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

Authors: 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

Source: Genome Biology, Vol 23, Iss 1, Pp 1-23 (2022)

Subject Terms: Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/113d5df19a8e44b995c6088b7988a543

The actions of methotrexate on endothelial cells are dependent on the shear stress-induced regulation of one carbon metabolism

Authors: Marie B. Lang, Kit-Yi Leung, Nicholas D.E. Greene, Kerri M. Malone, Gaye Saginc, Anna M. Randi, Allan Kiprianos, Robert T. Maughan, Charis Pericleous, Justin C. Mason

Source: Frontiers in Immunology, Vol 14 (2023)

Subject Terms: methotrexate, endothelial cells, one carbon metabolism, cardiovascular disease, shear stress, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2023.1209490/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/5d363a763a9c431a9c93d4a8e3417ea0

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

Authors: 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

Source: Genome Biology, Vol 22, Iss 1, Pp 1-30 (2021)

Subject Terms: Pan-genome, Genome graph, Accessory genome, Nanopore, Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/3bf384fd17904ec49e3cda3805c804b4

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

Authors: Grace A. Blackwell, Martin Hunt, Kerri M. Malone, Leandro Lima, Gal Horesh, Blaise T. F. Alako, Nicholas R. Thomson, Zamin Iqbal

Source: PLoS Biology, Vol 19, Iss 11 (2021)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8577725/?tool=EBI; https://doaj.org/toc/1544-9173; https://doaj.org/toc/1545-7885

Access URL: https://doaj.org/article/c01063cf412e499ab673a82efdc0d7bf

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

Authors: 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

Source: Wellcome Open Research, Vol 4 (2019)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://wellcomeopenresearch.org/articles/4-191/v1; https://doaj.org/toc/2398-502X

Access URL: https://doaj.org/article/13ce9ad14cbc4783b7d765b9e0628345

Relaxed Selection Drives a Noisy Noncoding Transcriptome in Members of the Mycobacterium tuberculosis Complex

Authors: Adam M. Dinan, Pin Tong, Amanda J. Lohan, Kevin M. Conlon, Aleksandra A. Miranda-CasoLuengo, Kerri M. Malone, Stephen V. Gordon, Brendan J. Loftus

Source: mBio, Vol 5, Iss 4 (2014)

Subject Terms: Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2150-7511

Access URL: https://doaj.org/article/dfb4712138a24332a916eb22066a1dc4

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

Authors: 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

Source: The Lancet Microbe, Vol 3, Iss 4, Pp e265-e273 (2022)

Subject Terms: Medicine (General), R5-920, Microbiology, QR1-502

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2666524721003013; https://doaj.org/toc/2666-5247

Access URL: https://doaj.org/article/5404bb0e9de24bc8bc42f357dff6c954

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

Authors: Grace A Blackwell, Martin Hunt, Kerri M Malone, Leandro Lima, Gal Horesh, Blaise T F Alako, Nicholas R Thomson, Zamin Iqbal

Source: PLoS Biology, Vol 19, Iss 11, p e3001421 (2021)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1544-9173; https://doaj.org/toc/1545-7885

Access URL: https://doaj.org/article/abce2d8928ac4d6098a60f51ffb57a54