Tuberculosis

Use of WGS and Omics to better understand the biology and behaviour of Mycobacterium tuberculosis

Malaria

Use of WGS and Omics to better understand the biology and genomic diversity of the malaria causing parasites (P. falciparum, P.vivax, P. knowlesi, P.ovale and P.malariae)

AMR

Coming



Flaviviruses

Coming

Vector

Coming

Methods

Use and creation of statistical methods and bioinformatics tools to tackle specific biological issues ( Data Visualization | NGS | PacBio | GWAS )



Teaching

Courses | Workshops

People

Team members and collaborators in the PathogenSeq group at LSHTM

Publications

Chronological list of Publications

Tuberculosis

Use of WGS and Omics to better understand the biology and behaviour of Mycobacterium tuberculosis

Poly TB

Web-based resource designed to explore Mycobacterium tuberculosis complex (MTBC) genomic variation at a global scale.

Global Drug Resistance Study

A study to investigate drug resistance in Mycobacterium tuberculosis (Mtb).

Karonga Diversity Study

Karonga Diversity Study

Kampala Study

Analysis of the genome of 51 clinical isolates of M. tuberculosis including drug resistant strains and longitudinal samples from individual patients from Kampala.

TDR TB Strain Bank

The Strain Bank is a collection of well characterized strains of M. tuberculosis that are available to the TB research community

Rapid DR Study

Web tool that rapidly analyses raw sequence data and predicts resistance and lineage in M. tuberculosis.

Molecular Barcode

SNP barcode for typing Mycobacterium tuberculosis.

PhyTB

Web-based tool to assist phylogenetic tree visualisation and identification of M. tuberculosis clade-informative polymorphisms.

M.aurum

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

PE/PPE

PE/PPE gene diversity project

Sequencing Variability

Mtb sequencing variability project

Malaria

Use of WGS and Omics to better understand the biology and genomic diversity of the malaria causing parasites (P. falciparum, P.vivax, P. knowlesi, P.ovale and P.malariae)

Plasmoview

PlasmoView is a web-tool that facilitates the investigation of Plasmodium falciparum polymorphisms across populations in malaria endemic regions and the presentation of allele frequencies on maps.

Genetic Barcode Study

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

Drug Resistance Map

Gametocyte Genomics Study

An understanding of the genetic mechanisms underlying Plasmodium falciparum gametocyte production could lead to new malaria control measures

AMR

Coming

Coming

Coming

Zika and flavivirus

Coming

Coming

Coming

Vector based Genomics

Coming

Coming

Coming

Methods

Use and creation of statistical methods and bioinformatics tools to tackle specific biological issues ( Data Visualization | NGS | PacBio | GWAS )

estMOI

Estimating multiplicity of infection using parasite deep sequencing data

VCF Viewer (VarB)

VarB software can read in multi-sample VCF files, and visualize and critically assess contents and identify informative markers

SnoopCGH

A Java desktop application for visualising and exploring comparative genomic hybridization (CGH) data.

In silico Spoligotyping

SpolPred is a software to predict the spoligotype of Mycobacterium tuberculosis samples from raw sequence reads

LD Bayesian Analysis (BALD)

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

Teaching

Courses | Workshops

GEID 2017

International Workshop in Epidemiology in Infectious Diseases in the Philippines | Course Dates: 3-7 July 2017

Infectious Disease 'Omics

Short Annual Course on Infectious Disease study using the latest 'Omics software and technologies | Course Dates: 19-21 September 2016

GEID 2016

International Workshop in Epidemiology in Infectious Diseases in Thailand

People

Team members and collaborators in the PathogenSeq group at LSHTM

TEAM MEMBERS

Taane Clark - Professor of Genomics and Global Health Send Mail
Susana Campino - Associate Professor Send Mail
Stephane Hue - Assistant Professor Send Mail
Joao Perdigao - FCT Post Doctoral Research Fellow Send Mail
Monica Campos - Research Fellow Send Mail
Ben Sobkowiak - Research Fellow Send Mail
Ernest Diez Benavente - Research Assistant and PhD Student Send Mail
Jody Phelan - BBRSC PhD Student Send Mail
Matt Ravenhall - BBRSC PhD Student Send Mail
Yaa Oppong - BBRSC PhD Student Send Mail

Wouter Deelder - PhD Student
Paula Gomez - MRC PhD Student
Matthew Higgins - BBRSC PhD Student
Amy Ibrahim - MRC PhD Student
To be announced - Bloomsbury Research Fund PhD Student

Alumni

Ifeyinwa Aniebo (PhD)
Francesc Coll (PhD)
Ana Rita Gomes
Afonso Guerra
Kim Mallard
Harold Ocholla (PhD)
Mark Preston
Hanif Bin Samad
Nuno Sepulveda

Stefan Panaiotov

Jean-Bosco Oudraogo
Issaka Zongo

Rick Fairhurst

Jaime Robledo

Cristophe Sola

Steffan Borrmann

Harold Ocholla

Mahamadou Diakite

Richard Anthony

Rumina Hasan

Pascal Michon

Isabel Portugal
Miguel Viveiros

Arnab Pain

Oumar Faye

Keertan Dheda
Rob Warren
Ruth McNerney

Tim Anderson
Francois Nosten
Prapat Suriyaphol
Surakameth Mahasirimongkol

Sanjib Bhakta
David Baker
Martin Hibberd
Colin Sutherland
Teun Bousema
Francesc Coll
David Conway
Julian Parkhill
Cally Roper
Nuno Sepulveda
Alister Craig
Chris Drakeley
Nick Furnham
Judith Glynn
Julius Hafalla
Martin Holland
Nigel Martin
Eleanor Riley
Brendan Wren
Julius Hafalla
Fady Mohareb
George Roussos

Bryan Greenhouse

Ma. Cecilia G. Ama
Raul Destura
Dodge Lim

Maxine Caws

YY Teo

Laura Gomez

Publications

Chronological list of publications.

  1. Dombrowski JG, Souza RM, Curry J, Hinton L, Silva NRM, Grignard L, Gonçalves L, Gomes A, Epiphanio S, Drakeley C, Huggett J, Clark TG, Campino S, Marinho C. G6PD deficiency alleles in a malaria endemic region in Western Brazilian Amazon. Malaria J. 2017 in press.

  2. Kanji A, Hasan R, Zaver A, Ali A, Ashraf M, Imtiaz K, Clark TG, McNerney R, Shafiq S, Hasan R. Alternate Efflux Pump Mechanism may Contribute to Drug Resistance in Extensively Drug Resistant (XDR) Isolates of Mycobacterium tuberculosis. Int J Myco. 2017 in press.

  3. Benavente ED, de Oliveira TC, Campino S, Ward Z, Chan W, Mohareb FR, Sutherland CJ, Ferreira M, Roper C, Clark TG. Using whole genomic variation in Plasmodium vivax malaria to reveal regions under selective pressure. PloS One 2017. 2017 May 11;12(5):e0177134.

  4. Gomes AR, Ravenhall M, Diez Benavente E, Talman A, Sutherland C, Roper C, Clark TG, Campino S. Genetic diversity of next generation antimalarial targets: a baseline for drug resistance surveillance programmes. International Journal for Parasitology: Drugs and Drug Resistance. 2017;7(2):174-180.

  5. Trimarsanto H, Benavente ED, Noviyanti R, Utami RA, Trianty L, Pava Z, Getachew S, Kim JY, Goo YK, Wangchuck S, Liu Y, Gao Q, Dowd S, Cheng Q, Clark TG, Price RN, Auburn S. VivaxGEN: An Open Access Platform for Comparative Analysis of Short Tandem Repeat Genotyping Data in Plasmodium vivax Populations. PloS Negl. Trop. Medicine. 2017 Mar 31;11(3):e0005465.

  6. Sepulveda N, Manjurano A, Campino SG, Lemnge M, Lusingu J, Olomi R, Rockett KA, Hubbart C, Jeffreys A, MalariaGEN, Clark TG & Riley EM & Drakeley CJ. Genetic signatures of malaria selection validated by association with current and historic measures of malaria transmission intensity. J Inf Diseas 2017; May 25. doi: 10.1093/infdis/jix250

  7. Dheda K, Gumbo T, Maartens G, Dooley KE, McNerney R, Murray M, Furin J, Nardell EA, London L, Lessem E, Theron G, van Helden P, Niemann S, Merker M, Dowdy D, Van Rie A, Siu GKH, Pasipanodya JG, Rodrigues C, Clark TG, et al. The epidemiology, pathogenesis, transmission, diagnosis, and management of multidrug-resistant, extensively drug-resistant, and incurable tuberculosis. Lancet Respir Med. 2017 Mar 15. pii: S2213-2600(17)30079-6.

  8. Last A, Roberts C, Coll F, Phelan J, Burr S, Cassama E, Nabicassa M, Cutcliffe L, Clarke I, Mabey D, Bailey R, …, Clark TG, Thomson N, Holland M. Genome wide association analysis in ocular Chlamydia trachomatis infection identifies genomic markers associated with disease severity. Nature Microbiology 2017;

  9. Lacerda E, Bowman E, Cliff J, Kingdon C, King E, Clark TG, Dockrell H, Riley E, Nacul L. Protocol for the UK ME/CFS Biobank - a Resource for High Quality Biomedical Research. Open Journal of Bioresources 2017; 4: 4, DOI: https://doi.org/10.5334/ojb.28

  10. Dheda K. Limberis J, Pietersen E, Phelan J, Theron G, Esmail A, Jayakumar J, Lesosky M, McNerney R, Fennelly K, van Helden P, Sirgel F, Pain A, Clark TG & Warren R. Molecular epidemiology, transmission dynamics, and outcomes of programmatically incurable TB in South Africa: a prospective cohort study. Lancet Resp. Med 2017; Jan 18. pii: S2213-2600(16)30433-7.

  11. Clarke GM, Rockett KA, …, Manjurano A, Sepúlveda N, Clark TG, et al. Multi-centre analysis of the association between severe malaria and multiple forms of G6PD deficiency. eLife 2017;6:e15085

  12. Andreu N, Phelan J, de Sessions P, Cliff JM, Clark TG, Hibberd M. Primary macrophages and J774 cells respond differently to infection with Mycobacterium tuberculosis. Sci Rep. 2017; Feb 8;7:42225. doi: 10.1038/srep42225.

  1. McNerney R, Clark TG, Campino S, Rodriguez C, Dolinger D, Smith L, Schito M. Removing the bottleneck in whole genome sequencing of M. tuberculosis for rapid drug resistance analysis: a call to action. Int J Infectious Dis. 2016 Dec 13. pii: S1201-9712(16)31642-3. doi: 10.1016/j.ijid.2016.11.422.

  2. Phelan J, O’Sullivan DM, Whale AS, Campino S, Viveiros M, Huggett J, Clark TG. The impact of DNA processing and sequencing technology on Mycobacterium tuberculosis genome characterisation and drug resistance profiling. Genome Medicine 2016, 8:132.

  3. Ravenhall M, Benavente ED, Mipando M, Jensen ATR, Sutherland CJ, Roper C, Kwiatkowski DP, Montgomery J, Phiri KS, Terlouw A, Craig A, Campino S, Ocholla H, Clark TG. Characterising the impact of sustained Sulfadoxine/Pyrimethamine use upon the Plasmodium falciparum population in Malawi. Malaria J. 2016. Nov 29;15(1):575. PMID: 27899115

  4. Refregier G, Abadia E, Matsumoto T, Ano H, Takashima T, Tsuyuguchi I, Aktas E, Panaiotov S, Phelan J, Coll F, McNerney R, Clark TG, Sola C. Combining host and pathogen data to reconstruct deep tuberculosis evolution: linking back Turkish and Japanese history to Paleolithic? Infect Genet Evol. 2016 Oct 13. pii: S1567-1348(16)30418-X

  5. Ansaria HR, Templeton TJ, Subudhi AK, Ramaprasad A, Tang J, Lu F, Naeem R, Oguike MC, DiezBenavente E, Clark TG, Sutherland CJ, Barnwell JW, Culleton R, Cao J, Pain A. 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 Parasitology 2016 Jul 5. pii: S0020-7519(16)30135-7. doi: 10.1016/j.ijpara.2016.05.009. PMID: 27392654

  6. Coker OO, Chaiprasert A, Ngamphiw C, Tongsima S, Regmi SM, Clark TG, Ong RTH, Teo Y, Prammananan T, Palittapongarnpim P. (2016) Genetic signatures of Mycobacterium tuberculosis Nonthaburi genotype revealed by whole genome analysis of isolates from tuberculous meningitis patients in Thailand. PeerJ 4:e1905. https://doi.org/10.7717/peerj.1905

  7. Phelan J, Coll F, McNerney R, Glynn JR, Campino S, Pain A, Clark TG. Recombination in PE and PPE multi-family genes contributes to genetic variation in Mycobacterium tuberculosis. BMC Genomics 2016 Feb 29;17(1):151. doi: 10.1186/s12864-016-2467-y

  8. Campino SG, Assefa S, Thompson E, Drought LG, Taylor C, Gorvett Z, Carret CJ, Flueck C, Ivens AC, Kwiatkowski DP, Alano P, Baker DA, Clark TG. Genomic variation in the A4 and F12 gametocyte non-producing malaria strains. Malaria J 2016 Apr 21;15(1):229. doi: 10.1186/s12936-016-1254-1.

  9. Phelan J, Coll F, McNerney R, Ascher DB, Furnham N, Coeck N, Hill-Cawthorne GA, Nair MB, Mallard K, Meehan C, Sola C, Hibberd M, Ramsey A, Pain A, Rigouts L, Clark TG. Whole genome association analysis of Mycobacterium tuberculosis clinical isolates provides insight into mutation position and the minimal inhibitory concentration of anti-tuberculosis drugs. BMC Medicine 2016, 14:31. doi: 10.1186/s12916-016-0575-9.

  10. Kim J-Y, Goo Y-K, Zo Y-G; Ji S-Y, Trimarsanto H; To S, Clark TG, Price R, Auburn S. Further evidence of increasing diversity of Plasmodium vivax in the Republic of Korea in recent years. PLoS One. 2016 Mar 18;11(3):e0151514. doi: 10.1371/journal.pone.0151514

  1. Getachew S, To S, Trimarsanto H, Ley-Thriemer K, Clark TG, Aseffa A, Petros B, Price RN, Auburn S. Variation in complexity of infection and transmission stability between neighbouring populations of Plasmodium vivax in Southern Ethiopia. PloS One 2015 Oct 15;10(10):e0140780.

  2. Moule MG, Spink N, Willcocks S, Lim J, Guerra-Assunção JA, Cia F, Senior N, Atkins H, Titball RW, Clark TG, Bancroft G, Cuccui J, Wren BW. Characterisation of new virulence factors involved in the intracellular growth and survival of Burkholderia pseudomallei. Infect. & Immun. (in press).

  3. Dalla Costa ER, Vasconcelos SEG, Esteves LS, Gomes HM, Gomes LL, Silva PEA, Perdigão J, Portugal I, Viveiros M, McNerney R, Pain A, Clark TG, Rastogi N, Unis G, Rossetti MLR, Suffys PN. Multidrug resistant Mycobacterium tuberculosis of the Latin American Mediterranean lineage wrongly identified as Mycobacterium pinnipedii (ST863) causing active tuberculosis in south Brazil. J Clin Microbiology 2015 Sep 23. pii: JCM.02012-15.

  4. Roberts CH, Franklin CS, Makalo P, …, Clark TG, Burton M, Mabey DCW, Bailey R, Barroso I, Holland MJ. Host genome-wide associations with pathology from ocular Chlamydia trachomatis infections converge on the metabolic cell cycle, cell surface receptors and associated signalling pathways. Nature Scientific Reports 2015; 5:17447.

  5. Assefa SA, Lim C, Preston MD, Duffy CW, Nair MB, Kadir KA, Goldberg JE, Neafsey D, Divis PCS, Clark TG, Duraisingh MT, Conway DJ, Pain A, Singh B. Population genomic structure and adaptation in the zoonotic malaria parasite Plasmodium knowlesi. Proc Natl Acad Sci USA 2015; 112(42): 13027-32.

  6. Sheen P, Requena D, Gilman RH, Gushiken E, Antiparra R, Lucero B, Lizárraga P, Cieza B, Roncal E, Grandjean L, Pain A, McNerney R, Clark TG, Moore D, Zimic M. A multiple genome analysis of Mycobacterium tuberculosis reveals specific genes and mutations associated with pyrazinamide resistance. Int J Mycobacteriology (in press).

  7. Shelton J, Risley P, De Silva N, Hubbart C, Jeffreys A, Rowlands K, Craik R, Cornelius V, Hensmann M, Molloy S, Sepulveda N, Clark TG et al. Genetic Determinants Of Anti-Malarial Acquired Immunity In A Large Multi-Centre Study. Malaria Journal 2015; Aug 28;14(1):333.

  8. Cairns M, Preston MD, Lawley T, Clark TG, Stabler R, Wren B. Genomic epidemiology of a protracted hospital outbreak caused by a toxin A negative, Clostridium difficile sublineage PCR Ribotype 017 strain in London, England. J Clin Micro 2015; Jul 15. pii: JCM.00648-15.

  9. Abdallah AM, Hill-Cawthorne G, Otto TD, Coll F, Ummels R, Adroub SA, Gao G, Guerra-Assunção AJ, Malas T, Naeem R, Zhang H, Panigrahi AK, Ali S, Mcnerney R, Brosch R, Clark TG, Behr MA, Bitter W, Pain A. Genomic expression catalogue of a global collection of BCG vaccine strains show evidence for highly diverged metabolic and cell-wall adaptations. Scientific Reports 2015; 5:15443.

  10. Kanji A, Hasan Z, Ali A, McNerney R, Mallard K, Coll F, Hill-Cawthorne C, Nair M, Clark TG, Zaver A, Jafri S, Hasan R. Characterization of genomic variations in SNPs of PE_PGRS genes reveals deletions and insertions in extensively drug resistant (XDR) M. tuberculosis strains from Pakistan. Int J Mycobacteriology 2015; 4, 73-79.

  11. Noviyanti R, Coutrier F, Utami RAS, Trimarsanto H, …, Clark TG, Price R, Auburn S. Contrasting transmission dynamics of co-endemic Plasmodium falciparum and P. vivax: implications for malaria control and elimination. PLoS Negl Trop Dis. 2015 May 7;9(5):e0003739. doi: 10.1371/journal.pntd.0003739

  12. Coll F, McNerney R, Preston MD, Guerra-Assunção JA, …, Pain A, Clark TG. Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences. Genome Medicine 2015; May 27; 7:51.

  13. Benavente ED, Coll F, Furnham N, McNerney R, Glynn JR, Campino S, Pain A, Mohareb FR, Clark TG. PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis. BMC Bioinformatics. 2015 May 13;16:155. doi: 10.1186/s12859-015-0603-3.

  14. Straimer J, Recker, Martin-Valls A, Preston M, Clark TG, Mueller A, Przyborski J, Borrmann S. Gene amplification fuels the acquisition of high-level anti-folate resistance in Plasmodium falciparum. Nature Commun. 2015 (in press)

  15. Phelan J, Coll F, McNerney R, Pain A, Bhakta S, Clark TG. Mycobacterium aurum genome sequence and investigating tuberculosis infection and drug resistance. Int J Mycobact. 2015; 4: 207–216.

  16. Samad H, Coll F, Preston MD, Ocholla H, Fairhurst RM, Clark TG. Imputation-based population genetics analysis of Plasmodium falciparum malaria parasites. PLoS Genet. 2015; 11(4):e1005131.

  17. Manjurano A, NadimB, Wangai M, Mtove G, MalariaGEN, Reyburn H, Drakeley CJ, Riley E, Clark TG. Polymorphisms in USP38, FREM3, SDC1, DDC and LOC727982 genes and differential susceptibility to severe malaria phenotypes in Tanzania. J Infectious Dis. 2015 J Mar 24. pii: jiv192.

  18. Bergval I, Schuitema A, de Ronde H, Coll F, Mallard K, Pain A, McNerney R, Clark TG, Anthony R. The majority of the 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. FEMS Microbiology Letters 2015 Jan;362(2):1-7.

  19. Manjurano A, Nadim B, Wangai M, Mtove G, Reyburn H, Riley E, Drakeley CJ, Clark TG. African Glucose-6-phosphate dehydrogenase alleles associated with protection from severe malaria in heterozygous females in Tanzania. PloS Genetics 2015 Feb 11;11(2):e1004960.

  20. Glynn JR, Guerra Assunção JA, Houben RMGJ, Mzembe T, Munthali L, Parkhill J, Crampin AC, Clark TG. Whole genome sequencing shows a low proportion of tuberculosis disease is attributable to close contacts in rural Malawi. PLoS One. 2015 Jul 16;10(7):e0132840

  21. Guerra-Assunção JA, Crampin AC, Houben RMGJ, Mzembe T, Mallard K, Coll F, Khan P, Banda L, Chiwaya A, Pereira RPA, McNerney R, Fine PEM, Parkhill J, Clark TG, Glynn JR. Large scale population-based whole genome sequencing of Mycobacterium tuberculosis provides insights into transmission in a high prevalence area. E-life 2015; 4:e05166.

  22. Ali A, Hasan Z, McNerney R, Mallard K, Hill-Cawthorne G, Coll F, Nair M, Pain A, Clark TG, Hasan R. Whole genome sequencing based characterization of extensively drug-resistant Mycobacterium tuberculosis isolates from Pakistan. PloS One 2015 Feb 26;10(2):e0117771.

  1. Guerra-Assunção JA, Houben RMGJ, Crampin AC, Mzembe T, Mallard K, Coll F, Khan P, Banda L, Chiwaya A, Pereira RPA, McNerney R, Harris D, Parkhill J, Clark TG, Glynn JR. Relapse or reinfection with tuberculosis: a whole genome sequencing approach in a population with high HIV prevalence. J Infectious Diseases 2014 Oct 21. pii: jiu574.

  2. Malaria Genomic Epidemiology Network (TG Clark, Senior statistical author). Reappraisal of known malaria resistance loci in a large multicenter study. Nature Genetics 2014; Sep 28. doi: 10.1038/ng.3107.

  3. Perdigão J, Silva H, Machado D, …. , Clark TG, Viveiros M, Portugal I. Unraveling the Mycobacterium tuberculosis genomic diversity and evolution in a high Multi and Extensive Drug resistance burden setting: the Lisboa family and tuberculosis in Lisbon, Portugal. BMC Genomics 2014, 15:991

  4. Takala-Harrison S, Jacob CG, Arze C, …., Clark TG, Miotto O, MacInnis B, Kwiatkowski DP, White NJ, Ringwald P, Plowe CV. Independent emergence of artemisinin resistant Plasmodium falciparum in Southeast Asia. J Infectious Disease 2014 Sep 1. pii: jiu491.

  5. Coll F, McNerney R, Guerra-Assunção JA, Glynn JR, Perdigão J, Viveiros M, Portugal I, Pain A, Martin N, Clark TG. A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. Nature Comm. 2014 Sep 1;5:4812. doi: 10.1038/ncomms5812.

  6. Liu Y, Auburn S, Cao J, Trimarsanto H, Zhou H, Gray K, Clark TG, Price RN, Cheng Q, Huang R, Gao Q. Genetic Diversity and Population Structure of Plasmodium vivax in Central China. Malaria J 2014 Jul 9;13(1):262

  7. Apinjoh TO, Anchang-Kimbi JK, Njua-Yafi C, Ngwai AN, Mugri RN, Clark TG, Rockett KA, Kwiatkowski DP, Achidi EA, MalariaGEN Consortium. Association of candidate gene polymorphisms with malaria and TGF-beta and IL10 levels in three regions of Cameroon: case -control study. Malaria Journal 2014, 13:236 DOI: 10.1186/1475-2875-13-236

  8. Hill-Cawthorne G, Hudson L, Mohamed M, Piepenburg O, Nair M, Dodgson A, Forrest M, Clark TG & Pain A. Recombinations in staphylococcal cassette chromosome mec elements compromise the molecular detection of methicillin resistance in Staphylococcus aureus. PloS One 2014 Jun 27;9(6):e101419.

  9. Henriques G, Hallett RL, Beshir KB, Gadalla N, Johnson RE, Burrow R, van Schalkwyk D, Sawa P, Omar SA, Clark TG, Bousema T, Sutherland CJ. Sub-microscopic Plasmodium falciparum persisting in Kenyan children immediately after ACT show directional selection at the pfmdr1, pfcrt, pfubp1 and pfap2mu loci. J Inf. Diseas. 2014 Jul 3. pii: jiu358.

  10. Maiga B, Dolo A, Campino S, Sepulveda N, Corran P, Rockett K, Troye-Blomberg M, Doumbo O, Clark TG. Glucose-6-phosphate dehydrogenase polymorphisms and mild malaria susceptibility in Dogon and Fulani, Mali. Malaria J 2014, Jul 11; 13(1):270.

  11. Preston MD, Campino S, Assefa SA, …., Sutherland CJ, Roper C, Clark TG. A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains. Nature Commun. 2014 Jun 13;5:4052. doi: 10.1038/ncomms5052.

  12. Ocholla H, Mipando M, … Craig A, Clark TG & Montgomery J. Whole-genome sequencing of Malawi Plasmodium falciparum isolates reveals selection pressure on genes encoding drug-response proteins and candidate vaccine antigens. J Infectious Disease 2014 Jun 19. pii: jiu349.

  13. Alsford S, Currier R, Guerra-Assunção JA, Clark TG, Horn D. An RNAi screen uncovers the major determinants of human serum sensitivity in Trypanosoma brucei brucei. PLoS Pathog. 2014 May 15;10(5):e1004130. doi: 10.1371/journal.ppat.1004130. eCollection 2014 May.

  14. Naeem R, Hidayah L, Preston MD, Clark TG, Pain A. SVAMP: Sequence Variation Analysis, Maps and Phylogeny. Bioinformatics 2014 Apr 23

  15. Kafsack BFC, Rovira-Graells N, Clark TG, Crowley VM, Campino SG, Williams AE, Drought LG, Kwiatkowski DP, Baker DA, Cortés A, Llinás M. A transcriptional switch underlies commitment to sexual development in malaria parasites. Nature. 2014 Feb 23. doi: 10.1038/nature12920.

  16. Sepulveda N, Manjurano A, Riley E, Drakeley C, Clark TG. On the performance of in tackling missing genotypes of the alpha-thalassemia locus in a malaria association study. Annals Human Genetics 2014 Jul;78(4):277-89

  17. Coll F, Preston M, Guerra-Assunção JA, Hill-Cawthorn G, Harris D, Perdigão J, Viveiros M, Portugal I, Drobniewski F, Gagneux S, Glynn JR, Pain A, Parkhill J, McNerney R, Martin N, Clark TG. PolyTB: A genomic variation map for Mycobacterium tuberculosis. Tuberculosis (Edinb). 2014 May;94(3):346-54. doi: 10.1016/j.tube.2014.02.005. Epub 2014 Feb 15.

  18. Moule MG, Hemsley CM, Seet Q, Senior NJ, Guerra A, Lim J, Champion OL, Sarkar-Tyson M, Clark TG, Tan P, Titball RW, Cuccui J, Wren BW. Genomewide saturation mutagenesis of Burkholderia pseudomallei reveals the essential gene set and identifies novel virulence determinants. MBio 2014, Feb 11;5(1).

  19. Mobegi VA, Duffy CW, Amambua-Ngwa A, Loua KM, Laman E, Nwakanma DC, MacInnis B, Aspeling-Jones H, Clark TG, Kwiatkowski DP, Conway DJ. Genome-wide analysis of local signatures of selection on the malaria parasite Plasmodium falciparum in West African populations of differing endemicity. Mol Bio Evol 2014 Jun;31(6):1490-9

  20. Assefa S, Campino S, Ocholla H, Sutherland CJ, Clark TG. estMOI: Estimating multiplicity of infection using parasite deep sequencing data. Bioinformatics 2014 May 1;30(9):1292-4. doi: 10.1093/bioinformatics/btu005. Epub 2014 Jan 17.

  1. Preston MD, Assefa S, Ocholla H, Sutherland CJ, Borrmann S, Nzila A, Michon P, Hien TT, Bousema T, Drakeley CJ, Zongo I, Ouedraogo JB, Djimde AA, Doumbo OK, Nosten F, Fairhurst RM, Conway DJ, Roper C, Clark TG. PlasmoView: A web-based resource to visualise global Plasmodium falciparum genomic variation. J Infect Dis. 2013 Dec 12.

  2. Apinjoh TO. Anchang-Kimbi JK, Yafi CN, Rockett KA, Mbunwe E, Besingi RN, Clark TG, Kwiatkowski DP, Achidi, EA Association between cytokine and Toll-like receptor gene polymorphisms and severe malaria in three regions of Cameroon. PloS One 2013; 8(11): e81071

  3. Nwakanma DC, Duffy CW, Amambua-Ngwa A, Oriero EC, Bojang KA, Pinder M, Drakeley CJ, Sutherland CJ, Milligan PJ, MacInnis B, Kwiatkowski DP, Clark TG, Greenwood BM, Conway DJ. Changes in malaria parasite drug resistance in The Gambia over a 25-year period related to genomic signatures of selection. J Infect. Disease 2013 Nov 21.

  4. Maiga B, Dolo A, Touré O, Dara V, Tapily A, Campino S, Sepulveda N, Corran P, Rockett K, Clark TG & Troye Blomberg M & Doumbo OK. Fcgamma Receptor IIa and malaria susceptibility in Fulani and Dogon living in an endemic area of Mali. Scand J Immunol. 2014 Jan;79(1):43-50. doi: 10.1111/sji.12122..

  5. Borrmann S, Mwai L, Abdirahnam A, Straimer J, Rippert A, Sasi P, Mosobo M, Lowe B, Campino S, Assefa S, Auburn S, Manske M, Maslen G, Peshu N, Kwiatkowski DP, Marsh K, Nzila A, Clark TG. Genome-wide screen identifies new candidate genes associated with artemisinin susceptibility in Plasmodium falciparum in Kenya. Scientific Reports 2013; Nov 25;3:3318. doi: 10.1038/srep03318.

  6. Maiga B, Dolo A, Touré O, Dara V, Tapily A, Campino S, Sepulveda N, Risley P, Corran P, Rockett KA, Kwiatkowski DP, The MalariaGEN Consortium, Clark TG & Troye Blomberg M & Doumbo OK. Human candidate polymorphisms involved in malaria susceptibility in sympatric ethnic groups in Mali. PLoS One. 2013 Oct 2;8(10):e75675..

  7. Clark TG, Mallard K, Coll F, Preston M, Assefa, S, …, Eisenach K, Joloba, M, Bentley, S, Parkhill J, Jones-López, E, McNerney, R. Transmission of Multidrug-Resistant Tuberculosis in Treatment Experienced Patients. PLoS One. 2013 Dec 11;8(12):e83012.

  8. Liu X, Ong RH, Pillai EN, Elzein AM, Small KS, Clark TG, Kwiatkowski DP, Teo YY. Detecting and characterizing genomic signatures of positive selection in global populations. Am J Hum Genet. 2013 May 22. doi:pii:

  9. Kariuki SM, Rockett KA, Clark TG, Reyburn H, Agbenyega T, Taylor TE, Williams T, MalariaGEN Consortium, Newton RJC. Phenotypes and Gene Polymorphisms of Malaria-associated Seizures in African Populations. Epilepsia 2013 Apr 24. doi: 10.1111/epi.12173.

  10. Band G, Le QS, … , Schuldt K, Clark TG, Small KS, Teo YY, Kwiatkowski DP, Rockett KR, Barrett JC, Spencer C, MalariaGEN. Imputation based meta-analysis of severe malaria in three African populations. PLoS Genet. 2013 May;9(5):e1003509. Epub 2013 May 23.

  11. Sepulveda N, Campino SG, Assefa S, Sutherland C, Pain A, Clark TG. A Poisson mixture modelling approach to detecting copy number variation in whole sequence coverage data. BMC Genomics 2013; 14(1):128

  12. Takala-Harrison S, Clark TG et al. Genetic loci associated with delayed clearance of Plasmodium falciparum following artemisinin treatment in Southeast Asia. Proc Natl Acad Sci U S A. 2013 Jan 2;110(1):240-5. doi: 10.1073/pnas.1211205110. Epub 2012 Dec 17.

  13. Auburn S, Marfurt J, Maslen G, Campino S, MacHunter B, Enny Kenangalem, Russell B, William T, Barber B, Yeo T, MacInnis B, Manske M, Miotto O, Clark TG, Anstey NM, Kwiatkowski D, Price RN. Effective preparation of Plasmodium vivax DNA for high-throughput whole-genome sequencing. PLoS One. 2013;8(1):e53160. doi: 10.1371/journal.pone.0053160. Epub 2013 Jan 4.

  1. Manjurano AM & Clark TG, Nadjm B, Mtove G, Wangai M, Sepulveda N, Campino S, Rockett KR, Richardson A, MalariaGEN consortium, Riley EM, Drakeley CJ, Reyburn H. Candidate human genetic polymorphisms and severe malaria in a Tanzanian population. PLoS One. 2012;7(10):e47463. doi: 10.1371/journal.pone.0047463. Epub 2012 Oct 29.

  2. Coll F, Mallard K, Preston M, McNerney R, Martin N, Clark TG. SpolPred: Rapid and accurate ascertainment of Mycobacterium tuberculosis strain types from short genomic sequences. Bioinformatics. 2012 Nov 15;28(22):2991-3. doi: 10.1093/bioinformatics/bts544. Epub 2012 Sep 26.

  3. Preston MD, Manske M, Horner N, Assefa S, Campino S, Auburn S, Zongo I, Ouédraogo JB, Nosten F, Anderson T, Clark TG. VarB: A visualisation and analysis tool for polymorphisms derived from sequence data. Bioinformatics. 2012 Nov 15;28(22):2983-2985. Epub 2012 Sep 13.

  4. Toure O, Konate S, Sissoko S, Amadou N, Barry A, Sall H, Diarra E, Poudiougou B, Sepulveda N, Campino S, Rockett KA, Clark TG & Thera MA & Doumbo O, in collaboration with the MalariaGEN Consortium. Candidate polymorphisms and severe malaria in a Malian population. PLoS ONE 7(9): e43987. doi:10.1371/journal.pone.0043987.

  5. Campino S, Clark TG. Genetic contribution to malaria susceptibility and resistance, in Genomic variation and genetic disorders of developing countries, Oxford University Press, New York (2012).

  6. Dunstan SJ, Rockett KA, Quyen NTN, Teo YY, Thai CO, Hang NT, Richardson A, Clark TG, de Vries J, Day N, O’Riordan SE, Kwiatkowski DP, Farrar J, Phu NH, MalariaGEN Consortium, Hien TT. Variation in human genes encoding adhesion and pro-inflammatory molecules are associated with severe malaria in the Vietnamese. Genes Immun. 2012 Jun 7. doi: 10.1038/gene.2012.25.

  7. da Silva Santos S, Clark TG, Campino S, Suarez-Mutis MC, Rockett KA, et al. (2012) Investigation of Host Candidate Malaria-Associated Risk/Protective SNPs in a Brazilian Amazonian Population. PLoS ONE 7(5): e36692. doi:10.1371/journal.pone.0036692

  8. Smith M, Campino S, Gu Y, Clark TG, Otto TD, Maslen G, Manske M, Imwong M, Dondorp AM, Kwiatkowski DP, Quail MA, Swerdlow HA. An In-Solution Hybridisation Method for the Isolation of Pathogen DNA from Human DNA-rich Clinical Samples for Analysis by NGS. The Open Genomics Journal, 5: 18-29; doi: 10.2174/1875693X01205010018.

  9. Auburn S, Campino S, Miotto O, Djimde AA, Zongo I, Manske M, Maslem G, Mangano V, Alcock D, MacInnis B, Rockett K, Clark TG, Doumbo OK, Ouédraogo JB, Kwiatkowski DP. Characterisation of Within-Host Plasmodium falciparum Diversity using Next-Generation Sequence Data. PLoS One. 2012;7(2):e32891. Epub 2012 Feb 29.

  10. Cliff JM, Lee J, Constantinou N, Cho J, Clark TG, Ronacher K, King EL, Lukey PT, Duncan K, van Helden P, Walzl G, Dockrell HM. Distinct phases of blood gene expression pattern through tuberculosis treatment reflect modulation of the humoral immune response. J Infect Diseas. 2012 Aug 7.

  11. Ghansah A, Rockett K, Clark TG, Wilson M, Koram K, Oduro R, Amego-Etego L, Anyorigiya T, Hudgson A, Milligan P, Rogers W, Kwiatkowski D. Haplotype analyses of haemoglobin C and haemoglobin S and the dynamics of the evolutionary response to malaria in Kassena-Nankana District of Ghana. PLoS One. 2012;7(4):e34565. Epub 2012 Apr 10.

  12. Lawley TD, Clare S, Walker AW, Stares MD, …, Clark TG, Parkhill J, Dougan G. Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile in mice. PLoS Pathog. 2012 Oct;8(10):e1002995. doi: 10.1371/journal.ppat.1002995. Epub 2012 Oct 25.

  13. Manske M, Miotto O, …., Clark TG (Statistics lead until Jan 2010), Newbold CN, Berriman M, MacInnis B, Kwiatkowski DP. Next-generation sequencing analysis of Plasmodium falciparum diversity within the host and across populations. Nature 2012 Jun 13. doi: 10.1038/nature11174.

  1. Manjurano A, Okell L, Lukindo T, Reyburn H, Olomi R, Roper C, Clark TG, Joseph S, Riley EM, Drakeley C. Association of sub-microscopic malaria parasite carriage with transmission intensity in north-eastern Tanzania. Malaria Journal 2011, 10:370

  2. Downing T, Imamura H, Decuypere, Clark TG et al. Whole genome sequencing of Leishmania donovani clinical lines reveals dynamic variation related to drug resistance. Genome Res. 2011 Dec;21(12):2143-56. Epub 2011 Oct 28.

  3. Robinson T, Campino S, …. Clark TG, Sutherland C. Drug-Resistant Genotypes and Multi-Clonality in Plasmodium falciparum Analysed by Direct Genome Sequencing from Peripheral Blood of Malaria Patients. PLoS One. 2011;6(8):e23204. Epub 2011

  4. Auburn S, Campino S, Clark TG et al.. An effective method to purify Plasmodium falciparum DNA directly from clinical blood samples for whole genome high-throughput sequencing. PLoS One. 2011;6(7):e22213. Epub 2011 Jul 18.

  5. Campino S, Auburn S, Kivinen K, … , Clark TG, Kwiatkowski DP. Population genetic analysis of Plasmodium parasites using a customized Illumina GoldenGate genotyping assay. PLoS One. 2011;6(6):e20251. Epub 2011 Jun 6.

  1. Sambo MR, Tovoada MJ, Benchimol C, Quinhentos V, Velosa R, Marques MI, Clark TG, Coutino A, Penha-Goncalves C. Transforming growth factor beta 2 and heme oxygenase 1 genes are risk factors for the cerebral malaria syndrome in Angolan children. Plos One 2010 Jun 16;5(6):e11141.

  2. Carroll RP, Segundo DS, Hollowood K, Marafioti T, Clark TG, Harden PN, Wood KJ. Immune Phenotype Predicts Risk for Posttransplantation Squamous Cell Carcinoma. J Am Soc Nephrol. 2010 Apr;21(4):713-22.

  3. Clark TG, Campino SG, Teo YY, Small K, Auburn S, Rockett KA, Kwiatkowski DP, Holmes CC. A Bayesian approach to assess differences in linkage disequilibrium patterns in genomewide association studies. Bioinformatics. 2010 Aug 15;26(16):1999-2003.

  4. Thye T, Vannberg FO, …., African TB Genetics Consortium (TG Clark = member of the TB statistical analysis group); Wellcome Trust Case Control Consortium, Morris AP, Meyer CG, Horstmann RD, Hill AV. Genome-wide association analyses identifies a susceptibility locus for tuberculosis on chromosome 18q11.2. Nat Genet. 2010 Sep; 42(9):739-41.

  5. Lawley TD, Clare S, Deakin LJ, Goulding D, Yea J, Raisen C, Lovell J, Cook F, Clark TG, Dougan G. A quantitative and practical method for monitoring Clostridium difficile spore decontamination. Appl Environ Microbiol. 2010 Aug 27.

  6. Auburn A, Fry AE, Clark TG, Campino S, Diakite M, Green A, Richardson A, Jallow M, Sisay-Joof F, Pinder M, Molyneux ME, Taylor TE, Rockett KA, Haldar K, Kwiatkowski DP. Further evidence supporting Gs signal transduction in severe malaria pathogenesis. PloS One 2010; 5(4):e10017.

  7. Sousa I, Clark TG, Holt R, Pagnamenta A, Mulder E, Bailey AJ, Battaglia A, Monaco AP, International Molecular Genetic Study of Autism Consortium (IMGSAC). Polymorphisms in leucine-rich repeat genes are associated with autism spectrum disorder susceptibility in populations of European ancestry. Molecular Autism 2010; 1:7.

  8. Daelemans C, Ritchie ME, Smits G, Abu-Amero S, Sudbery IM, Forrest MS, Campino S, Clark TG et al, High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta. BMC Genet. 2010 Apr 19;11:25.