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Castanet: a pipeline for rapid analysis of targeted multi-pathogen genomic data.
Published in:
Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae591
By:
- Mayne, Richard;
- Secret, Shannah;
- Geoghegan, Cyndi;
- Trebes, Amy;
- Kean, Kai;
- Reid, Kaitlin;
- Lin, Gu-Lung;
- Ansari, M Azim;
- Cesare, Mariateresa de;
- Bonsall, David;
- Elliott, Ivo;
- Piazza, Paolo;
- Brown, Anthony;
- Bray, James;
- Knight, Julian C;
- Harvala, Heli;
- Breuer, Judith;
- Simmonds, Peter;
- Bowden, Rory J;
- Golubchik, Tanya
Publication type:
Article
Evaluation of Viremia Frequencies of a Novel Human Pegivirus by Using Bioinformatic Screening and PCR.
Published in:
2016
By:
- Bonsall, David;
- Gregory, William F.;
- Ip, Camilla L. C.;
- Donfield, Sharyne;
- Iles, James;
- Ansari, M. Azim;
- Piazza, Paolo;
- Trebes, Amy;
- Brown, Anthony;
- Frater, John;
- Pybus, Oliver G.;
- Goulder, Phillip;
- Klenerman, Paul;
- Bowden, Rory;
- Gomperts, Edward D.;
- Barnes, Eleanor;
- Kapoor, Amit;
- Sharp, Colin P.;
- Simmonds, Peter
Publication type:
journal article
Using host genetics to infer the global spread and evolutionary history of HCV subtype 3a.
Published in:
Virus Evolution, 2021, v. 7, n. 2, p. 1, doi. 10.1093/ve/veab065
By:
- Lin, Shang-Kuan;
- Maio, Nicola De;
- Pedergnana, Vincent;
- Wu, Chieh-Hsi;
- Thézé, Julien;
- Wilson, Daniel J;
- Barnes, Eleanor;
- Ansari, M Azim
Publication type:
Article
The Design and Development of a Multi-HBV Antigen Encoded in Chimpanzee Adenoviral and Modified Vaccinia Ankara Viral Vectors; A Novel Therapeutic Vaccine Strategy against HBV.
Published in:
Vaccines, 2020, v. 8, n. 2, p. 184, doi. 10.3390/vaccines8020184
By:
- Chinnakannan, Senthil K.;
- Cargill, Tamsin N.;
- Donnison, Timothy A.;
- Ansari, M. Azim;
- Sebastian, Sarah;
- Lee, Lian Ni;
- Hutchings, Claire;
- Klenerman, Paul;
- Maini, Mala K.;
- Evans, Tom;
- Barnes, Eleanor
Publication type:
Article
Inference of the Properties of the Recombination Process from Whole Bacterial Genomes.
Published in:
Genetics, 2014, v. 196, n. 1, p. 253, doi. 10.1534/genetics.113.157172
By:
- Ansari, M. Azim;
- Didelot, Xavier
Publication type:
Article
Divergent trajectories of antiviral memory after SARS-CoV-2 infection.
Published in:
Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-28898-1
By:
- Tomic, Adriana;
- Skelly, Donal T.;
- Ogbe, Ane;
- O'Connor, Daniel;
- Pace, Matthew;
- Adland, Emily;
- Alexander, Frances;
- Ali, Mohammad;
- Allott, Kirk;
- Azim Ansari, M.;
- Belij-Rammerstorfer, Sandra;
- Bibi, Sagida;
- Blackwell, Luke;
- Brown, Anthony;
- Brown, Helen;
- Cavell, Breeze;
- Clutterbuck, Elizabeth A.;
- de Silva, Thushan;
- Eyre, David;
- Lumley, Sheila
Publication type:
Article
Publisher Correction: Distinct patterns of within-host virus populations between two subgroups of human respiratory syncytial virus.
Published in:
2021
By:
- Lin, Gu-Lung;
- Drysdale, Simon B.;
- Snape, Matthew D.;
- O'Connor, Daniel;
- Brown, Anthony;
- MacIntyre-Cockett, George;
- Mellado-Gomez, Esther;
- de Cesare, Mariateresa;
- Bonsall, David;
- Ansari, M. Azim;
- Öner, Deniz;
- Aerssens, Jeroen;
- Butler, Christopher;
- Bont, Louis;
- Openshaw, Peter;
- Martinón-Torres, Federico;
- Nair, Harish;
- Bowden, Rory;
- RESCEU Investigators;
- Campbell, Harry
Publication type:
Correction Notice
Distinct patterns of within-host virus populations between two subgroups of human respiratory syncytial virus.
Published in:
Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-25265-4
By:
- Lin, Gu-Lung;
- Drysdale, Simon B.;
- Snape, Matthew D.;
- O'Connor, Daniel;
- Brown, Anthony;
- MacIntyre-Cockett, George;
- Mellado-Gomez, Esther;
- de Cesare, Mariateresa;
- Bonsall, David;
- Ansari, M. Azim;
- Öner, Deniz;
- Aerssens, Jeroen;
- Butler, Christopher;
- Bont, Louis;
- Openshaw, Peter;
- Martinón-Torres, Federico;
- Nair, Harish;
- Bowden, Rory;
- RESCEU Investigators;
- Campbell, Harry
Publication type:
Article
T cell assays differentiate clinical and subclinical SARS-CoV-2 infections from cross-reactive antiviral responses.
Published in:
Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-21856-3
By:
- Ogbe, Ane;
- Kronsteiner, Barbara;
- Skelly, Donal T.;
- Pace, Matthew;
- Brown, Anthony;
- Adland, Emily;
- Adair, Kareena;
- Akhter, Hossain Delowar;
- Ali, Mohammad;
- Ali, Serat-E;
- Angyal, Adrienn;
- Ansari, M. Azim;
- Arancibia-Cárcamo, Carolina V.;
- Brown, Helen;
- Chinnakannan, Senthil;
- Conlon, Christopher;
- de Lara, Catherine;
- de Silva, Thushan;
- Dold, Christina;
- Dong, Tao
Publication type:
Article
Targeted metagenomics reveals association between severity and pathogen co-detection in infants with respiratory syncytial virus.
Published in:
Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-46648-3
By:
- Lin, Gu-Lung;
- Drysdale, Simon B.;
- Snape, Matthew D.;
- O'Connor, Daniel;
- Brown, Anthony;
- MacIntyre-Cockett, George;
- Mellado-Gomez, Esther;
- de Cesare, Mariateresa;
- Ansari, M. Azim;
- Bonsall, David;
- Bray, James E.;
- Jolley, Keith A.;
- Bowden, Rory;
- Aerssens, Jeroen;
- Bont, Louis;
- Openshaw, Peter J. M.;
- Martinon-Torres, Federico;
- Nair, Harish;
- Golubchik, Tanya;
- Pollard, Andrew J.
Publication type:
Article
Recombinational Switching of the Clostridium difficile S-Layer and a Novel Glycosylation Gene Cluster Revealed by Large-Scale Whole-Genome Sequencing.
Published in:
Journal of Infectious Diseases, 2013, v. 207, n. 4, p. 675, doi. 10.1093/infdis/jis734
By:
- Dingle, Kate E.;
- Didelot, Xavier;
- Ansari, M. Azim;
- Eyre, David W.;
- Vaughan, Alison;
- Griffiths, David;
- Ip, Camilla L. C.;
- Batty, Elizabeth M.;
- Golubchik, Tanya;
- Bowden, Rory;
- Jolley, Keith A.;
- Hood, Derek W.;
- Fawley, Warren N.;
- Walker, A. Sarah;
- Peto, Timothy E.;
- Wilcox, Mark H.;
- Crook, Derrick W.
Publication type:
Article
An HLA-I signature favouring KIR-educated Natural Killer cells mediates immune control of HIV in children and contrasts with the HLA-B-restricted CD8+ T-cell-mediated immune control in adults.
Published in:
PLoS Pathogens, 2021, v. 17, n. 11, p. 1, doi. 10.1371/journal.ppat.1010090
By:
- Adriano Vieira, Vinicius;
- Adland, Emily;
- Malone, David F. G.;
- Martin, Maureen P.;
- Groll, Andreas;
- Ansari, M. Azim;
- Garcia-Guerrero, Maria C.;
- Puertas, Mari C.;
- Muenchhoff, Maximilian;
- Guash, Claudia Fortuny;
- Brander, Christian;
- Martinez-Picado, Javier;
- Bamford, Alasdair;
- Tudor-Williams, Gareth;
- Ndung'u, Thumbi;
- Walker, Bruce D.;
- Ramsuran, Veron;
- Frater, John;
- Jooste, Pieter;
- Peppa, Dimitra
Publication type:
Article
Extensive C->U transition biases in the genomes of a wide range of mammalian RNA viruses; potential associations with transcriptional mutations, damage- or host-mediated editing of viral RNA.
Published in:
PLoS Pathogens, 2021, v. 17, n. 6, p. 1, doi. 10.1371/journal.ppat.1009596
By:
- Simmonds, Peter;
- Ansari, M. Azim
Publication type:
Article
HepFREEPak: protocol for a multi-centre, prospective observational study examining efficacy and impact of current therapies for the treatment of hepatitis C in Pakistan and reporting resistance to antiviral drugs: study protocol.
Published in:
BMC Public Health, 2023, v. 23, n. 1, p. 1, doi. 10.1186/s12889-023-17290-3
By:
- Arif, Ambreen;
- Hasnain, Aliya;
- Chaudhry, Auj;
- Asim, Muhammad;
- Shafqat, Muhammad Nabeel;
- Altaf, Abeer;
- Saba, Noor;
- Kemos, Polychronis;
- Ansari, M. Azim;
- Barnes, Eleanor;
- Metcalfe, Chris;
- Vickerman, Peter;
- Qureshi, Huma;
- Hamid, Saeed;
- Choudhry, Asad Ali;
- Niaz, Saad Khalid;
- Foster, Graham R.;
- Choudhry, Naheed
Publication type:
Article
Inference of Host–Pathogen Interaction Matrices from Genome-Wide Polymorphism Data.
Published in:
Molecular Biology & Evolution, 2024, v. 41, n. 9, p. 1, doi. 10.1093/molbev/msae176
By:
- Märkle, Hanna;
- John, Sona;
- Metzger, Lukas;
- Consortium, STOP-HCV;
- Ansari, M Azim;
- Pedergnana, Vincent;
- Tellier, Aurélien
Publication type:
Article
Efficient Inference of Recombination Hot Regions in Bacterial Genomes.
Published in:
Molecular Biology & Evolution, 2014, v. 31, n. 6, p. 1593, doi. 10.1093/molbev/msu082
By:
- Yahara, Koji;
- Didelot, Xavier;
- Ansari, M. Azim;
- Sheppard, Samuel K.;
- Falush, Daniel
Publication type:
Article
Illumina and Nanopore methods for whole genome sequencing of hepatitis B virus (HBV).
Published in:
Scientific Reports, 2019, v. 9, n. 1, p. N.PAG, doi. 10.1038/s41598-019-43524-9
By:
- McNaughton, Anna L.;
- Roberts, Hannah E.;
- Bonsall, David;
- de Cesare, Mariateresa;
- Mokaya, Jolynne;
- Lumley, Sheila F.;
- Golubchik, Tanya;
- Piazza, Paolo;
- Martin, Jacqueline B.;
- de Lara, Catherine;
- Brown, Anthony;
- Ansari, M. Azim;
- Bowden, Rory;
- Barnes, Eleanor;
- Matthews, Philippa C.
Publication type:
Article
HBV vaccination and PMTCT as elimination tools in the presence of HIV: insights from a clinical cohort and dynamic model.
Published in:
2019
By:
- McNaughton, Anna L.;
- Lourenço, José;
- Hattingh, Louise;
- Adland, Emily;
- Daniels, Samantha;
- Van Zyl, Anriette;
- Akiror, Connie S.;
- Wareing, Susan;
- Jeffery, Katie;
- Ansari, M. Azim;
- Klenerman, Paul;
- Goulder, Philip J. R.;
- Gupta, Sunetra;
- Jooste, Pieter;
- Matthews, Philippa C.
Publication type:
journal article
Phylogenetic Analysis of Hepatitis C Virus Infections in a Large Belgian Cohort Using Next-Generation Sequencing of Full-Length Genomes.
Published in:
Viruses (1999-4915), 2023, v. 15, n. 12, p. 2391, doi. 10.3390/v15122391
By:
- Christensen, Kasper T.;
- Pierard, Florian;
- Bonsall, David;
- Bowden, Rory;
- Barnes, Eleanor;
- Florence, Eric;
- Ansari, M. Azim;
- Nguyen, Dung;
- de Cesare, Mariateresa;
- Nevens, Frederik;
- Robaeys, Geert;
- Schrooten, Yoeri;
- Busschots, Dana;
- Simmonds, Peter;
- Vandamme, Anne-Mieke;
- Van Wijngaerden, Eric;
- Dierckx, Tim;
- Cuypers, Lize;
- Van Laethem, Kristel
Publication type:
Article
Interpreting Viral Deep Sequencing Data with GLUE.
Published in:
Viruses (1999-4915), 2019, v. 11, n. 4, p. 323, doi. 10.3390/v11040323
By:
- Singer, Joshua B.;
- Thomson, Emma C.;
- Hughes, Joseph;
- Aranday-Cortes, Elihu;
- McLauchlan, John;
- da Silva Filipe, Ana;
- Tong, Lily;
- Manso, Carmen F.;
- Gifford, Robert J.;
- Robertson, David L.;
- Barnes, Eleanor;
- Ansari, M. Azim;
- Mbisa, Jean L.;
- Bibby, David F.;
- Bradshaw, Daniel;
- Smith, David
Publication type:
Article
Microevolutionary analysis of Clostridium difficile genomes to investigate transmission.
Published in:
Genome Biology, 2012, v. 13, n. 12, p. 1, doi. 10.1186/gb-2012-13-12-r118
By:
- Didelot, Xavier;
- Eyre, David W.;
- Cule, Madeleine;
- Ip, Camilla L.C.;
- Ansari, M. Azim;
- Griffiths, David;
- Vaughan, Alison;
- O'Connor, Lily;
- Golubchik, Tanya;
- Batty, Elizabeth M.;
- Piazza, Paolo;
- Wilson, Daniel J.;
- Bowden, Rory;
- Donnelly, Peter J.;
- Dingle, Kate E.;
- Wilcox, Mark;
- Walker, A. Sarah;
- Crook, Derrick W.;
- Peto, Tim E. A.;
- Harding, Rosalind M.
Publication type:
Article
Efficacy of ultra-short, response-guided sofosbuvir and daclatasvir therapy for hepatitis C in a single-arm mechanistic pilot study.
Published in:
eLife, 2023, p. 1, doi. 10.7554/eLife.81801
By:
- Flower, Barnaby;
- Le Manh Hung;
- Mccabe, Leanne;
- Ansari, M. Azim;
- Chau Le Ngoc;
- Thu Vo Thi;
- Hang Vu Thi Kim;
- Phuong Nguyen Thi Ngoc;
- Le Thanh Phuong;
- Vo Minh Quang;
- Thuan Dang Trong;
- Thao Le Thi;
- Tran Nguyen Bao;
- Kingsley, Cherry;
- Smith, David;
- Hoglund, Richard M.;
- Tarning, Joel;
- Kestelyn, Evelyne;
- Pett, Sarah L.;
- van Doorn, Rogier
Publication type:
Article
Epstein-Barr virus reactivation in sepsis due to community-acquired pneumonia is associated with increased morbidity and an immunosuppressed host transcriptomic endotype.
Published in:
Scientific Reports, 2020, v. 10, n. 1, p. 1, doi. 10.1038/s41598-020-66713-3
By:
- Goh, Cyndi;
- Burnham, Katie L.;
- Ansari, M. Azim;
- de Cesare, Mariateresa;
- Golubchik, Tanya;
- Hutton, Paula;
- Overend, Lauren E.;
- Davenport, Emma E.;
- Hinds, Charles J.;
- Bowden, Rory;
- Knight, Julian C.
Publication type:
Article
Bayesian Inference of the Evolution of a Phenotype Distribution on a Phylogenetic Tree.
Published in:
Genetics, 2016, v. 204, n. 1, p. 89, doi. 10.1534/genetics.116.190496
By:
- Ansari, M. Azim;
- Didelot, Xavier
Publication type:
Article
Technical Validation of a Hepatitis C Virus Whole Genome Sequencing Assay for Detection of Genotype and Antiviral Resistance in the Clinical Pathway.
Published in:
Frontiers in Microbiology, 2020, v. 11, p. N.PAG, doi. 10.3389/fmicb.2020.576572
By:
- Manso, Carmen F.;
- Bibby, David F.;
- Lythgow, Kieren;
- Mohamed, Hodan;
- Myers, Richard;
- Williams, David;
- Piorkowska, Renata;
- Chan, Yuen T.;
- Bowden, Rory;
- Ansari, M. Azim;
- Ip, Camilla L. C.;
- Barnes, Eleanor;
- Bradshaw, Daniel;
- Mbisa, Jean L.
Publication type:
Article
Utility of a buccal swab point-of-care test for the IFNL4 genotype in the era of direct acting antivirals for hepatitis C virus.
Published in:
PLoS ONE, 2023, v. 17, n. 1, p. 1, doi. 10.1371/journal.pone.0280551
By:
- Sy, Aminata;
- McCabe, Leanne;
- Hudson, Emma;
- Ansari, Azim M.;
- Pedergnana, Vincent;
- Lin, Shang-Kuan;
- Santana, S.;
- Fiorino, Marzia;
- Ala, Aftab;
- Stone, Ben;
- Smith, M.;
- Nelson, Mark;
- Barclay, Stephen T.;
- McPherson, Stuart;
- Ryder, Stephen D.;
- Collier, Jane;
- Barnes, Eleanor;
- Walker, Ann Sarah;
- Pett, Sarah L.;
- Cooke, Graham
Publication type:
Article
Prevalence of resistanceassociated viral variants to the HIV-specific broadly neutralising antibody 10-1074 in a UK bNAb-naïve population.
Published in:
Frontiers in Immunology, 2024, p. 1, doi. 10.3389/fimmu.2024.1352123
By:
- Zacharopoulou, Panagiota;
- Lee, Ming;
- Oliveira, Thiago;
- Thornhill, John;
- Robinson, Nicola;
- Brown, Helen;
- Kinloch, Sabine;
- Goulder, Philip;
- Fox, Julie;
- Fidler, Sarah;
- Ansari, M. Azim;
- Frater, John
Publication type:
Article
Changes in the prevalence of hepatitis B and C viral infections in Sindh province, Pakistan: Findings from two sero‐surveys in 2007 and 2019.
Published in:
Journal of Viral Hepatitis, 2024, v. 31, n. 11, p. 645, doi. 10.1111/jvh.13986
By:
- Alamneh, Tesfa Sewunet;
- Walker, Josephine G.;
- Lim, Aaron G.;
- Alam, Ejaz;
- Hamid, Saeed;
- Foster, Graham R.;
- Choudhry, Naheed;
- Ansari, M. Azim;
- Qureshi, Huma;
- Vickerman, Peter
Publication type:
Article
Real world SOF/VEL/VOX retreatment outcomes and viral resistance analysis for HCV patients with prior failure to DAA therapy.
Published in:
Journal of Viral Hepatitis, 2021, v. 28, n. 9, p. 1256, doi. 10.1111/jvh.13549
By:
- Smith, David A.;
- Bradshaw, Daniel;
- Mbisa, Jean L;
- Manso, Carmen F.;
- Bibby, David F;
- Singer, Joshua B;
- Thomson, Emma C;
- da Silva Filipe, Ana;
- Aranday‐Cortes, Elihu;
- Ansari, M. Azim;
- Brown, Anthony;
- Hudson, Emma;
- Benselin, Jennifer;
- Healy, Brendan;
- Troke, Phil;
- McLauchlan, John;
- Barnes, Eleanor;
- Irving, William L.
Publication type:
Article
Global prevalence and phylogeny of hepatitis B virus (HBV) drug and vaccine resistance mutations.
Published in:
Journal of Viral Hepatitis, 2021, v. 28, n. 8, p. 1110, doi. 10.1111/jvh.13525
By:
- Mokaya, Jolynne;
- Vasylyeva, Tetyana I.;
- Barnes, Eleanor;
- Ansari, M. Azim;
- Pybus, Oliver G.;
- Matthews, Philippa C.
Publication type:
Article
Simultaneous Viral Whole-Genome Sequencing and Differential Expression Profiling in Respiratory Syncytial Virus Infection of Infants.
Published in:
2020
By:
- Lin, Gu-Lung;
- Golubchik, Tanya;
- Drysdale, Simon;
- O'Connor, Daniel;
- Jefferies, Kimberley;
- Brown, Anthony;
- Cesare, Mariateresa de;
- Bonsall, David;
- Ansari, M Azim;
- Aerssens, Jeroen;
- Bont, Louis;
- Openshaw, Peter;
- Martinón-Torres, Federico;
- Bowden, Rory;
- Pollard, Andrew J;
- Investigators, RESCEU;
- de Cesare, Mariateresa;
- RESCEU Investigators
Publication type:
journal article

Found: 31