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Taane Gregory Clark. Published 17 articles in journals.
Identificação

Identificação pessoal

Nome completo
Taane Gregory Clark

Nomes de citação

  • Clark, Taane

Identificadores de autor

Ciência ID
DD1B-2564-161C
ORCID iD
0000-0001-8985-9265
Formação
Grau Classificação
2001/10/01 - 2004/11/01
Concluído
 D.Phil (Doktor (PhD))
Especialização em Statistical Genetics
University of Oxford - Department of Statistics & Nuffield Department of Clinical Medicine, Reino Unido
Percurso profissional

Cargos e Funções

Categoria Profissional
Instituição de acolhimento 		Empregador
2017/01/01 - Atual Honorary Professor Universidade Nova de Lisboa Instituto de Higiene e Medicina Tropical, Portugal
Universidade Nova de Lisboa Instituto de Higiene e Medicina Tropical, Portugal
2016/01/01 - Atual Honorary Professor University of Cape Town Department of Medicine, África do Sul
University of Cape Town Department of Medicine, África do Sul
2009/12/01 - Atual Professor of Genomics and Global Health London School of Hygiene & Tropical Medicine, Reino Unido
London School of Hygiene & Tropical Medicine, Reino Unido
2018/01/01 - 2022/09/30 Director of The Applied Genomics Centre London School of Hygiene & Tropical Medicine, Reino Unido
London School of Hygiene & Tropical Medicine, Reino Unido
Projetos

Bolsa

Designação Financiadores
2018/01 - Atual Plasmodium species co-infections in Anopheles mosquitoes: a pilot study of parasite-vector interactions that define transmission in Africa
380545594
 Deutsche Forschungsgemeinschaft
2023/03 - 2026/03 GenES_VBD network (Genomic Epidemiology tools for the Surveillance of Vector Borne Diseases: applied to tick species, reservoirs, and pathogens
BB/X018156/1
 Biotechnology and Biological Sciences Research Council
2020/08 - 2024/08 "A genome-wide association study of myalgic encephalomyelitis / chronic fatigue syndrome(ME/CFS)"
MC_PC_20005
 Medical Research Council
2019/06 - 2023/06 A lung-oriented controlled human infection model using live BCG to evaluate tuberculosis immunopathogenicity and vaccine efficacy (TB-CHIM).
MR/S03563X/1
 Medical Research Council
2020/11 - 2023/03 Serological tools for COVID-19 control and vaccine roll-out in Southeast Asia
MR/V036890/1
 Medical Research Council
2022/08 - 2023/02 AI assisted genomic profiling for the personalisation of treatment and control of infections
MR/X005895/1
 Medical Research Council
2021/04 - 2023/02 Dietary patterns, microbiome, metabolome and cardiovascular disease risk in transitioning India
MR/V001221/1
 Medical Research Council
2020/01 - 2023/01 Using whole genome sequencing to reveal malaria parasite genetic diversity and drug resistance in Vietnam
MR/R026297/1
 Medical Research Council
2019/12 - 2022/12 Improving The Longevity Of New Infectious Disease Therapeutics Using Machine Learning / Artificial Intelligence In Early Stage Drug Discovery
MR/T000171/1
 Medical Research Council
2018/09 - 2022/09 Using whole genome sequencing to unravel the genetics underlying antimicrobial resistant pathogens
2089341
 Biotechnology and Biological Sciences Research Council
2019/04 - 2022/04 Using host-responses and pathogen genomics to improve diagnostics for tuberculosis in Bandung, Indonesia
MR/S01988X/1
 Medical Research Council
2017/09 - 2022/03 Development of a molecular barcoding tool for Plasmodium malaria
1906006
 Biotechnology and Biological Sciences Research Council
2018/09 - 2021/09 Using host-responses and pathogen genomics to improve diagnostics for tuberculosis in the Philippines
MR/R025576/1
 Medical Research Council
2017/09 - 2021/09 Whole-genome sequence analysis of Mycobacteria tuberculosis bacteria to identify the genetic determinants and mechanisms of anti-tuberculosis drug
1923132
 Medical Research Council
2019/07 - 2021/06 Dietary patterns, microbiome, metabolome and cardiovascular disease risk in transitioning India
MR/T008504/1
 Medical Research Council
2018/05 - 2021/05 Using genomics to trace Salmonella transmission and antimicrobial resistance (AMR) in the poultry and swine food chains in the Philippines
BB/R013063/1
 Biotechnology and Biological Sciences Research Council
2018/03 - 2021/03 Using whole genome sequencing to characterise drug resistant Mycobacterium tuberculosis in Thailand
MR/R020973/1
 Medical Research Council
2019/02 - 2021/02 Policy analysis of the drivers of antimicrobial resistance within Tanzania's one-health care systems
MR/S012796/1
 Medical Research Council
2016/09 - 2020/09 Mycobacterial determinants of survival and fitness within the bovine host
BB/N004590/1
 Biotechnology and Biological Sciences Research Council
2014/03 - 2020/02 Cardiovascular disease in Russia: strengthening evidence about causes, mechanisms, prevention and treatment.
100217/Z/12/A
 Wellcome Trust
2012/11 - 2020/02 Cardiovascular disease in Russia: strengthening evidence about causes, mechanisms, prevention and treatment.
100217/Z/12/Z
 Wellcome Trust
2016/03 - 2019/09 Understanding the transmission of tuberculosis using Mycobacterium tuberculosis sequence data
MR/N010469/1
 Medical Research Council
2015/03 - 2018/10 Geographic genetic profiling of human Plasmodium malaria
MR/M01360X/1
 Medical Research Council
2012/09 - 2018/03 The interactions between Clostridium difficile, intestinal microbiota and the host response in hospitalised patients
MR/K000551/1
 Medical Research Council
2016/03 - 2017/09 Zika: Zika virus surveillance in human and mosquito populations in Cape Verde
MC_PC_15103
 Medical Research Council
2011/06 - 2012/05 12 Months Bridging Funding for the Karonga Prevention Study
096249/Z/11/A
 Wellcome Trust
Produções

Publicações

Artigo em revista
  1. Guyeux C; Senelle G; Le Meur A; Supply P; Gaudin C; Phelan JE; Clark TG; et al. "Newly Identified Mycobacterium africanum Lineage 10, Central Africa.". Emerging infectious diseases (2024): http://europepmc.org/abstract/med/38407162.
    10.3201/eid3003.231466
  2. Thorpe J; Sawaengdee W; Ward D; Campos M; Wichukchinda N; Chaiyasirinroje B; Thanraka A; et al. "Multi-platform whole genome sequencing for tuberculosis clinical and surveillance applications.". Scientific reports (2024): http://europepmc.org/abstract/med/38431684.
    10.1038/s41598-024-55865-1
  3. Higgins M; Manko E; Ward D; Phelan JE; Nolder D; Sutherland CJ; Clark TG; Campino S. "New reference genomes to distinguish the sympatric malaria parasites, Plasmodium ovale curtisi and Plasmodium ovale wallikeri.". Scientific reports (2024): http://europepmc.org/abstract/med/38360879.
    10.1038/s41598-024-54382-5
  4. Mora JFB; Meclat VYB; Calayag AMB; Campino S; Hafalla JCR; Hibberd ML; Phelan JE; Clark TG; Rivera WL. "Genomic analysis of Salmonella enterica from Metropolitan Manila abattoirs and markets reveals insights into circulating virulence and antimicrobial resistance genotypes.". Frontiers in microbiology (2024): http://europepmc.org/abstract/med/38312499.
    10.3389/fmicb.2023.1304283
  5. Moss S; Pretorius E; Ceesay S; Hutchins H; da Silva ET; Ndiath MO; Jones RT; et al. "Genomic surveillance of Anopheles mosquitoes on the Bijagós Archipelago using custom targeted amplicon sequencing identifies mutations associated with insecticide resistance.". Parasites & vectors (2024): http://europepmc.org/abstract/med/38178249.
    10.1186/s13071-023-06085-5
  6. Ruth Charlotte Eccleston; Emilia Manko; Susana Campino; Taane G Clark; Nicholas Furnham. "A computational method for predicting the most likely evolutionary trajectories in the stepwise accumulation of resistance mutations". eLife (2023): https://doi.org/10.7554/eLife.84756.
    10.7554/eLife.84756
  7. Phelan JE; Turkiewicz A; Manko E; Thorpe J; Vanheer LN; van de Vegte-Bolmer M; Ngoc NTH; et al. "Rapid profiling of Plasmodium parasites from genome sequences to assist malaria control.". Genome medicine (2023): http://europepmc.org/abstract/med/37950308.
    10.1186/s13073-023-01247-7
  8. Acford-Palmer H; Campos M; Bandibabone J; N'Do S; Bantuzeko C; Zawadi B; Walker T; et al. "Detection of insecticide resistance markers in Anopheles funestus from the Democratic Republic of the Congo using a targeted amplicon sequencing panel.". Scientific reports (2023): http://europepmc.org/abstract/med/37833354.
    10.1038/s41598-023-44457-0
  9. Wang L; Campino S; Phelan J; Clark TG. "Mixed infections in genotypic drug-resistant Mycobacterium tuberculosis.". Scientific reports (2023): http://europepmc.org/abstract/med/37816829.
    10.1038/s41598-023-44341-x
  10. Gómez-González PJ; Grabowska AD; Tientcheu LD; Tsolaki AG; Hibberd ML; Campino S; Phelan JE; Clark TG. "Functional genetic variation in pe/ppe genes contributes to diversity in Mycobacterium tuberculosis lineages and potential interactions with the human host.". Frontiers in microbiology (2023): http://europepmc.org/abstract/med/37876785.
    10.3389/fmicb.2023.1244319
  11. Spadar A; Phelan JE; Clark TG; Campino S. "Large-scale reference-free analysis of flavivirus sequences in Aedes aegypti whole genome DNA sequencing data.". Parasites & vectors (2023): http://europepmc.org/abstract/med/37543604.
    10.1186/s13071-023-05898-8
  12. Nina Billows; Jody E Phelan; Dong Xia; Yonghong Peng; Taane G Clark; Yu-Mei Chang; Inanc Birol. "Feature weighted models to address lineage dependency in drug-resistance prediction from Mycobacterium tuberculosis genome sequences". Bioinformatics (2023): https://doi.org/10.1093/bioinformatics/btad428.
    10.1093/bioinformatics/btad428
  13. Mazumder R; Hussain A; Rahman MM; Phelan JE; Campino S; Abdullah A; Clark TG; Mondal D. "Genomic and functional portrait of multidrug-resistant, hydrogen sulfide (H2S)-producing variants of Escherichia coli.". Frontiers in microbiology (2023): http://europepmc.org/abstract/med/37577429.
    10.3389/fmicb.2023.1206757
  14. Osborne A; Phelan JE; Vanheer LN; Manjurano A; Gitaka J; Drakeley CJ; Kaneko A; et al. "High throughput human genotyping for variants associated with malarial disease outcomes using custom targeted amplicon sequencing.". Scientific reports (2023): http://europepmc.org/abstract/med/37495620.
    10.1038/s41598-023-39233-z
  15. Napier G; Couvin D; Refrégier G; Guyeux C; Meehan CJ; Sola C; Campino S; Phelan J; Clark TG. "Comparison of in silico predicted Mycobacterium tuberculosis spoligotypes and lineages from whole genome sequencing data.". Scientific reports (2023): http://europepmc.org/abstract/med/37443186.
    10.1038/s41598-023-38384-3
  16. Osborne A; Phelan JE; Kaneko A; Kagaya W; Chan C; Ngara M; Kongere J; et al. "Drug resistance profiling of asymptomatic and low-density Plasmodium falciparum malaria infections on Ngodhe island, Kenya, using custom dual-indexing next-generation sequencing.". Scientific reports (2023): http://europepmc.org/abstract/med/37452073.
    10.1038/s41598-023-38481-3
  17. Vanheer LN; Mahamar A; Manko E; Niambele SM; Sanogo K; Youssouf A; Dembele A; et al. "Genome-wide genetic variation and molecular surveillance of drug resistance in Plasmodium falciparum isolates from asymptomatic individuals in Ouélessébougou, Mali.". Scientific reports (2023): http://europepmc.org/abstract/med/37308503.
    10.1038/s41598-023-36002-w
  18. Mazumder R; Hussain A; Bhadra B; Phelan J; Campino S; Clark TG; Mondal D. "Case report: A successfully treated case of community-acquired urinary tract infection due to Klebsiella aerogenes in Bangladesh.". Frontiers in medicine (2023): http://europepmc.org/abstract/med/37435536.
    10.3389/fmed.2023.1206756
  19. Hussain A; Mazumder R; Ahmed A; Saima U; Phelan JE; Campino S; Ahmed D; et al. "Genome dynamics of high-risk resistant and hypervirulent Klebsiella pneumoniae clones in Dhaka, Bangladesh.". Frontiers in microbiology (2023): http://europepmc.org/abstract/med/37303793.
    10.3389/fmicb.2023.1184196
  20. Scott DAV; Benavente E; Libiseller-Egger J; Fedorov D; Phelan J; Ilina E; Tikhonova P; et al. "Bayesian compositional regression with microbiome features via variational inference.". BMC bioinformatics (2023): http://europepmc.org/abstract/med/37217852.
    10.1186/s12859-023-05219-x
  21. Qi Jiang; Hai-Can Liu; Qing-Yun Liu; Jody E. Phelan; Feng-Xi Tao; Xiu-Qin Zhao; Jian Wang; et al. "The Evolution and Transmission Dynamics of Multidrug-Resistant Tuberculosis in an Isolated High-Plateau Population of Tibet, China". Microbiology Spectrum (2023): https://doi.org/10.1128/spectrum.03991-22.
    10.1128/spectrum.03991-22
  22. Acford-Palmer H; Phelan JE; Tadesse FG; Kristan M; Collins E; Spadar A; Walker T; et al. "Identification of two insecticide resistance markers in Ethiopian Anopheles stephensi mosquitoes using a multiplex amplicon sequencing assay.". Scientific reports (2023): http://europepmc.org/abstract/med/37019918.
    10.1038/s41598-023-32336-7
  23. Moss S; Manko E; Vasileva H; Da Silva ET; Goncalves A; Osborne A; Phelan J; et al. "Population dynamics and drug resistance mutations in Plasmodium falciparum on the Bijagós Archipelago, Guinea-Bissau.". Scientific reports (2023): http://europepmc.org/abstract/med/37072433.
    10.1038/s41598-023-33176-1
  24. Kimla LJ; Clark TG; Banerjee S; Campino S. "JC Polyomavirus T-antigen protein expression and the risk of colorectal cancer: Systematic review and meta-analysis of case-control studies.". PloS one (2023): http://europepmc.org/abstract/med/37000859.
    10.1371/journal.pone.0283642
  25. Kristan M; Acford-Palmer H; Campos MO; Collins EL; Phelan J; Portwood NM; Pelloquin B; et al. "Towards environmental detection, quantification, and molecular characterization of Anopheles stephensi and Aedes aegypti from experimental larval breeding sites.". Scientific reports (2023): http://europepmc.org/abstract/med/36792622.
    10.1038/s41598-023-29657-y
  26. Phelan J; Gomez-Gonzalez PJ; Andreu N; Omae Y; Toyo-Oka L; Yanai H; Miyahara R; et al. "Genome-wide host-pathogen analyses reveal genetic interaction points in tuberculosis disease.". Nature communications (2023): http://europepmc.org/abstract/med/36725857.
    10.1038/s41467-023-36282-w
  27. Turkiewicz A; Manko E; Oresegun DR; Nolder D; Spadar A; Sutherland CJ; Cox-Singh J; et al. "Population genetic analysis of Plasmodium knowlesi reveals differential selection and exchange events between Borneo and Peninsular sub-populations.". Scientific reports (2023): http://europepmc.org/abstract/med/36750737.
    10.1038/s41598-023-29368-4
  28. Kouriba B; Arama C; Ouologuem DT; Cissoko Y; Diakite M; Beavogui AH; Wele M; et al. "IFN¿, TNFa polymorphisms and IFN¿ serum levels are associated with the clearance of drug-resistant P. falciparum in Malian children.". Cytokine (2023): http://europepmc.org/abstract/med/36773528.
    10.1016/j.cyto.2023.156137
  29. Julian Libiseller-Egger; Linfeng Wang; Wouter Deelder; Susana Campino; Taane G Clark; Jody E Phelan; Nicola Mulder. "TB-ML—a framework for comparing machine learning approaches to predict drug resistance of Mycobacterium tuberculosis". Bioinformatics Advances (2023): https://doi.org/10.1093/bioadv/vbad040.
    10.1093/bioadv/vbad040
  30. Spadar A; Perdigão J; Campino S; Clark TG. "Large-scale genomic analysis of global Klebsiella pneumoniae plasmids reveals multiple simultaneous clusters of carbapenem-resistant hypervirulent strains.". Genome medicine (2023): http://europepmc.org/abstract/med/36658655.
    10.1186/s13073-023-01153-y
  31. Napier G; Campino S; Phelan JE; Clark TG. "Large-scale genomic analysis of Mycobacterium tuberculosis reveals extent of target and compensatory mutations linked to multi-drug resistant tuberculosis.". Scientific reports (2023): http://europepmc.org/abstract/med/36635309.
    10.1038/s41598-023-27516-4
  32. Nguipdop-Djomo P; Oswald WE; Halliday KE; Cook S; Sturgess J; Sundaram N; Warren-Gash C; et al. "Risk factors for SARS-CoV-2 infection in primary and secondary school students and staff in England in the 2020/2021 school year: a longitudinal study.". International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases (2023): http://europepmc.org/abstract/med/36621754.
    10.1016/j.ijid.2022.12.030
  33. Ibrahim A; Manko E; Dombrowski JG; Campos M; Benavente ED; Nolder D; Sutherland CJ; et al. "Population-based genomic study of Plasmodium vivax malaria in seven Brazilian states and across South America.". Lancet regional health. Americas (2023): http://europepmc.org/abstract/med/36844008.
    10.1016/j.lana.2022.100420
  34. Scott D; Benavente E; Libiseller-Egger J; Fedorov D; Phelan J; Ilina E; Tikhonova P; et al. "Bayesian compositional regression with microbiome features via variational inference". BMC bioinformatics (2023): http://europepmc.org/abstract/PMC/PMC10201722.
  35. Julian Libiseller-Egger; Jody E. Phelan; Zachi I. Attia; Ernest Diez Benavente; Susana Campino; Paul A. Friedman; Francisco Lopez-Jimenez; David A. Leon; Taane G. Clark. "Deep learning-derived cardiovascular age shares a genetic basis with other cardiac phenotypes". Scientific Reports 12 1 (2022): http://dx.doi.org/10.1038/s41598-022-27254-z.
    10.1038/s41598-022-27254-z
  36. Kanwara Trisakul; Ditthawat Nonghanphithak; Pratchakan Chaiyachat; Orawee Kaewprasert; Kankanon Sakmongkoljit; Wipa Reechaipichitkul; Angkana Chaiprasert; et al. "High clustering rate and genotypic drug-susceptibility screening for the newly recommended anti-tuberculosis drugs among global extensively drug-resistant Mycobacterium tuberculosis isolates". Emerging Microbes & Infections (2022): https://doi.org/10.1080/22221751.2022.2099304.
    10.1080/22221751.2022.2099304
  37. Deelder W; Manko E; Phelan JE; Campino S; Palla L; Clark TG. "Geographical classification of malaria parasites through applying machine learning to whole genome sequence data.". Scientific reports (2022): http://europepmc.org/abstract/med/36476815.
    10.1038/s41598-022-25568-6
  38. Collins E; Phelan J; Hubner M; Spadar A; Campos M; Ward D; Acford-Palmer H; et al. "A next generation targeted amplicon sequencing method to screen for insecticide resistance mutations in Aedes aegypti populations reveals a rdl mutation in mosquitoes from Cabo Verde". PLoS neglected tropical diseases (2022): http://europepmc.org/abstract/PMC/PMC9746995.
  39. Collins EL; Phelan JE; Hubner M; Spadar A; Campos M; Ward D; Acford-Palmer H; et al. "A next generation targeted amplicon sequencing method to screen for insecticide resistance mutations in Aedes aegypti populations reveals a rdl mutation in mosquitoes from Cabo Verde.". PLoS neglected tropical diseases (2022): http://europepmc.org/abstract/med/36512510.
    10.1371/journal.pntd.0010935
  40. Dombrowski JG; Acford-Palmer H; Campos M; Separovic EPM; Epiphanio S; Clark TG; Campino S; Marinho CRF. "Genetic diversity of Plasmodium vivax isolates from pregnant women in the Western Brazilian Amazon: a prospective cohort study.". Lancet regional health. Americas (2022): http://europepmc.org/abstract/med/36844021.
    10.1016/j.lana.2022.100407
  41. Mazumder R; Hussain A; Phelan JE; Campino S; Haider SMA; Mahmud A; Ahmed D; et al. "Non-lactose fermenting Escherichia coli: Following in the footsteps of lactose fermenting E. coli high-risk clones.". Frontiers in microbiology (2022): http://europepmc.org/abstract/med/36406419.
    10.3389/fmicb.2022.1027494
  42. Khan AS; Phelan JE; Khan MT; Ali S; Qasim M; Mohammad N; Napier G; et al. "Genetic mutations underlying isoniazid-resistant Mycobacterium tuberculosis in Khyber Pakhtunkhwa, Pakistan.". Tuberculosis (Edinburgh, Scotland) (2022): http://europepmc.org/abstract/med/36463715.
    10.1016/j.tube.2022.102286
  43. Sundaram N; Abramsky T; Oswald WE; Cook S; Halliday KE; Nguipdop-Djomo P; Sturgess J; et al. "Implementation of COVID-19 Preventive Measures and Staff Well-Being in a Sample of English Schools 2020-2021.". The Journal of school health (2022): http://europepmc.org/abstract/med/36450450.
    10.1111/josh.13264
  44. Matthew Higgins; Oliver W. Stringer; Daniel Ward; Jennifer M. Andrews; Matthew S. Forrest; Susana Campino; Taane G. Clark. "Characterizing the Impact of Primer-Template Mismatches on Recombinase Polymerase Amplification". The Journal of Molecular Diagnostics (2022): https://doi.org/10.1016/j.jmoldx.2022.08.005.
    10.1016/j.jmoldx.2022.08.005
  45. Paula J Gómez-González; Susana Campino; Jody E Phelan; Taane G Clark. "Portable sequencing of Mycobacterium tuberculosis for clinical and epidemiological applications". Briefings in Bioinformatics (2022): https://doi.org/10.1093/bib/bbac256.
    10.1093/bib/bbac256
  46. Kuja JO; Kanoi BN; Balboa RF; Shiluli C; Maina M; Waweru H; Gathii K; et al. "Genomic surveillance of SARS-COV-2 reveals diverse circulating variant lineages in Nairobi and Kiambu Counties, Kenya.". BMC genomics (2022): http://europepmc.org/abstract/med/36050650.
    10.1186/s12864-022-08853-6
  47. Hargreaves JR; Langan SM; Oswald WE; Halliday KE; Sturgess J; Phelan J; Nguipdop-Djomo P; et al. "Epidemiology of SARS-CoV-2 infection among staff and students in a cohort of English primary and secondary schools during 2020-2021.". The Lancet regional health. Europe (2022): http://europepmc.org/abstract/med/36035630.
    10.1016/j.lanepe.2022.100471
  48. Spadar A; Perdigão J; Campino S; Clark TG. "Genomic analysis of hypervirulent Klebsiella pneumoniae reveals potential genetic markers for differentiation from classical strains.". Scientific reports (2022): http://europepmc.org/abstract/med/35953553.
    10.1038/s41598-022-17995-2
  49. Spadar A; Phelan J; Elias R; Modesto A; Caneiras C; Marques C; Lito L; et al. "Genomic epidemiological analysis of Klebsiella pneumoniae from Portuguese hospitals reveals insights into circulating antimicrobial resistance.". Scientific reports (2022): http://europepmc.org/abstract/med/35963896.
    10.1038/s41598-022-17996-1
  50. Campos M; Phelan J; Spadar A; Collins E; Gonçalves A; Pelloquin B; Vaselli NM; et al. "High-throughput barcoding method for the genetic surveillance of insecticide resistance and species identification in Anopheles gambiae complex malaria vectors.". Scientific reports (2022): http://europepmc.org/abstract/med/35974073.
    10.1038/s41598-022-17822-8
  51. Rita Elias; Anton Spadar; Jody Phelan; José Melo-Cristino; Luís Lito; Margarida Pinto; Luísa Gonçalves; et al. "A phylogenomic approach for the analysis of colistin resistance-associated genes in Klebsiella pneumoniae, its mutational diversity and implications for phenotypic resistance". International Journal of Antimicrobial Agents (2022): https://doi.org/10.1016/j.ijantimicag.2022.106581.
    10.1016/j.ijantimicag.2022.106581
  52. Montoya JC; Malabad JCM; Ang CF; Reyes LT; Basilio RP; Lim DR; Amarillo MLE; et al. "Molecular characterization of drug-resistant Mycobacterium tuberculosis among Filipino patients derived from the national tuberculosis prevalence survey Philippines 2016.". Tuberculosis (Edinburgh, Scotland) (2022): http://europepmc.org/abstract/med/35636102.
    10.1016/j.tube.2022.102211
  53. Napier G; Khan AS; Jabbar A; Khan MT; Ali S; Qasim M; Mohammad N; et al. "Characterisation of drug-resistant Mycobacterium tuberculosis mutations and transmission in Pakistan.". Scientific reports (2022): http://europepmc.org/abstract/med/35545649.
    10.1038/s41598-022-11795-4
  54. Phelan J; Deelder W; Ward D; Campino S; Hibberd ML; Clark TG. "COVID-profiler: a webserver for the analysis of SARS-CoV-2 sequencing data.". BMC bioinformatics (2022): http://europepmc.org/abstract/med/35428185.
    10.1186/s12859-022-04632-y
  55. Halliday KE; Nguipdop-Djomo P; Oswald WE; Sturgess J; Allen E; Sundaram N; Ireland G; et al. "The COVID-19 Schools Infection Survey in England: Protocol and participation profile for a prospective, observational cohort study.". JMIR research protocols (2022): http://europepmc.org/abstract/med/35635843.
    10.2196/34075
  56. Francesc Coll; Theodore Gouliouris; Sebastian Bruchmann; Jody Phelan; Kathy E. Raven; Taane G. Clark; Julian Parkhill; Sharon J. Peacock. "PowerBacGWAS: a computational pipeline to perform power calculations for bacterial genome-wide association studies". Communications Biology (2022): https://doi.org/10.1038/s42003-022-03194-2.
    10.1038/s42003-022-03194-2
  57. Deelder W; Napier G; Campino S; Palla L; Phelan J; Clark TG. "A modified decision tree approach to improve the prediction and mutation discovery for drug resistance in Mycobacterium tuberculosis.". BMC genomics (2022): http://europepmc.org/abstract/med/35016609.
    10.1186/s12864-022-08291-4
  58. Moss, S.; Manko, E.; Krishna, S.; Campino, S.; Clark, T.G.; Last, A.. "How has mass drug administration with dihydroartemisinin-piperaquine impacted molecular markers of drug resistance? A systematic review". Malaria Journal 21 1 (2022): http://www.scopus.com/inward/record.url?eid=2-s2.0-85131824815&partnerID=MN8TOARS.
    10.1186/s12936-022-04181-y
  59. Oresegun, D.R.; Thorpe, P.; Benavente, E.D.; Campino, S.; Muh, F.; Moon, R.W.; Clark, T.G.; Cox-Singh, J.. "De Novo Assembly of Plasmodium knowlesi Genomes From Clinical Samples Explains the Counterintuitive Intrachromosomal Organization of Variant SICAvar and kir Multiple Gene Family Members". Frontiers in Genetics 13 (2022): http://www.scopus.com/inward/record.url?eid=2-s2.0-85131887858&partnerID=MN8TOARS.
    10.3389/fgene.2022.855052
  60. O'Boyle, S.; Nacul, L.; Nacul, F.E.; Mudie, K.; Kingdon, C.C.; Cliff, J.M.; Clark, T.G.; Dockrell, H.M.; Lacerda, E.M.. "A Natural History of Disease Framework for Improving the Prevention, Management, and Research on Post-viral Fatigue Syndrome and Other Forms of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome". Frontiers in Medicine 8 (2022): http://www.scopus.com/inward/record.url?eid=2-s2.0-85124525885&partnerID=MN8TOARS.
    10.3389/fmed.2021.688159
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  285. Taane G. Clark; Maria De Iorio; Robert C. Griffths. "An Evolutionary Algorithm to Find Associations in Dense Genetic Maps". IEEE Transactions on Evolutionary Computation 12 3 (2008): 297-306. https://doi.org/10.1109%2Ftevc.2007.900984.
    10.1109/tevc.2007.900984
  286. Hoggart CJ; Clark TG; De Iorio M; Whittaker JC; Balding DJ. "Genome-wide significance for dense SNP and resequencing data.". Genetic epidemiology (2008): http://europepmc.org/abstract/med/18200594.
    10.1002/gepi.20292
  287. Teo YY; Small KS; Clark TG; Kwiatkowski DP. "Perturbation analysis: a simple method for filtering SNPs with erroneous genotyping in genome-wide association studies.". Annals of human genetics (2008): http://europepmc.org/abstract/med/18261185.
    10.1111/j.1469-1809.2007.00422.x
  288. Mangano VD; Luoni G; Rockett KA; Sirima BS; Konaté A; Forton J; Clark TG; et al. "Interferon regulatory factor-1 polymorphisms are associated with the control of Plasmodium falciparum infection.". Genes and immunity (2008): http://europepmc.org/abstract/med/18200030.
    10.1038/sj.gene.6364456
  289. Clark TG; Stewart M; Rye T; Smyth JF; Gourley C. "Validation of a new prognostic index for advanced epithelial ovarian cancer: results from its application to a UK-based cohort.". Journal of clinical oncology : official journal of the American Society of Clinical Oncology (2007): http://europepmc.org/abstract/med/18065745.
    10.1200/jco.2007.14.2976
  290. Hoggart CJ; Chadeau-Hyam M; Clark TG; Lampariello R; Whittaker JC; De Iorio M; Balding DJ. "Sequence-level population simulations over large genomic regions.". Genetics (2007): http://europepmc.org/abstract/med/17947444.
    10.1534/genetics.106.069088
  291. Teo YY; Inouye M; Small KS; Gwilliam R; Deloukas P; Kwiatkowski DP; Clark TG. "A genotype calling algorithm for the Illumina BeadArray platform.". Bioinformatics (Oxford, England) (2007): http://europepmc.org/abstract/med/17846035.
    10.1093/bioinformatics/btm443
  292. ENCODE Project Consortium; Birney E; Stamatoyannopoulos JA; Dutta A; Guigó R; Gingeras TR; Margulies EH; et al. "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.". Nature (2007): http://europepmc.org/abstract/med/17571346.
    10.1038/nature05874
  293. Munafò MR; Zetteler JI; Clark TG. "Personality and smoking status: a meta-analysis.". Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco (2007): http://europepmc.org/abstract/med/17365772.
    10.1080/14622200701188851
  294. Teo YY; Fry AE; Clark TG; Tai ES; Seielstad M. "On the usage of HWE for identifying genotyping errors.". Annals of human genetics (2007): http://europepmc.org/abstract/med/17388941.
    10.1111/j.1469-1809.2007.00356.x
  295. Keays DA; Clark TG; Campbell TG; Broxholme J; Valdar W. "Estimating the number of coding mutations in genotypic and phenotypic driven N-ethyl-N-nitrosourea (ENU) screens: revisited.". Mammalian genome : official journal of the International Mammalian Genome Society (2007): http://europepmc.org/abstract/med/17347895.
    10.1007/s00335-006-0065-z
  296. Clark TG; Andrew T; Cooper GM; Margulies EH; Mullikin JC; Balding DJ. "Functional constraint and small insertions and deletions in the ENCODE regions of the human genome.". Genome biology (2007): http://europepmc.org/abstract/med/17784950.
    10.1186/gb-2007-8-9-r180
  297. Munafo MR; Thiselton DL; Clark TG; Flint J. "Association of the NRG1 gene and schizophrenia: a meta-analysis.". Molecular psychiatry (2006): http://europepmc.org/abstract/med/16520822.
    10.1038/sj.mp.4001817
  298. Keays DA; Clark TG; Flint J. "Estimating the number of coding mutations in genotypic- and phenotypic-driven N-ethyl-N-nitrosourea (ENU) screens.". Mammalian genome : official journal of the International Mammalian Genome Society (2006): http://europepmc.org/abstract/med/16518690.
    10.1007/s00335-005-0101-4
  299. Clark TG; De Iorio M; Griffiths RC. "Bayesian logistic regression using a perfect phylogeny.". Biostatistics (Oxford, England) (2006): http://europepmc.org/abstract/med/16556611.
    10.1093/biostatistics/kxj030
  300. Clark TG; Murphy MF; Hey K; Drury M; Cheng KK; Aveyard P. "Does smoking influence survival in cancer patients through effects on respiratory and vascular disease?". European journal of cancer prevention : the official journal of the European Cancer Prevention Organisation (ECP) (2006): http://europepmc.org/abstract/med/16374237.
    10.1097/01.cej.0000186634.81753.45
  301. Bhatia M; Howard SC; Clark TG; Neale R; Qizilbash N; Murphy MF; Rothwell PM. "Apolipoproteins as predictors of ischaemic stroke in patients with a previous transient ischaemic attack.". Cerebrovascular diseases (Basel, Switzerland) (2006): http://europepmc.org/abstract/med/16490941.
    10.1159/000091537
  302. Munafò MR; Clark TG; Roberts KH; Johnstone EC. "Neuroticism mediates the association of the serotonin transporter gene with lifetime major depression.". Neuropsychobiology (2005): http://europepmc.org/abstract/med/16319503.
    10.1159/000089915
  303. Clark TG; De Iorio M; Griffiths RC; Farrall M. "Finding associations in dense genetic maps: a genetic algorithm approach.". Human heredity (2005): http://europepmc.org/abstract/med/16220001.
    10.1159/000088845
  304. Munafo MR; Bowes L; Clark TG; Flint J. "Lack of association of the COMT (Val158/108 Met) gene and schizophrenia: a meta-analysis of case-control studies.". Molecular psychiatry (2005): http://europepmc.org/abstract/med/15824744.
    10.1038/sj.mp.4001664
  305. Munafò MR; Clark T; Flint J. "Does measurement instrument moderate the association between the serotonin transporter gene and anxiety-related personality traits? A meta-analysis.". Molecular psychiatry (2005): http://europepmc.org/abstract/med/15599377.
    10.1038/sj.mp.4001627
  306. Munafò MR; Clark TG; Flint J. "Assessing publication bias in genetic association studies: evidence from a recent meta-analysis.". Psychiatry research (2004): http://europepmc.org/abstract/med/15572183.
    10.1016/j.psychres.2004.06.011
  307. Rothwell PM; Howard SC; Power DA; Gutnikov SA; Algra A; van Gijn J; Clark TG; Murphy MF; Warlow CP. "Fibrinogen concentration and risk of ischemic stroke and acute coronary events in 5113 patients with transient ischemic attack and minor ischemic stroke.". Stroke (2004): http://europepmc.org/abstract/med/15345800.
    10.1161/01.str.0000141701.36371.d1
  308. Munafò M; Clark T; Johnstone E; Murphy M; Walton R. "The genetic basis for smoking behavior: a systematic review and meta-analysis.". Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco (2004): http://europepmc.org/abstract/med/15370155.
    10.1080/14622200410001734030
  309. Whitlock G; Norton R; Clark T; Jackson R; MacMahon S. "Motor vehicle driver injury and marital status: a cohort study with prospective and retrospective driver injuries.". Injury prevention : journal of the International Society for Child and Adolescent Injury Prevention (2004): http://europepmc.org/abstract/med/14760024.
    10.1136/ip.2003.003020
  310. Clark TG; Bradburn MJ; Love SB; Altman DG. "Survival analysis part IV: further concepts and methods in survival analysis.". British journal of cancer (2003): http://europepmc.org/abstract/med/12942105.
    10.1038/sj.bjc.6601117
  311. Bradburn MJ; Clark TG; Love SB; Altman DG. "Survival analysis part II: multivariate data analysis--an introduction to concepts and methods.". British journal of cancer (2003): http://europepmc.org/abstract/med/12888808.
    10.1038/sj.bjc.6601119
  312. Bradburn MJ; Clark TG; Love SB; Altman DG. "Survival analysis Part III: multivariate data analysis -- choosing a model and assessing its adequacy and fit.". British journal of cancer (2003): http://europepmc.org/abstract/med/12915864.
    10.1038/sj.bjc.6601120
  313. Patel N; Goff LK; Clark T; Ford AM; Foot N; Lillington D; Hing S; et al. "Expression profile of wild-type ETV6 in childhood acute leukaemia.". British journal of haematology (2003): http://europepmc.org/abstract/med/12823350.
    10.1046/j.1365-2141.2003.04399.x
  314. Clark TG; Bradburn MJ; Love SB; Altman DG. "Survival analysis part I: basic concepts and first analyses.". British journal of cancer (2003): http://europepmc.org/abstract/med/12865907.
    10.1038/sj.bjc.6601118
  315. Whitlock G; Norton R; Clark T; Pledger M; Jackson R; MacMahon S. "Motor vehicle driver injury and socioeconomic status: a cohort study with prospective and retrospective driver injuries.". Journal of epidemiology and community health (2003): http://europepmc.org/abstract/med/12821697.
    10.1136/jech.57.7.512
  316. Munafò MR; Clark TG; Moore LR; Payne E; Walton R; Flint J. "Genetic polymorphisms and personality in healthy adults: a systematic review and meta-analysis.". Molecular psychiatry (2003): http://europepmc.org/abstract/med/12808427.
    10.1038/sj.mp.4001326
  317. Clark TG; Murphy MF; Rothwell PM. "Long term risks of stroke, myocardial infarction, and vascular death in "low risk" patients with a non-recent transient ischaemic attack.". Journal of neurology, neurosurgery, and psychiatry (2003): http://europepmc.org/abstract/med/12700296.
    10.1136/jnnp.74.5.577
  318. Briggs A; Clark T; Wolstenholme J; Clarke P. "Missing... presumed at random: cost-analysis of incomplete data.". Health economics (2003): http://europepmc.org/abstract/med/12720255.
    10.1002/hec.766
  319. Whitlock G; Norton R; Clark T; Jackson R; MacMahon S. "Is body mass index a risk factor for motor vehicle driver injury? A cohort study with prospective and retrospective outcomes.". International journal of epidemiology (2003): http://europepmc.org/abstract/med/12690027.
    10.1093/ije/dyg022
  320. Clark TG; Altman DG. "Developing a prognostic model in the presence of missing data: an ovarian cancer case study.". Journal of clinical epidemiology (2003): http://europepmc.org/abstract/med/12589867.
    10.1016/s0895-4356(02)00539-5
  321. Johnstone EC; Clark TG; Griffiths SE; Murphy MF; Walton RT. "Polymorphisms in dopamine metabolic enzymes and tobacco consumption in smokers: seeking confirmation of the association in a follow-up study.". Pharmacogenetics (2002): http://europepmc.org/abstract/med/12360111.
    10.1097/00008571-200210000-00012
  322. Clark TG; Altman DG; De Stavola BL. "Quantification of the completeness of follow-up.". Lancet (London, England) (2002): http://europepmc.org/abstract/med/11965278.
    10.1016/s0140-6736(02)08272-7
  323. Borley NR; Mortensen NJ; Chaudry MA; Mohammed S; Warren BF; George BD; Clark T; Jewell DP; Kettlewell MG. "Recurrence after abdominal surgery for Crohn's disease: relationship to disease site and surgical procedure.". Diseases of the colon and rectum (2002): http://europepmc.org/abstract/med/12068198.
    10.1007/s10350-004-6186-0
  324. Borley NR; Mortensen NJ; Chaudry MA; Mohammed S; Clarke T; Jewell DP. "Evidence for separate disease phenotypes in intestinal Crohn's disease.". The British journal of surgery (2002): http://europepmc.org/abstract/med/11856134.
    10.1046/j.1365-2168.2002.01987.x
  325. Whitlock G; Clark T. "The effect of missing values for covariates.". Epidemiology (Cambridge, Mass.) (2002): http://europepmc.org/abstract/med/11805596.
    10.1097/00001648-200201000-00019
  326. Clark TG; Stewart ME; Altman DG; Gabra H; Smyth JF. "A prognostic model for ovarian cancer.". British journal of cancer (2001): http://europepmc.org/abstract/med/11592763.
    10.1054/bjoc.2001.2030
  327. Whitlock G; Clark T; Vander Hoorn S; Rodgers A; Jackson R; Norton R; MacMahon S. "Random errors in the measurement of 10 cardiovascular risk factors.". European journal of epidemiology (2001): http://europepmc.org/abstract/med/12188008.
    10.1023/a:1016228410194
  328. Rodgers A; Walker N; Schug S; McKee A; Kehlet H; van Zundert A; Sage D; et al. "Reduction of postoperative mortality and morbidity with epidural or spinal anaesthesia: results from overview of randomised trials.". BMJ (Clinical research ed.) (2000): http://europepmc.org/abstract/med/11118174.
    10.1136/bmj.321.7275.1493
  329. MacMahon S; Sharpe N; Gamble G; Clague A; Mhurchu CN; Clark T; Hart H; Scott J; White H. "Randomized, placebo-controlled trial of the angiotensin-converting enzyme inhibitor, ramipril, in patients with coronary or other occlusive arterial disease. PART-2 Collaborative Research Group. Prevention of Atherosclerosis with Ramipril.". Journal of the American College of Cardiology (2000): http://europepmc.org/abstract/med/10933355.
    10.1016/s0735-1097(00)00736-1
  330. "Prevention of pulmonary embolism and deep vein thrombosis with low dose aspirin: Pulmonary Embolism Prevention (PEP) trial.". Lancet (London, England) (2000): http://europepmc.org/abstract/med/10776741.
  331. Neal BC; Rodgers A; Clark T; Gray H; Reid IR; Dunn L; MacMahon SW. "A systematic survey of 13 randomized trials of non-steroidal anti-inflammatory drugs for the prevention of heterotopic bone formation after major hip surgery.". Acta orthopaedica Scandinavica (2000): http://europepmc.org/abstract/med/10852316.
    10.1080/000164700317413076
  332. Neal BC; Rodgers A; Gray H; Clark T; Beaumont DD; House T; Douglas JE; Reid IR; MacMahon SW. "No effect of low-dose aspirin for the prevention of heterotopic bone formation after total hip replacement: a randomized trial of 2,649 patients.". Acta orthopaedica Scandinavica (2000): http://europepmc.org/abstract/med/10852317.
    10.1080/000164700317413085
  333. Micallef IN; Lillington DM; Apostolidis J; Amess JA; Neat M; Matthews J; Clark T; et al. "Therapy-related myelodysplasia and secondary acute myelogenous leukemia after high-dose therapy with autologous hematopoietic progenitor-cell support for lymphoid malignancies.". Journal of clinical oncology : official journal of the American Society of Clinical Oncology (2000): http://europepmc.org/abstract/med/10694543.
    10.1200/jco.2000.18.5.947
  334. Chalmers J; MacMahon S; Mancia G; Whitworth J; Beilin L; Hansson L; Neal B; et al. "1999 World Health Organization-International Society of Hypertension Guidelines for the management of hypertension. Guidelines sub-committee of the World Health Organization.". Clinical and experimental hypertension (New York, N.Y. : 1993) (1999): http://europepmc.org/abstract/med/10423121.
    10.3109/10641969909061028
  335. Walker N; Norton R; Vander Hoorn S; Rodgers A; MacMahon S; Clark T; Gray H. "Mortality after hip fracture: regional variations in New Zealand.". The New Zealand medical journal (1999): http://europepmc.org/abstract/med/10472890.
  336. "Blood pressure, cholesterol, and stroke in eastern Asia. Eastern Stroke and Coronary Heart Disease Collaborative Research Group.". Lancet (London, England) (1998): http://europepmc.org/abstract/med/9851379.
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