Publications

Whole-genome characterization of a colistin-resistant Klebsiella quasipneumoniae subsp. quasipneumoniae isolate from a urinary tract infection in Peshawar, Pakistan

A Waheed, SA Khan, S Ahmad, TA Khan, TG Clark

Brazilian Journal of Microbiology 57 (1), 169, 2026

Ciprofloxacin resistance in Klebsiella pneumoniae: phenotype prediction from genotype and global distribution of resistance determinants

KK Tsang, I Amke, DM Aanensen, J Abdulahi, A Aiken, MA Bachman, ...

Genome Medicine, 2026

Exploring genetic variation in insecticide resistance loci in Anopheles gambiae sl populations from Ghana

A Abdulai, S Moss, K Brandt-Templeton, E Collins, P Laan, IK Sraku, ...

Association between human genomes and mycobacterial genomes contributes to severity and transmissibility of pulmonary tuberculosis

P Tantivitayakul, P Kunhapan, M Boonbangyang, K Chaichoompu, ...

iScience 29 (10), 2026

Mutational profiling of ESX/type VII secretion system-associated genes in drug-resistant Mycobacterium tuberculosis from Khyber Pakhtunkhwa, Pakistan

N Muhammad, TA Khan, S Ali, MT Khan, IU Haq, AS Khan, S Ahmad, ...

International Journal of Medical Microbiology, 151748, 2026

Implications of edge cases for antimicrobial susceptibility predictions for rifampin, delamanid, and pretomanid with the WHO Mycobacterium tuberculosis mutation …

N Hermans, J Phelan, R Sorrentino, F Boysen, NL Sherry, P Miotto, ...

Microbiology spectrum 14 (10), e01821-26, 2026

Whole-Genome Sequencing Reveals the Resistome, Virulome, Pan-Genome Architecture, and Phylogenomic Diversity of Extensively Drug-Resistant Salmonella enterica Serovar Typhi in …

R Mehr, Q Ali, M Zahid, TA Khan, M Asghar, N Rehman, TG Clark, ...

Microorganisms 14 (10), 2225, 2026

Updated TB-Profiler: enhanced genotypic antimicrobial resistance prediction and relatedness analysis powered by a database of over 171,000 Mycobacterium tuberculosis genomes

JE Phelan, W Sawaengdee, J Thorpe, N Thawong, P Piboonsiri, ...

Genome Medicine, 2026

Malaria-Related Host Genetic Variation in an Endemic Population of Southern Senegal

BS Sambe, A Diagne, JE Phelan, N Billows, HAM Diatta, MKI Tan, ...

International journal of molecular sciences 27 (18), 8123, 2026

Genomic epidemiology of multidrug-resistant Klebsiella pneumoniae reveals lineage-specific resistance patterns with limited virulence determinants

A Waheed, SA Khan, TA Khan, S Ahmad, AA Khattak, TG Clark, ...

AIMS microbiology 12 (3), 610, 2026

Implications of edge cases for antimicrobial susceptibility predictions for rifampin, delamanid, and pretomanid with the WHO mutation catalog.

N Hermans, J Phelan, R Sorrentino, F Boysen, NL Sherry, P Miotto, ...

Synthesis, Characterization, and Inhibitory Potential of Fagonia arabica L. Phytochemicals Coated Gold Nanoparticles Against Drug‐Resistant Mycobacterium tuberculosis

F Mukhtar, MT Khan, MS Lodhi, I Ahmad, DS Alshaya, AA Al‐Qahtani, ...

Chemistry & biodiversity 23 (8), e71572, 2026

A recombinase polymerase amplification lateral flow assay (RPA-LF) for detection of Babesiadivergens-like parasites

ECJ Bin, K Hughes, C Whitehorn, M White, K Hansford, J Medlock, ...

Parasites & vectors, 2026

Whole-genome analysis of drug resistance and transmission patterns in Mycobacterium tuberculosis from Khyber Pakhtunkhwa, Pakistan

MF Khan, J Phelan, AS Anwar, SN Khan, A Ali, FM Awan, A Obaid, ...

Scientific Reports, 2026

Clinical and Genomic Characterization of High-Risk Multidrug-Resistant Klebsiella pneumoniae Lineages in Pakistan

AA Khattak, S Azam, N Rehman, M Asghar, A Waheed, S Ahmad, ...

Microorganisms 14 (7), 1462, 2026

Operationalising Environmental DNA (eDNA) Detection of Major Malaria Vector Species in Ghana

M Kristan, YA Afrane, S Moss, Y Akuamoah‐Boateng, ARM Sabtiu, ...

Molecular ecology resources 26 (5), e70154, 2026

High quality Chromosome-scale Genome Assembly of Phlebotomus perniciosus, a Vector of Zoonotic Leishmaniasis

J Thorpe, N Billows, T Becvar, E Collins, M Higgins, MS de Jesus, ...

Scientific data, 2026

Rapid whole-genome sequencing of Plasmodium DNA from cryptic malaria cases in UK travellers provides insights into infection origins, transmission and …

MKI Tan, N Billows, D Nolder, S Moss, JE Phelan, J Thorpe, JL Edgeworth, ...

Journal of Travel Medicine 33 (5), taag028, 2026

In Silico Mutational Analysis of Two-Component System Genes Associated with Colistin Resistance in Clinical Pseudomonas aeruginosa Isolates from Peshawar

B Ahmad, Q Ali, S Azam, M Asghar, N Rehman, GS Mujib, SS Shah, ...

Biomolecules 16 (7), 962, 2026

Corrigendum to" Emergence of novel sublineages of Mycobacterium tuberculosis in Pakistan"[Int. J. Med. Microbiol. 321 (2025) 151684]

MT Khan, C Zhu, AO Al Khatib, DS Alshaya, AA Al-Qahtani, I Ahmad, ...

International journal of medical microbiology: IJMM 322, 151719, 2026

The first chromosome-scale genome assembly for Dermacentor reticulatus: a key vector of tick-borne pathogens of public and veterinary health importance in Europe.

N Billows, ML White, J Thorpe, M Higgins, E Collins, MS de Jesus, ...

BMC biology, 2026

A Plasmodium falciparum Pangenome Resource to drive Structural Variant Discovery and assist Malaria Control

N Billows, J Thorpe, S Campino, TG Clark

bioRxiv, 2026.05. 19.726271, 2026

Global-scale population genetic analysis of Plasmodium falciparum identifies region-specific patterns of malaria parasite adaptation

N Billows, JG Dombrowski, J Thorpe, L Vanheer, S Moss, J Gitaka, ...

Nature communications, 2026

Phylogenomics of a NDM-1-Producing Providencia stuartii Strain from Portugal Reveals Global Clinical and Environmental Reservoirs

R Elias, M Seruca, V Mendes, W Hinthong, S Witteveen, R Lúzio, ...

Journal of Hospital Infection, 2026

Plasmodium knowlesi can adapt to infect Duffy-negative erythrocytes

M Zinga, A Ibrahim, F Mohring, S Chainarin, TK Jonsdottir, S Ngernna, ...

Blood 147 (18), 2132-2142, 2026

Focal inbreeding and clonal transmission of Plasmodium vivax in pre-elimination Vietnam

GC Ngwana-Joseph, NTH Binh, NTH Ngoc, J Phelan, S Campino, ...

bioRxiv, 2026.04. 21.719798, 2026

Genetic Characterization of First-Line Drug-Resistance Mutations in Multidrug-Resistant Mycobacterium tuberculosis

M Gul, S Ali, A Rehman, M Qasim, R Ali, JE Phelan, A Waheed, S Ahmad, ...

Pathogens 15 (5), 455, 2026

Novel Pfk13 and Pfubp1 genotypes in African Plasmodium falciparum isolates exhibiting reduced susceptibility to the antimalarials artemisinin and lumefantrine

S Pratt, DA van Schalkwyk, L Stewart, EF Hocke, S Mannan, C Berry, ...

Mbio 17 (4), e03676-25, 2026

A Recombinase Polymerase Amplification Lateral Flow Assay (RPA-LF) for detection of Babesia divergens

ECJ Bin, K Hughes, C Whitehorn, M White, K Hansford, J Medlock, ...

Genome-wide analyses of Mycobacterium tuberculosis complex isolates reveal insights into circulating lineages and drug resistance mutations in The Gambia

F Faal, N Top, O Jobe, SM Colley, A Ayorinde, A Mendy, B Sarr-Kuyateh, ...

Scientific reports 16 (1), 12005, 2026

Whole genome sequencing to inform the epidemiology of Plasmodium falciparum malaria in the elimination setting of Malaysia

MKI Tan, N Billows, PCS Divis, C Daneshvar, J Edgeworth, JC Singh, ...

BMC genomics 27 (1), 313, 2026

Kinetics of antimalarial antibodies in children with common haemoglobinopathies in a Tanzanian population

A Manjurano, N Sepulveda, S Mkumbaye, TG Clark, A Ndaro, CW Wang, ...

Frontiers in immunology 17, 1685626, 2026

Genomic Insights into Chromosomal Colistin Resistance and Virulence–Resistance Convergence in MDR/XDR Klebsiella pneumoniae from Tertiary Hospitals in …

A Waheed, SA Khan, S Ahmad, JE Phelan, GF Rani, S Campino, TA Khan, ...

Pathogens 15 (2), 218, 2026

Menaquinone depletion resensitises bedaquiline-resistant tuberculosis

J Wetzel, J Dallow, E Davis, WH Pearson, S Daems, M Govaerts, ...

bioRxiv, 2026

Malaria-GENOMAP: a web-based tool for exploring genomic variation of malaria parasites

J Thorpe, N Billows, GC Ngwana-Joseph, A Ibrahim, D Nolder, ...

Bioinformatics 42 (2), btag016, 2026

Malaria-MOI: A flexible and scalable tool for predicting multiplicity of infection in malaria parasites

N Billows, J Phelan, J Thorpe, LN Vanheer, MKI Tan, S Campino, ...

Genome medicine 18 (1), 22, 2026

The microevolutionary trajectory of endemic multidrug-resistant tuberculosis strains in Portugal toward increased drug resistance levels and its clinical significance

P Gomes, P Paixão, F Maltez, L Brum, JE Phelan, S Campino, TG Clark, ...

Frontiers in microbiology 16, 1716549, 2026

Whole Genome Sequencing of Drug-Resistant Vibrio cholerae Serotype Ogawa from an Outbreak in Khyber Pakhtunkhwa

A Ali, M Khan, TA Khan, S Ahmad, N Rahman, A Waheed, TG Clark

Pathogens 15 (1), 39, 2025

Highly conserved Plasmodium vivax genomes in Duffy-negative individuals from Sudan

RE Schroeder, S Ahmed, A Ford, M Elfaki, SO Hamad, TM Elfaki, ...

Scientific reports 15 (1), 44916, 2025

Enhancing whole genome DNA amplification of Plasmodium falciparum for advanced molecular surveillance in malaria control

MKI Tan, MCS de Jesus, JE Phelan, J Thorpe, D Ward, R Batra, A Patel, ...

Malaria journal 24 (1), 445, 2025

Novel zoonotic cases of Plasmodium simium from São Paulo with a reference genome of the Brazilian strain

E Manko, N Billows, M Higgins, D Ward, A Ibrahim, S Campino, ...

Scientific reports 15 (1), 43703, 2025

Comparative genomic insights into multidrug resistance in classical and hypervirulent K. pneumoniae clinical isolates

Azra, I Ullah, W Hinthong, JE Phelan, S Campino, IU Haq, ZU Din, ...

Scientific reports 15 (1), 43434, 2025

Genome-wide analysis of genetic diversity in Anopheles darlingi from Rondônia State, Brazil

S Moss, H Acford-Palmer, AO Andrade, E Manko, J Phelan, M Higgins, ...

Communications biology 9 (1), 52, 2025

Dissemination of arr-2 and arr-3 is associated with class 1 integrons in Klebsiella pneumoniae clinical isolates from Portugal

R Elias, A Modesto, D Machado, B Pereira, J Phelan, J Melo-Cristino, ...

Medical Microbiology and Immunology 214 (1), 6, 2025

Genetic insights into antimicrobial resistance and virulence characteristics of Salmonella enterica isolated from Nile tilapia sourced from retail markets in Thailand

JO Odoi, S Anuntawirun, N Roongrojmongkhon, W Singchat, T Panthum, ...

BMC microbiology 25 (1), 777, 2025

TOAST: a novel tool for designing targeted gene amplicons and an optimised set of primers for high-throughput sequencing in tuberculosis genomic studies

L Wang, N Thawong, J Thorpe, M Higgins, MTK Ik, W Sawaengdee, ...

BMC genomics 26 (1), 1058, 2025

Emergence of novel sublineages of Mycobacterium tuberculosis in Pakistan

MT Khan, C Zhu, AO Al Khatib, DS Alshaya, AA Al-Qahtani, I Ahmad, ...

International Journal of Medical Microbiology, 151684, 2025

Expanding Tuberculosis Drug Resistance Prediction beyond binary: Deep Learning for Minimum Inhibitory Concentration prediction

L Wang, S Campino, TG Clark, JE Phelan

INTEGRATIVE GENOMIC SEQUENCING AND MACHINE LEARNING APPROACHES FOR …, 2025

The role of cytochrome bc1 inhibitors in future tuberculosis treatment regimens

C Aguilar-Pérez, AJ Lenaerts, C Villellas, J Guillemont, J Dallow, ...

Nature communications 16 (1), 9344, 2025

A multi-stage machine learning framework for stepwise prediction of tuberculosis treatment outcomes: Integrating gradient boosted decision trees and feature-level analysis for …

L Wang, S Campino, TG Clark, JE Phelan

Decoding Positive Selection in Mycobacterium tuberculosis with Phylogeny-Guided Graph Attention Models

L Wang, S Campino, TG Clark, JE Phelan

arXiv preprint arXiv:2510.08703, 2025

Genomic insights into persistent infections, reinfections, and subspecies diversity of Mycobacteroides abscessus: a whole-genome sequencing study of Thai and global isolates

K Trisakul, A Sirichoat, A Nithichanon, S Rotcheewaphan, J Phelan, ...

Infection, Genetics and Evolution, 105838, 2025

Whole-Genome Sequencing Analysis of Drug-Resistant Salmonella Typhi in Children

M Riaz, S Ahmad, F Sattar, G Li, ZU Din, S Ahmad, Azra, A Waheed, ...

Pathogens 14 (10), 967, 2025

Genomic insights into pyrazinamide and fluoroquinolone resistance in multidrug-resistant tuberculosis in Khyber Pakhtunkhwa, Pakistan

ZU Din, F Ullah, AS Khan, S Ahmad, A Waheed, N Muhmmad, F Ali, ...

International Journal of Medical Microbiology, 151674, 2025

Emerging Rifampicin Resistance in M. tuberculosis: First Report on Characterization of a Novel rpoB (Ser431Phe) Mutation and Phylogenetic Lineages in Khyber Pakhtunkhwa, Pakistan

M Gul, S Ali, TA Khan, A Rehman, M Qasim, H Naveed, M Asiri, JE Phelan, ...

Whole-genome sequencing analysis of Burkholderia pseudomallei comparing drug-resistant and pan-susceptible isolates reveals novel biomarkers for drug resistance

Y Hinwan, N Nithimongkolchai, K Trisakul, B Kaewseekhao, ...

Infection, Genetics and Evolution 133, 105779, 2025

Global-scale population genetic analysis of Plasmodium falciparum identifies country-and region-specific patterns of malaria parasite adaptation

N Billows, JG Dombrowski, J Thorpe, L Vanheer, S Moss, J Gitaka, ...

Genomic decoding of drug-resistant tuberculosis transmission in Thailand over three decades

N Thawong, P Srilohasin, JE Phelan, W Phornsiricharoenphant, ...

Scientific reports 15 (1), 29617, 2025

Genome-wide analysis and longitudinal study of Klebsiella pneumoniae in Portugal: Tracing the evolution and spread of carbapenem resistance

R Elias, JE Phelan, L Lito, C Caneiras, C Marques, M Pinto, ...

International journal of antimicrobial agents, 107583, 2025

A timeline of reckoning: Tracking the historical rise of antimicrobial resistance across HIV, TB, and malaria

T Williamson, J Adderley, K Quinn, TG Clark, SR Lewin, C Doerig

Journal of global antimicrobial resistance, 2025

Genomic insights into Klebsiella pneumoniae: Virulence, resistance, and transmission in South and Southeast Asia

W Hinthong, J Phelan, A Hussain, R Mazumder, IU Haq, I Ullah, T Roberts, ...

International Journal of Medical Microbiology, 151666, 2025

Profiling insecticide resistance phenotypes and genotypes in Aedes aegypti populations across four regions in Puerto Rico

EL Collins, JM Quintana, R Morales, S Moss, H Acford-Palmer, M Higgins, ...

Scientific reports 15 (1), 26116, 2025

Complete and draft genome sequences of clinical Mycobacterium tuberculosis isolates from the Philippines

SM Rojas, MAA Tujan, AKC Valencia, JBG Capin, TJR Dizon, MCG Ama, ...

Microbiology resource announcements 14 (7), e00305-25, 2025

PPE50 variants as novel phylogeographic signatures of host-pathogen co-evolution in tuberculosis

C D’Souza, JE Phelan, PJ Gomez-Gonzalez, J Thorpe, TG Clark, ...

Communications biology 8 (1), 1024, 2025

Rapid detection of antibiotic resistance in Burkholderia pseudomallei using MALDI-TOF mass spectrometry

N Nithimongkolchai, Y Hinwan, K Trisakul, L Wonglakorn, ...

Scientific reports 15 (1), 21867, 2025

The ahpC c−54t compensatory mutation is not always a valid surrogate for isoniazid resistance in Mycobacterium tuberculosis

V Szél, JE Phelan, SB Georghiou, DL Dolinger, TG Clark, S Niemann, ...

Antimicrobial agents and chemotherapy 69 (6), e00265-25, 2025

Gametocyte production and transmission fitness of African and Asian Plasmodium falciparum isolates with differential susceptibility to artemisinins

NI Proellochs, C Andolina, J Ramjith, R Stoter, GJ van Gemert, ...

Antimicrobial agents and chemotherapy 69 (6), e01930-24, 2025

USE OF ENVIRONMENTAL DNA (EDNA) FOR MONITORING THE PRESENCE OF ANOPHELES STEPHENSI AND ASSOCIATED INSECTICIDE RESISTANCE …

M Kristan, H Acford-Palmer, MO Campos, E Collins, J Phelan, ...

AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE 112 (6), 2025

Genome wide population genetics and molecular surveillance of insecticide resistance in Anopheles stephensi mosquitoes from Awash Sebat Kilo in Ethiopia

H Acford-Palmer, FG Tadesse, E Manko, JE Phelan, M Higgins, ...

Scientific reports 15 (1), 16443, 2025

Genomic analysis of Mycobacterium tuberculosis in Thailand reveals circulating lineage diversity, transmission, and drug resistance mutations

N Thawong, P Srilohasin, JE Phelan, W Phornsiricharoenphant, ...

An open-access dashboard to interrogate the genetic diversity of Mycobacterium tuberculosis clinical isolates (vol 14, 24792, 2024)

J Phelan, K van den Heede, S Masyn, R Verbeeck, TG Clark, ...

SCIENTIFIC REPORTS 15 (1), 2025

Author Correction: An open-access dashboard to interrogate the genetic diversity of Mycobacterium tuberculosis clinical isolates

J Phelan, K Van den Heede, S Masyn, R Verbeeck, TG Clark, ...

Scientific Reports 15, 11565, 2025

Genome-wide analyses of Mycobacterium tuberculosis complex isolates reveal insights into circulating lineages and drug resistance mutations in The Gambia

L Tientcheu, F Faal, N Top, O Jobe, SM Colley, A Ayorinde, A Mendy, ...

Research Square, rs. 3. rs-5913893, 2025

A new method for detecting mixed Mycobacterium tuberculosis infection and reconstructing constituent strains provides insights into transmission

B Sobkowiak, P Cudahy, MH Chitwood, TG Clark, C Colijn, L Grandjean, ...

Genome medicine 17 (1), 8, 2025

Antibiotic Susceptibility Patterns and Virulence Profiles of Classical and Hypervirulent Klebsiella pneumoniae Strains Isolated from Clinical Samples in Khyber …

Azra, TA Khan, I Ul Haq, W Hinthong, S Campino, A Gohar, N Khan, ...

Pathogens 14 (1), 79, 2025

A novel tool for designing targeted gene amplicons and an optimised set of primers for high-throughput sequencing in tuberculosis genomic studies

L Wang, N Thawong, J Thorpe, M Higgins, MT Kia Ik, W Sawaengdee, ...

bioRxiv, 2025.01. 13.632698, 2025

Serological insights from SARS-CoV-2 heterologous prime and boost responses in Thailand

D Ward, L Pattarapreeyakul, R Pitaksalee, N Thawong, W Sawaengdee, ...

Scientific reports 15 (1), 1519, 2025

Application of a targeted amplicon sequencing panel to screen for insecticide resistance mutations in Anopheles darlingi populations from Brazil

H Acford-Palmer, AO Andrade, JE Phelan, RA Santana, SCP Lopes, ...

Scientific reports 15 (1), 731, 2025

Long short-term memory-based deep learning model for the discovery of antimicrobial peptides targeting Mycobacterium tuberculosis

L Wang, S Campino, TG Clark, JE Phelan

Bioinformatics advances 5 (1), vbaf274, 2025

Genomic analysis of global Plasmodium vivax populations reveals insights into the evolution of drug resistance

GC Ngwana-Joseph, JE Phelan, E Manko, JG Dombrowski, ...

Nature communications 15 (1), 10771, 2024

Genome sequencing of Plasmodium malariae identifies continental segregation and mutations associated with reduced pyrimethamine susceptibility

A Ibrahim, F Mohring, E Manko, DA van Schalkwyk, JE Phelan, D Nolder, ...

Nature communications 15 (1), 10779, 2024

TGV: suite of tools to visualize transmission graphs

JE Phelan, F Niazi, L Wang, GC Ngwana-Joseph, B Sobkowiak, T Cohen, ...

NAR genomics and bioinformatics 6 (4), lqae158, 2024

Longitudinal Immunological Analysis of Portuguese Healthcare Workers Across the COVID-19 Pandemic Reveals Differences in the Humoral Immune Response to Vaccines

L Vilela, A Silva, A Cruz, M Sousa, M Costa, F Fonseca, S Campino, ...

Vaccines 12 (12), 1358, 2024

Leveraging large-scale Mycobacterium tuberculosis whole genome sequence data to characterise drug-resistant mutations using machine learning and statistical …

SS Pruthi, N Billows, J Thorpe, S Campino, JE Phelan, F Mohareb, ...

Scientific reports 14 (1), 27091, 2024

Association of the humoral immune response with the inflammatory profile in Plasmodium vivax infections in pregnant women

RM Souza, MI Dos Santos, LC Gomes, BBP de Melo, EPM Separovic, ...

PLoS neglected tropical diseases 18 (11), e0012636, 2024

Insights into the use of cytochrome bc1 inhibitors for future therapeutic strategies for tuberculosis

CA Pérez, A Lenaerts, C Villellas, J Guillemont, J Dallow, H Painter, ...

An open-access dashboard to interrogate the genetic diversity of Mycobacterium tuberculosis clinical isolates

J Phelan, K Van den Heede, S Masyn, R Verbeeck, TG Clark, ...

Scientific reports 14 (1), 24792, 2024

Diversity, functional classification and genotyping of SHV β-lactamases in Klebsiella pneumoniae

KK Tsang, MMC Lam, RR Wick, KL Wyres, M Bachman, S Baker, K Barry, ...

Microbial genomics 10 (10), 001294, 2024

Phenotypic evidence of deltamethrin resistance and identification of selective sweeps in Anopheles mosquitoes on the Bijagós Archipelago, Guinea-Bissau

S Moss, RT Jones, E Pretorius, ET da Silva, M Higgins, M Kristan, ...

Scientific reports 14 (1), 22840, 2024

Whole genome sequence analysis of population structure and insecticide resistance markers in Anopheles melas from the Bijagós Archipelago, Guinea-Bissau

S Moss, E Pretorius, S Ceesay, ET da Silva, H Hutchins, MO Ndiath, ...

Parasites & vectors 17 (1), 396, 2024

Whole genome analysis of Plasmodium malariae identifies reduced susceptibility to pyrimethamine, validated using ortholog replacement in P. knowlesi

A Ibrahim, F Mohring, E Manko, D van Schalkwyk, J Phelan, D Nolder, ...

A Pan Plasmodium lateral flow recombinase polymerase amplification assay for monitoring malaria parasites in vectors and human populations

M Higgins, M Kristan, EL Collins, LA Messenger, JG Dombrowski, ...

Scientific reports 14 (1), 20165, 2024

Comparisons of genome assembly tools for characterization of Mycobacterium tuberculosis genomes using hybrid sequencing technologies

K Trisakul, Y Hinwan, J Eisiri, K Salao, A Chaiprasert, P Kamolwat, ...

PeerJ 12, e17964, 2024

Whole genome sequencing analysis of Mycobacterium tuberculosis reveals circulating strain types and drug-resistance mutations in the Philippines

L Wang, DR Lim, JE Phelan, LT Reyes, AG Palparan, MGC Sanchez, ...

Scientific reports 14 (1), 19602, 2024

Exploring the Antimicrobial Resistance Profile of Salmonella typhi and Its Clinical Burden

M Asghar, TA Khan, MN Séraphin, LF Schimke, O Cabral-Marques, ...

Antibiotics 13 (8), 765, 2024

Plasmodium falciparum population dynamics in East Africa and genomic surveillance along the Kenya-Uganda border

A Osborne, E Mańko, H Waweru, A Kaneko, K Kita, S Campino, J Gitaka, ...

Scientific reports 14 (1), 18051, 2024

Uncovering the genetic diversity in Aedes aegypti insecticide resistance genes through global comparative genomics

A Spadar, E Collins, LA Messenger, TG Clark, S Campino

Scientific Reports 14 (1), 13447, 2024

Large-scale statistical analysis of Mycobacterium tuberculosis genome sequences identifies compensatory mutations associated with multi-drug resistance

N Billows, J Phelan, D Xia, Y Peng, TG Clark, YM Chang

Scientific reports 14 (1), 12312, 2024

Exploring optimal drug targets through subtractive proteomics analysis and pangenomic insights for tailored drug design in tuberculosis

MF Khan, A Ali, HM Rehman, S Noor Khan, HM Hammad, M Waseem, ...

Scientific reports 14 (1), 10904, 2024

Genome-wide association study of global Plasmodium vivax populations provides insights into the evolution of drug resistance

G Ngwana-Joseph, J Phelan, E Manko, J Dombrowski, S dos Santos, ...

Multi-platform whole genome sequencing for tuberculosis clinical and surveillance applications

J Thorpe, W Sawaengdee, D Ward, M Campos, N Wichukchinda, ...

Scientific Reports 14 (1), 5201, 2024

Newly identified Mycobacterium africanum lineage 10, central Africa

C Guyeux, G Senelle, A Le Meur, P Supply, C Gaudin, JE Phelan, ...

Emerging infectious diseases 30 (3), 560, 2024

New reference genomes to distinguish the sympatric malaria parasites, Plasmodium ovale curtisi and Plasmodium ovale wallikeri

M Higgins, E Manko, D Ward, JE Phelan, D Nolder, CJ Sutherland, ...

Scientific reports 14 (1), 3843, 2024

Genomic analysis of Salmonella enterica from Metropolitan Manila abattoirs and markets reveals insights into circulating virulence and antimicrobial resistance …

JFB Mora, VYB Meclat, AMB Calayag, S Campino, JCR Hafalla, ...

Frontiers in microbiology 14, 1304283, 2024

Genomic surveillance of Anopheles mosquitoes on the Bijagós Archipelago using custom targeted amplicon sequencing identifies mutations associated with …

S Moss, E Pretorius, S Ceesay, H Hutchins, ET da Silva, MO Ndiath, ...

Parasites & vectors 17 (1), 10, 2024

A computational method for predicting the most likely evolutionary trajectories in the stepwise accumulation of resistance mutations

RC Eccleston, E Manko, S Campino, TG Clark, N Furnham

Elife 12, e84756, 2023

Rapid profiling of Plasmodium parasites from genome sequences to assist malaria control

JE Phelan, A Turkiewicz, E Manko, J Thorpe, LN Vanheer, ...

Genome medicine 15 (1), 96, 2023

Detection of insecticide resistance markers in Anopheles funestus from the Democratic Republic of the Congo using a targeted amplicon sequencing panel

H Acford-Palmer, M Campos, J Bandibabone, S N’Do, C Bantuzeko, ...

Scientific Reports 13 (1), 17363, 2023

Mixed infections in genotypic drug-resistant Mycobacterium tuberculosis

L Wang, S Campino, J Phelan, TG Clark

Scientific reports 13 (1), 17100, 2023

Functional genetic variation in pe/ppe genes contributes to diversity in Mycobacterium tuberculosis lineages and potential interactions with the human host

PJ Gómez-González, AD Grabowska, LD Tientcheu, AG Tsolaki, ...

Frontiers in microbiology 14, 1244319, 2023

Large-scale reference-free analysis of flavivirus sequences in Aedes aegypti whole genome DNA sequencing data

A Spadar, JE Phelan, TG Clark, S Campino

Parasites & vectors 16 (1), 265, 2023

Genomic and functional portrait of multidrug-resistant, hydrogen sulfide (H2S)-producing variants of Escherichia coli

R Mazumder, A Hussain, MM Rahman, JE Phelan, S Campino, ...

Frontiers in microbiology 14, 1206757, 2023

High throughput human genotyping for variants associated with malarial disease outcomes using custom targeted amplicon sequencing

A Osborne, JE Phelan, LN Vanheer, A Manjurano, J Gitaka, CJ Drakeley, ...

Scientific reports 13 (1), 12062, 2023

Drug resistance profiling of asymptomatic and low-density Plasmodium falciparum malaria infections on Ngodhe island, Kenya, using custom dual-indexing next …

A Osborne, JE Phelan, A Kaneko, W Kagaya, C Chan, M Ngara, ...

Scientific reports 13 (1), 11416, 2023

Comparison of in silico predicted Mycobacterium tuberculosis spoligotypes and lineages from whole genome sequencing data

G Napier, D Couvin, G Refrégier, C Guyeux, CJ Meehan, C Sola, ...

Scientific reports 13 (1), 11368, 2023

Feature weighted models to address lineage dependency in drug-resistance prediction from Mycobacterium tuberculosis genome sequences

N Billows, JE Phelan, D Xia, Y Peng, TG Clark, YM Chang

Bioinformatics 39 (7), btad428, 2023

Case report: A successfully treated case of community-acquired urinary tract infection due to Klebsiella aerogenes in Bangladesh

R Mazumder, A Hussain, B Bhadra, J Phelan, S Campino, TG Clark, ...

Frontiers in medicine 10, 1206756, 2023

Genome-wide genetic variation and molecular surveillance of drug resistance in Plasmodium falciparum isolates from asymptomatic individuals in …

LN Vanheer, A Mahamar, E Manko, SM Niambele, K Sanogo, A Youssouf, ...

Scientific reports 13 (1), 9522, 2023

Genome dynamics of high-risk resistant and hypervirulent Klebsiella pneumoniae clones in Dhaka, Bangladesh

A Hussain, R Mazumder, A Ahmed, U Saima, JE Phelan, S Campino, ...

Frontiers in microbiology 14, 1184196, 2023

Bayesian compositional regression with microbiome features via variational inference

DAV Scott, E Benavente, J Libiseller-Egger, D Fedorov, J Phelan, E Ilina, ...

BMC bioinformatics 24 (1), 210, 2023

Emergence of KPC-3- and OXA-181-producing ST13 and ST17 Klebsiella pneumoniae in Portugal: genomic insights on national and international dissemination

R Elias, A Spadar, APA Hendrickx, RA Bonnin, L Dortet, M Pinto, ...

Journal of Antimicrobial Chemotherapy 78 (5), 1300-1308, 2023

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Scientific Reports 13 (1), 6311, 2023

The evolution and transmission dynamics of multidrug-resistant tuberculosis in an isolated high-plateau population of Tibet, China

Q Jiang, HC Liu, QY Liu, JE Phelan, FX Tao, XQ Zhao, J Wang, JR Glynn, ...

Microbiology spectrum 11 (2), e03991-22, 2023

Identification of two insecticide resistance markers in Ethiopian Anopheles stephensi mosquitoes using a multiplex amplicon sequencing assay

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Scientific reports 13 (1), 5612, 2023

Validation and refinement of two interpretable models for coronavirus disease 2019 prognosis prediction

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World Journal of Traditional Chinese Medicine 9 (2), 191-200, 2023

IFNγ, TNFα polymorphisms and IFNγ serum levels are associated with the clearance of drug-resistant P. falciparum in Malian children

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Cytokine 164, 156137, 2023

JC Polyomavirus T-antigen protein expression and the risk of colorectal cancer: Systematic review and meta-analysis of case-control studies

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PLoS One 18 (3), e0283642, 2023

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P Nguipdop-Djomo, WE Oswald, KE Halliday, S Cook, J Sturgess, ...

International Journal of Infectious Diseases 128, 230-243, 2023

Towards environmental detection, quantification, and molecular characterization of Anopheles stephensi and Aedes aegypti from experimental larval breeding sites

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Scientific Reports 13 (1), 2729, 2023

Bayesian compositional regression with microbiome features via variational inference

S DAV, B ED, J LIBISELLER-EGGER, D FEDOROV, J PHELAN, E ILINA, ...

Population genetic analysis of Plasmodium knowlesi reveals differential selection and exchange events between Borneo and Peninsular sub-populations

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Scientific reports 13 (1), 2142, 2023

Genome-wide host-pathogen analyses reveal genetic interaction points in tuberculosis disease

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Nature communications 14 (1), 549, 2023

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The Lancet Regional Health–Americas 18, 2023

Genetic diversity of Plasmodium vivax isolates from pregnant women in the Western Brazilian Amazon: a prospective cohort study

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The Lancet Regional Health–Americas 18, 2023

Using whole genome sequencing data to identify strain-types, transmission enhancers and novel drug resistance mutations of Mycobacterium tuberculosis

G Napier

London School of Hygiene & Tropical Medicine, 2023

Large-scale genomic analysis of global Klebsiella pneumoniae plasmids reveals multiple simultaneous clusters of carbapenem-resistant hypervirulent strains

A Spadar, J Perdigão, S Campino, TG Clark

Genome medicine 15 (1), 3, 2023

Large-scale genomic analysis of Mycobacterium tuberculosis reveals extent of target and compensatory mutations linked to multi-drug resistant tuberculosis

G Napier, S Campino, JE Phelan, TG Clark

Scientific reports 13 (1), 623, 2023

Feature Weighted Models (FWM) to address lineage dependency in drug-resistance prediction from Mycobacterium tuberculosis genome sequences

N Billows, JE Phelan, D Xia, Y Peng, TG Clark, YM Chang

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DP Fernández Echeverri, GJ Vélez Tobón, A Tobón Castaño, S Campino, ...

Elsevier, 2023

TB-ML—a framework for comparing machine learning approaches to predict drug resistance of Mycobacterium tuberculosis

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Bioinformatics advances 3 (1), vbad040, 2023

Genetic diversity of Plasmodium vivax isolates from pregnant women in the Western Brazilian Amazon: aprospective cohort study

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The Lancet Regional Health. Americas 18, 1-11, 2023

Genetic mutations underlying isoniazid-resistant Mycobacterium tuberculosis in Khyber Pakhtunkhwa, Pakistan

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Tuberculosis 138, 102286, 2023

Combination of virulence and antibiotic resistance: a successful bacterial strategy to survive under hostile environments

A Hussain, R Mazumder, M Asadulghani, TG Clark, D Mondal

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Deep learning-derived cardiovascular age shares a genetic basis with other cardiac phenotypes

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Scientific reports 12 (1), 22625, 2022

High clustering rate and genotypic drug-susceptibility screening for the newly recommended anti-tuberculosis drugs among global extensively drug-resistant Mycobacterium …

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A next generation targeted amplicon sequencing method to screen for insecticide resistance mutations in Aedes aegypti populations reveals a rdl mutation in …

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Machine learning methods for infectious diseases: applications for tuberculosis and malaria

WA Deelder

London School of Hygiene & Tropical Medicine, 2022

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Scientific reports 12 (1), 21150, 2022

The COVID-19 Schools Infection Survey in England: protocol and participation profile for a prospective observational cohort study

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JMIR research protocols 11 (11), e34075, 2022

Non-lactose fermenting Escherichia coli: Following in the footsteps of lactose fermenting E. coli high-risk clones

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Characterizing the impact of primer-template mismatches on recombinase polymerase amplification

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Epidemiology of SARS-CoV-2 infection among staff and students in a cohort of English primary and secondary schools during 2020–2021

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The Lancet Regional Health–Europe 21, 2022

Portable sequencing of Mycobacterium tuberculosis for clinical and epidemiological applications

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Genomic surveillance of SARS-COV-2 reveals diverse circulating variant lineages in Nairobi and Kiambu Counties, Kenya

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BMC genomics 23 (1), 627, 2022

High-throughput barcoding method for the genetic surveillance of insecticide resistance and species identification in Anopheles gambiae complex malaria vectors

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Scientific reports 12 (1), 13893, 2022

Genomic epidemiological analysis of Klebsiella pneumoniae from Portuguese hospitals reveals insights into circulating antimicrobial resistance

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Scientific Reports 12 (1), 13791, 2022

Genomic analysis of hypervirulent Klebsiella pneumoniae reveals potential genetic markers for differentiation from classical strains

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Sero-epidemiological study of arbovirus infection following the 2015–2016 Zika virus outbreak in Cabo Verde

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Scientific Reports 12 (1), 11719, 2022

Molecular characterization of drug-resistant Mycobacterium tuberculosis among Filipino patients derived from the national tuberculosis prevalence survey Philippines 2016

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Malaria journal 21 (1), 186, 2022

A phylogenomic approach for the analysis of colistin resistance-associated genes in Klebsiella pneumoniae, its mutational diversity and implications for phenotypic resistance

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Scientific reports 12 (1), 7703, 2022

COVID-profiler: a webserver for the analysis of SARS-CoV-2 sequencing data

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PowerBacGWAS: a computational pipeline to perform power calculations for bacterial genome-wide association studies

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A modified decision tree approach to improve the prediction and mutation discovery for drug resistance in Mycobacterium tuberculosis

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Characterizing the genomic variation and population dynamics of Plasmodium falciparum malaria parasites in and around Lake Victoria, Kenya

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Scientific reports 11 (1), 14194, 2021

Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus

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Antibiotics 10 (6), 733, 2021

Using deep learning to identify recent positive selection in malaria parasite sequence data

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Malaria journal 20 (1), 270, 2021

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Nature communications 12 (1), 3160, 2021

An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities

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Scientific Reports 11 (1), 10590, 2021

Adverse pregnancy outcomes are associated with Plasmodium vivax malaria in a prospective cohort of women from the Brazilian Amazon

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Methylation analysis of Klebsiella pneumoniae from Portuguese hospitals

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Clusters of drug-resistant Mycobacterium tuberculosis detected by whole-genome sequence analysis of nationwide sample, Thailand, 2014–2017

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Emerging infectious diseases 27 (3), 813, 2021

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medRxiv, 2021.02. 19.21252065, 2021

Development and validation of a nomogram for assessing survival in patients with COVID-19 pneumonia

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A snapshot of translation in Mycobacterium tuberculosis during exponential growth and nutrient starvation revealed by ribosome profiling

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Cell Reports 34 (5), 2021

Studying accelerated cardiovascular ageing in Russian adults through a novel deep-learning ECG biomarker

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The antimalarial efficacy and mechanism of resistance of the novel chemotype DDD01034957

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An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets

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Studying accelerated cardiovascular ageing in Russian adults through a novel deep-learning ECG biomarker

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Antimicrobial Resistance & Infection Control 9 (1), 194, 2020

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Surveillance of Aedes aegypti populations in the city of Praia, Cape Verde: Zika virus infection, insecticide resistance and genetic diversity

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Nature medicine 26 (9), 1435-1443, 2020

How myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) progresses: the natural history of ME/CFS

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Whole genome sequencing of drug resistant Mycobacterium tuberculosis isolates from a high burden tuberculosis region of North West Pakistan.

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A comprehensive analysis of drug resistance molecular markers and Plasmodium falciparum genetic diversity in two malaria endemic sites in Mali

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Malaria journal 18 (1), 361, 2019

Whole genome sequencing of drug resistant Mycobacterium tuberculosis isolates from a high burden tuberculosis region of North West Pakistan

A Jabbar, JE Phelan, PF de Sessions, TA Khan, H Rahman, SN Khan, ...

Scientific reports 9 (1), 14996, 2019

Machine Learning Predicts Accurately Mycobacterium tuberculosis Drug Resistance From Whole Genome Sequencing Data

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Frontiers in genetics 10, 922, 2019

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Scientific reports 9 (1), 13718, 2019

How Myalgic encephalomyelitis/Chronic fatigue syndrome (ME/CFS) progresses: A framework for research and the prevention, treatment, and rehabilitation in ME/CFS

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The Lancet Respiratory Medicine Commission: 2019 update: epidemiology, pathogenesis, transmission, diagnosis, and management of multidrug-resistant and incurable tuberculosis

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The Lancet Respiratory Medicine 7 (9), 820-826, 2019

Clonal expansion across the seas as seen through CPLP-TB database: A joint effort in cataloguing Mycobacterium tuberculosis genetic diversity in Portuguese-speaking countries

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Whole genome sequencing of amplified Plasmodium knowlesi DNA from unprocessed blood reveals genetic exchange events between Malaysian Peninsular and …

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Scientific Reports 9 (1), 9873, 2019

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Mycobacterium tuberculosis whole genome sequencing provides insights into the Manila strain and drug-resistance mutations in the Philippines

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Scientific reports 9 (1), 9305, 2019

Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs

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Genome medicine 11 (1), 41, 2019

Rapid and iterative genome editing in the malaria parasite Plasmodium knowlesi provides new tools for P. vivax research

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Elife 8, e45829, 2019

An analysis of large structural variation in global Plasmodium falciparum isolates identifies a novel duplication of the chloroquine resistance associated gene

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Scientific Reports 9 (1), 8287, 2019

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London School of Hygiene & Tropical Medicine, 2019

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

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Scientific Reports 9 (1), 5204, 2019

Artemisinin resistance-associated markers in Plasmodium falciparum parasites from the China-Myanmar border: predicted structural stability of K13 propeller …

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BMC bioinformatics 20 (1), 136, 2019

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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 …

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A forward genetic screen reveals a primary role for Plasmodium falciparum Reticulocyte Binding Protein Homologue 2a and 2b in determining alternative erythrocyte invasion pathways

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PLoS pathogens 14 (11), e1007436, 2018

Hand grip strength as a clinical biomarker for ME/CFS and disease severity

LC Nacul, K Mudie, CC Kingdon, TG Clark, EM Lacerda

Frontiers in neurology 9, 992, 2018

Using whole genome sequence data to study genomic diversity and develop molecular barcodes to profile Plasmodium malaria parasites

E Díez Benavente

London School of Hygiene & Tropical Medicine, 2018

Global genetic diversity of var2csa in Plasmodium falciparum with implications for malaria in pregnancy and vaccine development

ED Benavente, DR Oresegun, PF de Sessions, EM Walker, C Roper, ...

Scientific Reports 8 (1), 15429, 2018

Understanding molecular consequences of putative drug resistant mutations in Mycobacterium tuberculosis

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Global expansion of Mycobacterium tuberculosis lineage 4 shaped by colonial migration and local adaptation

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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

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PLoS One 13 (8), e0201452, 2018

Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data

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Evidence for Host-Bacterial Co-evolution via Genome Sequence Analysis of 480 Thai Mycobacterium tuberculosis Lineage 1 Isolates

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Scientific reports 8 (1), 11597, 2018

Human candidate gene polymorphisms and risk of severe malaria in children in Kilifi, Kenya: a case-control association study

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The Lancet Haematology 5 (8), e333-e345, 2018

Global analysis of Plasmodium falciparum histidine-rich protein-2 (pfhrp2) and pfhrp3 gene deletions using whole-genome sequencing data and meta-analysis

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Infection, genetics and evolution 62, 211-219, 2018

Enrichment of clinically relevant organisms in spontaneous preterm-delivered placentas and reagent contamination across all clinical groups in a large pregnancy cohort in the …

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Genomic analysis of a pre-elimination Malaysian Plasmodium vivax population reveals selective pressures and changing transmission dynamics

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Nature communications 9 (1), 2585, 2018

Human coronavirus NL63 molecular epidemiology and evolutionary patterns in rural coastal Kenya

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The Journal of infectious diseases 217 (11), 1728-1739, 2018

Use of whole genome sequencing in surveillance of drug resistant tuberculosis

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Genome-wide analysis of multi-and extensively drug-resistant Mycobacterium tuberculosis (vol 50, pg 307, 2018)

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Nature genetics 50 (5), 764-764, 2018

Frequent Undetected Ward-Based Methicillin-Resistant Staphylococcus aureus Transmission Linked to Patient Sharing Between Hospitals

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Clinical Infectious Diseases 66 (6), 840-848, 2018

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

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International journal for parasitology 48 (3-4), 191-196, 2018

Population-based analysis of ocular Chlamydia trachomatis in trachoma-endemic West African communities identifies genomic markers of disease severity

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Genome medicine 10 (1), 15, 2018

Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis

F Coll, J Phelan, GA Hill-Cawthorne, MB Nair, K Mallard, S Ali, ...

Nature genetics 50 (2), 307-316, 2018

Novel genetic polymorphisms associated with severe malaria and under selective pressure in North-eastern Tanzania

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PLoS genetics 14 (1), e1007172, 2018

Methylation in Mycobacterium tuberculosis is lineage specific with associated mutations present globally

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Global genetic diversity of var2csa in Plasmodium falciparum with implications for malaria in pregnancy and vaccine development. Sci Rep 8: 15429

ED Benavente, DR Oresegun, PF de Sessions, EM Walker, C Roper, ...

Methylation in Mycobacterium tuberculosis is lineage specific with associated mutations present globally. Sci Rep 8: 160

J Phelan, PF de Sessions, L Tientcheu, J Perdigao, D Machado, R Hasan, ...

Population-based analysis of ocular Chlamydia trachomatis in trachoma-endemic West African communities identifies genomic markers of disease severity

HMB Seth-Smith, J Hadfield, LT Cutcliffe, IN Clarke, DCW Mabey, ...

Novel genetic polymorphisms associated with severe malaria and under selective pressure in North-eastern Tanzania

B Nadjm, G Mtove, H Wangai, C Maxwell, R Olomi

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AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE 99 (4), 533-533, 2018

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International journal for parasitology. Drugs and drug resistance, 2017

Genetic diversity of next generation antimalarial targets: A baseline for drug resistance surveillance programmes (vol 7, pg 174, 2017)

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INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 7 (3), 433-433, 2017

Role of Alanine Racemase Mutations in Mycobacterium tuberculosisd-Cycloserine Resistance

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Antimicrobial agents and chemotherapy 61 (12), 10.1128/aac. 01575-17, 2017

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

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ELUCIDATION OF THE DIVERGENT APICOPLAST GENOMES OF PLASMODIUM OVALE CURTISI AND P. OVALE WALLIKERI

MC Oguike, ED Benavente, TG Clark, HP Fuehrer, A Pain, CJ Sutherland

AMER SOC TROP MED & HYGIENE, 2017

Frequent undetected MRSA ward-based transmission linked to patient sharing between hospitals

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Clinical Infectious Diseases 66 (6), 2017

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

MC Campos, J Phelan, AF Francisco, MC Taylor, MD Lewis, A Pain, ...

Scientific reports 7 (1), 14407, 2017

Plasmodium falciparum infection during pregnancy impairs fetal head growth: prospective and populational-based retrospective studies

JG Dombrowski, RM de Souza, FA Lima, CL Bandeira, O Murillo, ...

bioRxiv, 203059, 2017

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

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BioMed Central Ltd., 2017

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

P Sheen, D Requena, E Gushiken, RH Gilman, R Antiparra, B Lucero, ...

BMC genomics 18 (1), 769, 2017

Analysis of nuclear and organellar genomes of Plasmodium knowlesi in humans reveals ancient population structure and recent recombination among host …

E Diez Benavente, P Florez de Sessions, RW Moon, AA Holder, ...

PLoS genetics 13 (9), e1007008, 2017

Structural nested mean models for assessing time-varying effect moderation

V Hoang, SK Medrek, M Pendurthi, C Kao, AD Parulekar, JC Yeung, ...

American Journal of Respiratory and Critical Care Medicine 196 (6), 782-784, 2017

Modest heterologous protection after Plasmodium falciparum sporozoite immunization: a double-blind randomized controlled clinical trial

J Walk, IJ Reuling, MC Behet, L Meerstein-Kessel, W Graumans, ...

BMC medicine 15 (1), 168, 2017

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

AR Gomes, M Ravenhall, ED Benavente, A Talman, C Sutherland, ...

International Journal for Parasitology: Drugs and Drug Resistance 7 (2), 174-180, 2017

Pyrazinamide resistance-conferring mutations in pncA and the transmission of multidrug resistant TB in Georgia

S Sengstake, IL Bergval, AR Schuitema, JL de Beer, J Phelan, ...

BMC infectious diseases 17 (1), 491, 2017

Malaria host candidate genes validated by association with current, recent, and historical measures of transmission intensity

N Sepúlveda, A Manjurano, SG Campino, M Lemnge, J Lusingu, R Olomi, ...

The Journal of infectious diseases 216 (1), 45-54, 2017

G6PD deficiency alleles in a malaria-endemic region in the Western Brazilian Amazon

JG Dombrowski, RM Souza, J Curry, L Hinton, NRM Silva, L Grignard, ...

Malaria journal 16 (1), 253, 2017

Genomic variation in Plasmodium vivax malaria reveals regions under selective pressure

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Outcomes, Infectiousness And Transmission Dynamics Of Patients With Extensively Drug Resistant Tuberculosis And Home-Discharged Patients With Programmatically Incurable Tb: A …

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The epidemiology, pathogenesis, transmission, diagnosis, and management of multidrug-resistant, extensively drug-resistant, and incurable tuberculosis

K Dheda, T Gumbo, G Maartens, KE Dooley, R McNerney, M Murray, ...

The lancet Respiratory medicine 5 (4), 291-360, 2017

Outcomes, infectiousness, and transmission dynamics of patients with extensively drug-resistant tuberculosis and home-discharged patients with programmatically incurable …

K Dheda, JD Limberis, E Pietersen, J Phelan, A Esmail, M Lesosky, ...

The lancet Respiratory medicine 5 (4), 269-281, 2017

VivaxGEN: An open access platform for comparative analysis of short tandem repeat genotyping data in Plasmodium vivax populations

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PLoS neglected tropical diseases 11 (3), e0005465, 2017

Removing the bottleneck in whole genome sequencing of Mycobacterium tuberculosis for rapid drug resistance analysis: a call to action

R McNerney, TG Clark, S Campino, C Rodrigues, D Dolinger, L Smith, ...

International journal of infectious diseases 56, 130-135, 2017

The UK ME/CFS biobank for biomedical research on myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) and multiple sclerosis

EM Lacerda, EW Bowman, JM Cliff, CC Kingdon, EC King, JS Lee, ...

Open journal of bioresources 4, 4, 2017

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

N Andreu, J Phelan, PF de Sessions, JM Cliff, TG Clark, ML Hibberd

Scientific reports 7 (1), 42225, 2017

Multi-centre analysis of the complex effects of G6PD deficiency on resistance to severe malaria

G Clarke, K Rockett, K Kivinen, C Hubbart, A Jeffreys, K Rowlands, ...

eLife 6, 2017

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

GM Clarke, K Rockett, K Kivinen, C Hubbart, AE Jeffreys, K Rowlands, ...

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Plasmodium falciparum infection during pregnancy impairs fetal head growth: prospective and populational-based retrospective studies

FM Cr, E Bevilacqua, O Murillo, LB Gonçalves, MP Ep, TG Clark, L Fa, ...

The epidemiology, pathogenesis, transmission, diagnosis, and management of multidrug-resistant, extensively drug-resistant, and incurable tuberculosis. Lancet Respiratory …

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N Andreu, J Phelan, PF De Sessions, JM Cliff, TG Clark, ML Hibberd

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JG Dombrowski, RM Souza, LC Gomes, BBP Melo, LA Gonçalves, ...

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Primary macrophages and J774 cells respond differently to infection with Mycobacterium tuberculosis. Sci Rep 7: 42225

N Andreu, J Phelan, PF De Sessions, JM Cliff, TG Clark, ML Hibberd

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JD Limberis, E Pietersen, J Phelan, A Esmail, M Lesosky, KP Fennelly, ...

American Journal of Respiratory and Critical Care Medicine 195, 2017

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

J Phelan, DM O’Sullivan, D Machado, J Ramos, AS Whale, J O’Grady, ...

Genome medicine 8 (1), 132, 2016

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

A Kanji, R Hasan, A Zaver, A Ali, K Imtiaz, M Ashraf, TG Clark, ...

International journal of mycobacteriology 5, S97-S98, 2016

Characterizing the impact of sustained sulfadoxine/pyrimethamine use upon the Plasmodium falciparum population in Malawi

M Ravenhall, ED Benavente, M Mipando, ATR Jensen, CJ Sutherland, ...

Malaria journal 15 (1), 575, 2016

Turkish and Japanese Mycobacterium tuberculosis sublineages share a remote common ancestor

G Refrégier, E Abadia, T Matsumoto, H Ano, T Takashima, I Tsuyuguchi, ...

Infection, genetics and evolution 45, 461-473, 2016

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

HR Ansari, TJ Templeton, AK Subudhi, A Ramaprasad, J Tang, F Lu, ...

International journal for parasitology 46 (11), 685-696, 2016

Outcomes of surgical fundoplication: The need for novel diagnostic tests for extra-oesophageal reflux symptoms

T Clark, C Gelder, V Menon

BRITISH JOURNAL OF SURGERY 103, 132-132, 2016

Genome-scale comparison of expanded gene families in Plasmodium

HR Ansari, TJ Templeton, AK Subudhi, A Ramaprasad, J Tang, F Lu, ...

Mortality of emergency abdominal surgery in high-, middle-and low-income countries

Journal of British Surgery 103 (8), 971-988, 2016

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GBJ Busby, G Band, Q Si Le, M Jallow, E Bougama, VD Mangano, ...

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Further evidence of increasing diversity of plasmodium vivax in the Republic of Korea in recent years.

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Genomic variation in two gametocyte non-producing Plasmodium falciparum clonal lines

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Malaria journal 15 (1), 229, 2016

Genetic signatures of Mycobacterium tuberculosis Nonthaburi genotype revealed by whole genome analysis of isolates from tuberculous meningitis patients in Thailand

OO Coker, A Chaiprasert, C Ngamphiw, S Tongsima, SM Regmi, TG Clark, ...

PeerJ 4, e1905, 2016

Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance

J Phelan, F Coll, R McNerney, DB Ascher, DEV Pires, N Furnham, ...

BMC medicine 14 (1), 31, 2016

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

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PLoS One 11 (3), e0151514, 2016

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bioRxiv, 043042, 2016

Characterization of new virulence factors involved in the intracellular growth and survival of Burkholderia pseudomallei

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Infection and immunity 84 (3), 701-710, 2016

Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages

JE Phelan, F Coll, I Bergval, RM Anthony, R Warren, SL Sampson, ...

BMC genomics 17 (1), 151, 2016

Ocular chlamydial genomic variants and disease severity in trachoma: a cross-sectional population-based genome-wide association study

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The Lancet 387, S63, 2016

The variability and reproducibility of whole genome sequencing technology for detecting resistance to anti-tuberculous drugs. Genome Med 8: 132

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G Refregier, E Abadia, T Matsumoto, H Ano, T Takashima, I Tsuyuguchi, ...

Supplementary Material for: Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance

J Phelan, F Coll, R McNerney, D Ascher, D Pires, N Furnham, N Coeck, ...

figshare, 2016

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J Phelan, F Coll, I Bergval, R Anthony, R Warren, S Sampson, NG Pittius, ...

figshare, 2016

Variation in complexity of infection and transmission stability between neighbouring populations of Plasmodium vivax in Southern Ethiopia.

SG Sisay Getachew, TSR To SheRen, H Trimarsanto, K Thriemer, ...

Multidrug-resistant Mycobacterium tuberculosis of the Latin American Mediterranean lineage, wrongly identified as Mycobacterium pinnipedii (spoligotype …

ERD Costa, SEG Vasconcelos, LS Esteves, HM Gomes, LL Gomes, ...

Multidrug-resistant Mycobacterium tuberculosis of the Latin American mediterranean lineage, wrongly identified as mycobacterium pinnipedii (Spoligotype International Type 863 …

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Journal of clinical microbiology 53 (12), 3805-3811, 2015

Conjunctival fibrosis and the innate barriers to Chlamydia trachomatis intracellular infection: a genome wide association study

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Scientific reports 5 (1), 17447, 2015

Genomic expression catalogue of a global collection of BCG vaccine strains show evidence for highly diverged metabolic and cell-wall adaptations

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Scientific reports 5 (1), 15443, 2015

Population genomic structure and adaptation in the zoonotic malaria parasite Plasmodium knowlesi

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Proceedings of the National Academy of Sciences 112 (42), 13027-13032, 2015

Variation in Complexity of Infection and Transmission Stability between Neighbouring Populations of Plasmodium vivax in Southern Ethiopia

S Getachew, S To, H Trimarsanto, K Thriemer, TG Clark, B Petros, ...

PloS one 10 (10), e0140780, 2015

GENOME SEQUENCING OF PLASMODIUM OVALE WALLIKERI

MC Oguike, I Aniebo, ED Bienevente, S Campino, TG Clark, O Gundogdu, ...

AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE 93 (4), 98-98, 2015

GENETIC SIGNATURES OF MALARIA SELECTION VALIDATED BY ASSOCIATION WITH CURRENT AND HISTORIC MEASURES OF MALARIA TRANSMISSION INTENSITY

N Sepulveda, A Manjurano, T Clark, E Riley, C Drakeley

AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE 93 (4), 280-280, 2015

Genomic epidemiology of a protracted hospital outbreak caused by a toxin A-negative Clostridium difficile sublineage PCR ribotype 017 strain in London, England

MD Cairns, MD Preston, TD Lawley, TG Clark, RA Stabler, BW Wren

Journal of clinical microbiology 53 (10), 3141-3147, 2015

USP38, FREM3, SDC1, DDC, and LOC727982 Gene Polymorphisms and Differential Susceptibility to Severe Malaria in Tanzania

A Manjurano, N Sepúlveda, B Nadjm, G Mtove, H Wangai, C Maxwell, ...

The Journal of infectious diseases 212 (7), 1129-1139, 2015

Author’s Statement

BFC Kafsack, N Rovira-Graells, TG Clark, C Bancells, VM Crowley, ...

April Elizabeth Williams, 52, 2015

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

J Phelan, A Maitra, R McNerney, M Nair, A Gupta, F Coll, A Pain, S Bhakta, ...

International journal of mycobacteriology 4 (3), 207-216, 2015

Genetic determinants of anti-malarial acquired immunity in a large multi-centre study

JMG Shelton, P Corran, P Risley, N Silva, C Hubbart, A Jeffreys, ...

Malaria journal 14 (1), 333, 2015

Whole genome sequencing shows a low proportion of tuberculosis disease is attributable to known close contacts in rural Malawi

JR Glynn, JA Guerra-Assunção, RMGJ Houben, L Sichali, T Mzembe, ...

PloS one 10 (7), e0132840, 2015

Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences

F Coll, R McNerney, MD Preston, JA Guerra-Assunção, A Warry, ...

Genome medicine 7 (1), 51, 2015

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

ED Benavente, F Coll, N Furnham, R McNerney, JR Glynn, S Campino, ...

BMC bioinformatics 16 (1), 155, 2015

Contrasting Transmission Dynamics of Co-endemic Plasmodium vivax and P. falciparum: Implications for Malaria Control and Elimination

R Noviyanti, F Coutrier, RAS Utami, H Trimarsanto, YK Tirta, L Trianty, ...

PLoS neglected tropical diseases 9 (5), e0003739, 2015

Imputation-Based Population Genetics Analysis of Plasmodium falciparum Malaria Parasites

H Samad, F Coll, MD Preston, H Ocholla, RM Fairhurst, TG Clark

PLoS genetics 11 (4), e1005131, 2015

Recurrence due to Relapse or Reinfection With Mycobacterium tuberculosis: A Whole-Genome Sequencing Approach in a Large, Population-Based Cohort With a …

JA Guerra-Assunção, RMGJ Houben, AC Crampin, T Mzembe, K Mallard, ...

The Journal of infectious diseases 211 (7), 1154-1163, 2015

Large-scale whole genome sequencing of M. tuberculosis provides insights into transmission in a high prevalence area

JA Guerra-Assunção, AC Crampin, R Houben, T Mzembe, K Mallard, ...

Elife 4, e05166, 2015

Genomic diversity of drug-resistant Mycobacterium tuberculosis isolates in Lisbon Portugal: Towards tuberculosis genomic epidemiology

J Perdigão, H Silva, D Machado, R Macedo, F Maltez, C Silva, L Jordao, ...

International Journal of Mycobacteriology 4, 27-28, 2015

Characterization of genomic variations in SNPs of PE_PGRS genes reveals deletions and insertions in extensively drug resistant (XDR) M. tuberculosis strains from Pakistan

A Kanji, Z Hasan, A Ali, R McNerney, K Mallard, F Coll, G Hill-Cawthorne, ...

International journal of mycobacteriology 4 (1), 73-79, 2015

Whole genome sequencing-based characterization of extensively drug resistant (XDR) strains of Mycobacterium tuberculosis from Pakistan

Z Hasan, A Ali, R McNerney, K Mallard, G Hill-Cawthorne, F Coll, M Nair, ...

International Journal of Mycobacteriology 4, 11-12, 2015

Independent Emergence of Artemisinin Resistance Mutations Among Plasmodium falciparum in Southeast Asia

S Takala-Harrison, CG Jacob, C Arze, MP Cummings, JC Silva, ...

The Journal of infectious diseases 211 (5), 670-679, 2015

Whole genome sequencing based characterization of extensively drug-resistant Mycobacterium tuberculosis isolates from Pakistan

A Ali, Z Hasan, R McNerney, K Mallard, G Hill-Cawthorne, F Coll, M Nair, ...

PloS one 10 (2), e0117771, 2015

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

A Manjurano, N Sepulveda, B Nadjm, G Mtove, H Wangai, C Maxwell, ...

PLoS genetics 11 (2), e1004960, 2015

Independent emergence of artemisinin resistance mutations among

S Takala-Harrison, CG Jacob, C Arze, MP Cummings, JC Silva, ...

Multidrug resistant Mycobacterium tuberculosis of the Latin American 1 Mediteranean lineage wrongly identified as Mycobacterium pinnipedii (ST863) 2 causing active tuberculosis …

LL Gomes, PA da Silva, J Perdigão, I Portugal, M Viveiros, R McNerney, ...

Large-scale whole genome sequencing of M. tuberculosis provides insights into transmission in a high prevalence area. Elife 4

J Guerra-Assunção, AC Crampin, R Houben, T Mzembe, K Mallard, F Coll, ...

eLife Sciences Publications, Ltd, 2015

Genomic expression catalogue of a global collection of BCG vaccine strains show evidence for highly diverged metabolic and cell-wall adaptations. Sci Rep 5: 15443

AM Abdallah, GA Hill-Cawthorne, TD Otto, F Coll, JA Guerra-Assunção, ...

Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences. Genome Med 7: 51

F Coll, R McNerney, MD Preston, JA Guerra-Assunção, A Warry, ...

The IVS data input to ITRF2014

A Nothnagel, W Alef, J Amagai, PH Andersen, J Anderson, T Andreeva, ...

GFZ Data Services, 2015

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

A Manjurano, N Sepúlveda, B Nadjm, G Mtove, H Wangai, C Maxwell, ...

PLoS Genet 11, e1004960, 2015

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 …

I Bergval, F Coll, A Schuitema, H de Ronde, K Mallard, A Pain, ...

FEMS microbiology letters 362 (2), fnu037, 2015

Directional Selection at the pfmdr1, pfcrt, pfubp1, and pfap2mu Loci of Plasmodium falciparum in Kenyan Children Treated With ACT

G Henriques, RL Hallett, KB Beshir, NB Gadalla, RE Johnson, R Burrow, ...

The Journal of infectious diseases 210 (12), 2001-2008, 2014

Whole-Genome Scans Provide Evidence of Adaptive Evolution in Malawian Plasmodium falciparum Isolates

H Ocholla, MD Preston, M Mipando, ATR Jensen, S Campino, B MacInnis, ...

The Journal of infectious diseases 210 (12), 1991-2000, 2014

Pathway-level analysis of a genome wide association scan coupled with transcriptome analysis reveals common repetitive signatures of innate defence and cell cycle interruption …

CH Roberts, C Franklin, S Molina-Gonzelez, F Payne, SE Burr, ...

IMMUNOLOGY 143, 161-161, 2014

Unraveling Mycobacterium tuberculosis genomic diversity and evolution in Lisbon, Portugal, a highly drug resistant setting

J Perdigão, H Silva, D Machado, R Macedo, F Maltez, C Silva, L Jordao, ...

BMC genomics 15 (1), 991, 2014

Reappraisal of known malaria resistance loci in a large multicenter study

Nature genetics 46 (11), 1197-1204, 2014

Impact of postoperative non-steroidal anti-inflammatory drugs on adverse events after gastrointestinal surgery

Journal of British Surgery 101 (11), 1413-1423, 2014

A robust SNP barcode for typing Mycobacterium tuberculosis complex strains

F Coll, R McNerney, JA Guerra-Assunção, JR Glynn, J Perdigão, ...

Nature communications 5 (1), 4812, 2014

SVAMP: sequence variation analysis, maps and phylogeny

R Naeem, L Hidayah, MD Preston, TG Clark, A Pain

Bioinformatics 30 (15), 2227-2229, 2014

Genetic diversity and population structure of Plasmodium vivax in Central China.

LYB Liu YaoBao, S Auburn, CJ Cao Jun, H Trimarsanto, ...

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

B Maiga, A Dolo, S Campino, N Sepulveda, P Corran, KA Rockett, ...

Malaria journal 13 (1), 270, 2014

Genetic diversity and population structure of Plasmodium vivax in Central China

Y Liu, S Auburn, J Cao, H Trimarsanto, H Zhou, KA Gray, TG Clark, ...

Malaria journal 13 (1), 262, 2014

On the Performance of Multiple Imputation Based on Chained Equations in Tackling Missing Data of the African α3.7‐Globin Deletion in a Malaria Association Study

N Sepulveda, A Manjurano, C Drakeley, TG Clark

Annals of human genetics 78 (4), 277-289, 2014

Recombinations in Staphylococcal Cassette Chromosome mec Elements Compromise the Molecular Detection of Methicillin Resistance in Staphylococcus aureus

GA Hill-Cawthorne, LO Hudson, MFA El Ghany, O Piepenburg, M Nair, ...

PloS one 9 (6), e101419, 2014

Association of candidate gene polymorphisms and TGF-beta/IL-10 levels with malaria in three regions of Cameroon: a case–control study

TO Apinjoh, JK Anchang-Kimbi, C Njua-Yafi, AN Ngwai, RN Mugri, ...

Malaria journal 13 (1), 236, 2014

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

MD Preston, S Campino, SA Assefa, DF Echeverry, H Ocholla, ...

Nature communications 5 (1), 4052, 2014

Genome-Wide Analysis of Selection on the Malaria Parasite Plasmodium falciparum in West African Populations of Differing Infection Endemicity

VA Mobegi, CW Duffy, A Amambua-Ngwa, KM Loua, E Laman, ...

Molecular biology and evolution 31 (6), 1490-1499, 2014

PlasmoView: A Web-based Resource to Visualise Global Plasmodium falciparum Genomic Variation

MD Preston, SA Assefa, H Ocholla, CJ Sutherland, S Borrmann, A Nzila, ...

The Journal of infectious diseases 209 (11), 1808-1815, 2014

Cathepsin-L Can Resist Lysis by Human Serum in Trypanosoma brucei brucei

S Alsford, RB Currier, JA Guerra-Assuncao, TG Clark, D Horn

PLoS pathogens 10 (5), e1004130, 2014

PolyTB: a genomic variation map for Mycobacterium tuberculosis

F Coll, M Preston, JA Guerra-Assunção, G Hill-Cawthorn, D Harris, ...

Tuberculosis 94 (3), 346-354, 2014

estMOI: estimating multiplicity of infection using parasite deep sequencing data

SA Assefa, MD Preston, S Campino, H Ocholla, CJ Sutherland, TG Clark

Bioinformatics 30 (9), 1292-1294, 2014

Changes in malaria parasite drug resistance in an endemic population over a 25-year period with resulting genomic evidence of selection

DC Nwakanma, CW Duffy, A Amambua-Ngwa, EC Oriero, KA Bojang, ...

The Journal of infectious diseases 209 (7), 1126-1135, 2014

A transcriptional switch underlies commitment to sexual development in malaria parasites

BFC Kafsack, N Rovira-Graells, TG Clark, C Bancells, VM Crowley, ...

Nature 507 (7491), 248-252, 2014

Genome-wide saturation mutagenesis of Burkholderia pseudomallei K96243 predicts essential genes and novel targets for antimicrobial development

MG Moule, CM Hemsley, Q Seet, JA Guerra-Assunção, J Lim, ...

MBio 5 (1), 10.1128/mbio. 00926-13, 2014

PolyTB: A genomic variation map for Mycobacterium tuberculosis

D Harris, J Perdigão, M Viveiros, I Portugal, F Drobniewski, S Gagneux, ...

Tuberculosis 30, 1e9, 2014

A robust SNP barcode for typing Mycobacterium tuberculosis complex strains

RF McNerney, JA Guerra-Assunção, JR Glynn, J Perdigão, M Viveiros, ...

Nat Commun 5, 4812, 2014

Malaria Genomic Epidemiology Network, Malaria Genomic Epidemiology Network. Reappraisal of known malaria resistance loci in a large multicenter study

KA Rockett, GM Clarke, K Fitzpatrick, C Hubbart, AE Jeffreys, K Rowlands, ...

Nat Genet 46 (11), 1197-204, 2014

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BF Kafsack, N Rovira-Graells, TG Clark, C Bancells, VM Crowley, ...

Nature 507 (7491), 248-252, 2014

A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. Nat Commun 5

F Coll, R McNerney, JA Guerra-Assunção, JR Glynn, J Perdigão, ...

A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains. Nat Commun 5: 4052

MD Preston, S Campino, SA Assefa, DF Echeverry, H Ocholla, ...

A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. Nat Commun 5: 4812

F Coll, R McNerney, JA Guerra-Assunção, JR Glynn, J Perdigão, ...

Whole genome sequencing shows a low proportion of tuberculosis disease is attributable to close contacts in rural Malawi

JR Glynn

Independent emergence of Plasmodium falciparum artemisinin resistance mutations in Southeast Asia

S Takala-Harrison, CG Jacob, C Arze, MP Cummings, JC Silva, ...

J Infect Dis 211 (670), 9, 2014

Fc gamma Receptor II a‐H 131 R Polymorphism and Malaria Susceptibility in Sympatric Ethnic Groups, Fulani and Dogon of M ali

B Maiga, A Dolo, O Touré, V Dara, A Tapily, S Campino, N Sepulveda, ...

Scandinavian journal of immunology 79 (1), 43-50, 2014

Elucidating emergence and transmission of multidrug-resistant tuberculosis in treatment experienced patients by whole genome sequencing

TG Clark, K Mallard, F Coll, M Preston, S Assefa, D Harris, S Ogwang, ...

PloS one 8 (12), e83012, 2013

Association of cytokine and Toll-like receptor gene polymorphisms with severe malaria in three regions of Cameroon

TO Apinjoh, JK Anchang-Kimbi, C Njua-Yafi, RN Mugri, AN Ngwai, ...

PloS one 8 (11), e81071, 2013

Genome-wide screen identifies new candidate genes associated with artemisinin susceptibility in Plasmodium falciparum in Kenya

S Borrmann, J Straimer, L Mwai, A Abdi, A Rippert, J Okombo, S Muriithi, ...

Scientific reports 3 (1), 3318, 2013

Human candidate polymorphisms in sympatric ethnic groups differing in malaria susceptibility in Mali

B Maiga, A Dolo, O Toure, V Dara, A Tapily, S Campino, N Sepulveda, ...

PLoS One 8 (10), e75675, 2013

Detecting and characterizing genomic signatures of positive selection in global populations

X Liu, RTH Ong, EN Pillai, AM Elzein, KS Small, TG Clark, ...

The American Journal of Human Genetics 92 (6), 866-881, 2013

The genetic risk of acute seizures in A frican children with falciparum malaria

SM Kariuki, K Rockett, TG Clark, H Reyburn, T Agbenyega, TE Taylor, ...

Epilepsia 54 (6), 990-1001, 2013

Imputation-based meta-analysis of severe malaria in three African populations

G Band, QS Le, L Jostins, M Pirinen, K Kivinen, M Jallow, F Sisay-Joof, ...

PLoS genetics 9 (5), e1003509, 2013

A Poisson hierarchical modelling approach to detecting copy number variation in sequence coverage data

N Sepúlveda, SG Campino, SA Assefa, CJ Sutherland, A Pain, TG Clark

BMC genomics 14 (1), 128, 2013

Effective Preparation of Plasmodium vivax Field Isolates for High-Throughput Whole Genome Sequencing

S Auburn, J Marfurt, G Maslen, S Campino, V Ruano Rubio, M Manske, ...

PLoS One 8 (1), e53160, 2013

Genetic loci associated with delayed clearance of Plasmodium falciparum following artemisinin treatment in Southeast Asia

S Takala-Harrison, TG Clark, CG Jacob, MP Cummings, O Miotto, ...

Proceedings of the National Academy of Sciences 110 (1), 240-245, 2013

Genetic loci associated with delayed clearance of

S Takala-Harrison, TG Clark, CG Jacob, MP Cummings, O Miotto, ...

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Genome-wide screen identifies new candidate genes associated with artemisinin susceptibility in Plasmodium falciparum in Kenya. Sci Rep 3: 3318

S Borrmann, J Straimer, L Mwai, A Abdi, A Rippert, J Okombo, S Muriithi, ...

Malaria Genomic Epidemiology Network; Malaria Genomic Epidemiological Network. Imputation-based meta-analysis of severe malaria in three African populations

G Band, QS Le, L Jostins, M Pirinen, K Kivinen, M Jallow, F Sisay-Joof, ...

PLoS Genet 9, e1003509, 2013

Genomic diversity in candidate virulence-associated genes in clinical strains of ocular Chlamydia trachomatis from a trachoma-hyperendemic population on the Bijagós Archipelago …

A Last, E Cassama, M Nabicassa, T Clark, F Coll, O Gundogdu, S Burr, ...

Distinct phases of blood gene expression pattern through tuberculosis treatment reflect modulation of the humoral immune response

JM Cliff, JS Lee, N Constantinou, JE Cho, TG Clark, K Ronacher, EC King, ...

The Journal of infectious diseases 207 (1), 18-29, 2013

SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences

F Coll, K Mallard, MD Preston, S Bentley, J Parkhill, R McNerney, N Martin, ...

Bioinformatics 28 (22), 2991-2993, 2012

VarB: a variation browsing and analysis tool for variants derived from next-generation sequencing data

MD Preston, M Manske, N Horner, S Assefa, S Campino, S Auburn, ...

Bioinformatics 28 (22), 2983-2985, 2012

Candidate human genetic polymorphisms and severe malaria in a Tanzanian population

A Manjurano, TG Clark, B Nadjm, G Mtove, H Wangai, N Sepulveda, ...

PloS one 7 (10), e47463, 2012

Targeted Restoration of the Intestinal Microbiota with a Simple, Defined Bacteriotherapy Resolves Relapsing Clostridium difficile Disease in Mice

TD Lawley, S Clare, AW Walker, MD Stares, TR Connor, C Raisen, ...

PLoS pathogens 8 (10), e1002995, 2012

Candidate polymorphisms and severe malaria in a Malian population

O Toure, S Konate, S Sissoko, A Niangaly, A Barry, AH Sall, E Diarra, ...

Public Library of Science 7 (9), e43987, 2012

Variation in human genes encoding adhesion and proinflammatory molecules are associated with severe malaria in the Vietnamese

SJ Dunstan, KA Rockett, NTN Quyen, YY Teo, CQ Thai, NT Hang, ...

Genes & Immunity 13 (6), 503-508, 2012

Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing

M Manske, O Miotto, S Campino, S Auburn, J Almagro-Garcia, G Maslen, ...

Nature 487 (7407), 375-379, 2012

Genomics and health in the developing world

D Kumar

Oxford University Press, 2012

Investigation of host candidate malaria-associated risk/protective SNPs in a Brazilian Amazonian population

S da Silva Santos, TG Clark, S Campino, MC Suarez-Mutis, KA Rockett, ...

PLoS One 7 (5), e36692, 2012

Haplotype analyses of haemoglobin C and haemoglobin S and the dynamics of the evolutionary response to malaria in Kassena-Nankana District of Ghana

A Ghansah, KA Rockett, TG Clark, MD Wilson, KA Koram, AR Oduro, ...

PloS one 7 (4), e34565, 2012

Characterization of within-host Plasmodium falciparum diversity using next-generation sequence data

S Auburn, S Campino, O Miotto, AA Djimde, I Zongo, M Manske, G Maslen, ...

PloS one 7 (2), e32891, 2012

VarB Plus: An Integrated Tool for Visualization of Genome Variation Datasets

L Hidayah

Investigation of Host Candidate Malaria-Associated Risk

S da Silva Santos, TG Clark, S Campino, MC Suarez-Mutis, KA Rockett

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Candidate polymorphisms and severe malaria in a Malian population. PLoS One7: e43987

O Toure, S Konate, S Sissoko, A Niagnaly, A Barry, AH Sall, E Diarra, ...

Gordon Dougan. Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice

D Trevor, SC Lawley, W Alan, MD Walker, TR Stares, CR Connor, ...

PLoS pathogens 8 (10), e1002995, 2012

An in-solution hybridisation method for the isolation of pathogen DNA from human DNA-rich clinical samples for analysis by NGS

M Smith, S Campino, Y Gu, TG Clark, TD Otto, G Maslen, M Manske, ...

The open genomics journal 5, 10.2174/1875693X01205010018, 2012

Association of sub-microscopic malaria parasite carriage with transmission intensity in north-eastern Tanzania

A Manjurano, L Okell, T Lukindo, H Reyburn, R Olomi, C Roper, TG Clark, ...

Malaria journal 10 (1), 370, 2011

Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance

T Downing, H Imamura, S Decuypere, TG Clark, GH Coombs, JA Cotton, ...

Genome research 21 (12), 2143-2156, 2011

Drug-Resistant Genotypes and Multi-Clonality in Plasmodium falciparum Analysed by Direct Genome Sequencing from Peripheral Blood of Malaria Patients

T Robinson, SG Campino, S Auburn, SA Assefa, SD Polley, M Manske, ...

PloS one 6 (8), e23204, 2011

HUMAN GENETIC POLYMORPHISMS AND THE RISK OF MALARIA-ASSOCIATED SEIZURES IN AFRICAN POPULATIONS

S Kariuki, K Rockett, T Clark, H Reyburn, T Agbenyega, T Taylor, ...

An Effective Method to Purify Plasmodium falciparum DNA Directly from Clinical Blood Samples for Whole Genome High-Throughput Sequencing

S Auburn, S Campino, TG Clark, AA Djimde, I Zongo, R Pinches, ...

PloS one 6 (7), e22213, 2011

Population Genetic Analysis of Plasmodium falciparum Parasites Using a Customized Illumina GoldenGate Genotyping Assay

S Campino, S Auburn, K Kivinen, I Zongo, JB Ouedraogo, V Mangano, ...

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Sch÷ nian G, Stark O, Sundar S, Vanaerschot M, Hertz-Fowler C, Dujardin JC, Berriman M. Whole genome sequencing of multiple leishmania donovani clinical isolates provides …

T Downing, H Imamura, S Decuypere, TG Clark, GH Coombs, JA Cotton, ...

Genome Res 21 (12), 2143-56, 2011

An Effective Method to Purify Plasmodium falciparum DNA Directly from Clinical Blood

S Auburn, S Campino, TG Clark, AA Djimde, I Zongo

Use of Purified Clostridium difficile Spores To Facilitate Evaluation of Health Care Disinfection Regimens

TD Lawley, S Clare, LJ Deakin, D Goulding, JL Yen, C Raisen, C Brandt, ...

Applied and environmental microbiology 76 (20), 6895-6900, 2010

Genome-wide association analyses identifies a susceptibility locus for tuberculosis on chromosome 18q11. 2

T Thye, FO Vannberg, SH Wong, E Owusu-Dabo, I Osei, J Gyapong, ...

Nature genetics 42 (9), 739-741, 2010

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

TG Clark, SG Campino, E Anastasi, S Auburn, YY Teo, K Small, ...

Bioinformatics 26 (16), 1999-2003, 2010

Transforming growth factor beta 2 and heme oxygenase 1 genes are risk factors for the cerebral malaria syndrome in Angolan children

MR Sambo, MJ Trovoada, C Benchimol, V Quinhentos, L Gonçalves, ...

PLoS One 5 (6), e11141, 2010

High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta

MS Forrest, ET Dermitzakis, S Abu-Amero, G Smits, P Stanier, ME Ritchie, ...

High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta

C Daelemans, ME Ritchie, G Smits, S Abu-Amero, IM Sudbery, MS Forrest, ...

BMC genetics 11 (1), 25, 2010

Further evidence supporting a role for gs signal transduction in severe malaria pathogenesis

S Auburn, AE Fry, TG Clark, S Campino, M Diakite, A Green, ...

PLoS One 5 (4), e10017, 2010

Immune phenotype predicts risk for posttransplantation squamous cell carcinoma

RP Carroll, D San Segundo, K Hollowood, T Marafioti, TG Clark, ...

Journal of the American Society of Nephrology: JASN 21 (4), 713, 2010

Polymorphisms in leucine-rich repeat genes are associated with autism spectrum disorder susceptibility in populations of European ancestry

I Sousa, TG Clark, R Holt, AT Pagnamenta, EJ Mulder, RB Minderaa, ...

Molecular autism 1 (1), 7, 2010

A Bayesian approach to assess differences in linkage disequilibrium patterns in genomewide association studies

TG Clark, SG Campino, YY Teo, K Small, S Auburn, KA Rockett, ...

Bioinformatics 26, 1999-2003, 2010

International Molecular Genetic Study of Autism Consortium (IMGSAC): Polymorphisms in leucinerich repeat genes are associated with autism spectrum disorder susceptibility in …

I Sousa, TG Clark, R Holt, AT Pagnamenta, EJ Mulder, RB Minderaa, ...

Mol Autism 1, 7, 2010

Research Polymorphisms in leucine-rich repeat genes are associated with autism spectrum disorder susceptibility in populations of European ancestry

I Sousa, TG Clark, R Holt, AT Pagnamenta, EJ Mulder, RB Minderaa

SnoopCGH: software for visualizing comparative genomic hybridization data

J Almagro-Garcia, M Manske, C Carret, S Campino, S Auburn, ...

Bioinformatics 25 (20), 2732-2733, 2009

Genome-wide comparisons of variation in linkage disequilibrium

YY Teo, AE Fry, K Bhattacharya, KS Small, DP Kwiatkowski, TG Clark

Genome research 19 (10), 1849-1860, 2009

Allelic heterogeneity of G6PD deficiency in West Africa and severe malaria susceptibility

TG Clark, AE Fry, S Auburn, S Campino, M Diakite, A Green, ...

European Journal of Human Genetics 17 (8), 1080-1085, 2009

Positive selection of a CD36 nonsense variant in sub-Saharan Africa, but no association with severe malaria phenotypes

AE Fry, A Ghansa, KS Small, A Palma, S Auburn, M Diakite, A Green, ...

Human molecular genetics 18 (14), 2683-2692, 2009

Genome-wide and fine-resolution association analysis of malaria in West Africa

M Jallow, YY Teo, KS Small, KA Rockett, P Deloukas, TG Clark, K Kivinen, ...

Nature genetics 41 (6), 657-665, 2009

MET and autism susceptibility: family and case–control studies

I Sousa, TG Clark, C Toma, K Kobayashi, M Choma, R Holt, NH Sykes, ...

European Journal of Human Genetics 17 (6), 749-758, 2009

TLR9 polymorphisms in African populations: no association with severe malaria, but evidence of cis-variants acting on gene expression

S Campino, J Forton, S Auburn, A Fry, M Diakite, A Richardson, J Hull, ...

Malaria Journal 8 (1), 44, 2009

Tumor necrosis factor and lymphotoxin-α polymorphisms and severe malaria in African populations

TG Clark, M Diakite, S Auburn, S Campino, AE Fry, A Green, ...

The Journal of infectious diseases 199 (4), 569-575, 2009

A genetic association study in the Gambia using tagging polymorphisms in the major histocompatibility complex class III region implicates a HLA-B associated transcript 2 …

M Diakite, TG Clark, S Auburn, S Campino, AE Fry, A Green, AP Morris, ...

Human genetics 125 (1), 105-109, 2009

Power consequences of linkage disequilibrium variation between populations

YY Teo, KS Small, AE Fry, Y Wu, DP Kwiatkowski, TG Clark

Genetic Epidemiology: The Official Publication of the International Genetic …, 2009

Lack of association of interferon regulatory factor 1 with severe malaria in affected child-parental trio studies across three African populations

VD Mangano, TG Clark, S Auburn, S Campino, M Diakite, AE Fry, A Green, ...

PLoS One 4 (1), e4206, 2009

KWIATKOWSKI DP WELLCOME TRUST CASE CONTROL C, MALARIA GENOMIC EPIDEMIOLOGY N. Genome-wide and fine-resolution association analysis of malaria in West Africa

M Jallow, YY Teo, KS Small, KA Rockett, P Deloukas, TG Clark, K Kivinen, ...

Nat Genet 41, 657-65, 2009

A cost-effective method to purify Plasmodium DNA from clinical malaria samples for “next generation” whole genome sequencing

S Auburn, S Campino, AA Djimde, I Zongo, TG Clark, V Mangano, ...

Mahamadou Thera, Marita Troye-Blomberg, Thomas N Williams, Michael Wilson, and Dominic P Kwiatkowski. Genome-wide and fine-resolution association analysis of malaria in West Africa

M Jallow, YY Teo, KS Small, KA Rockett, P Deloukas, TG Clark, K Kivinen, ...

Nature Genetics 41 (6), 657-665, 2009

Lack of Association of Interferon Regulatory Factor 1 with Severe Malaria in Affected

VD Mangano, TG Clark, S Auburn, S Campino, M Diakite

High Numbers of FOXP3 (+) T Cells and Poor Lymphocyte Proliferation Identifies Patients at High Risk of Developing Squamous Cell Cancer after Renal Transplantation.

R Carroll, D Arribas, T Clark, P Harden, K Wood

Validating Discovered Cis-Acting Regulatory Genetic Variants: Application of an Allele Specific Expression Approach to HapMap Populations

S Campino, J Forton, S Raj, B Mohr, S Auburn, A Fry, VD Mangano, ...

PLoS One 3 (12), e4105, 2008

A global network for investigating the genomic epidemiology of malaria

Project Management Committee Agbenyega Tsiri 2 Carucci Dan 36 Cook Katharine ...

Nature 456 (7223), 732-737, 2008

Assessing genuine parents-offspring trios for genetic association studies

YY Teo, AE Fry, MA Sanjoaquin, B Pederson, KS Small, KA Rockett, ...

Human heredity 67 (1), 26-37, 2008

The genome of the simian and human malaria parasite Plasmodium knowlesi

A Pain, U Böhme, AE Berry, K Mungall, RD Finn, AP Jackson, T Mourier, ...

Nature 455 (7214), 799-803, 2008

An evolutionary algorithm to find associations in dense genetic maps

TG Clark, M De Iorio, RC Griffths

IEEE transactions on evolutionary computation 12 (3), 297-306, 2008

BRLMM: An improved genotype calling method for the GeneChip human mapping 500K array set

YY Teo, KS Small, TG Clark, DP Kwiatkowski

ANNALS OF HUMAN GENETICS 72, 368-374, 2008

Perturbation analysis: a simple method for filtering SNPs with erroneous genotyping in genome‐wide association studies

YY Teo, KS Small, TG Clark, DP Kwiatkowski

Annals of human genetics 72 (3), 368-374, 2008

Interferon regulatory factor-1 polymorphisms are associated with the control of Plasmodium falciparum infection

VD Mangano, G Luoni, KA Rockett, BS Sirima, A Konaté, J Forton, ...

Genes & Immunity 9 (2), 122-129, 2008

Genome‐wide significance for dense SNP and resequencing data

CJ Hoggart, TG Clark, M De Iorio, JC Whittaker, DJ Balding

Genetic Epidemiology: The Official Publication of the International Genetic …, 2008

A simple method for filtering SNPs with erroneous genotyping in genome-wide association studies

YY Teo, KS Small, TG Clark, DP Kwiatkowski

Annals of Human Genome, 2008

Interferon-gamma signalling pathway in protection against malaria: new insights from a genetic approach

V Mangano, T Clark, S Auburn, S Campino, M Diakite, A Fry, A Green, ...

A global network for genomic epidemiology of malaria

MalariaGEN Consortium

Nature, 2008

Validation of a new prognostic index for advanced epithelial ovarian cancer: results from its application to a UK-based cohort

C Gourley

Journal of clinical oncology 25 (35), 5669-5670, 2007

Sequence-level population simulations over large genomic regions

CJ Hoggart, M Chadeau-Hyam, TG Clark, R Lampariello, JC Whittaker, ...

Genetics 177 (3), 1725-1731, 2007

A genotype calling algorithm for the Illumina BeadArray platform

YY Teo, M Inouye, KS Small, R Gwilliam, P Deloukas, DP Kwiatkowski, ...

Bioinformatics 23 (20), 2741-2746, 2007

A genotype calling algorithm for the Illumina BeadArray platform

KS Small, R Gwilliam, P Deloukas, DP Kwiatkowski, YY Teo, TG Clark, ...

Bioinformatics 23 (20), 2741-2746, 2007

Functional constraint and small insertions and deletions in the ENCODE regions of the human genome

TG Clark, T Andrew, GM Cooper, EH Margulies, JC Mullikin, DJ Balding

Genome biology 8 (9), R180, 2007

Data sheet: Sentrix HumanHap550 genotyping BeadChip

YY Teo, AE Fry, TG Clark, ES Tai, M Seielstad

ANNALS OF HUMAN GENETICS 71, 701-703, 2007

On the usage of HWE for identifying genotyping errors.

YY Teo, AE Fry, TG Clark, ES Tai, M Seielstad

Annals of Human genetics 71 (5), 701, 2007

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Management Group Liefer Laura A. 51 Wetterstrand Kris A. 51 Good Peter J. 51 ...

nature 447 (7146), 799-816, 2007

Personality and smoking status: A meta-analysis

MR Munafo, JI Zetteler, TG Clark

Nicotine & Tobacco Research 9 (3), 405-413, 2007

Estimating the number of coding mutations in genotypic and phenotypic driven N-ethyl-N-nitrosourea (ENU) screens: revisited: D. A. KEAYS ET AL.

DA Keays, TG Clark, TG Campbell, J Broxholme, W Valdar

Mammalian genome 18 (2), 123-124, 2007

Interferon Regulatory Factor 1 and susceptibility to malaria.

V Mangano, G Luoni, K Rockett, B Sirima, A Konatè, J Forton, T Clark, ...

Structured additive regression for categorical space-time data. A mixed model approach.

AA Abiodun, BA Oyejola, AA Abiodun, PK Andersen, O Borgan, RD Gill, ...

Asian Journal of Mathematics & Statistics 5 (1), 74-79, 2007

Bayesian logistic regression using a perfect phylogeny

TG Clark, M De Iorio, RC Griffiths

Biostatistics 8 (1), 32-52, 2007

Association of the NRG1 gene and schizophrenia: a meta-analysis

MR Munafo, DL Thiselton, TG Clark, J Flint

Molecular psychiatry 11 (6), 539-546, 2006

Apolipoproteins as predictors of ischaemic stroke in patients with a previous transient ischaemic attack

M Bhatia, SC Howard, TG Clark, R Neale, N Qizilbash, MFG Murphy, ...

Cerebrovascular Diseases 21 (5-6), 323-328, 2006

Estimating the number of coding mutations in genotypic- and phenotypic-driven N-ethyl-N-nitrosourea (ENU) screens: D.A. KEAYS ET AL.

DA Keays, TG Clark, J Flint

Mammalian genome 17 (3), 230-238, 2006

Neuroticism mediates the association of the serotonin transporter gene with lifetime major depression

MR Munafò, TG Clark, KH Roberts, EC Johnstone

Neuropsychobiology 53 (1), 1-8, 2006

Does smoking influence survival in cancer patients through effects on respiratory and vascular disease?

TG Clark, MFG Murphy, K Hey, M Drury, KK Cheng, P Aveyard

European journal of cancer prevention 15 (1), 87-90, 2006

Journal of Undergraduate Research, Volume VI, 2006

P Faletra, A Schuetz, D Cherkerzian, T Clark

DOESC (USDOE Office of Science (SC)(United States)), 2006

Finding associations in dense genetic maps: a genetic algorithm approach

TG Clark, M De Iorio, RC Griffiths, M Farrall

Human Heredity 60 (2), 97-108, 2005

Association of the dopamine-β-hydroxylase gene with nicotine dependence: No evidence for mediation by personality

JI Zetteler, TG Clark, EC Johnstone, MR Munafò

Personality and individual differences 39 (6), 1113-1122, 2005

Promise and pitfalls in the meta-analysis of genetic association studies: a response to Sen and Schinka

MR Munafo, T Clark, J Flint

Molecular Psychiatry 10 (10), 895-897, 2005

Meta-analysis of genetic association studies: Limitations, and directions for future research

M Munafo, T Clark, J Flint

Analysis of IL10 haplotypic associations with severe malaria

JN Wilson, K Rockett, M Jallow, M Pinder, F Sisay-Joof, M Newport, ...

Genes & Immunity 6 (6), 462-466, 2005

Lack of association of the COMT (Val158/108 Met) gene and schizophrenia: a meta-analysis of case–control studies

MR Munafo, L Bowes, TG Clark, J Flint

Molecular psychiatry 10 (8), 765-770, 2005

Does measurement instrument moderate the association between the serotonin transporter gene and anxiety-related personality traits? A meta-analysis

MR Munafo, T Clark, J Flint

Molecular psychiatry 10 (4), 415-419, 2005

Sequence-level population genomic simulations

DJ Balding, T Clark, CJ Hoggart

WILEY-LISS 29 (3), 235-236, 2005

Assessing publication bias in genetic association studies: evidence from a recent meta-analysis

MR Munafò, TG Clark, J Flint

Psychiatry research 129 (1), 39-44, 2004

Fibrinogen concentration and risk of ischemic stroke and acute coronary events in 5113 patients with transient ischemic attack and minor ischemic stroke

PM Rothwell, SC Howard, DA Power, SA Gutnikov, A Algra, J van Gijn, ...

Stroke 35 (10), 2300-2305, 2004

Are there sex differences in the association between the 5HTT gene and neuroticism? A meta-analysis

MR Munafò, TG Clark, J Flint

Personality and Individual Differences 37 (3), 621-626, 2004

The genetic basis for smoking behavior: a systematic review and meta-analysis

MR Munafo, TG Clark, EC Johnstone, MFG Murphy, RT Walton

Nicotine & Tobacco Research 6 (4), 583-597, 2004

Apolipoproteins predict ischaemic stroke in patients with a previous transient ischaemic attack

M Bhatia, S Howard, T Clark, M Murphy, P Rothwell

Motor vehicle driver injury and marital status: a cohort study with prospective and retrospective driver injuries

G Whitlock, R Norton, T Clark, R Jackson, S MacMahon

Injury prevention 10 (1), 33-36, 2004

the Cerebrovascular Cohort Studies Collaboration: Fibrinogen concentration and risk of ischaemic stroke and acute coronary events in 5113 patients with transient ischaemic …

PM Rothwell, SC Howard, DA Power, SA Gutnikov, A Algra, J van Gijn, ...

Stroke 35, 2300-2305, 2004

Thegeneticbasisforsmokingbehaviour: Asystematic reviewandmeta-analysis

MR Munafo, TG Clark, EC Johnstone, MFG Murphy

NicotineandTobaccoResearch6, 2004

Statistical methods for finding associations in dense genetic regions

TG Clark

University of Oxford, 2004

Should intensive preventive treatment be continued indefinitely after a transient ischaemic attack?

E Flossmann, T Clark, M Murphy, P Rothwell

Survival analysis part IV: further concepts and methods in survival analysis

TG Clark, MJ Bradburn, SB Love, DG Altman

British journal of cancer 89 (5), 781-786, 2003

Survival analysis Part III: multivariate data analysis–choosing a model and assessing its adequacy and fit

MJ Bradburn, TG Clark, SB Love, DG Altman

British journal of cancer 89 (4), 605-611, 2003

Survival analysis part II: multivariate data analysis–an introduction to concepts and methods

MJ Bradburn, TG Clark, SB Love, DG Altman

British journal of cancer 89 (3), 431-436, 2003

Expression profile of wild‐type ETV6 in childhood acute leukaemia

N Patel, LK Goff, T Clark, AM Ford, N Foot, D Lillington, S Hing, ...

British journal of haematology 122 (1), 94-98, 2003

Motor vehicle driver injury and socioeconomic status: a cohort study with prospective and retrospective driver injuries

G Whitlock, R Norton, T Clark, M Pledger, R Jackson, S MacMahon

Journal of epidemiology and community health 57 (7), 512-516, 2003

Survival analysis part I: basic concepts and first analyses

TG Clark, MJ Bradburn, SB Love, DG Altman

British journal of cancer 89 (2), 232-238, 2003

Long term risks of stroke, myocardial infarction, and vascular death in “low risk” patients with a non-recent transient ischaemic attack

TG Clark, MFG Murphy, PM Rothwell

Journal of Neurology, Neurosurgery & Psychiatry 74 (5), 577-580, 2003

Missing.... presumed at random: cost‐analysis of incomplete data

A Briggs, T Clark, J Wolstenholme, P Clarke

Health economics 12 (5), 377-392, 2003

Genetic polymorphisms and personality in healthy adults: a systematic review and meta-analysis

MR Munafo, TG Clark, LR Moore, E Payne, R Walton, J Flint

Molecular psychiatry 8 (5), 471-484, 2003

Is body mass index a risk factor for motor vehicle driver injury? A cohort study with prospective and retrospective outcomes

G Whitlock, R Norton, T Clark, R Jackson, S MacMahon

International journal of epidemiology 32 (1), 147-149, 2003

Survival analysis part III: Basic concepts and first analyses

MJ Bradburn, TG Clark, SB Love, DG Altman

British Journal of Cancer 89, 605-611, 2003

List of contents

JR Kelley, JM Duggan, KM Dunn, K Jordan, PR Croft, EB Fortescue, ...

J Clin Epidemiol 56 (12), 1248-1260, 2003

Developing a prognostic model in the presence of missing data: an ovarian cancer case study

TG Clark, DG Altman

Journal of clinical epidemiology 56 (1), 28-37, 2003

Polymorphisms in dopamine metabolic enzymes and tobacco consumption in smokers: seeking confirmation of the association in a follow-up study

EC Johnstone, TG Clark, SE Griffiths, MFG Murphy, RT Walton

Pharmacogenetics and Genomics 12 (7), 585-587, 2002

Quantification of the completeness of follow-up

TG Clark, DG Altman, BL De Stavola

The Lancet 359 (9314), 1309-1310, 2002

Recurrence after abdominal surgery for Crohn’s disease: relationship to disease site and surgical procedure

NR Borley, NJMC Mortensen, MA Chaudry, S Mohammed, BF Warren, ...

Diseases of the colon & rectum 45 (3), 377-383, 2002

Evidence for separate disease phenotypes in intestinal Crohn's disease

JDP Borley NR, Mortensen NJ, Chaudry MA, Mohammed S, Clarke T

Br J Surg 89 (2), 201-5, 2002

ERULF (Energy Research Undergraduate Laboratory Fellowship)

P Faletra, K Franz, T Clark, K Manning, C Musick, K Sokolski

The effect of missing values for covariates

G Whitlock, T Clark

Epidemiology 13 (1), 113, 2002

Comparative expression profiles of ETV6, CBFA2 and ETV6-CBFA2 in disease and remission states in childhood acute leukemia.

N Patel, L Goff, T Clark, N Foot, D Lillington, S Hing, K Pritchard-Jones, ...

Blood 98 (11), 163b-163b, 2001

Random errors in the measurement of 10 cardiovascular risk factors

G Whitlock, T Clark, S Vander Hoorn, A Rodgers, R Jackson, R Norton, ...

European journal of epidemiology 17 (10), 907-909, 2001

A prognostic model for ovarian cancer

TG Clark, ME Stewart, DG Altman, H Gabra, JF Smyth

British journal of cancer 85 (7), 944-952, 2001

Expression profile of ETV6, CBFA2 and ETV6-CBFA2 in childhood ALL and AML

N Patel, L Goff, LK Jones, T Clark, T Foot, D Lillington, S Hing, ...

British Journal of Cancer 85, 31-31, 2001

Blood pressure, cholesterol and cardiovascular diseases in eastern Asia

A Rodgers

PhD Thesis-University of Auckland, 2001

Stewart ME. A1tman DG. et a1. A pr0l; no6tic modelfor ovarian caBcer

C TG

Br J~ nce 85 (7), 944-952, 2001