientific article published on 27 March 2007

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

PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis

scientific article published on 13 May 2015

PlasmoView: a web-based resource to visualise global Plasmodium falciparum genomic variation

scientific article

PolyTB: a genomic variation map for Mycobacterium tuberculosis

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

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

scientific article

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

scientific article

Population-based analysis of ocular Chlamydia trachomatis in trachoma-endemic West African communities identifies genomic markers of disease severity

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

Power consequences of linkage disequilibrium variation between populations

scientific article published on February 2009

Primary macrophages and J774 cells respond differently to infection with Mycobacterium tuberculosis

scientific article published on 08 February 2017

Probing Differences in Gene Essentiality Between the Human and Animal Adapted Lineages of the <i>Mycobacterium tuberculosis</i> Complex Using TnSeq

scientific article published on 24 December 2021

Rapid and iterative genome editing in the malaria parasite Plasmodium knowlesi provides new tools for P. vivax research.

scientific article published on 17 June 2019

Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences

scientific article published on 27 May 2015

Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages

scientific article

Recombinations in staphylococcal cassette chromosome mec elements compromise the molecular detection of methicillin resistance in Staphylococcus aureus

scientific article

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

Robust barcoding and identification of Mycobacterium tuberculosis lineages for epidemiological and clinical studies

scientific article published on 14 December 2020

Robust detection of point mutations involved in multidrug-resistant Mycobacterium tuberculosis in the presence of co-occurrent resistance markers

scientific article published on 21 December 2020

Role of alanine racemase mutations in Mycobacterium tuberculosis D-cycloserine resistance

scientific article published on 2 October 2017

SV-Pop: population-based structural variant analysis and visualization

scientific article published on 13 March 2019

SVAMP: sequence variation analysis, maps and phylogeny

scientific article published on 3 April 2014

Sequence-level population simulations over large genomic regions

scientific article published on 18 October 2007

Single nucleotide polymorphisms in efflux pumps genes in extensively drug resistant Mycobacterium tuberculosis isolates from Pakistan

scientific article

SnoopCGH: software for visualizing comparative genomic hybridization data

scientific article (publication date: 15 October 2009)

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

scientific article published on 26 September 2012

TLR9 polymorphisms in African populations: no association with severe malaria, but evidence of cis-variants acting on gene expression

scientific article published on 13 March 2009

Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice

scientific article

The antimalarial efficacy and mechanism of resistance of the novel chemotype DDD01034957

scientific article published on 21 January 2021

The draft genome of Mycobacterium aurum, a potential model organism for investigating drugs against Mycobacterium tuberculosis and Mycobacterium leprae

scientific article published on 4 June 2015

The epidemiology, pathogenesis, transmission, diagnosis, and management of multidrug-resistant, extensively drug-resistant, and incurable tuberculosis

scientific article

The variability and reproducibility of whole genome sequencing technology for detecting resistance to anti-tuberculous drugs

scientific article

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

scientific article published on February 2009

Turkish and Japanese Mycobacterium tuberculosis sublineages share a remote common ancestor

scientific article published on 13 October 2016

USP38, FREM3, SDC1, DDC, and LOC727982 Gene Polymorphisms and Differential Susceptibility to Severe Malaria in Tanzania

scientific article

Understanding molecular consequences of putative drug resistant mutations in Mycobacterium tuberculosis

scientific article published in Scientific Reports

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

scientific article

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

scientific article published on 27 August 2010

Use of whole genome sequencing in surveillance of drug resistant tuberculosis

scientific article

Validating discovered Cis-acting regulatory genetic variants: application of an allele specific expression approach to HapMap populations

scientific article

VarB: a variation browsing and analysis tool for variants derived from next-generation sequencing data

scientific article (publication date: 15 November 2012)

Variation in Complexity of Infection and Transmission Stability between Neighbouring Populations of Plasmodium vivax in Southern Ethiopia

scientific article published on 15 October 2015

VivaxGEN: An open access platform for comparative analysis of short tandem repeat genotyping data in Plasmodium vivax populations

scientific article

Whole genome sequencing based characterization of extensively drug-resistant Mycobacterium tuberculosis isolates from Pakistan

scientific article

Whole genome sequencing of amplified Plasmodium knowlesi DNA from unprocessed blood reveals genetic exchange events between Malaysian Peninsular and Borneo subpopulations

scientific article published on 08 July 2019

Whole genome sequencing of drug resistant Mycobacterium tuberculosis isolates from a high burden tuberculosis region of North West Pakistan

scientific article published on 18 October 2019

Whole-genome scans provide evidence of adaptive evolution in Malawian Plasmodium falciparum isolates

scientific article

estMOI: estimating multiplicity of infection using parasite deep sequencing data

scientific article

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