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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
Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning.
Published in:
Scientific Reports, 2022, v. 12, n. 1, p. 1, doi. 10.1038/s41598-022-15661-1
By:
- Nickbakhsh, Sema;
- Hughes, Joseph;
- Christofidis, Nicolaos;
- Griffiths, Emily;
- Shaaban, Sharif;
- Enright, Jessica;
- Smollett, Katherine;
- Nomikou, Kyriaki;
- Palmalux, Natasha;
- Tong, Lily;
- Carmichael, Stephen;
- Sreenu, Vattipally B.;
- Orton, Richard;
- Goldstein, Emily J.;
- Tomb, Rachael M.;
- The COVID-19 Genomics UK (COG-UK) Consortium;
- Robson, Samuel C.;
- Connor, Thomas R.;
- Loman, Nicholas J.;
- Golubchik, Tanya
Publication type:
Article
Blood donation screening for hepatitis B virus core antibodies: The importance of confirmatory testing and initial implication for rare blood donor groups.
Published in:
Vox Sanguinis, 2024, v. 119, n. 5, p. 447, doi. 10.1111/vox.13608
By:
- Fu, Michael X.;
- Ingram, Jennifer;
- Roberts, Courtney;
- Nurmi, Visa;
- Watkins, Emma;
- Dempsey, Nina;
- Golubchik, Tanya;
- Breuer, Judith;
- Brailsford, Su;
- Irving, William L.;
- Andersson, Monique;
- Simmonds, Peter;
- Harvala, Heli
Publication type:
Article
Reconstruction of the historic time course of blood‐borne virus contamination of clotting factor concentrates, 1974–1992.
Published in:
Journal of Medical Virology, 2024, v. 96, n. 7, p. 1, doi. 10.1002/jmv.29774
By:
- McClure, C. Patrick;
- Kean, Kai;
- Reid, Kaitlin;
- Mayne, Richard;
- Fu, Michael X.;
- Rajendra, Piya;
- Gates, Shannah;
- Breuer, Judy;
- Harvala, Heli;
- Golubchik, Tanya;
- Tarr, Alexander W.;
- Irving, William L.;
- Makris, Michael;
- Simmonds, Peter
Publication type:
Article
Validation of an HIV whole genome sequencing method for HIV drug resistance testing in an Australian clinical microbiology laboratory.
Published in:
Journal of Medical Virology, 2023, v. 95, n. 12, p. 1, doi. 10.1002/jmv.29273
By:
- Jenkins, Frances;
- Le, Thomas;
- Farhat, Rima;
- Pinto, Angie;
- Anzari, Azim;
- Bonsall, David;
- Golubchik, Tanya;
- Bowden, Rory;
- Lee, Frederick J.;
- van Hal, Sebastiaan J.
Publication type:
Article
Ultrasensitive PCR system for HBV DNA detection: Risk stratification for occult hepatitis B virus infection in English blood donors.
Published in:
Journal of Medical Virology, 2023, v. 95, n. 10, p. 1, doi. 10.1002/jmv.29144
By:
- Fu, Michael X.;
- Simmonds, Peter;
- Andreani, Julien;
- Baklan, Hatice;
- Webster, Mhairi;
- Asadi, Romisa;
- Golubchik, Tanya;
- Breuer, Judith;
- Ijaz, Samreen;
- Ushiro‐Lumb, Ines;
- Brailsford, Su;
- Irving, William L.;
- Andersson, Monique;
- Harvala, Heli
Publication type:
Article
Postpandemic rebound of adeno‐associated virus type 2 (AAV2) infections temporally associated with an outbreak of unexplained severe acute hepatitis in children in the United Kingdom.
Published in:
Journal of Medical Virology, 2023, v. 95, n. 7, p. 1, doi. 10.1002/jmv.28921
By:
- Gates, Shannah;
- Andreani, Julien;
- Dewar, Rebecca;
- Smith, Donald B.;
- Templeton, Kate;
- Child, Harry T.;
- Breuer, Judy;
- Golubchik, Tanya;
- Bassano, Irene;
- Wade, Matthew J.;
- Jeffries, Aaron R.;
- Simmonds, Peter;
- Harvala, Heli
Publication type:
Article
Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load.
Published in:
Virus Evolution, 2022, v. 8, n. 1, p. 1, doi. 10.1093/ve/veac022
By:
- Zhao, Lele;
- Wymant, Chris;
- Blanquart, François;
- Golubchik, Tanya;
- Gall, Astrid;
- Bakker, Margreet;
- Bezemer, Daniela;
- Hall, Matthew;
- Ong, Swee Hoe;
- Albert, Jan;
- Bannert, Norbert;
- Fellay, Jacques;
- Grabowski, M Kate;
- Gunsenheimer-Bartmeyer, Barbara;
- Günthard, Huldrych F;
- Kivelä, Pia;
- Kouyos, Roger D;
- Laeyendecker, Oliver;
- Meyer, Laurence;
- Porter, Kholoud
Publication type:
Article
Severe infections emerge from commensal bacteria by adaptive evolution.
Published in:
eLife, 2017, p. 1, doi. 10.7554/eLife.30637
By:
- Young, Bernadette C.;
- Chieh-Hsi Wu;
- Gordon, N. Claire;
- Cole, Kevin;
- Pric, James R.;
- Liu, Elian;
- Sheppard, Anna E.;
- Perera, Sanuki;
- Charlesworth, Jane;
- Golubchik, Tanya;
- Iqbal, Zamin;
- Bowden, Rory;
- Massey, Ruth C.;
- Paul, John;
- Crook, Derrick W.;
- Peto, Timothy E.;
- Walker, A. Sarah;
- Llewelyn, Martin J.;
- Wyllie, David H.;
- Wilson, Daniel J.
Publication type:
Article
Pneumococcal genome sequencing tracks a vaccine escape variant formed through a multi-fragment recombination event.
Published in:
Nature Genetics, 2012, v. 44, n. 3, p. 352, doi. 10.1038/ng.1072
By:
- Golubchik, Tanya;
- Brueggemann, Angela B;
- Street, Teresa;
- Gertz, Robert E;
- Spencer, Chris C A;
- Ho, Thien;
- Giannoulatou, Eleni;
- Link-Gelles, Ruth;
- Harding, Rosalind M;
- Beall, Bernard;
- Peto, Tim E A;
- Moore, Matthew R;
- Donnelly, Peter;
- Crook, Derrick W;
- Bowden, Rory
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
Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses.
Published in:
Genome Medicine, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13073-024-01380-x
By:
- Buddle, Sarah;
- Forrest, Leysa;
- Akinsuyi, Naomi;
- Martin Bernal, Luz Marina;
- Brooks, Tony;
- Venturini, Cristina;
- Miller, Charles;
- Brown, Julianne R.;
- Storey, Nathaniel;
- Atkinson, Laura;
- Best, Timothy;
- Roy, Sunando;
- Goldsworthy, Sian;
- Castellano, Sergi;
- Simmonds, Peter;
- Harvala, Heli;
- Golubchik, Tanya;
- Williams, Rachel;
- Breuer, Judith;
- Morfopoulou, Sofia
Publication type:
Article
Asymptomatic <i>Clostridium difficile</i> Colonisation and Onward Transmission.
Published in:
PLoS ONE, 2013, v. 8, n. 11, p. 1, doi. 10.1371/journal.pone.0078445
By:
- Eyre, David W.;
- Griffiths, David;
- Vaughan, Alison;
- Golubchik, Tanya;
- Acharya, Milind;
- O’Connor, Lily;
- Crook, Derrick W.;
- Walker, A. Sarah;
- Peto, Tim E. A.
Publication type:
Article
A Modified RNA-Seq Approach for Whole Genome Sequencing of RNA Viruses from Faecal and Blood Samples.
Published in:
PLoS ONE, 2013, v. 8, n. 6, p. 1, doi. 10.1371/journal.pone.0066129
By:
- Batty, Elizabeth M.;
- Wong, T. H. Nicholas;
- Trebes, Amy;
- Argoud, Karène;
- Attar, Moustafa;
- Buck, David;
- Ip, Camilla L. C.;
- Golubchik, Tanya;
- Cule, Madeleine;
- Bowden, Rory;
- Manganis, Charis;
- Klenerman, Paul;
- Barnes, Eleanor;
- Walker, A. Sarah;
- Wyllie, David H.;
- Wilson, Daniel J.;
- Dingle, Kate E.;
- Peto, Tim E. A.;
- Crook, Derrick W.;
- Piazza, Paolo
Publication type:
Article
Within-Host Evolution of <i>Staphylococcus aureus</i> during Asymptomatic Carriage
Published in:
PLoS ONE, 2013, v. 8, n. 5, p. 1, doi. 10.1371/journal.pone.0061319
By:
- Golubchik, Tanya;
- Batty, Elizabeth M.;
- Miller, Ruth R.;
- Farr, Helen;
- Young, Bernadette C.;
- Larner-Svensson, Hanna;
- Fung, Rowena;
- Godwin, Heather;
- Knox, Kyle;
- Votintseva, Antonina;
- Everitt, Richard G.;
- Street, Teresa;
- Cule, Madeleine;
- Ip, Camilla L. C.;
- Didelot, Xavier;
- Peto, Timothy E. A.;
- Harding, Rosalind M.;
- Wilson, Daniel J.;
- Crook, Derrick W.;
- Bowden, Rory
Publication type:
Article
Identification of Antigens Specific to Non-Tuberculous Mycobacteria: The Mce Family of Proteins as a Target of T Cell Immune Responses.
Published in:
PLoS ONE, 2011, v. 6, n. 10, p. 1, doi. 10.1371/journal.pone.0026434
By:
- Checkley, Anna M.;
- Wyllie, David H.;
- Scriba, Thomas J.;
- Golubchik, Tanya;
- Hill, Adrian V. S.;
- Hanekom, Willem A.;
- McShane, Helen
Publication type:
Article
Clinical Clostridium difficile: Clonality and Pathogenicity Locus Diversity.
Published in:
PLoS ONE, 2011, v. 6, n. 5, p. 1, doi. 10.1371/journal.pone.0019993
By:
- Dingle, Kate E.;
- Griffiths, David;
- Didelot, Xavier;
- Evans, Jessica;
- Vaughan, Alison;
- Kachrimanidou, Melina;
- Stoesser, Nicole;
- Jolley, Keith A.;
- Golubchik, Tanya;
- Harding, Rosalind M.;
- Peto, Tim E.;
- Fawley, Warren;
- Walker, A. Sarah;
- Wilcox, Mark;
- Crook, Derrick W.
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
Deep-sequence phylogenetics to quantify patterns of HIV transmission in the context of a universal testing and treatment trial - BCPP/Ya Tsie trial.
Published in:
eLife, 2022, p. 1, doi. 10.7554/eLife.72657
By:
- Magosi, Lerato E.;
- Yinfeng Zhang;
- Golubchik, Tanya;
- DeGruttola, Victor;
- Tchetgen, Eric Tchetgen;
- Novitsky, Vladimir;
- Moore, Janet;
- Bachanas, Pam;
- Segolodi, Tebogo;
- Lebelonyane, Refeletswe;
- Holme, Molly Pretorius;
- Moyo, Sikhulile;
- Makhema, Joseph;
- Lockman, Shahin;
- Fraser, Christophe;
- Essex, Myron Max;
- Lipsitch, Marc
Publication type:
Article
Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis.
Published in:
Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-09139-4
By:
- Ratmann, Oliver;
- Grabowski, M. Kate;
- Hall, Matthew;
- Golubchik, Tanya;
- Wymant, Chris;
- Abeler-Dörner, Lucie;
- Bonsall, David;
- Hoppe, Anne;
- Brown, Andrew Leigh;
- de Oliveira, Tulio;
- Gall, Astrid;
- Kellam, Paul;
- Pillay, Deenan;
- Kagaayi, Joseph;
- Kigozi, Godfrey;
- Quinn, Thomas C.;
- Wawer, Maria J.;
- Laeyendecker, Oliver;
- Serwadda, David;
- Gray, Ronald H.
Publication type:
Article
PHYLOSCANNER: Inferring Transmission from Within- and Between-Host Pathogen Genetic Diversity.
Published in:
Molecular Biology & Evolution, 2018, v. 35, n. 3, p. 719, doi. 10.1093/molbev/msx304
By:
- Wymant, Chris;
- Hall, Matthew;
- Ratmann, Oliver;
- Bonsall, David;
- Golubchik, Tanya;
- Cesare, Mariateresa de;
- Gall, Astrid;
- Cornelissen, Marion;
- Fraser, Christophe;
- Consortium, STOP-HCV
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
Corrigendum: Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis.
Published in:
Nature Communications, 2016, v. 7, n. 4, p. 11465, doi. 10.1038/ncomms11465
By:
- Bradley, Phelim;
- Gordon, N. Claire;
- Walker, Timothy M.;
- Dunn, Laura;
- Heys, Simon;
- Huang, Bill;
- Earle, Sarah;
- Pankhurst, Louise J.;
- Anson, Luke;
- de Cesare, Mariateresa;
- Piazza, Paolo;
- Votintseva, Antonina A.;
- Golubchik, Tanya;
- Wilson, Daniel J.;
- Wyllie, David H.;
- Diel, Roland;
- Niemann, Stefan;
- Feuerriegel, Silke;
- Kohl, Thomas A.;
- Ismail, Nazir
Publication type:
Article
Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis.
Published in:
Nature Communications, 2015, v. 6, n. 12, p. 10063, doi. 10.1038/ncomms10063
By:
- Bradley, Phelim;
- Gordon, N. Claire;
- Walker, Timothy M.;
- Dunn, Laura;
- Heys, Simon;
- Huang, Bill;
- Earle, Sarah;
- Pankhurst, Louise J.;
- Anson, Luke;
- de Cesare, Mariateresa;
- Piazza, Paolo;
- Votintseva, Antonina A.;
- Golubchik, Tanya;
- Wilson, Daniel J.;
- Wyllie, David H.;
- Diel, Roland;
- Niemann, Stefan;
- Feuerriegel, Silke;
- Kohl, Thomas A.;
- Ismail, Nazir
Publication type:
Article
Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus.
Published in:
Nature Communications, 2014, v. 5, n. 5, p. 3956, doi. 10.1038/ncomms4956
By:
- Everitt, Richard G.;
- Didelot, Xavier;
- Batty, Elizabeth M.;
- Miller, Ruth R;
- Knox, Kyle;
- Young, Bernadette C.;
- Bowden, Rory;
- Auton, Adam;
- Votintseva, Antonina;
- Larner-Svensson, Hanna;
- Charlesworth, Jane;
- Golubchik, Tanya;
- Ip, Camilla L. C.;
- Godwin, Heather;
- Fung, Rowena;
- Peto, Tim E. A.;
- Walker, A. Sarah;
- Crook, Derrick W.;
- Wilson, Daniel J.
Publication type:
Article
Phylogenetic and Demographic Characterization of Directed HIV-1 Transmission Using Deep Sequences from High-Risk and General Population Cohorts/Groups in Uganda.
Published in:
Viruses (1999-4915), 2020, v. 12, n. 3, p. 331, doi. 10.3390/v12030331
By:
- Bbosa, Nicholas;
- Ssemwanga, Deogratius;
- Ssekagiri, Alfred;
- Xi, Xiaoyue;
- Mayanja, Yunia;
- Bahemuka, Ubaldo;
- Seeley, Janet;
- Pillay, Deenan;
- Abeler-Dörner, Lucie;
- Golubchik, Tanya;
- Fraser, Christophe;
- Kaleebu, Pontiano;
- Ratmann, Oliver
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
Evolutionary History of the Clostridium difficile Pathogenicity Locus.
Published in:
Genome Biology & Evolution, 2014, v. 6, n. 1, p. 36, doi. 10.1093/gbe/evt204
By:
- Dingle, Kate E.;
- Elliott, Briony;
- Robinson, Esther;
- Griffiths, David;
- Eyre, David W.;
- Stoesser, Nicole;
- Vaughan, Alison;
- Golubchik, Tanya;
- Fawley, Warren N.;
- Wilcox, Mark H.;
- Peto, Timothy E.;
- Walker, A. Sarah;
- Riley, Thomas V.;
- Crook, Derrick W.;
- Didelot, Xavier
Publication type:
Article
Reply to Mills and Linkin.
Published in:
2014
By:
- Price, James R.;
- Golubchik, Tanya;
- Wilson, Daniel J.;
- Crook, Derrick W.;
- Walker, A. Sarah;
- Peto, Timothy E. A.;
- Paul, John;
- Llewelyn, Martin J.
Publication type:
Letter to the Editor
Whole-Genome Sequencing Shows That Patient-to-Patient Transmission Rarely Accounts for Acquisition of Staphylococcus aureus in an Intensive Care Unit.
Published in:
Clinical Infectious Diseases, 2014, v. 58, n. 5, p. 609, doi. 10.1093/cid/cit807
By:
- Price, James R.;
- Golubchik, Tanya;
- Cole, Kevin;
- Wilson, Daniel J.;
- Crook, Derrick W.;
- Thwaites, Guy E.;
- Bowden, Rory;
- Walker, A. Sarah;
- Peto, Timothy E. A.;
- Paul, John;
- Llewelyn, Martin J.
Publication type:
Article
Mind the Gaps: Evidence of Bias in Estimates of Multiple Sequence Alignments.
Published in:
Molecular Biology & Evolution, 2007, v. 24, n. 11, p. 2433, doi. 10.1093/molbev/msm176
By:
- Golubchik, Tanya;
- Wise, Michael J.;
- Easteal, Simon;
- Jermiin, Lars S.
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
Absence of detectable monkeypox virus DNA in 11,000 English blood donations during the 2022 outbreak.
Published in:
Transfusion, 2023, v. 63, n. 4, p. 690, doi. 10.1111/trf.17266
By:
- Knight, Chanice;
- Andreani, Julien;
- Garrett, Neil;
- Winter, Mark;
- Golubchik, Tanya;
- Breuer, Judy;
- Reynolds, Claire;
- Brailsford, Susan R.;
- Harvala, Heli;
- Simmonds, Peter
Publication type:
Article
Recombination and Population Structure in Salmonella enterica.
Published in:
PLoS Genetics, 2011, v. 7, n. 7, p. 1, doi. 10.1371/journal.pgen.1002191
By:
- Didelot, Xavier;
- Bowden, Rory;
- Street, Teresa;
- Golubchik, Tanya;
- Spencer, Chris;
- McVean, Gil;
- Sangal, Vartul;
- Anjum, Muna F.;
- Achtman, Mark;
- Falush, Daniel;
- Donnelly, Peter
Publication type:
Article
Oxford Screening CSF and Respiratory samples (‘OSCAR’): results of a pilot study to screen clinical samples from a diagnostic microbiology laboratory for viruses using Illumina next generation sequencing.
Published in:
BMC Research Notes, 2018, v. 11, p. 1, doi. 10.1186/s13104-018-3234-8
By:
- Sharp, Colin;
- Golubchik, Tanya;
- Gregory, William F.;
- McNaughton, Anna L.;
- Gow, Nicholas;
- Selvaratnam, Mathyruban;
- Mirea, Alina;
- Foster, Dona;
- Andersson, Monique;
- Klenerman, Paul;
- Jeffery, Katie;
- Matthews, Philippa C.
Publication type:
Article
Clinical and Viral Factors Associated With Disease Severity and Subsequent Wheezing in Infants With Respiratory Syncytial Virus Infection.
Published in:
2022
By:
- McGinley, Joseph P;
- Lin, Gu Lung;
- Öner, Deniz;
- Golubchik, Tanya;
- O'Connor, Daniel;
- Snape, Matthew D;
- Gruselle, Olivier;
- Langedijk, Annefleur C;
- Wildenbeest, Joanne;
- Openshaw, Peter;
- Nair, Harish;
- Aerssens, Jeroen;
- Bont, Louis;
- Martinón-Torres, Federico;
- Drysdale, Simon B;
- Pollard, Andrew J;
- Investigators, the RESCEU;
- RESCEU Investigators
Publication type:
journal article
Human Immunodeficiency Virus (HIV) Genetic Diversity Informs Stage of HIV-1 Infection Among Patients Receiving Antiretroviral Therapy in Botswana.
Published in:
2022
By:
- Ragonnet-Cronin, Manon;
- Golubchik, Tanya;
- Moyo, Sikhulile;
- Fraser, Christophe;
- Essex, Max;
- Novitsky, Vlad;
- Volz, Erik
Publication type:
journal article
Virological and serological characterization of critically ill patients with COVID-19 in the UK: Interactions of viral load, antibody status and B.1.1.7 variant infection.
Published in:
2021
By:
- Ratcliff, Jeremy;
- Nguyen, Dung;
- Fish, Matthew;
- Rynne, Jennifer;
- Jennings, Aislinn;
- Williams, Sarah;
- Al-Beidh, Farah;
- Bonsall, David;
- Evans, Amy;
- Golubchik, Tanya;
- Gordon, Anthony C;
- Lamikanra, Abigail;
- Tsang, Pat;
- Ciccone, Nick A;
- Leuscher, Ullrich;
- Slack, Wendy;
- Laing, Emma;
- Mouncey, Paul R;
- Ziyenge, Sheba;
- Oliveira, Marta
Publication type:
journal 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
Performance of a high-throughput next-generation sequencing method for analysis of HIV drug resistance and viral load.
Published in:
2020
By:
- Fogel, Jessica M;
- Bonsall, David;
- Cummings, Vanessa;
- Bowden, Rory;
- Golubchik, Tanya;
- Cesare, Mariateresa de;
- Wilson, Ethan A;
- Gamble, Theresa;
- Rio, Carlos del;
- Batey, D Scott;
- Mayer, Kenneth H;
- Farley, Jason E;
- Hughes, James P;
- Remien, Robert H;
- Beyrer, Chris;
- Fraser, Christophe;
- Eshleman, Susan H;
- de Cesare, Mariateresa;
- Del Rio, Carlos
Publication type:
journal article
High prevalence of integrase mutation L74I in West African HIV-1 subtypes prior to integrase inhibitor treatment.
Published in:
2020
By:
- Bouzidi, Kate El;
- Kemp, Steven A;
- Datir, Rawlings P;
- Murtala-Ibrahim, Fati;
- Aliyu, Ahmad;
- Kwaghe, Vivian;
- Frampton, Dan;
- Roy, Sunando;
- Breuer, Judith;
- Sabin, Caroline A;
- Ogbanufe, Obinna;
- Charurat, Man E;
- Bonsall, David;
- Golubchik, Tanya;
- Fraser, Christophe;
- Dakum, Patrick;
- Ndembi, Nicaise;
- Gupta, Ravindra K;
- El Bouzidi, Kate
Publication type:
journal article
SARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY.4.2.
Published in:
BMC Infectious Diseases, 2022, v. 22, n. 1, p. 1, doi. 10.1186/s12879-022-07628-4
By:
- Eales, Oliver;
- Page, Andrew J.;
- de Oliveira Martins, Leonardo;
- Wang, Haowei;
- Bodinier, Barbara;
- Haw, David;
- Jonnerby, Jakob;
- Atchison, Christina;
- The COVID-19 Genomics UK (COG-UK) Consortium;
- Robson, Samuel C.;
- Connor, Thomas R.;
- Loman, Nicholas J.;
- Golubchik, Tanya;
- Nunez, Rocio T. Martinez;
- Bonsall, David;
- Rambaut, Andrew;
- Snell, Luke B.;
- Livett, Rich;
- Ludden, Catherine;
- Corden, Sally
Publication type:
Article
Correction: Viral burden is associated with age, vaccination, and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection-related sampling bias.
Published in:
2023
By:
- Fryer, Helen R.;
- Golubchik, Tanya;
- Hall, Matthew;
- Fraser, Christophe;
- Hinch, Robert;
- Ferretti, Luca;
- Thomson, Laura;
- Nurtay, Anel;
- Pellis, Lorenzo;
- House, Thomas;
- MacIntyre-Cockett, George;
- Trebes, Amy;
- Buck, David;
- Piazza, Paolo;
- Green, Angie;
- Lonie, Lorne J;
- Smith, Darren;
- Bashton, Matthew;
- Crown, Matthew;
- Nelson, Andrew
Publication type:
Correction Notice
Viral burden is associated with age, vaccination, and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection-related sampling bias.
Published in:
PLoS Pathogens, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.ppat.1011461
By:
- Fryer, Helen R.;
- Golubchik, Tanya;
- Hall, Matthew;
- Fraser, Christophe;
- Hinch, Robert;
- Ferretti, Luca;
- Thomson, Laura;
- Nurtay, Anel;
- Pellis, Lorenzo;
- House, Thomas;
- MacIntyre-Cockett, George;
- Trebes, Amy;
- Buck, David;
- Piazza, Paolo;
- Green, Angie;
- Lonie, Lorne J;
- Smith, Darren;
- Bashton, Matthew;
- Crown, Matthew;
- Nelson, Andrew
Publication type:
Article

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