Taane G Clark

Summary

Affiliation: London School of Hygiene and Tropical Medicine
Country: UK

Publications

  1. pmc Unraveling Mycobacterium tuberculosis genomic diversity and evolution in Lisbon, Portugal, a highly drug resistant setting
    João Perdigão
    Centro de Patogenese Molecular, URIA, Faculdade de Farmacia da Universidade de Lisboa, Av, Prof, Gama Pinto, 1649 003 Lisboa, Portugal
    BMC Genomics 15:991. 2014
  2. pmc Association of candidate gene polymorphisms and TGF-beta/IL-10 levels with malaria in three regions of Cameroon: a case-control study
    Tobias O Apinjoh
    Department of Biochemistry and Molecular Biology, University of Buea, Buea, Cameroon
    Malar J 13:236. 2014
  3. pmc Genetic diversity and population structure of Plasmodium vivax in Central China
    Yaobao Liu
    Medical College of Soochow University, Suzhou, Jiangsu, People s Republic of China
    Malar J 13:262. 2014
  4. pmc Glucose-6-phosphate dehydrogenase polymorphisms and susceptibility to mild malaria in Dogon and Fulani, Mali
    Bakary Maiga
    Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, Faculty of Medicine, Pharmacy and Odonto Stomatology, USTTB, BP 1805 Bamako, Mali
    Malar J 13:270. 2014
  5. pmc Candidate polymorphisms and severe malaria in a Malian population
    Ousmane Toure
    Malaria Research and Training Centre, Faculty of Medicine, Pharmacy and Dentistry, University of Bamako, Bamako, Mali
    PLoS ONE 7:e43987. 2012
  6. pmc Association of sub-microscopic malaria parasite carriage with transmission intensity in north-eastern Tanzania
    Alphaxard Manjurano
    Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, WC1E 7HT, London, UK
    Malar J 10:370. 2011
  7. pmc A Bayesian approach using covariance of single nucleotide polymorphism data to detect differences in linkage disequilibrium patterns between groups of individuals
    Taane G Clark
    Department of Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, London, UK
    Bioinformatics 26:1999-2003. 2010
  8. pmc estMOI: estimating multiplicity of infection using parasite deep sequencing data
    Samuel A Assefa
    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
    Bioinformatics 30:1292-4. 2014
  9. doi request reprint Genome-wide significance for dense SNP and resequencing data
    Clive J Hoggart
    Department of Epidemiology and Public Health, Imperial College London, Norfolk Place, London, UK
    Genet Epidemiol 32:179-85. 2008
  10. pmc PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis
    Ernest D Benavente
    Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel St, London, UK
    BMC Bioinformatics 16:155. 2015

Collaborators

Detail Information

Publications27

  1. pmc Unraveling Mycobacterium tuberculosis genomic diversity and evolution in Lisbon, Portugal, a highly drug resistant setting
    João Perdigão
    Centro de Patogenese Molecular, URIA, Faculdade de Farmacia da Universidade de Lisboa, Av, Prof, Gama Pinto, 1649 003 Lisboa, Portugal
    BMC Genomics 15:991. 2014
    ..In Lisbon, Portugal, specific and successful XDR-TB strains have been found in circulation for almost two decades...
  2. pmc Association of candidate gene polymorphisms and TGF-beta/IL-10 levels with malaria in three regions of Cameroon: a case-control study
    Tobias O Apinjoh
    Department of Biochemistry and Molecular Biology, University of Buea, Buea, Cameroon
    Malar J 13:236. 2014
    ....
  3. pmc Genetic diversity and population structure of Plasmodium vivax in Central China
    Yaobao Liu
    Medical College of Soochow University, Suzhou, Jiangsu, People s Republic of China
    Malar J 13:262. 2014
    ..The impact of these changes on the local parasite population, and concurrent risks of future resurgence, was assessed...
  4. pmc Glucose-6-phosphate dehydrogenase polymorphisms and susceptibility to mild malaria in Dogon and Fulani, Mali
    Bakary Maiga
    Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, Faculty of Medicine, Pharmacy and Odonto Stomatology, USTTB, BP 1805 Bamako, Mali
    Malar J 13:270. 2014
    ..There is evidence to suggest that other G6PD deficiency alleles may be common in some regions of West Africa, and that allelic heterogeneity could explain these discrepancies...
  5. pmc Candidate polymorphisms and severe malaria in a Malian population
    Ousmane Toure
    Malaria Research and Training Centre, Faculty of Medicine, Pharmacy and Dentistry, University of Bamako, Bamako, Mali
    PLoS ONE 7:e43987. 2012
    ..It also demonstrates the need for establishing the region-specific repertoire of functional variation in important genes, including the glucose-6-phosphatase deficiency gene, before embarking on focused genotyping...
  6. pmc Association of sub-microscopic malaria parasite carriage with transmission intensity in north-eastern Tanzania
    Alphaxard Manjurano
    Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, WC1E 7HT, London, UK
    Malar J 10:370. 2011
    ..The PCR prevalence was then compared against other measures of transmission intensity collected in the same area...
  7. pmc A Bayesian approach using covariance of single nucleotide polymorphism data to detect differences in linkage disequilibrium patterns between groups of individuals
    Taane G Clark
    Department of Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, London, UK
    Bioinformatics 26:1999-2003. 2010
    ..Quantifying differences in linkage disequilibrium (LD) between sub-groups can highlight genetic regions or sites under selection and/or associated with disease, and may have utility in trans-ethnic mapping studies...
  8. pmc estMOI: estimating multiplicity of infection using parasite deep sequencing data
    Samuel A Assefa
    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
    Bioinformatics 30:1292-4. 2014
    ..The method is implemented within the estMOI software. When applied to clinical P.falciparum isolates from three continents, we find that multiple infections are common, especially in regions with high transmission...
  9. doi request reprint Genome-wide significance for dense SNP and resequencing data
    Clive J Hoggart
    Department of Epidemiology and Public Health, Imperial College London, Norfolk Place, London, UK
    Genet Epidemiol 32:179-85. 2008
    ..We compare our results for sequence data to those derived by the HapMap Consortium and find notable differences which may be due to the small sample sizes used in the HapMap estimate...
  10. pmc PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis
    Ernest D Benavente
    Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel St, London, UK
    BMC Bioinformatics 16:155. 2015
    ..One roadblock to strain investigation is the lack of user-interactive solutions to interrogate and visualise variation within a phylogenetic tree setting...
  11. pmc Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance
    Jody Phelan
    Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
    BMC Med 14:31. 2016
    ..Protein structure and interaction modelling are used to understand the functional effects of putative mutations and provide insight into the molecular mechanisms leading to resistance...
  12. pmc A robust SNP barcode for typing Mycobacterium tuberculosis complex strains
    Francesc Coll
    Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
    Nat Commun 5:4812. 2014
    ..It may be used to classify clinical isolates to evaluate tools to control the disease, including therapeutics and vaccines whose effectiveness may vary by strain type...
  13. pmc Whole Genome Sequencing Shows a Low Proportion of Tuberculosis Disease Is Attributable to Known Close Contacts in Rural Malawi
    Judith R Glynn
    Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
    PLoS ONE 10:e0132840. 2015
    ..The proportion of tuberculosis attributable to transmission from close contacts is not well known. Comparison of the genome of strains from index patients and prior contacts allows transmission to be confirmed or excluded...
  14. pmc Imputation-based population genetics analysis of Plasmodium falciparum malaria parasites
    Hanif Samad
    Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
    PLoS Genet 11:e1005131. 2015
    ..falciparum genotypes is a viable strategy for conducting accurate large-scale population genetics and association analyses, and supporting global surveillance for drug resistance markers and candidate vaccine antigens...
  15. pmc A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains
    Mark D Preston
    Immunology and Infection Department, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
    Nat Commun 5:4052. 2014
    ..We design a 23-SNP barcode that is highly predictive (~92%) and easily adapted to aid case management in the field and survey parasite migration worldwide. ..
  16. pmc Elucidating emergence and transmission of multidrug-resistant tuberculosis in treatment experienced patients by whole genome sequencing
    Taane G Clark
    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
    PLoS ONE 8:e83012. 2013
    ..We have used whole genome analysis to investigate M. tuberculosis strains isolated from treatment experienced patients with MDR-TB in Uganda over a period of four years...
  17. pmc A Poisson hierarchical modelling approach to detecting copy number variation in sequence coverage data
    Nuno Sepúlveda
    London School of Hygiene and Tropical Medicine, London, UK
    BMC Genomics 14:128. 2013
    ....
  18. pmc SVAMP: sequence variation analysis, maps and phylogeny
    Raeece Naeem
    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
    Bioinformatics 30:2227-9. 2014
    ..We also demonstrate the scalability and accuracy of our software on 245 Plasmodium falciparum malaria isolates from three continents...
  19. pmc SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences
    Francesc Coll
    Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
    Bioinformatics 28:2991-3. 2012
    ..Our results demonstrate the usefulness of the tool and its role in revealing experimental limitations...
  20. pmc VarB: a variation browsing and analysis tool for variants derived from next-generation sequencing data
    Mark D Preston
    Faculties of Epidemiology and Population Health and Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
    Bioinformatics 28:2983-5. 2012
    ....
  21. pmc Functional constraint and small insertions and deletions in the ENCODE regions of the human genome
    Taane G Clark
    Department of Epidemiology and Public Health, Imperial College, Norfolk Place, London, W2 1PG, UK
    Genome Biol 8:R180. 2007
    ..We relate indels to known genomic annotation features and measures of evolutionary constraint...
  22. pmc Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages
    Jody E Phelan
    Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, WC1E 7HT, London, UK
    BMC Genomics 17:151. 2016
    ..They are hypothesised to be important virulence factors involved with host-pathogen interactions, but their high genetic variability and complexity of analysis means they are typically disregarded in genome studies...
  23. pmc Population genomic structure and adaptation in the zoonotic malaria parasite Plasmodium knowlesi
    Samuel Assefa
    Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, London, WC1E 7HT United Kingdom
    Proc Natl Acad Sci U S A 112:13027-32. 2015
    ..57), and scans of haplotype homozygosity implicate several genomic regions as being under recent positive selection. ..
  24. pmc 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
    Nuno Sepúlveda
    London School of Hygiene and Tropical Medicine, London, UK Centre of Statistics and Applications of University of Lisbon, Lisbon, Portugal
    Ann Hum Genet 78:277-89. 2014
    ..We argue that these postimputation estimates are reasonably unbiased, as a result of a good study design based on matching key socio-environmental factors. ..
  25. doi request reprint Distinct phases of blood gene expression pattern through tuberculosis treatment reflect modulation of the humoral immune response
    Jacqueline M Cliff
    Immunology and Infection Department, London School of Hygiene and Tropical Medicine, London, United Kingdom
    J Infect Dis 207:18-29. 2013
    ..We hypothesized that early alterations in peripheral immunity could be measured by gene expression profiling in tuberculosis patients undergoing successful conventional combination treatment...
  26. pmc Candidate human genetic polymorphisms and severe malaria in a Tanzanian population
    Alphaxard Manjurano
    Joint Malaria Programme, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
    PLoS ONE 7:e47463. 2012
    ..Further studies are required to test the generality of these associations and to understand their functional consequences...
  27. ncbi request reprint Finding associations in dense genetic maps: a genetic algorithm approach
    Taane G Clark
    Department of Epidemiology and Public Health, Imperial College, St Mary s Campus, Norfolk Place, London W2 1PG, UK
    Hum Hered 60:97-108. 2005
    ..We demonstrate our method and the flexibility of logic tree structure with variable nodal lengths on simulated data from a coalescent model, as well as data from a candidate gene study of quantitative genetic variation...