| Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans I Comas, M Coscolla, T Luo, S Borrell, KE Holt, M Kato-Maeda, J Parkhill, ... Nature genetics 45 (10), 1176-1182, 2013 | 644 | 2013 |
| High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi KE Holt, J Parkhill, CJ Mazzoni, P Roumagnac, FX Weill, I Goodhead, ... Nature genetics 40 (8), 987-993, 2008 | 459 | 2008 |
| Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4 New England Journal of Medicine 365 (8), 718-724, 2011 | 457 | 2011 |
| Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype RA Kingsley, CL Msefula, NR Thomson, S Kariuki, KE Holt, MA Gordon, ... Genome research 19 (12), 2279-2287, 2009 | 379 | 2009 |
| SRST2: Rapid genomic surveillance for public health and hospital microbiology labs M Inouye, H Dashnow, LA Raven, MB Schultz, BJ Pope, T Tomita, J Zobel, ... Genome Medicine 6 (11), 1-16, 2014 | 371 | 2014 |
| The Infant Nasopharyngeal Microbiome Impacts Severity of Lower Respiratory Infection and Risk of Asthma Development SM Teo, D Mok, K Pham, M Kusel, M Serralha, N Troy, BJ Holt, BJ Hales, ... Cell Host and Microbe 17 (5), 704-715, 2015 | 346 | 2015 |
| Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health KE Holt, H Wertheim, RN Zadoks, S Baker, CA Whitehouse, D Dance, ... Proceedings of the National Academy of Sciences 112 (27), E3574-E3581, 2015 | 345 | 2015 |
| Unicycler: resolving bacterial genome assemblies from short and long sequencing reads RR Wick, LM Judd, CL Gorrie, KE Holt PLOS Computational Biology 13 (6), e1005595, 2017 | 328 | 2017 |
| Evolutionary dynamics of Clostridium difficile over short and long time scales M He, M Sebaihia, TD Lawley, RA Stabler, LF Dawson, MJ Martin, KE Holt, ... Proceedings of the National Academy of Sciences 107 (16), 7527, 2010 | 313 | 2010 |
| An immunoepidemiological approach to asthma: identification of in-vitro T cell response patterns associated with different wheezing phenotypes in children T Heaton, J Rowe, S Turner, RC Aalberse, N De Klerk, D Suriyaarachchi, ... The Lancet 365 (9454), 142-149, 2005 | 307 | 2005 |
| Bandage: interactive visualization of de novo genome assemblies RR Wick, MB Schultz, J Zobel, KE Holt Bioinformatics 31 (20), 3350-2, 2015 | 237 | 2015 |
| Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter-and intracontinental transmission events VK Wong, S Baker, DJ Pickard, J Parkhill, AJ Page, NA Feasey, ... Nature Genetics 47 (6), 632-639, 2015 | 209 | 2015 |
| Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe KE Holt, S Baker, FX Weill, EC Holmes, A Kitchen, J Yu, V Sangal, ... Nature genetics 44 (9), 1056-1059, 2012 | 175 | 2012 |
| Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi K Holt, N Thomson, J Wain, G Langridge, R Hasan, Z Bhutta, M Quail, ... BMC genomics 10 (1), 36, 2009 | 135 | 2009 |
| Typhoid in Kenya is associated with a dominant multidrug-resistant Salmonella enterica serovar Typhi haplotype that is also widespread in Southeast Asia S Kariuki, G Revathi, J Kiiru, DM Mengo, J Mwituria, J Muyodi, A Munyalo, ... Journal of clinical microbiology 48 (6), 2171, 2010 | 118 | 2010 |
| On the origin of Mycobacterium ulcerans, the causative agent of buruli ulcer KD Doig, KE Holt, JAM Fyfe, CJ Lavender, M Eddyani, F Portaels, ... BMC genomics 13 (1), 258, 2012 | 107 | 2012 |
| Beginner’s guide to comparative bacterial genome analysis using next-generation sequence data DJ Edwards, KE Holt Microb Inform Exp 3 (1), 2, 2013 | 99 | 2013 |
| Short read sequence typing (SRST): multi-locus sequence types from short reads M Inouye, TC Conway, J Zobel, KE Holt BMC genomics 13 (1), 338, 2012 | 86 | 2012 |
| Emergence of a Globally Dominant IncHI1 Plasmid Type Associated with Multiple Drug Resistant Typhoid KE Holt, MD Phan, S Baker, PT Duy, TVT Nga, S Nair, AK Turner, C Walsh, ... PLoS Neglected Tropical Diseases 5 (7), e1245, 2011 | 86 | 2011 |
| Tracking the establishment of local endemic populations of an emergent enteric pathogen KE Holt, TVT Nga, DP Thanh, H Vinh, DW Kim, MPV Tra, JI Campbell, ... Proceedings of the National Academy of Sciences 110 (43), 17522-17527, 2013 | 83 | 2013 |
Stephen BakerUniversity of OxfordVerified email at ndm.ox.ac.uk