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publications.csv
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"Author","doi","issn","journal","title","year","PMID"
"Anton Spadar,João Perdigão,Susana Campino,Taane G Clark","10.1186/s13073-023-01153-y","1756-994X","Genome Medicine","Large-scale genomic analysis of global Klebsiella pneumoniae plasmids reveals multiple simultaneous clusters of carbapenem-resistant hypervirulent strains","2023"
"Patrick Nguipdop-Djomo,William E Oswald,Katherine E Halliday,Sarah Cook,Joanna Sturgess,Neisha Sundaram,Charlotte Warren-Gash,Paul EM Fine,Judith Glynn,Elizabeth Allen,Taane G Clark,Benjamin Ford,Alison Judd,Georgina Ireland,John Poh,Chris Bonell,Fiona Dawe,Emma Rourke,Ian Diamond,Shamez N Ladhani,Sinéad M Langan,James Hargreaves,Punam Mangtani","10.1016/j.ijid.2022.12.030","12019712","International Journal of Infectious Diseases","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","2023"
"Gary Napier,Susana Campino,Jody E Phelan,Taane G Clark","10.1038/s41598-023-27516-4","2045-2322","Scientific Reports","Large-scale genomic analysis of Mycobacterium tuberculosis reveals extent of target and compensatory mutations linked to multi-drug resistant tuberculosis","2023"
"Amy Ibrahim,Emilia Manko,Jamille G Dombrowski,Mónica Campos,Ernest Diez Benavente,Debbie Nolder,Colin J Sutherland,Francois Nosten,Diana Fernandez,Gabriel Vélez-Tobón,Alberto Tobón Castaño,Anna Caroline C Aguiar,Dhelio Batista Pereira,Simone da Silva Santos,Martha Suarez-Mutis,Silvia Maria Di Santi,Andrea Regina de Souza Baptista,Ricardo Luiz Dantas Machado,Claudio RF Marinho,Taane G Clark,Susana Campino","10.1016/j.lana.2022.100420","2667193X","The Lancet Regional Health - Americas","Population-based genomic study of Plasmodium vivax malaria in seven Brazilian states and across South America","2023"
"Itzhak Zachi Attia,Andrew S Tseng,Ernest Diez Benavente,Jose R Medina-Inojosa,Taane G Clark,Sofia Malyutina,Suraj Kapa,Henrik Schirmer,Alexander V Kudryavtsev,Peter A Noseworthy,Rickey E Carter,Andrew Ryabikov,Pablo Perel,Paul A Friedman,David A Leon,Francisco Lopez-Jimenez","10.1016/j.ijcard.2020.12.065","01675273","International Journal of Cardiology","External validation of a deep learning electrocardiogram algorithm to detect ventricular dysfunction","2021"
"Celia Miguel-Blanco,James M Murithi,Ernest Diez Benavente,Fiona Angrisano,Katarzyna A Sala,Donelly A van Schalkwyk,Manu Vanaerschot,Frank Schwach,Matthew J Fuchter,Oliver Billker,Colin J Sutherland,Susana G Campino,Taane G Clark,Andrew M Blagborough,David A Fidock,Esperanza Herreros,Francisco Javier Gamo,Jake Baum,Michael J Delves","10.1038/s41598-021-81343-z","2045-2322","Scientific Reports","The antimalarial efficacy and mechanism of resistance of the novel chemotype DDD01034957","2021"
"Gasto Frumence,Leonard EG Mboera,Bugwesa Z Katale,Calvin Sindato,Sharadhuli Kimera,Anna Durrance-Bagale,Stephen E Mshana,Taane G Clark,Mark M Rweyemamu,Helena Legido-Quigley,Mecky Matee","10.1016/j.jgar.2021.02.027","22137165","Journal of Global Antimicrobial Resistance","Policy actors and human and animal health practitioners’ perceptions of antimicrobial use and resistance in Tanzania: A qualitative study","2021"
"Anton Spadar,João Perdigão,Jody Phelan,James Charleston,Ana Modesto,Rita Elias,Paola Florez de Sessions,Martin L Hibberd,Susana Campino,Aida Duarte,Taane G Clark","10.1038/s41598-021-85724-2","2045-2322","Scientific Reports","Methylation analysis of Klebsiella pneumoniae from Portuguese hospitals","2021"
"Silvania Da Veiga Leal,Daniel Ward,Susana Campino,Ernest Diez Benavente,Amy Ibrahim,Tânia Claret,Varela Isaías,Davidson Monteiro,Taane G Clark,Luzia Gonçalves,Tomas Valdez,Maria da Luz Lima Mendonça,Henrique Silveira,Fatima Nogueira","10.1186/s12936-021-03708-z","1475-2875","Malaria Journal","Drug resistance profile and clonality of Plasmodium falciparum parasites in Cape Verde: the 2017 malaria outbreak","2021"
"Gasto Frumence,Leonard E G Mboera,Calvin Sindato,Bugwesa Z Katale,Sharadhuli Kimera,Emmy Metta,Anna Durrance-Bagale,Anne-Sophie Jung,Stephen E Mshana,Taane G Clark,Mark Rweyemamu,Helena Legido-Quigley,Mecky I N Matee","10.3390/antibiotics10030273","2079-6382","Antibiotics","The Governance and Implementation of the National Action Plan on Antimicrobial Resistance in Tanzania: A Qualitative Study","2021"
"Nuno Sepúlveda,Lynn Grignard,Jonathan Curry,Laleta Mahey,Guido J H Bastiaens,Alfred B Tiono,Joseph Okebe,Sam A Coulibaly,Bronner P Gonçalves,Muna Affara,Alphonse Ouédraogo,Edith C Bougouma,Guillaume S Sanou,Issa Nébié,Kjerstin Lanke,Sodiomon B Sirima,Alassane Dicko,Umberto d’Alessandro,Taane G Clark,Susana Campino,Ingrid Chen,Alice C Eziefula,Roly Gosling,Teun Bousema,Chris Drakeley","10.3389/fgene.2021.645688","1664-8021","Frontiers in Genetics","G6PD Polymorphisms and Hemolysis After Antimalarial Treatment With Low Single-Dose Primaquine: A Pooled Analysis of Six African Clinical Trials","2021"
"Jamille Gregório Dombrowski,Holly Acford-Palmer,Monica Campos,Erika Paula Machado Separovic,Sabrina Epiphanio,Taane Gregory Clark,Susana Campino,Claudio Romero Farias Marinho","10.1016/j.lana.2022.100407","2667193X","The Lancet Regional Health - Americas","Genetic diversity of Plasmodium vivax isolates from pregnant women in the Western Brazilian Amazon: A prospective cohort study","2023"
"Denise M O’Sullivan,Ronan M Doyle,Sasithon Temisak,Nicholas Redshaw,Alexandra S Whale,Grace Logan,Jiabin Huang,Nicole Fischer,Gregory C A Amos,Mark D Preston,Julian R Marchesi,Josef Wagner,Julian Parkhill,Yair Motro,Hubert Denise,Robert D Finn,Kathryn A Harris,Gemma L Kay,Justin O’Grady,Emma Ransom-Jones,Huihai Wu,Emma Laing,David J Studholme,Ernest Diez Benavente,Jody Phelan,Taane G Clark,Jacob Moran-Gilad,Jim F Huggett","10.1038/s41598-021-89881-2","2045-2322","Scientific Reports","An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities","2021"
"Ernest Diez Benavente,Emilia Manko,Jody Phelan,Monica Campos,Debbie Nolder,Diana Fernandez,Gabriel Velez-Tobon,Alberto Tobón Castaño,Jamille G Dombrowski,Claudio R F Marinho,Anna Caroline C Aguiar,Dhelio Batista Pereira,Kanlaya Sriprawat,Francois Nosten,Robert Moon,Colin J Sutherland,Susana Campino,Taane G Clark","10.1038/s41467-021-23422-3","2041-1723","Nature Communications","Distinctive genetic structure and selection patterns in Plasmodium vivax from South Asia and East Africa","2021"
"Wouter Deelder,Ernest Diez Benavente,Jody Phelan,Emilia Manko,Susana Campino,Luigi Palla,Taane G Clark","10.1186/s12936-021-03788-x","1475-2875","Malaria Journal","Using deep learning to identify recent positive selection in malaria parasite sequence data","2021"
"Gasto Frumence,Leonard E G Mboera,Calvin Sindato,Anna Durrance-Bagale,Anne-Sophie Jung,Stephen E Mshana,Taane G Clark,Helena Legido-Quigley,Mecky I Matee","10.3390/antibiotics10060733","2079-6382","Antibiotics","Practices and Challenges of Veterinary Paraprofessionals in Regards to Antimicrobial Use and Resistance in Animals in Dar Es Salaam, Tanzania","2021"
"André Silva-Pinto,João Domingos,Margarida Cardoso,Ana Reis,Ernest Diez Benavente,João Paulo Caldas,Cláudia Conceição,Cristina Toscano,Teresa Baptista-Fernandes,Taane G Clark,Kamal Mansinho,Susana Campino,Fatima Nogueira","10.1016/j.ijid.2021.07.008","12019712","International Journal of Infectious Diseases","Artemether-lumefantrine treatment failure of uncomplicated Plasmodium falciparum malaria in travellers coming from Angola and Mozambique","2021"
"Tanushree Tunstall,Jody Phelan,Charlotte Eccleston,Taane G Clark,Nicholas Furnham","10.3389/fmolb.2021.619403","2296-889X","Frontiers in Molecular Biosciences","Structural and Genomic Insights Into Pyrazinamide Resistance in Mycobacterium tuberculosis Underlie Differences Between Ancient and Modern Lineages","2021"
"Anna Durrance-Bagale,Anne-Sophie Jung,Gasto Frumence,Leonard Mboera,Stephen E Mshana,Calvin Sindato,Taane G Clark,Mecky Matee,Helena Legido-Quigley","10.3390/antibiotics10080991","2079-6382","Antibiotics","Framing the Drivers of Antimicrobial Resistance in Tanzania","2021"
"Ashley Osborne,Emilia Manko,Mika Takeda,Akira Kaneko,Wataru Kagaya,Chim Chan,Mtakai Ngara,James Kongere,Kiyoshi Kita,Susana Campino,Osamu Kaneko,Jesse Gitaka,Taane G Clark","10.1038/s41598-021-99192-1","2045-2322","Scientific Reports","Characterizing the genomic variation and population dynamics of Plasmodium falciparum malaria parasites in and around Lake Victoria, Kenya","2021"
"Jaciara de Lourdes do Carmo Guimarães Diniz,Andrea von Groll,Gisela Unis,Elis Regina Dalla-Costa,Maria Lúcia Rosa Rossetti,Júlia Silveira Vianna,Daniela Fernandes Ramos,Ana Júlia Reis,Priscila Cristina Bartolomeu Halicki,João Luis Rheingantz Scaini,Yasmin Castillos de Ibrahim das Neves,Jody Phelan,Ana Rita Gomes,Susana Campino,Karina dos Santos Machado,Adriano Velasque Werhli,Arnab Pain,Taane Gregory Clark,João Perdigão,Miguel Viveiros,Isabel Portugal,Pedro Eduardo Almeida Silva","10.1016/j.tube.2021.102137","14729792","Tuberculosis","Whole-genome sequencing as a tool for studying the microevolution of drug-resistant serial Mycobacterium tuberculosis isolates","2021"
"Mayreli Ortiz,Miriam Jauset-Rubio,Vasso Skouridou,Diana Machado,Miguel Viveiros,Taane G Clark,Anna Simonova,David Kodr,Michal Hocek,Ciara K O’Sullivan","10.1021/acssensors.1c01710","2379-3694","ACS Sensors","Electrochemical Detection of Single-Nucleotide Polymorphism Associated with Rifampicin Resistance in <i>Mycobacterium tuberculosis</i> Using Solid-Phase Primer Elongation with Ferrocene-Linked Redox-Labeled Nucleotides","2021"
"Rita Elias,José Melo-Cristino,Luís Lito,Margarida Pinto,Luísa Gonçalves,Susana Campino,Taane G Clark,Aida Duarte,João Perdigão","10.3390/diagnostics11122352","2075-4418","Diagnostics","Klebsiella pneumoniae and Colistin Susceptibility Testing: Performance Evaluation for Broth Microdilution, Agar Dilution and Minimum Inhibitory Concentration Test Strips and Impact of the “Skipped Well” Phenomenon","2021"
"Amanda J Gibson,Ian J Passmore,Valwynne Faulkner,Dong Xia,Irene Nobeli,Jennifer Stiens,Sam Willcocks,Taane G Clark,Ben Sobkowiak,Dirk Werling,Bernardo Villarreal-Ramos,Brendan W Wren,Sharon L Kendall","10.3389/fvets.2021.760717","2297-1769","Frontiers in Veterinary Science","Probing Differences in Gene Essentiality Between the Human and Animal Adapted Lineages of the Mycobacterium tuberculosis Complex Using TnSeq","2021"
"Wouter Deelder,Gary Napier,Susana Campino,Luigi Palla,Jody Phelan,Taane G Clark","10.1186/s12864-022-08291-4","1471-2164","BMC Genomics","A modified decision tree approach to improve the prediction and mutation discovery for drug resistance in Mycobacterium tuberculosis","2022"
"Shennae O'Boyle,Luis Nacul,Flavio E Nacul,Kathleen Mudie,Caroline C Kingdon,Jacqueline M Cliff,Taane G Clark,Hazel M Dockrell,Eliana M Lacerda","10.3389/fmed.2021.688159","2296-858X","Frontiers in Medicine","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","2022"
"Francesc Coll,Theodore Gouliouris,Sebastian Bruchmann,Jody Phelan,Kathy E Raven,Taane G Clark,Julian Parkhill,Sharon J Peacock","10.1038/s42003-022-03194-2","2399-3642","Communications Biology","PowerBacGWAS: a computational pipeline to perform power calculations for bacterial genome-wide association studies","2022"
"Jody Phelan,Wouter Deelder,Daniel Ward,Susana Campino,Martin L Hibberd,Taane G Clark","10.1186/s12859-022-04632-y","1471-2105","BMC Bioinformatics","COVID-profiler: a webserver for the analysis of SARS-CoV-2 sequencing data","2022"
"Katherine E Halliday,Patrick Nguipdop-Djomo,William E Oswald,Joanna Sturgess,Elizabeth Allen,Neisha Sundaram,Georgina Ireland,John Poh,Samreen Ijaz,Justin Shute,Ian Diamond,Emma Rourke,Fiona Dawe,Alison Judd,Taane Clark,W John Edmunds,Chris Bonell,Punam Mangtani,Shamez N Ladhani,Sinéad M Langan,James Hargreaves","10.2196/34075","1929-0748","JMIR Research Protocols","The COVID-19 Schools Infection Survey in England: Protocol and Participation Profile for a Prospective Observational Cohort Study","2022"
"Damilola R Oresegun,Peter Thorpe,Ernest Diez Benavente,Susana Campino,Fauzi Muh,Robert William Moon,Taane Gregory Clark,Janet Cox-Singh","10.3389/fgene.2022.855052","1664-8021","Frontiers in Genetics","De Novo Assembly of Plasmodium knowlesi Genomes From Clinical Samples Explains the Counterintuitive Intrachromosomal Organization of Variant SICAvar and kir Multiple Gene Family Members","2022"
"Rita Elias,Anton Spadar,Jody Phelan,José Melo-Cristino,Luís Lito,Margarida Pinto,Luísa Gonçalves,Susana Campino,Taane G Clark,Aida Duarte,João Perdigão","10.1016/j.ijantimicag.2022.106581","09248579","International Journal of Antimicrobial Agents","A phylogenomic approach for the analysis of colistin resistance-associated genes in Klebsiella pneumoniae, its mutational diversity and implications for phenotypic resistance","2022"
"Sophie Moss,Emilia Mańko,Sanjeev Krishna,Susana Campino,Taane G Clark,Anna Last","10.1186/s12936-022-04181-y","1475-2875","Malaria Journal","How has mass drug administration with dihydroartemisinin-piperaquine impacted molecular markers of drug resistance? A systematic review","2022"
"Kanwara Trisakul,Ditthawat Nonghanphithak,Pratchakan Chaiyachat,Orawee Kaewprasert,Kankanon Sakmongkoljit,Wipa Reechaipichitkul,Angkana Chaiprasert,David Blair,Taane G Clark,Kiatichai Faksri","10.1080/22221751.2022.2099304","2222-1751","Emerging Microbes & Infections","High clustering rate and genotypic drug-susceptibility screening for the newly recommended anti-tuberculosis drugs among global extensively drug-resistant <i>Mycobacterium tuberculosis</i> isolates","2022"
"Daniel Ward,Ana Rita Gomes,Kevin K A Tetteh,Nuno Sepúlveda,Lara Ferrero Gomez,Susana Campino,Taane G Clark","10.1038/s41598-022-16115-4","2045-2322","Scientific Reports","Sero-epidemiological study of arbovirus infection following the 2015–2016 Zika virus outbreak in Cabo Verde","2022"
"Paula J Gómez-González,Susana Campino,Jody E Phelan,Taane G Clark","10.1093/bib/bbac256","1467-5463","Briefings in Bioinformatics","Portable sequencing of <i>Mycobacterium tuberculosis</i> for clinical and epidemiological applications","2022"
"Anton Spadar,João Perdigão,Susana Campino,Taane G Clark","10.1038/s41598-022-17995-2","2045-2322","Scientific Reports","Genomic analysis of hypervirulent Klebsiella pneumoniae reveals potential genetic markers for differentiation from classical strains","2022"
"Anton Spadar,Jody Phelan,Rita Elias,Ana Modesto,Cátia Caneiras,Cátia Marques,Luís Lito,Margarida Pinto,Patrícia Cavaco-Silva,Helena Ferreira,Constança Pomba,Gabriela J Da Silva,Maria José Saavedra,José Melo-Cristino,Aida Duarte,Susana Campino,João Perdigão,Taane G Clark","10.1038/s41598-022-17996-1","2045-2322","Scientific Reports","Genomic epidemiological analysis of Klebsiella pneumoniae from Portuguese hospitals reveals insights into circulating antimicrobial resistance","2022"
"Monica Campos,Jody Phelan,Anton Spadar,Emma Collins,Adéritow Gonçalves,Bethanie Pelloquin,Natasha Marcella Vaselli,Anne Meiwald,Emma Clark,Caleb Stica,James Orsborne,Moussa Sylla,Constant Edi,Denka Camara,Abdul Rahim Mohammed,Yaw Asare Afrane,Mojca Kristan,Thomas Walker,Lara Ferrero Gomez,Louisa A Messenger,Taane G Clark,Susana Campino","10.1038/s41598-022-17822-8","2045-2322","Scientific Reports","High-throughput barcoding method for the genetic surveillance of insecticide resistance and species identification in Anopheles gambiae complex malaria vectors","2022"
"James R Hargreaves,Sinéad M Langan,William E Oswald,Katherine E Halliday,Joanna Sturgess,Jody Phelan,Patrick Nguipdop-Djomo,Benjamin Ford,Elizabeth Allen,Neisha Sundaram,Georgina Ireland,John Poh,Samreen Ijaz,Ian Diamond,Emma Rourke,Fiona Dawe,Alison Judd,Charlotte Warren-Gash,Taane G Clark,Judith R Glynn,W John Edmunds,Chris Bonell,Punam Mangtani,Shamez N Ladhani,Tanya Abramsky,Shazaad Ahmad,Felicity Aiano,Frances Baawuah,Urszula Bankiewicz,Sarah Batt,Joanne Beckmann,Ami Bhavsar,Bernadette Brent,Andrew Brent,Simon Brouwer,Kevin Brown,Richard Browne,Kevin Childs,Sarah Cook,Simon Cousens,Ieuan Day,Antonio Felton,Paul Fine,David Foster,Joanna Garstang,David Gates,Claire Grant,Bethany Griffiths-Tong,Claire Hele,Rowan Hemsi,Pete Jones,Helena Jordan,Adam Kucharski,Andrea Lacey,Rebecca Leeson,Ffion Lelii,Philip Lovely,Madeleine Lunskey,Chris McLanachan,James Munday,Ifeanyichukwu Okike,Kathleen O'Reilly,Penelope Parker,Annabel Powell,Sarah Proud,Mary Ramsay,Lee Rudd,Timothy Russell,Justin Shute,Nerissa Tilouche,Charmaine Virgin,Sian-Elin Wyatt,KELLY YEO","10.1016/j.lanepe.2022.100471","26667762","The Lancet Regional Health - Europe","Epidemiology of SARS-CoV-2 infection among staff and students in a cohort of English primary and secondary schools during 2020–2021","2022"
"Josiah O Kuja,Bernard N Kanoi,Renzo F Balboa,Clement Shiluli,Michael Maina,Harrison Waweru,Kimita Gathii,Mary Mungai,Moses Masika,Omu Anzala,Matilu Mwau,Taane G Clark,John Waitumbi,Jesse Gitaka","10.1186/s12864-022-08853-6","1471-2164","BMC Genomics","Genomic surveillance of SARS-COV-2 reveals diverse circulating variant lineages in Nairobi and Kiambu Counties, Kenya","2022"
"Matthew Higgins,Oliver W Stringer,Daniel Ward,Jennifer M Andrews,Matthew S Forrest,Susana Campino,Taane G Clark","10.1016/j.jmoldx.2022.08.005","15251578","The Journal of Molecular Diagnostics","Characterizing the Impact of Primer-Template Mismatches on Recombinase Polymerase Amplification","2022"
"Razib Mazumder,Arif Hussain,Jody E Phelan,Susana Campino,S M Arefeen Haider,Araf Mahmud,Dilruba Ahmed,Md Asadulghani,Taane G Clark,Dinesh Mondal","10.3389/fmicb.2022.1027494","1664-302X","Frontiers in Microbiology","Non-lactose fermenting Escherichia coli: Following in the footsteps of lactose fermenting E. coli high-risk clones","2022"
"Anwar Sheed Khan,Jody E Phelan,Muhammad Tahir Khan,Sajid Ali,Muhammad Qasim,Noor Mohammad,Gary Napier,Sajjad Ahmad,Jamshed Alam,Baharullah Khattak,Susana Campino,Taane G Clark,Taj Ali Khan","10.1016/j.tube.2022.102286","14729792","Tuberculosis","Genetic mutations underlying isoniazid-resistant Mycobacterium tuberculosis in Khyber Pakhtunkhwa, Pakistan","2023"
"Wouter Deelder,Emilia Manko,Jody E Phelan,Susana Campino,Luigi Palla,Taane G Clark","10.1038/s41598-022-25568-6","2045-2322","Scientific Reports","Geographical classification of malaria parasites through applying machine learning to whole genome sequence data","2022"
"Emma L Collins,Jody E Phelan,Magdalena Hubner,Anton Spadar,Monica Campos,Daniel Ward,Holly Acford-Palmer,Ana Rita Gomes,Keily Silva,Lara Ferrero Gomez,Taane G Clark,Susana Campino","10.1371/journal.pntd.0010935","1935-2735","PLOS Neglected Tropical Diseases","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","2022"
"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","10.1038/s41598-022-27254-z","2045-2322","Scientific Reports","Deep learning-derived cardiovascular age shares a genetic basis with other cardiac phenotypes","2022"
"Jody E Phelan,Francesc Coll,Indra Bergval,Richard M Anthony,Rob Warren,Samantha L Sampson,Nicolaas C Gey van Pittius,Judith R Glynn,Amelia C Crampin,Adriana Alves,Theolis Barbosa Bessa,Susana Campino,Keertan Dheda,Louis Grandjean,Rumina Hasan,Zahra Hasan,Anabela Miranda,David Moore,Stefan Panaiotov,Joao Perdigao,Isabel Portugal,Patricia Sheen,Erivelton de Oliveira Sousa,Elizabeth M Streicher,Paul D van Helden,Miguel Viveiros,Martin L Hibberd,Arnab Pain,Ruth McNerney,Taane G Clark","10.1186/s12864-016-2467-y","1471-2164","BMC genomics","Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages.","2016","26923687"
"Benjamin Sobkowiak,Judith R Glynn,Rein M G J Houben,Kim Mallard,Jody E Phelan,José Afonso Guerra-Assunção,Louis Banda,Themba Mzembe,Miguel Viveiros,Ruth McNerney,Julian Parkhill,Amelia C Crampin,Taane G Clark","10.1186/s12864-018-4988-z","1471-2164","BMC Genomics","Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data","2018"
"Stephanie Portelli,Jody E Phelan,David B Ascher,Taane G Clark,Nicholas Furnham","10.1038/s41598-018-33370-6","2045-2322","Scientific Reports","Understanding molecular consequences of putative drug resistant mutations in Mycobacterium tuberculosis","2018"
"Paula J Gomez-Gonzalez,Nuria Andreu,Jody E Phelan,Paola Florez de Sessions,Judith R Glynn,Amelia C Crampin,Susana Campino,Philip D Butcher,Martin L Hibberd,Taane G Clark","10.1038/s41598-019-41692-2","2045-2322","Scientific Reports","An integrated whole genome analysis of Mycobacterium tuberculosis reveals insights into relationship between its genome, transcriptome and methylome","2019"
"Jody E Phelan,Denise M O’Sullivan,Diana Machado,Jorge Ramos,Yaa E A Oppong,Susana Campino,Justin O’Grady,Ruth McNerney,Martin L Hibberd,Miguel Viveiros,Jim F Huggett,Taane G Clark","10.1186/s13073-019-0650-x","1756-994X","Genome Medicine","Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs","2019"
"Jody E Phelan,Dodge R Lim,Satoshi Mitarai,Paola Florez de Sessions,Ma Angelica A Tujan,Lorenzo T Reyes,Inez Andrea P Medado,Alma G Palparan,Ahmad Nazri Mohamed Naim,Song Jie,Edelwisa Segubre-Mercado,Beatriz Simoes,Susana Campino,Julius C Hafalla,Yoshiro Murase,Yuta Morishige,Martin L Hibberd,Seiya Kato,Ma Cecilia G Ama,Taane G Clark","10.1038/s41598-019-45566-5","2045-2322","Scientific Reports","Mycobacterium tuberculosis whole genome sequencing provides insights into the Manila strain and drug-resistance mutations in the Philippines","2019"
"João Perdigão,Pedro Gomes,Anabela Miranda,Fernando Maltez,Diana Machado,Carla Silva,Jody E Phelan,Laura Brum,Susana Campino,Isabel Couto,Miguel Viveiros,Taane G Clark,Isabel Portugal","10.1038/s41598-020-59558-3","2045-2322","Scientific Reports","Using genomics to understand the origin and dispersion of multidrug and extensively drug resistant tuberculosis in Portugal","2020"
"Bugwesa Z Katale,Peter M Mbelele,Nsiande A Lema,Susana Campino,Stephen E Mshana,Mark M Rweyemamu,Jody E Phelan,Julius D Keyyu,Mtebe Majigo,Erasto V Mbugi,Hazel M Dockrell,Taane G Clark,Mecky I Matee,Stellah Mpagama","10.1186/s12864-020-6577-1","1471-2164","BMC Genomics","Whole genome sequencing of Mycobacterium tuberculosis isolates and clinical outcomes of patients treated for multidrug-resistant tuberculosis in Tanzania","2020"
"Prapaporn Srilohasin,Therdsak Prammananan,Kiatichai Faksri,Jody E Phelan,Prapat Suriyaphol,Phalin Kamolwat,Saijai Smithtikarn,Areeya Disratthakit,Sanjib Mani Regmi,Manoon Leechawengwongs,Rick Twee-Hee Ong,Yik Ying Teo,Sissades Tongsima,Taane G Clark,Angkana Chaiprasert","10.1080/22221751.2020.1852891","2222-1751","Emerging Microbes & Infections","Genomic evidence supporting the clonal expansion of extensively drug-resistant tuberculosis bacteria belonging to a rare proto <b>-</b> Beijing genotype","2020"
"Daniel Ward,Matthew Higgins,Jody E Phelan,Martin L Hibberd,Susana Campino,Taane G Clark","10.1186/s13073-020-00822-6","1756-994X","Genome Medicine","An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets","2021"
"Elizabeth B Sawyer,Jody E Phelan,Taane G Clark,Teresa Cortes","10.1016/j.celrep.2021.108695","22111247","Cell Reports","A snapshot of translation in Mycobacterium tuberculosis during exponential growth and nutrient starvation revealed by ribosome profiling","2021"
"Ditthawat Nonghanphithak,Angkana Chaiprasert,Saijai Smithtikarn,Phalin Kamolwat,Petchawan Pungrassami,Virasakdi Chongsuvivatwong,Surakameth Mahasirimongkol,Wipa Reechaipichitkul,Chaniya Leepiyasakulchai,Jody E Phelan,David Blair,Taane G Clark,Kiatichai Faksri","10.3201/eid2703.204364","1080-6040","Emerging Infectious Diseases","Clusters of Drug-Resistant <i>Mycobacterium tuberculosis</i> Detected by Whole-Genome Sequence Analysis of Nationwide Sample, Thailand, 2014–2017","2021"
"Anton Spadar,Jody E Phelan,Ernest Diez Benavente,Monica Campos,Lara Ferrero Gomez,Fady Mohareb,Taane G Clark,Susana Campino","10.1186/s13071-021-04828-w","1756-3305","Parasites & Vectors","Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus","2021"
"Anwar Sheed Khan,Jody E Phelan,Muhammad Tahir Khan,Sajid Ali,Muhammad Qasim,Gary Napier,Susana Campino,Sajjad Ahmad,Otavio Cabral-Marques,Shulin Zhang,Hazir Rahman,Dong-Qing Wei,Taane G Clark,Taj Ali Khan","10.1038/s41598-021-93501-4","2045-2322","Scientific Reports","Characterization of rifampicin-resistant Mycobacterium tuberculosis in Khyber Pakhtunkhwa, Pakistan","2021"
"Anwar Sheed Khan,Jody E Phelan,Muhammad Tahir Khan,Sajid Ali,Muhammad Qasim,Gary Napier,Susana Campino,Sajjad Ahmad,Otavio Cabral-Marques,Shulin Zhang,Hazir Rahman,Dong-Qing Wei,Taane G Clark,Taj Ali Khan","10.1038/s41598-021-94687-3","2045-2322","Scientific Reports","Author Correction: Characterization of rifampicin-resistant Mycobacterium tuberculosis in Khyber Pakhtunkhwa, Pakistan","2021"
"Paula J Gómez-González,Joao Perdigao,Pedro Gomes,Zully M Puyen,David Santos-Lazaro,Gary Napier,Martin L Hibberd,Miguel Viveiros,Isabel Portugal,Susana Campino,Jody E Phelan,Taane G Clark","10.1038/s41598-021-98862-4","2045-2322","Scientific Reports","Genetic diversity of candidate loci linked to Mycobacterium tuberculosis resistance to bedaquiline, delamanid and pretomanid","2021"
"Laura C Gomes,Susana Campino,Cláudio R F Marinho,Taane G Clark,Jody E Phelan","10.1099/mgen.0.000724","2057-5858","Microbial Genomics","Whole genome sequencing reveals large deletions and other loss of function mutations in Mycobacterium tuberculosis drug resistance genes","2021"
"Dennis Mujuni,Dianah Linda Kasemire,Ivan Ibanda,Joel Kabugo,Andrew Nsawotebba,Jody E Phelan,Robert Kaos Majwala,Didas Tugumisirize,Abdunoor Nyombi,Beatrice Orena,Irene Turyahabwe,Henry Byabajungu,Diana Nadunga,Kenneth Musisi,Moses Lutakoome Joloba,Willy Ssengooba","10.1186/s12879-022-07339-w","1471-2334","BMC Infectious Diseases","Molecular characterisation of second-line drug resistance among drug resistant tuberculosis patients tested in Uganda: a two and a half-year’s review","2022"
"Gary Napier,Anwar Sheed Khan,Abdul Jabbar,Muhammad Tahir Khan,Sajid Ali,Muhammad Qasim,Noor Mohammad,Rumina Hasan,Zahra Hasan,Susana Campino,Sajjad Ahmad,Baharullah Khattak,Simon J Waddell,Taj Ali Khan,Jody E Phelan,Taane G Clark","10.1038/s41598-022-11795-4","2045-2322","Scientific Reports","Characterisation of drug-resistant Mycobacterium tuberculosis mutations and transmission in Pakistan","2022"
"Jaime C Montoya,John Carlo M Malabad,Concepcion F Ang,Lorenzo T Reyes,Ramon P Basilio,Dodge R Lim,Maria Lourdes E Amarillo,Ma Cecilia G Ama,Jody E Phelan,Martin L Hibberd,Taane G Clark","10.1016/j.tube.2022.102211","14729792","Tuberculosis","Molecular characterization of drug-resistant Mycobacterium tuberculosis among Filipino patients derived from the national tuberculosis prevalence survey Philippines 2016","2022"
"Maria Rosário Sambo,Maria Jesus Trovoada,Carla Benchimol,Vatúsia Quinhentos,Lígia Gonçalves,Rute Velosa,Maria Isabel Marques,Nuno Sepúlveda,Taane G Clark,Stefan Mustafa,Oswald Wagner,António Coutinho,Carlos Penha-Gonçalves","10.1371/journal.pone.0011141","1932-6203","PLoS ONE","Transforming Growth Factor Beta 2 and Heme Oxygenase 1 Genes Are Risk Factors for the Cerebral Malaria Syndrome in Angolan Children","2010"
"Robert P Carroll,David San Segundo,Kevin Hollowood,Teresa Marafioti,Taane G Clark,Paul N Harden,Kathryn J Wood","10.1681/ASN.2009060669","1046-6673","Journal of the American Society of Nephrology","Immune Phenotype Predicts Risk for Posttransplantation Squamous Cell Carcinoma","2010"
"Taane G Clark,Susana G Campino,Elisa Anastasi,Sarah Auburn,Yik Y Teo,Kerrin Small,Kirk A Rockett,Dominic P Kwiatkowski,Christopher C Holmes","10.1093/bioinformatics/btq327","1367-4811","Bioinformatics","A Bayesian approach using covariance of single nucleotide polymorphism data to detect differences in linkage disequilibrium patterns between groups of individuals","2010"
"Sarah Auburn,Andrew E Fry,Taane G Clark,Susana Campino,Mahamadou Diakite,Angela Green,Anna Richardson,Muminatou Jallow,Fatou Sisay-Joof,Margaret Pinder,Malcolm E Molyneux,Terrie E Taylor,Kasturi Haldar,Kirk A Rockett,Dominic P Kwiatkowski","10.1371/journal.pone.0010017","1932-6203","PLoS ONE","Further Evidence Supporting a Role for Gs Signal Transduction in Severe Malaria Pathogenesis","2010"
"Inês Sousa,Taane G Clark,Richard Holt,Alistair T Pagnamenta,Erik J Mulder,Ruud B Minderaa,Anthony J Bailey,Agatino Battaglia,Sabine M Klauck,Fritz Poustka,Anthony P Monaco","10.1186/2040-2392-1-7","2040-2392","Molecular Autism","Polymorphisms in leucine-rich repeat genes are associated with autism spectrum disorder susceptibility in populations of European ancestry","2010"
"Caroline Daelemans,Matthew E Ritchie,Guillaume Smits,Sayeda Abu-Amero,Ian M Sudbery,Matthew S Forrest,Susana Campino,Taane G Clark,Philip Stanier,Dominic Kwiatkowski,Panos Deloukas,Emmanouil T Dermitzakis,Simon Tavaré,Gudrun E Moore,Ian Dunham","10.1186/1471-2156-11-25","1471-2156","BMC Genetics","High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta","2010"
"Susana Campino,Sarah Auburn,Katja Kivinen,Issaka Zongo,Jean-Bosco Ouedraogo,Valentina Mangano,Abdoulaye Djimde,Ogobara K Doumbo,Steven M Kiara,Alexis Nzila,Steffen Borrmann,Kevin Marsh,Pascal Michon,Ivo Mueller,Peter Siba,Hongying Jiang,Xin-Zhuan Su,Chanaki Amaratunga,Duong Socheat,Rick M Fairhurst,Mallika Imwong,Timothy Anderson,François Nosten,Nicholas J White,Rhian Gwilliam,Panos Deloukas,Bronwyn MacInnis,Christopher I Newbold,Kirk Rockett,Taane G Clark,Dominic P Kwiatkowski","10.1371/journal.pone.0020251","1932-6203","PLoS ONE","Population Genetic Analysis of Plasmodium falciparum Parasites Using a Customized Illumina GoldenGate Genotyping Assay","2011"
"Sarah Auburn,Susana Campino,Taane G Clark,Abdoulaye A Djimde,Issaka Zongo,Robert Pinches,Magnus Manske,Valentina Mangano,Daniel Alcock,Elisa Anastasi,Gareth Maslen,Bronwyn MacInnis,Kirk Rockett,David Modiano,Christopher I Newbold,Ogobara K Doumbo,Jean Bosco Ouédraogo,Dominic P Kwiatkowski","10.1371/journal.pone.0022213","1932-6203","PLoS ONE","An Effective Method to Purify Plasmodium falciparum DNA Directly from Clinical Blood Samples for Whole Genome High-Throughput Sequencing","2011"
"Timothy Robinson,Susana G Campino,Sarah Auburn,Samuel A Assefa,Spencer D Polley,Magnus Manske,Bronwyn MacInnis,Kirk A Rockett,Gareth L Maslen,Mandy Sanders,Michael A Quail,Peter L Chiodini,Dominic P Kwiatkowski,Taane G Clark,Colin J Sutherland","10.1371/journal.pone.0023204","1932-6203","PLoS ONE","Drug-Resistant Genotypes and Multi-Clonality in Plasmodium falciparum Analysed by Direct Genome Sequencing from Peripheral Blood of Malaria Patients","2011"
"Tim Downing,Hideo Imamura,Saskia Decuypere,Taane G Clark,Graham H Coombs,James A Cotton,James D Hilley,Simonne de Doncker,Ilse Maes,Jeremy C Mottram,Mike A Quail,Suman Rijal,Mandy Sanders,Gabriele Schönian,Olivia Stark,Shyam Sundar,Manu Vanaerschot,Christiane Hertz-Fowler,Jean-Claude Dujardin,Matthew Berriman","10.1101/gr.123430.111","1088-9051","Genome Research","Whole genome sequencing of multiple <i>Leishmania donovani</i> clinical isolates provides insights into population structure and mechanisms of drug resistance","2011"
"Alphaxard Manjurano,Lucy Okell,Tedson Lukindo,Hugh Reyburn,Raimos Olomi,Cally Roper,Taane G Clark,Sarah Joseph,Eleanor M Riley,Chris Drakeley","10.1186/1475-2875-10-370","1475-2875","Malaria Journal","Association of sub-microscopic malaria parasite carriage with transmission intensity in north-eastern Tanzania","2011"
"Alphaxard Manjurano,Taane G Clark,Behzad Nadjm,George Mtove,Hannah Wangai,Nuno Sepulveda,Susana G Campino,Caroline Maxwell,Raimos Olomi,Kirk R Rockett,Anna Jeffreys,Eleanor M Riley,Hugh Reyburn,Christopher Drakeley","10.1371/journal.pone.0047463","1932-6203","PLoS ONE","Candidate Human Genetic Polymorphisms and Severe Malaria in a Tanzanian Population","2012"
"Francesc Coll,Kim Mallard,Mark D Preston,Stephen Bentley,Julian Parkhill,Ruth McNerney,Nigel Martin,Taane G Clark","10.1093/bioinformatics/bts544","1367-4811","Bioinformatics","SpolPred: rapid and accurate prediction of <i>Mycobacterium tuberculosis</i> spoligotypes from short genomic sequences","2012"
"Mark D Preston,Magnus Manske,Neil Horner,Samuel Assefa,Susana Campino,Sarah Auburn,Issaka Zongo,Jean-Bosco Ouedraogo,Francois Nosten,Tim Anderson,Taane G Clark","10.1093/bioinformatics/bts557","1367-4811","Bioinformatics","VarB: a variation browsing and analysis tool for variants derived from next-generation sequencing data","2012"
"Ousmane Toure,Salimata Konate,Sibiri Sissoko,Amadou Niangaly,Abdoulaye Barry,Abdourahmane H Sall,Elisabeth Diarra,Belco Poudiougou,Nuno Sepulveda,Susana Campino,Kirk A Rockett,Taane G Clark,Mahamadou A Thera,Ogobara Doumbo","10.1371/journal.pone.0043987","1932-6203","PLoS ONE","Candidate Polymorphisms and Severe Malaria in a Malian Population","2012"
"S J Dunstan,K A Rockett,N T N Quyen,Y Y Teo,C Q Thai,N T Hang,A Jeffreys,T G Clark,K S Small,C P Simmons,N Day,S E O'Riordan,D P Kwiatkowski,J Farrar,N H Phu,T T Hien","10.1038/gene.2012.25","1466-4879","Genes & Immunity","Variation in human genes encoding adhesion and proinflammatory molecules are associated with severe malaria in the Vietnamese","2012"
"Simone da Silva Santos,Taane G Clark,Susana Campino,Martha Cecília Suarez-Mutis,Kirk A Rockett,Dominic P Kwiatkowski,Octavio Fernandes","10.1371/journal.pone.0036692","1932-6203","PLoS ONE","Investigation of Host Candidate Malaria-Associated Risk/Protective SNPs in a Brazilian Amazonian Population","2012"
"Sarah Auburn,Susana Campino,Olivo Miotto,Abdoulaye A Djimde,Issaka Zongo,Magnus Manske,Gareth Maslen,Valentina Mangano,Daniel Alcock,Bronwyn MacInnis,Kirk A Rockett,Taane G Clark,Ogobara K Doumbo,Jean Bosco Ouédraogo,Dominic P Kwiatkowski","10.1371/journal.pone.0032891","1932-6203","PLoS ONE","Characterization of Within-Host Plasmodium falciparum Diversity Using Next-Generation Sequence Data","2012"
"Jacqueline M Cliff,Ji-Sook Lee,Nicholas Constantinou,Jang-Eun Cho,Taane G Clark,Katharina Ronacher,Elizabeth C King,Pauline T Lukey,Ken Duncan,Paul D Van Helden,Gerhard Walzl,Hazel M Dockrell","10.1093/infdis/jis499","1537-6613","The Journal of Infectious Diseases","Distinct Phases of Blood Gene Expression Pattern Through Tuberculosis Treatment Reflect Modulation of the Humoral Immune Response","2013"
"Anita Ghansah,Kirk A Rockett,Taane G Clark,Michael D Wilson,Kwadwo A Koram,Abraham R Oduro,Lucas Amenga-Etego,Thomas Anyorigiya,Abraham Hodgson,Paul Milligan,William O Rogers,Dominic P Kwiatkowski","10.1371/journal.pone.0034565","1932-6203","PLoS ONE","Haplotype Analyses of Haemoglobin C and Haemoglobin S and the Dynamics of the Evolutionary Response to Malaria in Kassena-Nankana District of Ghana","2012"
"Trevor D Lawley,Simon Clare,Alan W Walker,Mark D Stares,Thomas R Connor,Claire Raisen,David Goulding,Roland Rad,Fernanda Schreiber,Cordelia Brandt,Laura J Deakin,Derek J Pickard,Sylvia H Duncan,Harry J Flint,Taane G Clark,Julian Parkhill,Gordon Dougan","10.1371/journal.ppat.1002995","1553-7374","PLoS Pathogens","Targeted Restoration of the Intestinal Microbiota with a Simple, Defined Bacteriotherapy Resolves Relapsing Clostridium difficile Disease in Mice","2012"
"Magnus Manske,Olivo Miotto,Susana Campino,Sarah Auburn,Jacob Almagro-Garcia,Gareth Maslen,Jack O’Brien,Abdoulaye Djimde,Ogobara Doumbo,Issaka Zongo,Jean-Bosco Ouedraogo,Pascal Michon,Ivo Mueller,Peter Siba,Alexis Nzila,Steffen Borrmann,Steven M Kiara,Kevin Marsh,Hongying Jiang,Xin-Zhuan Su,Chanaki Amaratunga,Rick Fairhurst,Duong Socheat,Francois Nosten,Mallika Imwong,Nicholas J White,Mandy Sanders,Elisa Anastasi,Dan Alcock,Eleanor Drury,Samuel Oyola,Michael A Quail,Daniel J Turner,Valentin Ruano-Rubio,Dushyanth Jyothi,Lucas Amenga-Etego,Christina Hubbart,Anna Jeffreys,Kate Rowlands,Colin Sutherland,Cally Roper,Valentina Mangano,David Modiano,John C Tan,Michael T Ferdig,Alfred Amambua-Ngwa,David J Conway,Shannon Takala-Harrison,Christopher V Plowe,Julian C Rayner,Kirk A Rockett,Taane G Clark,Chris I Newbold,Matthew Berriman,Bronwyn MacInnis,Dominic P Kwiatkowski","10.1038/nature11174","0028-0836","Nature","Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing","2012"
"Mark D Preston,Samuel A Assefa,Harold Ocholla,Colin J Sutherland,Steffen Borrmann,Alexis Nzila,Pascal Michon,Tran Tinh Hien,Teun Bousema,Christopher J Drakeley,Issaka Zongo,Jean-Bosco Ouédraogo,Abdoulaye A Djimde,Ogobara K Doumbo,Francois Nosten,Rick M Fairhurst,David J Conway,Cally Roper,Taane G Clark","10.1093/infdis/jit812","1537-6613","The Journal of Infectious Diseases","PlasmoView: A Web-based Resource to Visualise Global Plasmodium falciparum Genomic Variation","2014"
"Tobias O Apinjoh,Judith K Anchang-Kimbi,Clarisse Njua-Yafi,Regina N Mugri,Andre N Ngwai,Kirk A Rockett,Eric Mbunwe,Richard N Besingi,Taane G Clark,Dominic P Kwiatkowski,Eric A Achidi","10.1371/journal.pone.0081071","1932-6203","PLoS ONE","Association of Cytokine and Toll-Like Receptor Gene Polymorphisms with Severe Malaria in Three Regions of Cameroon","2013","24312262"
"Davis C Nwakanma,Craig W Duffy,Alfred Amambua-Ngwa,Eniyou C Oriero,Kalifa A Bojang,Margaret Pinder,Chris J Drakeley,Colin J Sutherland,Paul J Milligan,Bronwyn MacInnis,Dominic P Kwiatkowski,Taane G Clark,Brian M Greenwood,David J Conway","10.1093/infdis/jit618","1537-6613","The Journal of Infectious Diseases","Changes in Malaria Parasite Drug Resistance in an Endemic Population Over a 25-Year Period With Resulting Genomic Evidence of Selection","2014"
"B Maiga,A Dolo,O Touré,V Dara,A Tapily,S Campino,N Sepulveda,P Corran,K Rockett,T G Clark,M Troye Blomberg,O K Doumbo","10.1111/sji.12122","0300-9475","Scandinavian Journal of Immunology","Fc gamma Receptor <scp>II</scp> a‐ <scp>H</scp> 131 <scp>R</scp> Polymorphism and Malaria Susceptibility in Sympatric Ethnic Groups, Fulani and Dogon of <scp>M</scp> ali","2014"
"Steffen Borrmann,Judith Straimer,Leah Mwai,Abdirahman Abdi,Anja Rippert,John Okombo,Steven Muriithi,Philip Sasi,Moses Mosobo Kortok,Brett Lowe,Susana Campino,Samuel Assefa,Sarah Auburn,Magnus Manske,Gareth Maslen,Norbert Peshu,Dominic P Kwiatkowski,Kevin Marsh,Alexis Nzila,Taane G Clark","10.1038/srep03318","2045-2322","Scientific Reports","Genome-wide screen identifies new candidate genes associated with artemisinin susceptibility in Plasmodium falciparum in Kenya","2013"
"Bakary Maiga,Amagana Dolo,Ousmane Touré,Victor Dara,Amadou Tapily,Susana Campino,Nuno Sepulveda,Paul Risley,Nilupa Silva,Patrick Corran,Kirk A Rockett,Dominic Kwiatkowski,MalariaGEN Consortium,Taane G Clark,Marita Troye-Blomberg,Ogobara K Doumbo","10.1371/journal.pone.0075675","1932-6203","PloS one","Human candidate polymorphisms in sympatric ethnic groups differing in malaria susceptibility in Mali.","2013","24098393"
"Taane G Clark,Kim Mallard,Francesc Coll,Mark Preston,Samuel Assefa,David Harris,Sam Ogwang,Francis Mumbowa,Bruce Kirenga,Denise M O’Sullivan,Alphonse Okwera,Kathleen D Eisenach,Moses Joloba,Stephen D Bentley,Jerrold J Ellner,Julian Parkhill,Edward C Jones-López,Ruth McNerney","10.1371/journal.pone.0083012","1932-6203","PLoS ONE","Elucidating Emergence and Transmission of Multidrug-Resistant Tuberculosis in Treatment Experienced Patients by Whole Genome Sequencing","2013"
"Xuanyao Liu,Rick Twee-Hee Ong,Esakimuthu Nisha Pillai,Abier M Elzein,Kerrin S Small,Taane G Clark,Dominic P Kwiatkowski,Yik-Ying Teo","10.1016/j.ajhg.2013.04.021","1537-6605","American journal of human genetics","Detecting and characterizing genomic signatures of positive selection in global populations.","2013","23731540"
"Symon M Kariuki,Kirk Rockett,Taane G Clark,Hugh Reyburn,Tsiri Agbenyega,Terrie E Taylor,Gretchen L Birbeck,Thomas N Williams,Charles R J C Newton","10.1111/epi.12173","0013-9580","Epilepsia","The genetic risk of acute seizures in <scp>A</scp> frican children with falciparum malaria","2013"
"Gavin Band,Quang Si Le,Luke Jostins,Matti Pirinen,Katja Kivinen,Muminatou Jallow,Fatoumatta Sisay-Joof,Kalifa Bojang,Margaret Pinder,Giorgio Sirugo,David J Conway,Vysaul Nyirongo,David Kachala,Malcolm Molyneux,Terrie Taylor,Carolyne Ndila,Norbert Peshu,Kevin Marsh,Thomas N Williams,Daniel Alcock,Robert Andrews,Sarah Edkins,Emma Gray,Christina Hubbart,Anna Jeffreys,Kate Rowlands,Kathrin Schuldt,Taane G Clark,Kerrin S Small,Yik Ying Teo,Dominic P Kwiatkowski,Kirk A Rockett,Jeffrey C Barrett,Chris C A Spencer","10.1371/annotation/adc2beaf-4bee-4e22-925b-6788d62fe029","1553-7404","PLoS Genetics","Correction: Imputation-Based Meta-Analysis of Severe Malaria in Three African Populations","2013"
"Nuno Sepúlveda,Susana G Campino,Samuel A Assefa,Colin J Sutherland,Arnab Pain,Taane G Clark","10.1186/1471-2164-14-128","1471-2164","BMC Genomics","A Poisson hierarchical modelling approach to detecting copy number variation in sequence coverage data","2013"
"Shannon Takala-Harrison,Taane G Clark,Christopher G Jacob,Michael P Cummings,Olivo Miotto,Arjen M Dondorp,Mark M Fukuda,Francois Nosten,Harald Noedl,Mallika Imwong,Delia Bethell,Youry Se,Chanthap Lon,Stuart D Tyner,David L Saunders,Duong Socheat,Frederic Ariey,Aung Pyae Phyo,Peter Starzengruber,Hans-Peter Fuehrer,Paul Swoboda,Kasia Stepniewska,Jennifer Flegg,Cesar Arze,Gustavo C Cerqueira,Joana C Silva,Stacy M Ricklefs,Stephen F Porcella,Robert M Stephens,Matthew Adams,Leo J Kenefic,Susana Campino,Sarah Auburn,Bronwyn MacInnis,Dominic P Kwiatkowski,Xin-zhuan Su,Nicholas J White,Pascal Ringwald,Christopher V Plowe","10.1073/pnas.1211205110","0027-8424","Proceedings of the National Academy of Sciences","Genetic loci associated with delayed clearance of <i>Plasmodium falciparum</i> following artemisinin treatment in Southeast Asia","2013"
"Sarah Auburn,Jutta Marfurt,Gareth Maslen,Susana Campino,Valentin Ruano Rubio,Magnus Manske,Barbara MacHunter,Enny Kenangalem,Rintis Noviyanti,Leily Trianty,Boni Sebayang,Grennady Wirjanata,Kanlaya Sriprawat,Daniel Alcock,Bronwyn MacInnis,Olivo Miotto,Taane G Clark,Bruce Russell,Nicholas M Anstey,François Nosten,Dominic P Kwiatkowski,Ric N Price","10.1371/journal.pone.0053160","1932-6203","PLoS ONE","Effective Preparation of Plasmodium vivax Field Isolates for High-Throughput Whole Genome Sequencing","2013"
"José Afonso Guerra-Assunção,Rein M G J Houben,Amelia C Crampin,Themba Mzembe,Kim Mallard,Francesc Coll,Palwasha Khan,Louis Banda,Arthur Chiwaya,Rui P A Pereira,Ruth McNerney,David Harris,Julian Parkhill,Taane G Clark,Judith R Glynn","10.1093/infdis/jiu574","0022-1899","Journal of Infectious Diseases","Recurrence due to Relapse or Reinfection With <i>Mycobacterium tuberculosis</i> : A Whole-Genome Sequencing Approach in a Large, Population-Based Cohort With a High HIV Infection Prevalence and Active Follow-up","2015"
"João Perdigão,Hugo Silva,Diana Machado,Rita Macedo,Fernando Maltez,Carla Silva,Luisa Jordao,Isabel Couto,Kim Mallard,Francesc Coll,Grant A Hill-Cawthorne,Ruth McNerney,Arnab Pain,Taane G Clark,Miguel Viveiros,Isabel Portugal","10.1186/1471-2164-15-991","1471-2164","BMC genomics","Unraveling Mycobacterium tuberculosis genomic diversity and evolution in Lisbon, Portugal, a highly drug resistant setting.","2014","25407810"
"Shannon Takala-Harrison,Christopher G Jacob,Cesar Arze,Michael P Cummings,Joana C Silva,Arjen M Dondorp,Mark M Fukuda,Tran Tinh Hien,Mayfong Mayxay,Harald Noedl,Francois Nosten,Myat P Kyaw,Nguyen Thanh Thuy Nhien,Mallika Imwong,Delia Bethell,Youry Se,Chanthap Lon,Stuart D Tyner,David L Saunders,Frederic Ariey,Odile Mercereau-Puijalon,Didier Menard,Paul N Newton,Maniphone Khanthavong,Bouasy Hongvanthong,Peter Starzengruber,Hans-Peter Fuehrer,Paul Swoboda,Wasif A Khan,Aung Pyae Phyo,Myaing M Nyunt,Myat H Nyunt,Tyler S Brown,Matthew Adams,Christopher S Pepin,Jason Bailey,John C Tan,Michael T Ferdig,Taane G Clark,Olivo Miotto,Bronwyn MacInnis,Dominic P Kwiatkowski,Nicholas J White,Pascal Ringwald,Christopher V Plowe","10.1093/infdis/jiu491","1537-6613","The Journal of infectious diseases","Independent emergence of artemisinin resistance mutations among Plasmodium falciparum in Southeast Asia.","2015","25180241"
"Francesc Coll,Ruth McNerney,José Afonso Guerra-Assunção,Judith R Glynn,João Perdigão,Miguel Viveiros,Isabel Portugal,Arnab Pain,Nigel Martin,Taane G Clark","10.1038/ncomms5812","2041-1723","Nature Communications","A robust SNP barcode for typing Mycobacterium tuberculosis complex strains","2014"
"Yaobao Liu,Sarah Auburn,Jun Cao,Hidayat Trimarsanto,Huayun Zhou,Karen-Ann Gray,Taane G Clark,Ric N Price,Qin Cheng,Rui Huang,Qi Gao","10.1186/1475-2875-13-262","1475-2875","Malaria Journal","Genetic diversity and population structure of Plasmodium vivax in Central China","2014"
"Tobias O Apinjoh,Judith K Anchang-Kimbi,Clarisse Njua-Yafi,André N Ngwai,Regina N Mugri,Taane G Clark,Kirk A Rockett,Dominic P Kwiatkowski,Eric A Achidi","10.1186/1475-2875-13-236","1475-2875","Malaria Journal","Association of candidate gene polymorphisms and TGF-beta/IL-10 levels with malaria in three regions of Cameroon: a case–control study","2014"
"Grant A Hill-Cawthorne,Lyndsey O Hudson,Moataz Fouad Abd El Ghany,Olaf Piepenburg,Mridul Nair,Andrew Dodgson,Matthew S Forrest,Taane G Clark,Arnab Pain","10.1371/journal.pone.0101419","1932-6203","PLoS ONE","Recombinations in Staphylococcal Cassette Chromosome mec Elements Compromise the Molecular Detection of Methicillin Resistance in Staphylococcus aureus","2014"
"Gisela Henriques,Rachel L Hallett,Khalid B Beshir,Nahla B Gadalla,Rachel E Johnson,Rebekah Burrow,Donelly A van Schalkwyk,Patrick Sawa,Sabah A Omar,Taane G Clark,Teun Bousema,Colin J Sutherland","10.1093/infdis/jiu358","1537-6613","The Journal of infectious diseases","Directional selection at the pfmdr1, pfcrt, pfubp1, and pfap2mu loci of Plasmodium falciparum in Kenyan children treated with ACT.","2014","24994911"
"Bakary Maiga,Amagana Dolo,Susana Campino,Nuno Sepulveda,Patrick Corran,Kirk A Rockett,Marita Troye-Blomberg,Ogobara K Doumbo,Taane G Clark","10.1186/1475-2875-13-270","1475-2875","Malaria Journal","Glucose-6-phosphate dehydrogenase polymorphisms and susceptibility to mild malaria in Dogon and Fulani, Mali","2014"
"Mark D Preston,Susana Campino,Samuel A Assefa,Diego F Echeverry,Harold Ocholla,Alfred Amambua-Ngwa,Lindsay B Stewart,David J Conway,Steffen Borrmann,Pascal Michon,Issaka Zongo,Jean-Bosco Ouédraogo,Abdoulaye A Djimde,Ogobara K Doumbo,Francois Nosten,Arnab Pain,Teun Bousema,Chris J Drakeley,Rick M Fairhurst,Colin J Sutherland,Cally Roper,Taane G Clark","10.1038/ncomms5052","2041-1723","Nature Communications","A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains","2014"
"Harold Ocholla,Mark D Preston,Mwapatsa Mipando,Anja T R Jensen,Susana Campino,Bronwyn MacInnis,Daniel Alcock,Anja Terlouw,Issaka Zongo,Jean-Bosco Oudraogo,Abdoulaye A Djimde,Samuel Assefa,Ogobara K Doumbo,Steffen Borrmann,Alexis Nzila,Kevin Marsh,Rick M Fairhurst,Francois Nosten,Tim J C Anderson,Dominic P Kwiatkowski,Alister Craig,Taane G Clark,Jacqui Montgomery","10.1093/infdis/jiu349","1537-6613","The Journal of infectious diseases","Whole-genome scans provide evidence of adaptive evolution in Malawian Plasmodium falciparum isolates.","2014","24948693"
"Sam Alsford,Rachel B Currier,José Afonso Guerra-Assunção,Taane G Clark,David Horn","10.1371/journal.ppat.1004130","1553-7374","PLoS Pathogens","Cathepsin-L Can Resist Lysis by Human Serum in Trypanosoma brucei brucei","2014"
"Raeece Naeem,Lailatul Hidayah,Mark D Preston,Taane G Clark,Arnab Pain","10.1093/bioinformatics/btu176","1367-4811","Bioinformatics","SVAMP: sequence variation analysis, maps and phylogeny","2014"
"Björn F C Kafsack,Núria Rovira-Graells,Taane G Clark,Cristina Bancells,Valerie M Crowley,Susana G Campino,April E Williams,Laura G Drought,Dominic P Kwiatkowski,David A Baker,Alfred Cortés,Manuel Llinás","10.1038/nature12920","0028-0836","Nature","A transcriptional switch underlies commitment to sexual development in malaria parasites","2014"
"Francesc Coll,Mark Preston,José Afonso Guerra-Assunção,Grant Hill-Cawthorn,David Harris,João Perdigão,Miguel Viveiros,Isabel Portugal,Francis Drobniewski,Sebastien Gagneux,Judith R Glynn,Arnab Pain,Julian Parkhill,Ruth McNerney,Nigel Martin,Taane G Clark","10.1016/j.tube.2014.02.005","14729792","Tuberculosis","PolyTB: A genomic variation map for Mycobacterium tuberculosis","2014"
"Madeleine G Moule,Claudia M Hemsley,Qihui Seet,José Afonso Guerra-Assunção,Jiali Lim,Mitali Sarkar-Tyson,Taane G Clark,Patrick B O Tan,Richard W Titball,Jon Cuccui,Brendan W Wren","10.1128/mBio.00926-13","2161-2129","mBio","Genome-Wide Saturation Mutagenesis of Burkholderia pseudomallei K96243 Predicts Essential Genes and Novel Targets for Antimicrobial Development","2014"
"Victor A Mobegi,Craig W Duffy,Alfred Amambua-Ngwa,Kovana M Loua,Eugene Laman,Davis C Nwakanma,Bronwyn MacInnis,Harvey Aspeling-Jones,Lee Murray,Taane G Clark,Dominic P Kwiatkowski,David J Conway","10.1093/molbev/msu106","1537-1719","Molecular biology and evolution","Genome-wide analysis of selection on the malaria parasite Plasmodium falciparum in West African populations of differing infection endemicity.","2014","24644299"
"Samuel A Assefa,Mark D Preston,Susana Campino,Harold Ocholla,Colin J Sutherland,Taane G Clark","10.1093/bioinformatics/btu005","1367-4811","Bioinformatics","estMOI: estimating multiplicity of infection using parasite deep sequencing data","2014"
"Sisay Getachew,Sheren To,Hidayat Trimarsanto,Kamala Thriemer,Taane G Clark,Beyene Petros,Abraham Aseffa,Ric N Price,Sarah Auburn","10.1371/journal.pone.0140780","1932-6203","PLOS ONE","Variation in Complexity of Infection and Transmission Stability between Neighbouring Populations of Plasmodium vivax in Southern Ethiopia","2015"
"Madeleine G Moule,Natasha Spink,Sam Willcocks,Jiali Lim,José Afonso Guerra-Assunção,Felipe Cia,Olivia L Champion,Nicola J Senior,Helen S Atkins,Taane Clark,Gregory J Bancroft,Jon Cuccui,Brendan W Wren","10.1128/IAI.01102-15","1098-5522","Infection and immunity","Characterization of New Virulence Factors Involved in the Intracellular Growth and Survival of Burkholderia pseudomallei.","2015","26712202"
"Francisco Rogerlândio Martins-Melo,Juliana Maria Trindade Bezerra,David Soeiro Barbosa,Mariângela Carneiro,Kleydson Bonfim Andrade,Antonio Luiz Pinho Ribeiro,Mohsen Naghavi,Guilherme Loureiro Werneck","10.1186/s12963-020-00203-6","1478-7954","Population Health Metrics","The burden of tuberculosis and attributable risk factors in Brazil, 1990–2017: results from the Global Burden of Disease Study 2017","2020"
"Chrissy h Roberts,Christopher S Franklin,Pateh Makalo,Hassan Joof,Isatou Sarr,Olaimatu S Mahdi,Ansumana Sillah,Momodou Bah,Felicity Payne,Anna E Jeffreys,William Bottomley,Angels Natividad,Sandra Molina-Gonzalez,Sarah E Burr,Mark Preston,Dominic Kwiatkowski,Kirk A Rockett,Taane G Clark,Matthew J Burton,David C W Mabey,Robin Bailey,Inês Barroso,Martin J Holland","10.1038/srep17447","2045-2322","Scientific Reports","Conjunctival fibrosis and the innate barriers to Chlamydia trachomatis intracellular infection: a genome wide association study","2015"
"Samuel Assefa,Caeul Lim,Mark D Preston,Craig W Duffy,Mridul B Nair,Sabir A Adroub,Khamisah A Kadir,Jonathan M Goldberg,Daniel E Neafsey,Paul Divis,Taane G Clark,Manoj T Duraisingh,David J Conway,Arnab Pain,Balbir Singh","10.1073/pnas.1509534112","1091-6490","Proceedings of the National Academy of Sciences of the United States of America","Population genomic structure and adaptation in the zoonotic malaria parasite Plasmodium knowlesi.","2015","26438871"
"Jennifer M G Shelton,Patrick Corran,Paul Risley,Nilupa Silva,Christina Hubbart,Anna Jeffreys,Kate Rowlands,Rachel Craik,Victoria Cornelius,Meike Hensmann,Sile Molloy,Nuno Sepulveda,Taane G Clark,Gavin Band,Geraldine M Clarke,Christopher C A Spencer,Angeliki Kerasidou,Susana Campino,Sarah Auburn,Adama Tall,Alioune Badara Ly,Odile Mercereau-Puijalon,Anavaj Sakuntabhai,Abdoulaye Djimdé,Boubacar Maiga,Ousmane Touré,Ogobara K Doumbo,Amagana Dolo,Marita Troye-Blomberg,Valentina D Mangano,Frederica Verra,David Modiano,Edith Bougouma,Sodiomon B Sirima,Muntaser Ibrahim,Ayman Hussain,Nahid Eid,Abier Elzein,Hiba Mohammed,Ahmed Elhassan,Ibrahim Elhassan,Thomas N Williams,Carolyne Ndila,Alexander Macharia,Kevin Marsh,Alphaxard Manjurano,Hugh Reyburn,Martha Lemnge,Deus Ishengoma,Richard Carter,Nadira Karunaweera,Deepika Fernando,Rajika Dewasurendra,Christopher J Drakeley,Eleanor M Riley,Dominic P Kwiatkowski,Kirk A Rockett","10.1186/s12936-015-0833-x","1475-2875","Malaria Journal","Genetic determinants of anti-malarial acquired immunity in a large multi-centre study","2015"
"M D Cairns,M D Preston,T D Lawley,T G Clark,R A Stabler,B W Wren","10.1128/JCM.00648-15","1098-660X","Journal of clinical microbiology","Genomic Epidemiology of a Protracted Hospital Outbreak Caused by a Toxin A-Negative Clostridium difficile Sublineage PCR Ribotype 017 Strain in London, England.","2015","26179308"
"Abdallah M Abdallah,Grant A Hill-Cawthorne,Thomas D Otto,Francesc Coll,José Afonso Guerra-Assunção,Ge Gao,Raeece Naeem,Hifzur Ansari,Tareq B Malas,Sabir A Adroub,Theo Verboom,Roy Ummels,Huoming Zhang,Aswini Kumar Panigrahi,Ruth McNerney,Roland Brosch,Taane G Clark,Marcel A Behr,Wilbert Bitter,Arnab Pain","10.1038/srep15443","2045-2322","Scientific reports","Genomic expression catalogue of a global collection of BCG vaccine strains show evidence for highly diverged metabolic and cell-wall adaptations.","2015","26487098"
"Akbar Kanji,Zahra Hasan,Asho Ali,Ruth McNerney,Kim Mallard,Francesc Coll,Grant Hill-Cawthorne,Mridul Nair,Taane G Clark,Ambreen Zaver,Sana Jafri,Rumina Hasan","10.1016/j.ijmyco.2014.11.049","2212-554X","International journal of mycobacteriology","Characterization of genomic variations in SNPs of PE_PGRS genes reveals deletions and insertions in extensively drug resistant (XDR) M. tuberculosis strains from Pakistan.","2015","26655202"
"Rintis Noviyanti,Farah Coutrier,Retno A S Utami,Hidayat Trimarsanto,Yusrifar K Tirta,Leily Trianty,Andreas Kusuma,Inge Sutanto,Ayleen Kosasih,Rita Kusriastuti,William A Hawley,Ferdinand Laihad,Neil Lobo,Jutta Marfurt,Taane G Clark,Ric N Price,Sarah Auburn","10.1371/journal.pntd.0003739","1935-2735","PLOS Neglected Tropical Diseases","Contrasting Transmission Dynamics of Co-endemic Plasmodium vivax and P. falciparum: Implications for Malaria Control and Elimination","2015"
"Francesc Coll,Ruth McNerney,Mark D Preston,José Afonso Guerra-Assunção,Andrew Warry,Grant Hill-Cawthorne,Kim Mallard,Mridul Nair,Anabela Miranda,Adriana Alves,João Perdigão,Miguel Viveiros,Isabel Portugal,Zahra Hasan,Rumina Hasan,Judith R Glynn,Nigel Martin,Arnab Pain,Taane G Clark","10.1186/s13073-015-0164-0","1756-994X","Genome Medicine","Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences","2015"
"Ernest D Benavente,Francesc Coll,Nick Furnham,Ruth McNerney,Judith R Glynn,Susana Campino,Arnab Pain,Fady R Mohareb,Taane G Clark","10.1186/s12859-015-0603-3","1471-2105","BMC Bioinformatics","PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis","2015"
"Jody Phelan,Arundhati Maitra,Ruth McNerney,Mridul Nair,Antima Gupta,Francesc Coll,Arnab Pain,Sanjib Bhakta,Taane G Clark","10.1016/j.ijmyco.2015.05.001","2212-554X","International journal of mycobacteriology","The draft genome of Mycobacterium aurum, a potential model organism for investigating drugs against Mycobacterium tuberculosis and Mycobacterium leprae.","2015","27649868"
"Hanif Samad,Francesc Coll,Mark D Preston,Harold Ocholla,Rick M Fairhurst,Taane G Clark","10.1371/journal.pgen.1005131","1553-7404","PLoS genetics","Imputation-based population genetics analysis of Plasmodium falciparum malaria parasites.","2015","25928499"
"Alphaxard Manjurano,Nuno Sepúlveda,Behzad Nadjm,George Mtove,Hannah Wangai,Caroline Maxwell,Raimos Olomi,Hugh Reyburn,Christopher J Drakeley,Eleanor M Riley,Taane G Clark","10.1093/infdis/jiv192","0022-1899","Journal of Infectious Diseases","<i>USP38, FREM3, SDC1, DDC,</i> and <i>LOC727982</i> Gene Polymorphisms and Differential Susceptibility to Severe Malaria in Tanzania","2015"
"Indra Bergval,Francesc Coll,Anja Schuitema,Hans de Ronde,Kim Mallard,Arnab Pain,Ruth McNerney,Taane G Clark,Richard M Anthony","10.1093/femsle/fnu037","1574-6968","FEMS microbiology letters","A proportion of mutations fixed in the genomes of in vitro selected isogenic drug-resistant Mycobacterium tuberculosis mutants can be detected as minority variants in the parent culture.","2015","25670707"
"Alphaxard Manjurano,Nuno Sepulveda,Behzad Nadjm,George Mtove,Hannah Wangai,Caroline Maxwell,Raimos Olomi,Hugh Reyburn,Eleanor M Riley,Christopher J Drakeley,Taane G Clark,MalariaGEN Consortium","10.1371/journal.pgen.1004960","1553-7404","PLoS genetics","African glucose-6-phosphate dehydrogenase alleles associated with protection from severe malaria in heterozygous females in Tanzania.","2015","25671784"
"Judith R Glynn,José Afonso Guerra-Assunção,Rein M G J Houben,Lifted Sichali,Themba Mzembe,Lorrain K Mwaungulu,J Nimrod Mwaungulu,Ruth McNerney,Palwasha Khan,Julian Parkhill,Amelia C Crampin,Taane G Clark","10.1371/journal.pone.0132840","1932-6203","PLOS ONE","Whole Genome Sequencing Shows a Low Proportion of Tuberculosis Disease Is Attributable to Known Close Contacts in Rural Malawi","2015"
"J A Guerra-Assunção,A C Crampin,R M G J Houben,T Mzembe,K Mallard,F Coll,P Khan,L Banda,A Chiwaya,R P A Pereira,R McNerney,P E M Fine,J Parkhill,T G Clark,J R Glynn","10.7554/eLife.05166","2050-084X","eLife","Large-scale whole genome sequencing of M. tuberculosis provides insights into transmission in a high prevalence area.","2015","25732036"
"Asho Ali,Zahra Hasan,Ruth McNerney,Kim Mallard,Grant Hill-Cawthorne,Francesc Coll,Mridul Nair,Arnab Pain,Taane G Clark,Rumina Hasan","10.1371/journal.pone.0117771","1932-6203","PloS one","Whole genome sequencing based characterization of extensively drug-resistant Mycobacterium tuberculosis isolates from Pakistan.","2015","25719196"
"Ruth McNerney,Taane G Clark,Susana Campino,Camilla Rodrigues,David Dolinger,Liezel Smith,Andrea M Cabibbe,Keertan Dheda,Marco Schito","10.1016/j.ijid.2016.11.422","12019712","International Journal of Infectious Diseases","Removing the bottleneck in whole genome sequencing of Mycobacterium tuberculosis for rapid drug resistance analysis: a call to action","2017"
"Matt Ravenhall,Ernest Diez Benavente,Mwapatsa Mipando,Anja T R Jensen,Colin J Sutherland,Cally Roper,Nuno Sepúlveda,Dominic P Kwiatkowski,Jacqui Montgomery,Kamija S Phiri,Anja Terlouw,Alister Craig,Susana Campino,Harold Ocholla,Taane G Clark","10.1186/s12936-016-1634-6","1475-2875","Malaria journal","Characterizing the impact of sustained sulfadoxine/pyrimethamine use upon the Plasmodium falciparum population in Malawi.","2016","27899115"
"Hifzur Rahman Ansari,Thomas J Templeton,Amit Kumar Subudhi,Abhinay Ramaprasad,Jianxia Tang,Feng Lu,Raeece Naeem,Yasmeen Hashish,Mary C Oguike,Ernest Diez Benavente,Taane G Clark,Colin J Sutherland,John W Barnwell,Richard Culleton,Jun Cao,Arnab Pain","10.1016/j.ijpara.2016.05.009","1879-0135","International journal for parasitology","Genome-scale comparison of expanded gene families in Plasmodium ovale wallikeri and Plasmodium ovale curtisi with Plasmodium malariae and with other Plasmodium species.","2016","27392654"
"Olabisi Oluwabukola Coker,Angkana Chaiprasert,Chumpol Ngamphiw,Sissades Tongsima,Sanjib Mani Regmi,Taane G Clark,Rick Twee Hee Ong,Yik-Ying Teo,Therdsak Prammananan,Prasit Palittapongarnpim","10.7717/peerj.1905","2167-8359","PeerJ","Genetic signatures of <i>Mycobacterium tuberculosis</i> Nonthaburi genotype revealed by whole genome analysis of isolates from tuberculous meningitis patients in Thailand","2016"
"Susana Campino,Ernest Diez Benavente,Samuel Assefa,Eloise Thompson,Laura G Drought,Catherine J Taylor,Zaria Gorvett,Celine K Carret,Christian Flueck,Al C Ivens,Dominic P Kwiatkowski,Pietro Alano,David A Baker,Taane G Clark","10.1186/s12936-016-1254-1","1475-2875","Malaria Journal","Genomic variation in two gametocyte non-producing Plasmodium falciparum clonal lines","2016"
"Jody Phelan,Francesc Coll,Ruth McNerney,David B Ascher,Douglas E V Pires,Nick Furnham,Nele Coeck,Grant A Hill-Cawthorne,Mridul B Nair,Kim Mallard,Andrew Ramsay,Susana Campino,Martin L Hibberd,Arnab Pain,Leen Rigouts,Taane G Clark","10.1186/s12916-016-0575-9","1741-7015","BMC Medicine","Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance","2016"
"Jung-Yeon Kim,Youn-Kyoung Goo,Young-Gun Zo,So-Young Ji,Hidayat Trimarsanto,Sheren To,Taane G Clark,Ric N Price,Sarah Auburn","10.1371/journal.pone.0151514","1932-6203","PLOS ONE","Further Evidence of Increasing Diversity of Plasmodium vivax in the Republic of Korea in Recent Years","2016"
"Patricia Sheen,David Requena,Eduardo Gushiken,Robert H Gilman,Ricardo Antiparra,Bryan Lucero,Pilar Lizárraga,Basilio Cieza,Elisa Roncal,Louis Grandjean,Arnab Pain,Ruth McNerney,Taane G Clark,David Moore,Mirko Zimic","10.1186/s12864-017-4146-z","1471-2164","BMC Genomics","A multiple genome analysis of Mycobacterium tuberculosis reveals specific novel genes and mutations associated with pyrazinamide resistance","2017"
"Yoshio Nakatani,Helen K Opel-Reading,Matthias Merker,Diana Machado,Sönke Andres,S Siva Kumar,Danesh Moradigaravand,Francesc Coll,João Perdigão,Isabel Portugal,Thomas Schön,Dina Nair,K R Uma Devi,Thomas A Kohl,Patrick Beckert,Taane G Clark,Gugu Maphalala,Derrick Khumalo,Roland Diel,Kadri Klaos,Htin Lin Aung,Gregory M Cook,Julian Parkhill,Sharon J Peacock,Soumya Swaminathan,Miguel Viveiros,Stefan Niemann,Kurt L Krause,Claudio U Köser","10.1128/AAC.01575-17","1098-6596","Antimicrobial agents and chemotherapy","Role of Alanine Racemase Mutations in Mycobacterium tuberculosis d-Cycloserine Resistance.","2017","28971867"
"Mônica C Campos,Jody Phelan,Amanda F Francisco,Martin C Taylor,Michael D Lewis,Arnab Pain,Taane G Clark,John M Kelly","10.1038/s41598-017-14986-6","2045-2322","Scientific reports","Genome-wide mutagenesis and multi-drug resistance in American trypanosomes induced by the front-line drug benznidazole.","2017","29089615"
"Olga Tosas Auguet,Richard A Stabler,Jason Betley,Mark D Preston,Mandeep Dhaliwal,Michael Gaunt,Avgousta Ioannou,Nergish Desai,Tacim Karadag,Rahul Batra,Jonathan A Otter,Helene Marbach,Taane G Clark,Jonathan D Edgeworth","10.1093/cid/cix901","1058-4838","Clinical Infectious Diseases","Frequent Undetected Ward-Based Methicillin-Resistant Staphylococcus aureus Transmission Linked to Patient Sharing Between Hospitals","2018"
"Ernest Diez Benavente,Paola Florez de Sessions,Robert W Moon,Anthony A Holder,Michael J Blackman,Cally Roper,Christopher J Drakeley,Arnab Pain,Colin J Sutherland,Martin L Hibberd,Susana Campino,Taane G Clark","10.1371/journal.pgen.1007008","1553-7404","PLOS Genetics","Analysis of nuclear and organellar genomes of Plasmodium knowlesi in humans reveals ancient population structure and recent recombination among host-specific subpopulations","2017"
"Akbar Kanji,Rumina Hasan,Asho Ali,Ambreen Zaver,Ying Zhang,Kehkashan Imtiaz,Wanliang Shi,Taane G Clark,Ruth McNerney,Jody Phelan,Shoaib Rao,Samreen Shafiq,Zahra Hasan","10.1016/j.tube.2017.07.012","14729792","Tuberculosis","Single nucleotide polymorphisms in efflux pumps genes in extensively drug resistant Mycobacterium tuberculosis isolates from Pakistan","2017"
"Sarah Sengstake,Indra L Bergval,Anja R Schuitema,Jessica L de Beer,Jody Phelan,Rina de Zwaan,Taane G Clark,Dick van Soolingen,Richard M Anthony","10.1186/s12879-017-2594-3","1471-2334","BMC Infectious Diseases","Pyrazinamide resistance-conferring mutations in pncA and the transmission of multidrug resistant TB in Georgia","2017"
"Jamille G Dombrowski,Rodrigo M Souza,Jonathan Curry,Laura Hinton,Natercia R M Silva,Lynn Grignard,Ligia A Gonçalves,Ana Rita Gomes,Sabrina Epiphanio,Chris Drakeley,Jim Huggett,Taane G Clark,Susana Campino,Claudio R F Marinho","10.1186/s12936-017-1889-6","1475-2875","Malaria Journal","G6PD deficiency alleles in a malaria-endemic region in the Western Brazilian Amazon","2017"
"Ernest Diez Benavente,Zoe Ward,Wilson Chan,Fady R Mohareb,Colin J Sutherland,Cally Roper,Susana Campino,Taane G Clark","10.1371/journal.pone.0177134","1932-6203","PloS one","Genomic variation in Plasmodium vivax malaria reveals regions under selective pressure.","2017","28493919"
"Ana Rita Gomes,Matt Ravenhall,Ernest Diez Benavente,Arthur Talman,Colin Sutherland,Cally Roper,Taane G Clark,Susana Campino","10.1016/j.ijpddr.2017.03.001","2211-3207","International journal for parasitology. Drugs and drug resistance","Genetic diversity of next generation antimalarial targets: A baseline for drug resistance surveillance programmes.","2017","28376349"
"Jona Walk,Isaie J Reuling,Marije C Behet,Lisette Meerstein-Kessel,Wouter Graumans,Geert-Jan van Gemert,Rianne Siebelink-Stoter,Marga van de Vegte-Bolmer,Thorsten Janssen,Karina Teelen,Johannes H W de Wilt,Quirijn de Mast,André J van der Ven,Ernest Diez Benavente,Susana Campino,Taane G Clark,Martijn A Huynen,Cornelus C Hermsen,Else M Bijker,Anja Scholzen,Robert W Sauerwein","10.1186/s12916-017-0923-4","1741-7015","BMC Medicine","Modest heterologous protection after Plasmodium falciparum sporozoite immunization: a double-blind randomized controlled clinical trial","2017"
"Hidayat Trimarsanto,Ernest D Benavente,Rintis Noviyanti,Retno Ayu Setya Utami,Leily Trianty,Zuleima Pava,Sisay Getachew,Jung-Yeon Kim,Youn-Kyoung Goo,Sonam Wangchuck,Yaobao Liu,Qi Gao,Simone Dowd,Qin Cheng,Taane G Clark,Ric N Price,Sarah Auburn","10.1371/journal.pntd.0005465","1935-2735","PLoS neglected tropical diseases","VivaxGEN: An open access platform for comparative analysis of short tandem repeat genotyping data in Plasmodium vivax populations.","2017","28362818"
"Nuno Sepúlveda,Alphaxard Manjurano,Susana G Campino,Martha Lemnge,John Lusingu,Raimos Olomi,Kirk A Rockett,Christina Hubbart,Anna Jeffreys,Kate Rowlands,Taane G Clark,Eleanor M Riley,Chris J Drakeley","10.1093/infdis/jix250","0022-1899","The Journal of Infectious Diseases","Malaria Host Candidate Genes Validated by Association With Current, Recent, and Historical Measures of Transmission Intensity","2017"
"Keertan Dheda,Tawanda Gumbo,Gary Maartens,Kelly E Dooley,Ruth McNerney,Megan Murray,Jennifer Furin,Edward A Nardell,Leslie London,Erica Lessem,Grant Theron,Paul van Helden,Stefan Niemann,Matthias Merker,David Dowdy,Annelies Van Rie,Gilman K H Siu,Jotam G Pasipanodya,Camilla Rodrigues,Taane G Clark,Frik A Sirgel,Aliasgar Esmail,Hsien-Ho Lin,Sachin R Atre,H Simon Schaaf,Kwok Chiu Chang,Christoph Lange,Payam Nahid,Zarir F Udwadia,C Robert Horsburgh,Gavin J Churchyard,Dick Menzies,Anneke C Hesseling,Eric Nuermberger,Helen McIlleron,Kevin P Fennelly,Eric Goemaere,Ernesto Jaramillo,Marcus Low,Carolina Morán Jara,Nesri Padayatchi,Robin M Warren","10.1016/S2213-2600(17)30079-6","2213-2619","The Lancet. Respiratory medicine","The epidemiology, pathogenesis, transmission, diagnosis, and management of multidrug-resistant, extensively drug-resistant, and incurable tuberculosis.","2017","28344011"
"A R Last,H Pickering,C H Roberts,F Coll,J Phelan,S E Burr,E Cassama,M Nabicassa,H M B Seth-Smith,J Hadfield,L T Cutcliffe,I N Clarke,D C W Mabey,R L Bailey,T G Clark,N R Thomson,M J Holland","10.1186/s13073-018-0521-x","1756-994X","Genome medicine","Population-based analysis of ocular Chlamydia trachomatis in trachoma-endemic West African communities identifies genomic markers of disease severity.","2018","29482619"
"Eliana M Lacerda,Erinna W Bowman,Jacqueline M Cliff,Caroline C Kingdon,Elizabeth C King,Ji-Sook Lee,Taane G Clark,Hazel M Dockrell,Eleanor M Riley,Hayley Curran,Luis Nacul","10.5334/ojb.28","2056-5542","Open Journal of Bioresources","The UK ME/CFS Biobank for biomedical research on Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) and Multiple Sclerosis","2017"
"Keertan Dheda,Jason D Limberis,Elize Pietersen,Jody Phelan,Aliasgar Esmail,Maia Lesosky,Kevin P Fennelly,Julian te Riele,Barbara Mastrapa,Elizabeth M Streicher,Tania Dolby,Abdallah M Abdallah,Fathia Ben-Rached,John Simpson,Liezel Smith,Tawanda Gumbo,Paul van Helden,Frederick A Sirgel,Ruth McNerney,Grant Theron,Arnab Pain,Taane G Clark,Robin M Warren","10.1016/S2213-2600(16)30433-7","22132600","The Lancet Respiratory Medicine","Outcomes, infectiousness, and transmission dynamics of patients with extensively drug-resistant tuberculosis and home-discharged patients with programmatically incurable tuberculosis: a prospective cohort study","2017"
"Nuria Andreu,Jody Phelan,Paola F de Sessions,Jacqueline M Cliff,Taane G Clark,Martin L Hibberd","10.1038/srep42225","2045-2322","Scientific Reports","Primary macrophages and J774 cells respond differently to infection with Mycobacterium tuberculosis","2017"
"Sarah Cook,Sofia Malyutina,Alexander V Kudryavtsev,Maria Averina,Natalia Bobrova,Sergey Boytsov,Soren Brage,Taane G Clark,Ernest Diez Benavente,Anne Elise Eggen,Laila A Hopstock,Alun Hughes,Heidi Johansen,Kamila Kholmatova,Anastasiya Kichigina,Anna Kontsevaya,Michael Kornev,Darryl Leong,Per Magnus,Ellisiv Mathiesen,Martin McKee,Katy Morgan,Odd Nilssen,Ilya Plakhov,Jennifer K Quint,Alicja Rapala,Andrey Ryabikov,Lyudmila Saburova,Henrik Schirmer,Marina Shapkina,Suhail Shiekh,Vladimir M Shkolnikov,Michael Stylidis,Michael Voevoda,Kate Westgate,David A Leon","10.12688/wellcomeopenres.14619.2","2398-502X","Wellcome Open Research","Know Your Heart: Rationale, design and conduct of a cross-sectional study of cardiovascular structure, function and risk factors in 4500 men and women aged 35-69 years from two Russian cities, 2015-18","2018"
"Monica C Campos,Jamille G Dombrowski,Jody Phelan,Claudio R F Marinho,Martin Hibberd,Taane G Clark,Susana Campino","10.1371/journal.pone.0201452","1932-6203","PLOS ONE","Zika might not be acting alone: Using an ecological study approach to investigate potential co-acting risk factors for an unusual pattern of microcephaly in Brazil","2018"
"Matthew Higgins,Matt Ravenhall,Daniel Ward,Jody Phelan,Amy Ibrahim,Matthew S Forrest,Taane G Clark,Susana Campino","10.1093/bioinformatics/bty701","1367-4803","Bioinformatics","PrimedRPA: primer design for recombinase polymerase amplification assays","2019"
"Prasit Palittapongarnpim,Pravech Ajawatanawong,Wasna Viratyosin,Nat Smittipat,Areeya Disratthakit,Surakameth Mahasirimongkol,Hideki Yanai,Norio Yamada,Supalert Nedsuwan,Worarat Imasanguan,Pacharee Kantipong,Boonchai Chaiyasirinroje,Jiraporn Wongyai,Licht Toyo-oka,Jody Phelan,Julian Parkhill,Taane G Clark,Martin L Hibberd,Wuthiwat Ruengchai,Panawun Palittapongarnpim,Tada Juthayothin,Sissades Tongsima,Katsushi Tokunaga","10.1038/s41598-018-29986-3","2045-2322","Scientific Reports","Evidence for Host-Bacterial Co-evolution via Genome Sequence Analysis of 480 Thai Mycobacterium tuberculosis Lineage 1 Isolates","2018"
"Carolyne M Ndila,Sophie Uyoga,Alexander W Macharia,Gideon Nyutu,Norbert Peshu,John Ojal,Mohammed Shebe,Kennedy O Awuondo,Neema Mturi,Benjamin Tsofa,Nuno Sepúlveda,Taane G Clark,Gavin Band,Geraldine Clarke,Kate Rowlands,Christina Hubbart,Anna Jeffreys,Silvia Kariuki,Kevin Marsh,Margaret Mackinnon,Kathryn Maitland,Dominic P Kwiatkowski,Kirk A Rockett,Thomas N Williams,Amadou Abathina,Ismaela Abubakar,Eric Achidi,Tsiri Agbenyega,Mohammed Aiyegbo,Alex Akoto,Angela Allen,Stephen Allen,Lucas Amenga-Etego,Folakemi Amodu,Olukemi Amodu,Judith Anchang-Kimbi,Nana Ansah,Patrick Ansah,Daniel Ansong,Sampson Antwi,Thomas Anyorigiya,Tobias Apinjoh,Emmanuel Asafo-Agyei,Victor Asoala,Frank Atuguba,Sarah Auburn,Abdou Bah,Kariatou Bamba,Germana Bancone,Gavin Band,David Barnwell,Abdoulaye Barry,Evasius Bauni,Richard Besingi,Kalifa Bojang,Edith Bougouma,Susan Bull,George Busby,Abdoulie Camara,Landing Camara,Susana Campino,Richard Carter,Dan Carucci,Climent Casals-Pascual,Ndey Ceesay,Pa Ceesay,Tran Chau,Ly Chuong,Taane Clark,Geraldine Clarke,Ramou Cole-Ceesay,David Conway,Katharine Cook,Olivia Cook,Victoria Cornelius,Patrick Corran,Simon Correa,Sharon Cox,Rachel Craik,Bakary Danso,Timothy Davis,Nicholas Day,Panos Deloukas,Awa Dembele,Jantina deVries,Rajika Dewasurendra,Mahamadou Diakite,Elizabeth Diarra,Yaya Dibba,Andrea Diss,Abdoulaye Djimdé,Amagana Dolo,Ogobara Doumbo,Alan Doyle,Chris Drakeley,Eleanor Drury,Patrick Duffy,Sarah Dunstan,Augustine Ebonyi,Ahmed Elhassan,Ibrahim Elhassan,Abier Elzein,Anthony Enimil,Pamela Esangbedo,Jennifer Evans,Julie Evans,Jeremy Farrar,Deepika Fernando,Kathryn Fitzpatrick,Janet Fullah,Jacob Garcia,Anita Ghansah,Michael Gottleib,Angie Green,Lee Hart,Meike Hennsman,Tran Hien,Nguyen Hieu,Eliza Hilton,Abraham Hodgson,Rolf Horstmann,Christina Hubbart,Catherine Hughes,Ayman Hussein,Robert Hutton,Muntaser Ibrahim,Deus Ishengoma,Jula Jaiteh,Mariatou Jallow,Muminatou Jallow,Kebba Jammeh,Momodou Jasseh,Anna Jeffreys,Amie Jobarteh,Kimberly Johnson,Sarah Joseph,Dushyanth Jyothi,David Kachala,Dorcas Kamuya,Haddy Kanyi,Harin Karunajeewa,Nadira Karunaweera,Momodou Keita,Angeliki Kerasidou,Aja Khan,Katja Kivinen,Gilbert Kokwaro,Amadou Konate,Salimata Konate,Kwadwo Koram,Dominic Kwiatkowski,Moses Laman,Si Le,Ellen Leffler,Martha Lemnge,Enmoore Lin,Alioune Ly,Alexander Macharia,Bronwyn MacInnis,Nguyen Mai,Julie Makani,Cinzia Malangone,Valentina Mangano,Alphaxard Manjurano,Lamin Manneh,Laurens Manning,Magnus Manske,Kevin Marsh,Vicki Marsh,Gareth Maslen,Caroline Maxwell,Eric Mbunwe,Marilyn McCreight,Daniel Mead,Alieu Mendy,Anthony Mendy,Nathan Mensah,Pascal Michon,Alistair Miles,Olivo Miotto,David Modiano,Hiba Mohamed,Sile Molloy,Malcolm Molyneux,Sassy Molyneux,Mike Moore,Catherine Moyes,Frank Mtei,George Mtove,Ivo Mueller,Regina Mugri,Annie Munthali,Theonest Mutabingwa,Behzad Nadjm,Andre Ndi,Carolyne Ndila,Charles Newton,Amadou Niangaly,Haddy Njie,Jalimory Njie,Madi Njie,Malick Njie,Sophie Njie,Labes Njiragoma,Francis Nkrumah,Neema Ntunthama,Aceme Nyika,Vysaul Nyirongo,John O'Brien,Herbert Obu,Abraham Oduro,Alex Ofori,Subulade Olaniyan,Rasaq Olaosebikan,Tom Oluoch,Olayemi Omotade,Olajumoke Oni,Emmanuel Onykwelu,Daniel Opi,Adebola Orimadegun,Sean O'Riordan,Issa Ouedraogo,Samuel Oyola,Michael Parker,Richard Pearson,Paul Pensulo,Norbert Peshu,Ajib Phiri,Nguyen Phu,Margaret Pinder,Matti Pirinen,Chris Plowe,Claire Potter,Belco Poudiougou,Odile Puijalon,Nguyen Quyen,Ioannis Ragoussis,Jiannis Ragoussis,Oba Rasheed,John Reeder,Hugh Reyburn,Eleanor Riley,Paul Risley,Kirk Rockett,Joanne Rodford,Jane Rogers,William Rogers,Kate Rowlands,Valentín Ruano-Rubio,Kumba Sabally-Ceesay,Abubacar Sadiq,Momodou Saidy-Khan,Horeja Saine,Anavaj Sakuntabhai,Abdourahmane Sall,David Sambian,Idrissa Sambou,Miguel SanJoaquin,Nuno Sepúlveda,Shivang Shah,Jennifer Shelton,Peter Siba,Nilupa Silva,Cameron Simmons,Jaques Simpore,Pratap Singhasivanon,Dinh Sinh,Sodiomon Sirima,Giorgio Sirugo,Fatoumatta Sisay-Joof,Sibiry Sissoko,Kerrin Small,Elilan Somaskantharajah,Chris Spencer,Jim Stalker,Marryat Stevens,Prapat Suriyaphol,Justice Sylverken,Bintou Taal,Adama Tall,Terrie Taylor,Yik Teo,Cao Thai,Mahamadou Thera,Vincent Titanji,Ousmane Toure,Marita Troye-Blomberg,Stanley Usen,Sophie Uyoga,Aaron Vanderwal,Hannah Wangai,Renee Watson,Thomas Williams,Michael Wilson,Rebecca Wrigley,Clarisse Yafi,Lawrence Yamoah","10.1016/S2352-3026(18)30107-8","23523026","The Lancet Haematology","Human candidate gene polymorphisms and risk of severe malaria in children in Kilifi, Kenya: a case-control association study","2018"
"Sarah Auburn,Ernest D Benavente,Olivo Miotto,Richard D Pearson,Roberto Amato,Matthew J Grigg,Bridget E Barber,Timothy William,Irene Handayuni,Jutta Marfurt,Hidayat Trimarsanto,Rintis Noviyanti,Kanlaya Sriprawat,Francois Nosten,Susana Campino,Taane G Clark,Nicholas M Anstey,Dominic P Kwiatkowski,Ric N Price","10.1038/s41467-018-04965-4","2041-1723","Nature Communications","Genomic analysis of a pre-elimination Malaysian Plasmodium vivax population reveals selective pressures and changing transmission dynamics","2018"
"Lydia J Leon,Ronan Doyle,Ernest Diez-Benavente,Taane G Clark,Nigel Klein,Philip Stanier,Gudrun E Moore","10.1128/AEM.00483-18","0099-2240","Applied and Environmental Microbiology","Enrichment of Clinically Relevant Organisms in Spontaneous Preterm-Delivered Placentas and Reagent Contamination across All Clinical Groups in a Large Pregnancy Cohort in the United Kingdom","2018"
"Nuno Sepúlveda,Jody Phelan,Ernest Diez-Benavente,Susana Campino,Taane G Clark,Heidi Hopkins,Colin Sutherland,Chris J Drakeley,Khalid B Beshir","10.1016/j.meegid.2018.04.039","15671348","Infection, Genetics and Evolution","Global analysis of Plasmodium falciparum histidine-rich protein-2 (pfhrp2) and pfhrp3 gene deletions using whole-genome sequencing data and meta-analysis","2018"
"Ruth McNerney,Matteo Zignol,Taane G Clark","10.1080/14787210.2018.1472577","1478-7210","Expert Review of Anti-infective Therapy","Use of whole genome sequencing in surveillance of drug resistant tuberculosis","2018"
"João Perdigão,Carla Silva,Jaciara Diniz,Catarina Pereira,Diana Machado,Jorge Ramos,Hugo Silva,Fernanda Abilleira,Clarice Brum,Ana J Reis,Maíra Macedo,João L Scaini,Ana B Silva,Leonardo Esteves,Rita Macedo,Fernando Maltez,Sofia Clemente,Elizabeth Coelho,Sofia Viegas,Paulo Rabna,Amabélia Rodrigues,Nuno Taveira,Luísa Jordao,Afrânio Kritski,José R Lapa e Silva,Igor Mokrousov,David Couvin,Nalin Rastogi,Isabel Couto,Arnab Pain,Ruth McNerney,Taane G Clark,Andrea von Groll,Elis R Dalla-Costa,Maria Lúcia Rossetti,Pedro EA Silva,Miguel Viveiros,Isabel Portugal","10.1016/j.meegid.2018.03.011","15671348","Infection, Genetics and Evolution","Clonal expansion across the seas as seen through CPLP-TB database: A joint effort in cataloguing Mycobacterium tuberculosis genetic diversity in Portuguese-speaking countries","2019"
"Matt Ravenhall,Susana Campino,Nuno Sepúlveda,Alphaxard Manjurano,Behzad Nadjm,George Mtove,Hannah Wangai,Caroline Maxwell,Raimos Olomi,Hugh Reyburn,Christopher J Drakeley,Eleanor M Riley,Taane G Clark","10.1371/journal.pgen.1007172","1553-7404","PLOS Genetics","Novel genetic polymorphisms associated with severe malaria and under selective pressure in North-eastern Tanzania","2018"
"Francesc Coll,Jody Phelan,Grant A Hill-Cawthorne,Mridul B Nair,Kim Mallard,Shahjahan Ali,Abdallah M Abdallah,Saad Alghamdi,Mona Alsomali,Abdallah O Ahmed,Stephanie Portelli,Yaa Oppong,Adriana Alves,Theolis Barbosa Bessa,Susana Campino,Maxine Caws,Anirvan Chatterjee,Amelia C Crampin,Keertan Dheda,Nicholas Furnham,Judith R Glynn,Louis Grandjean,Dang Minh Ha,Rumina Hasan,Zahra Hasan,Martin L Hibberd,Moses Joloba,Edward C Jones-López,Tomoshige Matsumoto,Anabela Miranda,David J Moore,Nora Mocillo,Stefan Panaiotov,Julian Parkhill,Carlos Penha,João Perdigão,Isabel Portugal,Zineb Rchiad,Jaime Robledo,Patricia Sheen,Nashwa Talaat Shesha,Frik A Sirgel,Christophe Sola,Erivelton Oliveira Sousa,Elizabeth M Streicher,Paul Van Helden,Miguel Viveiros,Robert M Warren,Ruth McNerney,Arnab Pain,Taane G Clark","10.1038/s41588-017-0029-0","1061-4036","Nature Genetics","Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis","2018"
"Ernest Diez Benavente,Paola Florez de Sessions,Robert W Moon,Munira Grainger,Anthony A Holder,Michael J Blackman,Cally Roper,Christopher J Drakeley,Arnab Pain,Colin J Sutherland,Martin L Hibberd,Susana Campino,Taane G Clark","10.1016/j.ijpara.2017.09.008","00207519","International Journal for Parasitology","A reference genome and methylome for the Plasmodium knowlesi A1-H.1 line","2018"
"Lynn Grignard,Catherine Mair,Jonathan Curry,Laleta Mahey,Guide J H Bastiaens,Alfred B Tiono,Joseph Okebe,Sam A Coulibaly,Bronner P Gonçalves,Muna Affara,Alphonse Ouédraogo,Edith C Bougouma,Guillaume S Sanou,Issa Nébié,Kjerstin H W Lanke,Sodiomon B Sirima,Umberto d’Alessandro,Taane G Clark,Susana Campino,Teun Bousema,Chris Drakeley","10.1186/s12936-019-2648-7","1475-2875","Malaria Journal","Bead-based assays to simultaneously detect multiple human inherited blood disorders associated with malaria","2019"
"Sofia Santos Costa,Benjamin Sobkowiak,Ricardo Parreira,Jonathan D Edgeworth,Miguel Viveiros,Taane G Clark,Isabel Couto","10.3389/fgene.2018.00710","1664-8021","Frontiers in Genetics","Genetic Diversity of norA, Coding for a Main Efflux Pump of Staphylococcus aureus","2019"
"Joanna B Broad,Zhenqiang Wu,Taane G Clark,David Musson,Rebekah Jaung,Bruce Arroll,Ian P Bissett,Martin J Connolly","10.1080/03008207.2019.1570169","1607-8438","Connective tissue research","Diverticulosis and nine connective tissue disorders: epidemiological support for an association.","2019","30719942"
"Yaa E A Oppong,Jody Phelan,João Perdigão,Diana Machado,Anabela Miranda,Isabel Portugal,Miguel Viveiros,Taane G Clark,Martin L Hibberd","10.1186/s12864-019-5615-3","1471-2164","BMC Genomics","Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance","2019"
"Jamille Gregório Dombrowski,Rodrigo Medeiros de Souza,Flávia Afonso Lima,Carla Letícia Bandeira,Oscar Murillo,Douglas de Sousa Costa,Erika Paula Machado Peixoto,Marielton Dos Passos Cunha,Paolo Marinho de Andrade Zanotto,Estela Bevilacqua,Marcos Augusto Grigolin Grisotto,Antonio Carlos Pedroso de Lima,Julio da Motta Singer,Susana Campino,Taane Gregory Clark,Sabrina Epiphanio,Lígia Antunes Gonçalves,Cláudio Romero Farias Marinho","10.1001/jamanetworkopen.2019.3300","2574-3805","JAMA network open","Association of Malaria Infection During Pregnancy With Head Circumference of Newborns in the Brazilian Amazon.","2019","31050780"
"Yan He,Susana Campino,Ernest Diez Benavente,David C Warhurst,Khalid B Beshir,Inke Lubis,Ana Rita Gomes,Jun Feng,Wang Jiazhi,Xiaodong Sun,Fang Huang,Lin-Hua Tang,Colin J Sutherland,Taane G Clark","10.1371/journal.pone.0213686","1932-6203","PloS one","Artemisinin resistance-associated markers in Plasmodium falciparum parasites from the China-Myanmar border: predicted structural stability of K13 propeller variants detected in a low-prevalence area.","2019","30883571"
"Matt Ravenhall,Susana Campino,Taane G Clark","10.1186/s12859-019-2718-4","1471-2105","BMC Bioinformatics","SV-Pop: population-based structural variant analysis and visualization","2019"
"Luis Nacul,Barbara de Barros,Caroline C Kingdon,Jacqueline M Cliff,Taane G Clark,Kathleen Mudie,Hazel M Dockrell,Eliana M Lacerda","10.3390/diagnostics9020041","2075-4418","Diagnostics (Basel, Switzerland)","Evidence of Clinical Pathology Abnormalities in People with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) from an Analytic Cross-Sectional Study.","2019","30974900"
"Matt Ravenhall,Ernest Diez Benavente,Colin J Sutherland,David A Baker,Susana Campino,Taane G Clark","10.1038/s41598-019-44599-0","2045-2322","Scientific Reports","An analysis of large structural variation in global Plasmodium falciparum isolates identifies a novel duplication of the chloroquine resistance associated gene","2019"
"Franziska Mohring,Melissa Natalie Hart,Thomas A Rawlinson,Ryan Henrici,James A Charleston,Ernest Diez Benavente,Avnish Patel,Joanna Hall,Neil Almond,Susana Campino,Taane G Clark,Colin J Sutherland,David A Baker,Simon J Draper,Robert William Moon","10.7554/eLife.45829","2050-084X","eLife","Rapid and iterative genome editing in the malaria parasite Plasmodium knowlesi provides new tools for P. vivax research.","2019","31205002"
"Jody E Phelan,Denise M O’Sullivan,Diana Machado,Jorge Ramos,Yaa E A Oppong,Susana Campino,Justin O’Grady,Ruth McNerney,Martin L Hibberd,Miguel Viveiros,Jim F Huggett,Taane G Clark","10.1186/s13073-019-0650-x","1756-994X","Genome Medicine","Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs","2019"
"Jody E Phelan,Dodge R Lim,Satoshi Mitarai,Paola Florez de Sessions,Ma Angelica A Tujan,Lorenzo T Reyes,Inez Andrea P Medado,Alma G Palparan,Ahmad Nazri Mohamed Naim,Song Jie,Edelwisa Segubre-Mercado,Beatriz Simoes,Susana Campino,Julius C Hafalla,Yoshiro Murase,Yuta Morishige,Martin L Hibberd,Seiya Kato,Ma Cecilia G Ama,Taane G Clark","10.1038/s41598-019-45566-5","2045-2322","Scientific reports","Mycobacterium tuberculosis whole genome sequencing provides insights into the Manila strain and drug-resistance mutations in the Philippines.","2019","31243306"
"Ernest Diez Benavente,Ana Rita Gomes,Jeremy Ryan De Silva,Matthew Grigg,Harriet Walker,Bridget E Barber,Timothy William,Tsin Wen Yeo,Paola Florez de Sessions,Abhinay Ramaprasad,Amy Ibrahim,James Charleston,Martin L Hibberd,Arnab Pain,Robert W Moon,Sarah Auburn,Lau Yee Ling,Nicholas M Anstey,Taane G Clark,Susana Campino","10.1038/s41598-019-46398-z","2045-2322","Scientific Reports","Whole genome sequencing of amplified Plasmodium knowlesi DNA from unprocessed blood reveals genetic exchange events between Malaysian Peninsular and Borneo subpopulations","2019"
"Wouter Deelder,Sofia Christakoudi,Jody Phelan,Ernest Diez Benavente,Susana Campino,Ruth McNerney,Luigi Palla,Taane G Clark","10.3389/fgene.2019.00922","1664-8021","Frontiers in Genetics","Machine Learning Predicts Accurately Mycobacterium tuberculosis Drug Resistance From Whole Genome Sequencing Data","2019"
"Pravech Ajawatanawong,Hideki Yanai,Nat Smittipat,Areeya Disratthakit,Norio Yamada,Reiko Miyahara,Supalert Nedsuwan,Worarat Imasanguan,Pacharee Kantipong,Boonchai Chaiyasirinroje,Jiraporn Wongyai,Supada Plitphonganphim,Pornpen Tantivitayakul,Jody Phelan,Julian Parkhill,Taane G Clark,Martin L Hibberd,Wuthiwat Ruangchai,Panawun Palittapongarnpim,Tada Juthayothin,Yuttapong Thawornwattana,Wasna Viratyosin,Sissades Tongsima,Surakameth Mahasirimongkol,Katsushi Tokunaga,Prasit Palittapongarnpim","10.1038/s41598-019-50078-3","2045-2322","Scientific Reports","A novel Ancestral Beijing sublineage of Mycobacterium tuberculosis suggests the transition site to Modern Beijing sublineages","2019"
"Abdul Jabbar,Jody E Phelan,Paola Florez de Sessions,Taj Ali Khan,Hazir Rahman,Sadiq Noor Khan,Daire M Cantillon,Leticia Muraro Wildner,Sajid Ali,Susana Campino,Simon J Waddell,Taane G Clark","10.1038/s41598-019-51562-6","2045-2322","Scientific Reports","Whole genome sequencing of drug resistant Mycobacterium tuberculosis isolates from a high burden tuberculosis region of North West Pakistan","2019"
"Seidina A S Diakité,Karim Traoré,Ibrahim Sanogo,Taane G Clark,Susana Campino,Modibo Sangaré,Djeneba Dabitao,Antoine Dara,Drissa S Konaté,Fousseyni Doucouré,Amadou Cissé,Bourama Keita,Mory Doumbouya,Merepen A Guindo,Mahamoudou B Toure,Nafomon Sogoba,Seydou Doumbia,Gordon A Awandare,Mahamadou Diakité","10.1186/s12936-019-2986-5","1475-2875","Malaria Journal","A comprehensive analysis of drug resistance molecular markers and Plasmodium falciparum genetic diversity in two malaria endemic sites in Mali","2019"
"Benjamin Sobkowiak,Louis Banda,Themba Mzembe,Amelia C Crampin,Judith R Glynn,Taane G Clark","10.1099/mgen.0.000361","2057-5858","Microbial Genomics","Bayesian reconstruction of Mycobacterium tuberculosis transmission networks in a high incidence area over two decades in Malawi reveals associated risk factors and genomic variants","2020"
"João Perdigão,Ana Modesto,A L Pereira,O Neto,V Matos,A Godinho,Jody Phelan,James Charleston,Anton Spadar,Paola Florez de Sessions,Martin Hibberd,Susana Campino,A Costa,F Fernandes,F Ferreira,A B Correia,Luisa Gonçalves,Taane G Clark,Aida Duarte","10.1099/mgen.0.000349","2057-5858","Microbial Genomics","Whole-genome sequencing resolves a polyclonal outbreak by extended-spectrum beta-lactam and carbapenem-resistant Klebsiella pneumoniae in a Portuguese tertiary-care hospital","2019"
"Ernest Diez Benavente,Monica Campos,Jody Phelan,Debbie Nolder,Jamille G Dombrowski,Claudio R F Marinho,Kanlaya Sriprawat,Aimee R Taylor,James Watson,Cally Roper,Francois Nosten,Colin J Sutherland,Susana Campino,Taane G Clark","10.1371/journal.pgen.1008576","1553-7404","PLOS Genetics","A molecular barcode to inform the geographical origin and transmission dynamics of Plasmodium vivax malaria","2020"
"Ronan M Doyle,Denise M O'Sullivan,Sean D Aller,Sebastian Bruchmann,Taane Clark,Andreu Coello Pelegrin,Martin Cormican,Ernest Diez Benavente,Matthew J Ellington,Elaine McGrath,Yair Motro,Thi Phuong Thuy Nguyen,Jody Phelan,Liam P Shaw,Richard A Stabler,Alex van Belkum,Lucy van Dorp,Neil Woodford,Jacob Moran-Gilad,Jim F Huggett,Kathryn A Harris","10.1099/mgen.0.000335","2057-5858","Microbial Genomics","Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: an inter-laboratory study","2020"
"Anna Turkiewicz and Emilia Manko and Damiola R. Oresegun and Debbie Nolder and Anton Spadar and Colin J. Sutherland and Janet Cox-Singh and Robert W. Moon and Yee-Ling Lau and Susana Campino and Taane G. Clark","10.1038/s41598-023-29368-4","2045-2322","Scientific Reports","Population genetic analysis of Plasmodium knowlesi reveals differential selection and exchange events between Borneo and Peninsular sub-populations","2023"