Virus genomics and evolution: the transformative effect of new technologies and multidisciplinary collaboration on virus research and outbreak management by Ip, C, Pybus, O, Gardy, J

Are prorocentroid dinoflagellates monophyletic? A study of 25 species based on nuclear and mitochondrial genes. by Murray, S, Ip, C, Moore, R, Nagahama, Y, Fukuyo, Y

Evolutionary dynamics of Enterococcus faecium reveals complex genomic relationships between isolates with independent emergence of vancomycin resistance. by van Hal, S, Ip, C, Anzari, M, Wilson, D, Espedido, B, Jensen, S, Bowden, R

ve-SEQ: Robust, unbiased enrichment for streamlined detection and whole-genome sequencing of HCV and other highly diverse pathogens by Bowden, R, Bonsall, D, Ansari, M, Ip, C, Trebes, A, Brown, A, Klenerman, P, Buck, D, Piazza, P, Barnes, E

Comparison of next generation sequencing technologies for the comprehensive assessment of full-length hepatitis C viral genomes by Ip, C, Ansari, M, Brown, A, Bowden, R, Bonsall, D, Hudson, E, Klenerman, P, Piazza, P, Trebes, A, Barnes, E, Simmonds, P, STOP-HCV Consortium

Resistance analysis of genotype 3 hepatitis C virus indicates subtypes inherently resistant to nonstructural protein 5A inhibitors by Smith, D, Magri, A, Bonsall, D, Ip, C, Trebes, A, Brown, A, Piazza, P, Bowden, R, Nguyen, D, STOP-HCV Consortium, Ansari, M, Simmonds, P, Barnes, E

Healthcare-associated outbreak of meticillin-resistant Staphylococcus aureus bacteraemia: role of a cryptic variant of an epidemic clone. by Miller, R, Price, JR, Batty, E, Didelot, X, Wyllie, D, Golubchik, T, Crook, D, Paul, J, Peto, T, Wilson, D, Cule, M, Ip, C, Day, N, Moore, C, Bowden, R, Llewelyn, M

Recombinational switching of the Clostridium difficile S-layer and a novel glycosylation gene cluster revealed by large-scale whole-genome sequencing. by Dingle, K, Didelot, X, Ansari, M, Eyre, D, Vaughan, A, Griffiths, D, Ip, C, Batty, E, Golubchik, T, Bowden, R, Jolley, K, Hood, D, Fawley, W, Walker, A, Peto, T, Wilcox, M, Crook, D

Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. by Walker, T, Ip, C, Harrell, R, Evans, J, Kapatai, G, Dedicoat, M, Eyre, D, Wilson, D, Hawkey, P, Crook, D, Parkhill, J, Harris, D, Walker, A, Bowden, R, Monk, P, Smith, E, Peto, T

A modified RNA-Seq approach for whole genome sequencing of RNA viruses from faecal and blood samples. by Batty, E, Wong, T, Trebes, A, Argoud, K, Attar, M, Buck, D, Ip, C, Golubchik, T, Cule, M, Bowden, R, Manganis, C, Klenerman, P, Barnes, E, Walker, A, Wyllie, D, Wilson, D, Dingle, K, Peto, T, Crook, D, Piazza, P

Evaluation of viremia frequencies of a novel human pegivirus by using bioinformatic screening and PCR by Bonsall, D, Gregory, W, Ip, C, Donfield, S, Iles, J, Ansari, M, Piazza, P, Trebes, A, Brown, A, Frater, J, Pybus, O, Goulder, P, Klenerman, P, Bowden, R, Gomperts, E, Barnes, E, Kapoor, A, Sharp, C, Simmonds, P

Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus by Everitt, R, Didelot, X, Batty, E, Miller, R, Knox, K, Young, B, Bowden, R, Auton, A, Votintseva, A, Larner-Svensson, H, Charlesworth, J, Golubchik, T, Ip, C, Godwin, H, Fung, R, Peto, T, Walker, A, Crook, D, Wilson, D

A modified RNA-Seq approach for whole genome sequencing of RNA viruses from faecal and blood samples by Batty, E, Wong, T, Trebes, A, Argoud, K, Attar, M, Buck, D, Ip, C, Golubchik, T, Cule, M, Bowden, R, Manganis, C, Klenerman, P, Barnes, E, Walker, A, Wyllie, D, Wilson, D, Dingle, K, Peto, T, Crook, D, Piazza, P

Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus. by Everitt, R, Didelot, X, Batty, E, Miller, R, Knox, K, Young, B, Bowden, R, Auton, A, Votintseva, A, Larner-Svensson, H, Charlesworth, J, Golubchik, T, Ip, C, Godwin, H, Fung, R, Peto, T, Walker, A, Crook, D, Wilson, D

Within-host evolution of Staphylococcus aureus during asymptomatic carriage by Golubchik, T, Batty, E, Miller, R, Farr, H, Young, B, Larner-Svensson, H, Fung, R, Godwin, H, Knox, K, Votintseva, A, Everitt, R, Street, T, Cule, M, Ip, C, Didelot, X, Peto, T, Harding, R, Wilson, D, Crook, D, Bowden, R

Within-host evolution of Staphylococcus aureus during asymptomatic carriage. by Golubchik, T, Batty, E, Miller, R, Farr, H, Young, B, Larner-Svensson, H, Fung, R, Godwin, H, Knox, K, Votintseva, A, Everitt, R, Street, T, Cule, M, Ip, C, Didelot, X, Peto, T, Harding, R, Wilson, D, Crook, D, Bowden, R

Microevolutionary analysis of Clostridium difficile genomes to investigate transmission. by Didelot, X, Eyre, D, Cule, M, Ip, C, Ansari, M, Griffiths, D, Vaughan, A, O'Connor, L, Golubchik, T, Batty, E, Piazza, P, Wilson, D, Bowden, R, Donnelly, P, Dingle, K, Wilcox, M, Walker, A, Crook, D, Peto, T, Harding, R

A pilot study of rapid benchtop sequencing of Staphylococcus aureus and Clostridium difficile for outbreak detection and surveillance by Eyre, D, Golubchik, T, Gordon, N, Bowden, R, Piazza, P, Batty, E, Ip, C, Wilson, D, Didelot, X, O'Connor, L, Lay, R, Buck, D, Kearns, A, Shaw, A, Paul, J, Wilcox, M, Donnelly, P, Peto, T, Walker, A, Crook, D

Sequencing of human genomes with nanopore technology by Bowden, R, Davies, R, Heger, A, Pagnamenta, A, De Cesare, M, Oikkonen, L, Parkes, D, Freeman, C, Dhalla, F, Patel, S, Popitsch, N, Ip, C, Roberts, H, Salatino, S, Lockstone, H, Lunter, G, Taylor, J, Buck, D, Simpson, M, Donnelly, P

Diverse sources of C. difficile infection identified on whole-genome sequencing. by Eyre, D, Cule, M, Wilson, D, Griffiths, D, Vaughan, A, O'Connor, L, Ip, C, Golubchik, T, Batty, E, Finney, J, Wyllie, D, Didelot, X, Piazza, P, Bowden, R, Dingle, K, Harding, R, Crook, D, Wilcox, M, Peto, T, Walker, A