Gramtools enables multiscale variation analysis with genome graphs

by Brice Letcher, Martin Hunt, Zamin Iqbal
Published 2021-09-01

Role for gene conversion in the evolution of cell-surface antigens of the malaria parasite Plasmodium falciparum.

by Brice Letcher, Sorina Maciuca, Zamin Iqbal
Published 2024-03-01

Inferring Strain Mixture within Clinical Plasmodium falciparum Isolates from Genomic Sequence Data.

by John D O'Brien, Zamin Iqbal, Jason Wendler, Lucas Amenga-Etego
Published 2016-06-01

Towards Point-of-Care Diagnosis of Pulmonary Tuberculosis and Drug Susceptibility Testing by Whole Genome Sequencing of DNA Isolated from Sputum

by Kayzad S. Nilgiriwala, Louise Pankhurst, Ali Vaughan, Zamin Iqbal, Derrick Crook, Anirvan Chatterjee, Nerges Mistry
Published 2017-12-01

High-Accuracy HLA Type Inference from Whole-Genome Sequencing Data Using Population Reference Graphs.

by Alexander T Dilthey, Pierre-Antoine Gourraud, Alexander J Mentzer, Nezih Cereb, Zamin Iqbal, Gil McVean
Published 2016-10-01

Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences.

by Grace A Blackwell, Martin Hunt, Kerri M Malone, Leandro Lima, Gal Horesh, Blaise T F Alako, Nicholas R Thomson, Zamin Iqbal
Published 2021-11-01

Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences

by Grace A. Blackwell, Martin Hunt, Kerri M. Malone, Leandro Lima, Gal Horesh, Blaise T. F. Alako, Nicholas R. Thomson, Zamin Iqbal
Published 2021-11-01

GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning

by Matthias I. Gröschel, Martin Owens, Luca Freschi, Roger Vargas, Maximilian G. Marin, Jody Phelan, Zamin Iqbal, Avika Dixit, Maha R. Farhat
Published 2021-08-01

Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs.

by Richard M Leggett, Ricardo H Ramirez-Gonzalez, Walter Verweij, Cintia G Kawashima, Zamin Iqbal, Jonathan D G Jones, Mario Caccamo, Daniel Maclean
Published 2013-01-01

Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs

by Rachel M. Colquhoun, Michael B. Hall, Leandro Lima, Leah W. Roberts, Kerri M. Malone, Martin Hunt, Brice Letcher, Jane Hawkey, Sophie George, Louise Pankhurst, Zamin Iqbal
Published 2021-09-01

Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes

by Martin Hunt, Brice Letcher, Kerri M. Malone, Giang Nguyen, Michael B. Hall, Rachel M. Colquhoun, Leandro Lima, Michael C. Schatz, Srividya Ramakrishnan, CRyPTIC consortium, Zamin Iqbal
Published 2022-07-01

Drug-Resistant Tuberculosis in Pet Ring-Tailed Lemur, Madagascar

by Marni LaFleur, Kim E. Reuter, Michael B. Hall, Hoby H. Rasoanaivo, Stuart McKernan, Paulo Ranaivomanana, Anita Michel, Marie Sylvianne Rabodoarivelo, Zamin Iqbal, Niaina Rakotosamimanana, Simon Grandjean Lapierre
Published 2021-03-01

Rapid Whole-Genome Sequencing for Surveillance of Salmonella enterica Serovar Enteritidis

by Henk C. den Bakker, Marc W. Allard, Dianna Bopp, Eric W. Brown, John Fontana, Zamin Iqbal, Aristea Kinney, Ronald Limberger, Kimberlee A. Musser, Matthew Shudt, Errol Strain, Martin Wiedmann, William J. Wolfgang
Published 2014-08-01

The global distribution and spread of the mobilized colistin resistance gene mcr-1

by Ruobing Wang, Lucy van Dorp, Liam P. Shaw, Phelim Bradley, Qi Wang, Xiaojuan Wang, Longyang Jin, Qing Zhang, Yuqing Liu, Adrien Rieux, Thamarai Dorai-Schneiders, Lucy Anne Weinert, Zamin Iqbal, Xavier Didelot, Hui Wang, Francois Balloux
Published 2018-03-01

SNP-IT Tool for Identifying Subspecies and Associated Lineages of Mycobacterium tuberculosis Complex

by Samuel Lipworth, Rana Jajou, Albert de Neeling, Phelim Bradley, Wim van der Hoek, Gugu Maphalala, Maryline Bonnet, Elizabeth Sanchez-Padilla, Roland Diel, Stefan Niemann, Zamin Iqbal, Grace Smith, Tim Peto, Derrick Crook, Timothy Walker, Dick van Soolingen
Published 2019-03-01

Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei

by Jane Hawkey, Kalani Paranagama, Kate S. Baker, Rebecca J. Bengtsson, François-Xavier Weill, Nicholas R. Thomson, Stephen Baker, Louise Cerdeira, Zamin Iqbal, Martin Hunt, Danielle J. Ingle, Timothy J. Dallman, Claire Jenkins, Deborah A. Williamson, Kathryn E. Holt
Published 2021-05-01

Severe infections emerge from commensal bacteria by adaptive evolution

by Bernadette C Young, Chieh-Hsi Wu, N Claire Gordon, Kevin Cole, James R Price, Elian Liu, Anna E Sheppard, Sanuki Perera, Jane Charlesworth, Tanya Golubchik, Zamin Iqbal, Rory Bowden, Ruth C Massey, John Paul, Derrick W Crook, Timothy E Peto, A Sarah Walker, Martin J Llewelyn, David H Wyllie, Daniel J Wilson
Published 2017-12-01

Correction: Corrigendum: Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis

by Phelim Bradley, N. Claire Gordon, Timothy M. Walker, Laura Dunn, Simon Heys, Bill Huang, Sarah Earle, Louise J. Pankhurst, Luke Anson, Mariateresa de Cesare, Paolo Piazza, Antonina A. Votintseva, Tanya Golubchik, Daniel J. Wilson, David H. Wyllie, Roland Diel, Stefan Niemann, Silke Feuerriegel, Thomas A. Kohl, Nazir Ismail, Shaheed V. Omar, E. Grace Smith, David Buck, Gil McVean, A. Sarah Walker, Tim E. A. Peto, Derrick W. Crook, Zamin Iqbal
Published 2016-04-01

Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe [version 1; peer review: 2 approved, 1 approved with reservations]

by Martin Hunt, Phelim Bradley, Simon Grandjean Lapierre, Simon Heys, Mark Thomsit, Michael B. Hall, Kerri M. Malone, Penelope Wintringer, Timothy M. Walker, Daniela M. Cirillo, Iñaki Comas, Maha R. Farhat, Phillip Fowler, Jennifer Gardy, Nazir Ismail, Thomas A. Kohl, Vanessa Mathys, Matthias Merker, Stefan Niemann, Shaheed Vally Omar, Vitali Sintchenko, Grace Smith, Dick van Soolingen, Philip Supply, Sabira Tahseen, Mark Wilcox, Irena Arandjelovic, Tim E. A. Peto, Derrick W. Crook, Zamin Iqbal
Published 2019-12-01

The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis

by Timothy M Walker, DPhil, Paolo Miotto, PhD, Claudio U Köser, PhD, Philip W Fowler, PhD, Jeff Knaggs, BSc, Zamin Iqbal, DPhil, Martin Hunt, PhD, Leonid Chindelevitch, PhD, Maha R Farhat, MD, Daniela Maria Cirillo, PhD, Iñaki Comas, PhD, James Posey, PhD, Shaheed V Omar, PhD, Timothy EA Peto, ProfFRCP, Anita Suresh, MSc, Swapna Uplekar, PhD, Sacha Laurent, PhD, Rebecca E Colman, PhD, Carl-Michael Nathanson, PhD, Matteo Zignol, MD, Ann Sarah Walker, ProfPhD, Derrick W Crook, ProfFRCPath, Nazir Ismail, FRCPath [SA], Timothy C Rodwell, ProfMD, A Sarah Walker, Adrie J C Steyn, Ajit Lalvani, Alain Baulard, Alan Christoffels, Alberto Mendoza-Ticona, Alberto Trovato, Alena Skrahina, Alexander S Lachapelle, Alice Brankin, Amy Piatek, Ana Gibertoni Cruz, Anastasia Koch, Andrea Maurizio Cabibbe, Andrea Spitaleri, Angela P Brandao, Angkana Chaiprasert, Anita Suresh, Anna Barbova, Annelies Van Rie, Arash Ghodousi, Arnold Bainomugisa, Ayan Mandal, Aysha Roohi, Babak Javid, Baoli Zhu, Brice Letcher, Camilla Rodrigues, Camus Nimmo, Carl-Michael NATHANSON, Carla Duncan, Christopher Coulter, Christian Utpatel, Chunfa Liu, Clara Grazian, Clare Kong, Claudio U Köser, Daniel J Wilson, Daniela Maria Cirillo, Daniela Matias, Danielle Jorgensen, Danila Zimenkov, Darren Chetty, David AJ Moore, David A Clifton, Derrick W Crook, Dick van Soolingen, Dongxin Liu, Donna Kohlerschmidt, Draurio Barreira, Dumisani Ngcamu, Elias David Santos Lazaro, Ellis Kelly, Emanuele Borroni, Emma Roycroft, Emmanuel Andre, Erik C Böttger, Esther Robinson, Fabrizio Menardo, Flavia F Mendes, Frances B Jamieson, Francesc Coll, George Fu Gao, George W Kasule, Gian Maria Rossolini, Gillian Rodger, E Grace Smith, Graeme Meintjes, Guy Thwaites, Harald Hoffmann, Heidi Albert, Helen Cox, Ian F Laurenson, Iñaki Comas, Irena Arandjelovic, Ivan Barilar, Jaime Robledo, James Millard, James Johnston, Jamie Posey, Jason R Andrews, Jeff Knaggs, Jennifer Gardy, Jennifer Guthrie, Jill Taylor, Jim Werngren, John Metcalfe, Jorge Coronel, Joseph Shea, Joshua Carter, Juliana MW Pinhata, Julianne V Kus, Katharina Todt, Kathryn Holt, Kayzad S Nilgiriwala, Kelen T Ghisi, Kerri M Malone, Kiatichai Faksri, Kimberlee A Musser, Lavania Joseph, Leen Rigouts, Leonid Chindelevitch, Lisa Jarrett, Louis Grandjean, Lucilaine Ferrazoli, Mabel Rodrigues, Maha Farhat, Marco Schito, Margaret M Fitzgibbon, Marguerite Massinga Loembé, Maria Wijkander, Marie Ballif, Marie-Sylvianne Rabodoarivelo, Marina Mihalic, Mark WILCOX, Martin Hunt, Matteo ZIGNOL, Matthias Merker, Matthias Egger, Max O'Donnell, Maxine Caws, Mei-Hua Wu, Michael G Whitfield, Michael Inouye, Mikael Mansjö, Minh Ha Dang Thi, Moses Joloba, SM Mostofa Kamal, Nana Okozi, Nazir ISMAIL, Nerges Mistry, Nhung N Hoang, Niaina Rakotosamimanana, Nicholas I Paton, Paola M V Rancoita, Paolo Miotto, Pascal Lapierre, Patricia J Hall, Patrick Tang, Pauline Claxton, Penelope Wintringer, Peter M Keller, Phan Vuong Khac Thai, Philip W Fowler, Philip Supply, Prapaporn Srilohasin, Prapat Suriyaphol, Priti Rathod, Priti Kambli, Ramona Groenheit, Rebecca E Colman, Rick Twee-Hee Ong, Robin M Warren, Robert J Wilkinson, Roland Diel, Rosangela S Oliveira, Rukhsar Khot, Ruwen Jou, Sabira Tahseen, Sacha Laurent, Saheer Gharbia, Samaneh Kouchaki, Sanchi Shah, Sara Plesnik, Sarah G Earle, Sarah Dunstan, Sarah J Hoosdally, Satoshi Mitarai, Sebastien Gagneux, Shaheed V Omar, Shen-Yuan Yao, Simon Grandjean Lapierre, Simone Battaglia, Stefan Niemann, Sushil Pandey, Swapna Uplekar, Tanya A Halse, Ted Cohen, Teresa Cortes, Therdsak Prammananan, Thomas A Kohl, Nguyen T T Thuong, Tik Ying Teo, Timothy E A Peto, Timothy C Rodwell, Timothy William, Timothy M Walker, Thomas R Rogers, Utkarsha Surve, Vanessa Mathys, Victoria Furió, Victoria Cook, Srinivasan Vijay, Vincent Escuyer, Viola Dreyer, Vitali Sintchenko, Vonthanak Saphonn, Walter Solano, Wan-Hsuan Lin, Wayne van Gemert, Wencong He, Yang Yang, Yanlin Zhao, Youwen Qin, Yu-Xin Xiao, Zahra Hasan, Zamin Iqbal, Zully M Puyen
Published 2022-04-01