Local Persistence of Novel MRSA Lineage after Hospital Ward Outbreak, Cambridge, UK, 2011–2013

by Toleman, Michelle S., Reuter, Sandra, Coll, Francesc, Harrison, Ewan M., Peacock, Sharon J.
Published 2016

Imputation-Based Population Genetics Analysis of Plasmodium falciparum Malaria Parasites

by Samad, Hanif, Coll, Francesc, Preston, Mark D., Ocholla, Harold, Fairhurst, Rick M., Clark, Taane G.
Published 2015

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

by Coll, Francesc, Mallard, Kim, Preston, Mark D., Bentley, Stephen, Parkhill, Julian, McNerney, Ruth, Martin, Nigel, Clark, Taane G.
Published 2012

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

by Benavente, Ernest D, Coll, Francesc, Furnham, Nick, McNerney, Ruth, Glynn, Judith R, Campino, Susana, Pain, Arnab, Mohareb, Fady R, Clark, Taane G
Published 2015

A robust SNP barcode for typing Mycobacterium tuberculosis complex strains

by Coll, Francesc, McNerney, Ruth, Guerra-Assunção, José Afonso, Glynn, Judith R., Perdigão, João, Viveiros, Miguel, Portugal, Isabel, Pain, Arnab, Martin, Nigel, Clark, Taane G.
Published 2014

Whole Genome Sequencing Based Characterization of Extensively Drug-Resistant Mycobacterium tuberculosis Isolates from Pakistan

by Ali, Asho, Hasan, Zahra, McNerney, Ruth, Mallard, Kim, Hill-Cawthorne, Grant, Coll, Francesc, Nair, Mridul, Pain, Arnab, Clark, Taane G., Hasan, Rumina
Published 2015

Systematic Surveillance Detects Multiple Silent Introductions and Household Transmission of Methicillin-Resistant Staphylococcus aureus USA300 in the East of England

by Toleman, Michelle S., Reuter, Sandra, Coll, Francesc, Harrison, Ewan M., Blane, Beth, Brown, Nicholas M., Török, M. Estée, Parkhill, Julian, Peacock, Sharon J.
Published 2016

PolyTB: A genomic variation map for Mycobacterium tuberculosis

by Coll, Francesc, Preston, Mark, Guerra-Assunção, José Afonso, Hill-Cawthorn, Grant, Harris, David, Perdigão, João, Viveiros, Miguel, Portugal, Isabel, Drobniewski, Francis, Gagneux, Sebastien, Glynn, Judith R., Pain, Arnab, Parkhill, Julian, McNerney, Ruth, Martin, Nigel, Clark, Taane G.
Published 2014

Transmission of methicillin-resistant Staphylococcus aureus in long-term care facilities and their related healthcare networks

by Harrison, Ewan M., Ludden, Catherine, Brodrick, Hayley J., Blane, Beth, Brennan, Gráinne, Morris, Dearbháile, Coll, Francesc, Reuter, Sandra, Brown, Nicholas M., Holmes, Mark A., O’Connell, Brian, Parkhill, Julian, Török, M. Estee, Cormican, Martin, Peacock, Sharon J.
Published 2016

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

by Perdigão, João, Silva, Hugo, Machado, Diana, Macedo, Rita, Maltez, Fernando, Silva, Carla, Jordao, Luisa, Couto, Isabel, Mallard, Kim, Coll, Francesc, Hill-Cawthorne, Grant A, McNerney, Ruth, Pain, Arnab, Clark, Taane G, Viveiros, Miguel, Portugal, Isabel
Published 2014

Elucidating Emergence and Transmission of Multidrug-Resistant Tuberculosis in Treatment Experienced Patients by Whole Genome Sequencing

by Clark, Taane G., Mallard, Kim, Coll, Francesc, Preston, Mark, Assefa, Samuel, Harris, David, Ogwang, Sam, Mumbowa, Francis, Kirenga, Bruce, O’Sullivan, Denise M., Okwera, Alphonse, Eisenach, Kathleen D., Joloba, Moses, Bentley, Stephen D., Ellner, Jerrold J., Parkhill, Julian, Jones-López, Edward C., McNerney, Ruth
Published 2013

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

by Phelan, Jody, Coll, Francesc, McNerney, Ruth, Ascher, David B., Pires, Douglas E. V., Furnham, Nick, Coeck, Nele, Hill-Cawthorne, Grant A., Nair, Mridul B., Mallard, Kim, Ramsay, Andrew, Campino, Susana, Hibberd, Martin L., Pain, Arnab, Rigouts, Leen, Clark, Taane G.
Published 2016

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

by Abdallah, Abdallah M., Hill-Cawthorne, Grant A., Otto, Thomas D., Coll, Francesc, Guerra-Assunção, José Afonso, Gao, Ge, Naeem, Raeece, Ansari, Hifzur, Malas, Tareq B., Adroub, Sabir A., Verboom, Theo, Ummels, Roy, Zhang, Huoming, Panigrahi, Aswini Kumar, McNerney, Ruth, Brosch, Roland, Clark, Taane G., Behr, Marcel A., Bitter, Wilbert, Pain, Arnab
Published 2015

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

by Coll, Francesc, McNerney, Ruth, Preston, Mark D, Guerra-Assunção, José Afonso, Warry, Andrew, Hill-Cawthorne, Grant, Mallard, Kim, Nair, Mridul, Miranda, Anabela, Alves, Adriana, Perdigão, João, Viveiros, Miguel, Portugal, Isabel, Hasan, Zahra, Hasan, Rumina, Glynn, Judith R, Martin, Nigel, Pain, Arnab, Clark, Taane G
Published 2015

Recurrence due to Relapse or Reinfection With Mycobacterium tuberculosis: A Whole-Genome Sequencing Approach in a Large, Population-Based Cohort With a High HIV Infection Prevalenc...

by Guerra-Assunção, José Afonso, Houben, Rein M. G. J., Crampin, Amelia C., Mzembe, Themba, Mallard, Kim, Coll, Francesc, Khan, Palwasha, Banda, Louis, Chiwaya, Arthur, Pereira, Rui P. A., McNerney, Ruth, Harris, David, Parkhill, Julian, Clark, Taane G., Glynn, Judith R.
Published 2015

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

by Phelan, Jody E., Coll, Francesc, Bergval, Indra, Anthony, Richard M., Warren, Rob, Sampson, Samantha L., Gey van Pittius, Nicolaas C., Glynn, Judith R., Crampin, Amelia C., Alves, Adriana, Bessa, Theolis Barbosa, Campino, Susana, Dheda, Keertan, Grandjean, Louis, Hasan, Rumina, Hasan, Zahra, Miranda, Anabela, Moore, David, Panaiotov, Stefan, Perdigao, Joao, Portugal, Isabel, Sheen, Patricia, de Oliveira Sousa, Erivelton, Streicher, Elizabeth M., van Helden, Paul D., Viveiros, Miguel, Hibberd, Martin L., Pain, Arnab, McNerney, Ruth, Clark, Taane G.
Published 2016