Taane G Clark

Taane G Clark

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Taane G Clark

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

Connect Tissue Res 2019 Jul 5;60(4):389-398. Epub 2019 Feb 5.

f Waitemata District Health Board , University of Auckland, and Geriatrician , Auckland , New Zealand.

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http://dx.doi.org/10.1080/03008207.2019.1570169DOI Listing
July 2019

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

BMC Bioinformatics 2019 Mar 13;20(1):136. Epub 2019 Mar 13.

Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.

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http://dx.doi.org/10.1186/s12859-019-2718-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6417133PMC
March 2019

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

BMC Genomics 2019 Mar 29;20(1):252. Epub 2019 Mar 29.

Pathogen Molecular Biology Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.

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http://dx.doi.org/10.1186/s12864-019-5615-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6440112PMC
March 2019

PrimedRPA: primer design for recombinase polymerase amplification assays.

Bioinformatics 2019 Feb;35(4):682-684

Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine (LSHTM), London, UK.

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http://dx.doi.org/10.1093/bioinformatics/bty701DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6379019PMC
February 2019

Genetic Diversity of , Coding for a Main Efflux Pump of .

Front Genet 2018 9;9:710. Epub 2019 Jan 9.

Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade NOVA de Lisboa, Lisbon, Portugal.

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http://dx.doi.org/10.3389/fgene.2018.00710DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6333699PMC
January 2019

Hand Grip Strength as a Clinical Biomarker for ME/CFS and Disease Severity.

Front Neurol 2018 27;9:992. Epub 2018 Nov 27.

Department of Clinical Research, Faculty of Infectious and Tropical Diseases, International Centre for Evidence in Disability, London School of Hygiene and Tropical Medicine, London, United Kingdom.

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http://dx.doi.org/10.3389/fneur.2018.00992DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6277492PMC
November 2018

Understanding molecular consequences of putative drug resistant mutations in Mycobacterium tuberculosis.

Sci Rep 2018 Oct 18;8(1):15356. Epub 2018 Oct 18.

Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.

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http://www.nature.com/articles/s41598-018-33370-6
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http://dx.doi.org/10.1038/s41598-018-33370-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6193939PMC
October 2018

Use of whole genome sequencing in surveillance of drug resistant tuberculosis.

Expert Rev Anti Infect Ther 2018 05 9;16(5):433-442. Epub 2018 May 9.

c Faculty of Infectious and Tropical Diseases and Faculty of Epidemiology and Population Health , London School of Hygiene & Tropical Medicine , London , United Kingdom.

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http://dx.doi.org/10.1080/14787210.2018.1472577DOI Listing
May 2018

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

Int J Parasitol 2018 03 16;48(3-4):191-196. Epub 2017 Dec 16.

Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom; Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom. Electronic address:

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http://dx.doi.org/10.1016/j.ijpara.2017.09.008DOI Listing
March 2018

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

Tuberculosis (Edinb) 2017 12 3;107:20-30. Epub 2017 Aug 3.

Department of Pathology and Laboratory Medicine, Aga Khan University Hospital, Karachi, Pakistan. Electronic address:

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http://dx.doi.org/10.1016/j.tube.2017.07.012DOI Listing
December 2017

A multiple genome analysis of Mycobacterium tuberculosis reveals specific novel genes and mutations associated with pyrazinamide resistance.

BMC Genomics 2017 Oct 11;18(1):769. Epub 2017 Oct 11.

Laboratorio de Bioinformática y Biología Molecular. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martín de Porras, 31, Lima, Peru.

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http://dx.doi.org/10.1186/s12864-017-4146-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5637355PMC
October 2017

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

Sci Rep 2017 10 31;7(1):14407. Epub 2017 Oct 31.

Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.

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http://dx.doi.org/10.1038/s41598-017-14986-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5663738PMC
October 2017

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

Int J Parasitol Drugs Drug Resist 2017 08 9;7(2):174-180. Epub 2017 Mar 9.

Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK. Electronic address:

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http://dx.doi.org/10.1016/j.ijpddr.2017.03.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5379905PMC
August 2017

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

Sci Rep 2017 02 8;7:42225. Epub 2017 Feb 8.

Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, London, UK.

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http://dx.doi.org/10.1038/srep42225DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5296737PMC
February 2017

The UK ME/CFS Biobank for biomedical research on Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) and Multiple Sclerosis.

Open J Bioresour 2017 20;4. Epub 2017 Feb 20.

CureME Research Team, International Centre for Evidence in Disability (ICED), Department of Clinical Research (CRD), Faculty of Infectious and Tropical Diseases at the London School of Hygiene & Tropical Medicine, Keppel St, London WC1E 7HT, UK.

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http://dx.doi.org/10.5334/ojb.28DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5482226PMC
February 2017

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

Elife 2017 01 9;6. Epub 2017 Jan 9.

Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.

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http://dx.doi.org/10.7554/eLife.15085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5222559PMC
January 2017

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

Genome Med 2016 12 22;8(1):132. Epub 2016 Dec 22.

Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT, London, UK.

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http://dx.doi.org/10.1186/s13073-016-0385-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5178084PMC
December 2016

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

Int J Mycobacteriol 2016 Dec 22;5 Suppl 1:S97-S98. Epub 2016 Nov 22.

Department of Pathology and Laboratory Medicine, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan. Electronic address:

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http://dx.doi.org/10.1016/j.ijmyco.2016.09.064DOI Listing
December 2016

Turkish and Japanese Mycobacterium tuberculosis sublineages share a remote common ancestor.

Infect Genet Evol 2016 11 14;45:461-473. Epub 2016 Oct 14.

Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.

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http://dx.doi.org/10.1016/j.meegid.2016.10.009DOI Listing
November 2016

Genome-scale comparison of expanded gene families in Plasmodium ovale wallikeri and Plasmodium ovale curtisi with Plasmodium malariae and with other Plasmodium species.

Int J Parasitol 2016 10 5;46(11):685-96. Epub 2016 Jul 5.

Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah 23955-6900, Saudi Arabia; Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, N20 W10 Kita-ku, Sapporo 001-0020, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.ijpara.2016.05.009DOI Listing
October 2016

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

PLoS One 2016 18;11(3):e0151514. Epub 2016 Mar 18.

Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT 0810, Australia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0151514PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4798397PMC
August 2016

Whole Genome Sequencing Shows a Low Proportion of Tuberculosis Disease Is Attributable to Known Close Contacts in Rural Malawi.

PLoS One 2015 16;10(7):e0132840. Epub 2015 Jul 16.

Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom; Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0132840PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4504505PMC
April 2016

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

Int J Mycobacteriol 2015 09 4;4(3):207-16. Epub 2015 Jun 4.

Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom.

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http://dx.doi.org/10.1016/j.ijmyco.2015.05.001DOI Listing
September 2015

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

BMC Bioinformatics 2015 May 13;16:155. Epub 2015 May 13.

Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel St, London, UK.

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http://dx.doi.org/10.1186/s12859-015-0603-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4429496PMC
May 2015

Imputation-based population genetics analysis of Plasmodium falciparum malaria parasites.

PLoS Genet 2015 Apr 30;11(4):e1005131. Epub 2015 Apr 30.

Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom; Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.1005131DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4415759PMC
April 2015

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

PLoS Genet 2015 Feb 11;11(2):e1004960. Epub 2015 Feb 11.

Pathogen Molecular Biology Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom; Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.1004960DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4335500PMC
February 2015

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

J Infect Dis 2014 Dec 3;210(12):2001-8. Epub 2014 Jul 3.

Department of Immunology and Infection, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, United Kingdom.

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http://dx.doi.org/10.1093/infdis/jiu358DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4241946PMC
December 2014

A robust SNP barcode for typing Mycobacterium tuberculosis complex strains.

Nat Commun 2014 Sep 1;5:4812. Epub 2014 Sep 1.

1] Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK [2] Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.

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http://dx.doi.org/10.1038/ncomms5812DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4166679PMC
September 2014

SVAMP: sequence variation analysis, maps and phylogeny.

Bioinformatics 2014 Aug 3;30(15):2227-9. Epub 2014 Apr 3.

Pathogen Genomics Laboratory, Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia and Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.

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http://dx.doi.org/10.1093/bioinformatics/btu176DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4103593PMC
August 2014

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.

Ann Hum Genet 2014 Jul;78(4):277-89

London School of Hygiene and Tropical Medicine, London, UK; Centre of Statistics and Applications of University of Lisbon, Lisbon, Portugal.

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http://dx.doi.org/10.1111/ahg.12065DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4140543PMC
July 2014

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

Malar J 2014 Jul 11;13:270. Epub 2014 Jul 11.

Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, Faculty of Medicine, Pharmacy and Odonto - Stomatology, USTTB, BP 1805 Bamako, Mali.

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http://dx.doi.org/10.1186/1475-2875-13-270DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4110528PMC
July 2014

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

Mol Biol Evol 2014 Jun 18;31(6):1490-9. Epub 2014 Mar 18.

Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, London, United KingdomMedical Research Council Unit, Fajara, Banjul, The Gambia

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http://dx.doi.org/10.1093/molbev/msu106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4032133PMC
June 2014

estMOI: estimating multiplicity of infection using parasite deep sequencing data.

Bioinformatics 2014 May 17;30(9):1292-4. Epub 2014 Jan 17.

London School of Hygiene and Tropical Medicine, WC1E 7HT, London, UK, Wellcome Trust Sanger Institute, CB10 1SA, Hinxton, UK and Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Box 30096 BT3, Blantyre, Malawia.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btu005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3998131PMC
May 2014

PolyTB: a genomic variation map for Mycobacterium tuberculosis.

Tuberculosis (Edinb) 2014 May 15;94(3):346-54. Epub 2014 Feb 15.

Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK.

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http://dx.doi.org/10.1016/j.tube.2014.02.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4066953PMC
May 2014

Cathepsin-L can resist lysis by human serum in Trypanosoma brucei brucei.

PLoS Pathog 2014 May 15;10(5):e1004130. Epub 2014 May 15.

Division of Biological Chemistry & Drug Discovery, College of Life Sciences, University of Dundee, Dundee, United Kingdom.

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http://dx.doi.org/10.1371/journal.ppat.1004130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4022737PMC
May 2014

A transcriptional switch underlies commitment to sexual development in malaria parasites.

Nature 2014 Mar 23;507(7491):248-52. Epub 2014 Feb 23.

1] Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA [2] Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA [3] Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA (B.F.C.K.); Department of Molecular Biology and Center for Infectious Disease Dynamics, The Pennsylvania State University, State College, Pennsylvania 16802, USA (V.M.C., M.L.).

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http://dx.doi.org/10.1038/nature12920DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4040541PMC
March 2014