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Breadcrumb Charles Swanton Swanton lab Cancer Evolution and Genome Instability Laboratory : Publications Lab contentLab contentIn this section Overview Areas of interest Publications Members Vacancies Illustration of chromosomes from a cancer cell showing large-scale alterations. Toggle to view hero caption PublicationsYear published2024 (4)2023 (43)2022 (26)2021 (40)2020 (43)2019 (26)2018 (26)2017 (36)2016 (24)2015 (19) Facet Year publishedResearch topicsGenome Integrity & Repair (287)Tumour Biology (287)Computational & Systems Biology (286)Chemical Biology & High Throughput (285)Human Biology & Physiology (285)Signalling & Oncogenes (284)Model Organisms (58)Cell Biology (55)Immunology (45)Stem Cells (44)Cell Cycle & Chromosomes (42)Infectious Disease (35)Structural Biology & Biophysics (32)Metabolism (30)Neurosciences (30)Biochemistry & Proteomics (25)Gene Expression (20)Imaging (19)Developmental Biology (18)Synthetic Biology (4)Microfabrication & Bioengineering (2) (-)Genetics & Genomics (287) Facet Research topicsPublication typeJournal article (287)Primary research (169)Review (66)Commentary (23)Letter (13)Editorial (7)Method (5)Biography (1)Obituary (1)Policy letter (1) Facet Publication typeJournalAnnals of Oncology (32)Cancer Discovery (15)Nature (15)Nature Communications (13)Cancer Cell (12)Cell (12)Nature Cancer (11)Nature Medicine (11)The Lancet (10)Nature Reviews Clinical Oncology (8)Cancer Research (7)Nature Genetics (7)Lancet Oncology (5)Genome Biology (4)Journal of Clinical Oncology (4)Lancet (4)npj Breast Cancer (4)Science (4)Science Translational Medicine (4)British Journal of Cancer (3)Cell Reports (3)Nature Biotechnology (3)New England Journal of Medicine (3)Oncogene (3)PLOS Medicine (3)The Lancet Oncology (3)Annual Review of Cancer Biology (2)Cancer Prevention Research (2)Cold Spring Harbor Perspectives in Medicine (2)European Journal of Cancer (2)European Urology (2)Gastroenterology (2)Immunity (2)Journal of Clinical Investigation (2)Journal of Experimental Medicine (2)Journal of Thoracic Oncology (2)Lancet Infectious Diseases (2)Methods in Molecular Biology (2)Nature Ecology and Evolution (2)PLOS ONE (2)Trends in Cancer (2)Annals of Translational Medicine (1)ASCO Educational Book (1)Autophagy (1)Biochemical Society Transactions (1)BMC Bioinformatics (1)BMC Medical Genomics (1)BMC Medicine (1)BMJ (1)CA: a cancer journal for clinicians (1)Cancer Immunology, Immunotherapy (1)Cancers (Basel) (1)Cell Cycle (1)Cell Reports Medicine (1)Clinical cancer research (1)Clinical Oncology (1)Current Opinion in Systems Biology (1)Current Opinion in Urology (1)Disease Models & Mechanisms (1)eLife (1)EMBO Molecular Medicine (1)Epilepsy and Behavior (1)ESMO Open (1)Frontiers in Oncology (1)Frontiers in Pharmacology (1)Immuno-Oncology and Technology (1)Immunological Reviews (1)International Journal of Cancer (1)Journal for ImmunoTherapy of Cancer (1)Journal of the Royal Society of Medicine (1)Molecular & Cellular Oncology (1)Molecular and Cellular Oncology (1)Mutagenesis (1)NAR Cancer (1)Nature Aging (1)Nature Protocols (1)Nature Reviews Cancer (1)Nature Reviews Disease Primers (1)Nature Reviews Drug Discovery (1)Nature Reviews Genetics (1)Nature Reviews Urology (1)Neuro-Oncology (1)Nucleic Acids Research (1)Oncotarget (1)Open Biology (1)PLOS Biology (1)PLoS Computational Biology (1)Preventive Medicine (1)Proceedings of the National Academy of Sciences of USA (1)Seminars in Cancer Biology (1)Supportive Care in Cancer (1)The EMBO Journal (1)Trends in Cell Biology (1)Tumori Journal (1)Wellcome Open Research (1) Facet Journal Publications Displaying 1 - 20 of 287Last updated : 28 March 2024 02:48 COVID-19 in non-hospitalised adults caused by either SARS-CoV-2 sub-variants Omicron BA.1, BA.2, BA.4/5 or Delta associates with similar illness duration, symptom severity and viral kinetics, irrespective of vaccination history Authors (37) Hermaleigh Townsley Joshua Gahir Timothy W Russell David GreenwoodEdward Carr Matala Dyke[...]Sonia Gandhi Adam J KucharskiCharles SwantonDavid LV Bauer Emma C Wall PLOS ONE Published 21 March 2024 Crick labs/ facilitiesRobert J WilkinsonCharles SwantonGeorge KassiotisSonia GandhiSteve GamblinRupert BealeDavid LV BauerBiological Research FacilityBioinformatics and BiostatisticsAdvanced SequencingFull details Divergent performance of vaccines in the UK autumn 2023 COVID-19 booster campaign Authors (22) Marianne Shawe-Taylor David Greenwood Agnieszka Hobbs Giulia DowgierBecky PennTheo Sanderson[...]Sonia GandhiEdward CarrMary WuDavid LV Bauer Emma C Wall The Lancet Published 11 March 2024 Crick labs/ facilitiesCharles SwantonGeorge KassiotisSonia GandhiSteve GamblinMike BlackmanRupert BealeDavid LV BauerWorldwide Influenza CentreStructural BiologyHigh Throughput ScreeningBioinformatics and BiostatisticsAdvanced SequencingScientific computingFull details Combined analyses of within-host SARS-CoV-2 viral kinetics and information on past exposures to the virus in a human cohort identifies intrinsic differences of Omicron and Delta variants Authors (26) Timothy W Russell Hermaleigh Townsley Sam Abbott Joel HellewellEdward Carr Lloyd AC Chapman[...]Charles SwantonRupert BealeDavid LV Bauer Emma C Wall Adam J Kucharski PLOS Biology Published 30 January 2024 Crick labs/ facilitiesCharles SwantonSonia GandhiSteve GamblinRupert BealeDavid LV BauerWorldwide Influenza CentreBiological Research FacilityAdvanced SequencingFull details The artificial intelligence-based model ANORAK improves histopathological grading of lung adenocarcinoma Authors (20) Xiaoxi Pan Khalid AbdulJabbar Jose Coelho-Lima Anca-Ioana Grapa Hanyun Zhang Alvin Ho Kwan Cheung[...] TRACERx ConsortiumCharles Swanton Yinyin Yuan John Le Quesne David A Moore Nature Cancer Published 1 February 2024 Crick labs/ facilitiesPeter Van LooSamra TurajlicCharles SwantonErik SahaiGeorge KassiotisFlow CytometryExperimental HistopathologyBiological Research FacilityBioinformatics and BiostatisticsAdvanced SequencingScientific computingFull details Breaking the performance ceiling for neoantigen immunogenicity prediction Authors (12) Hugh O'Brien Max Salm Laura Morton Maciej Szukszto Felix O'Farrell Charlotte Boulton[...] Yardena SamuelsCharles Swanton Marc R Mansour Sine Reker Hadrup Sergio A Quezada Nature Cancer Published 1 December 2023 Crick labsCharles SwantonFull details SARS-CoV-2 mucosal neutralising immunity after vaccination Authors (38)Edward Carr Guilia Dowgier David Greenwood Lou S Herman Agnieszka Hobbs Martina Ragno[...]Charles SwantonSonia GandhiDavid LV Bauer Emma WallMary Wu Lancet Infectious Diseases Published 1 January 2024 Crick labs/ facilitiesCharles SwantonGeorge KassiotisSonia GandhiSteve GamblinRupert BealeDavid LV BauerWorldwide Influenza CentreHigh Throughput ScreeningBiological Research FacilityAdvanced SequencingFull details The role of APOBEC3B in lung tumor evolution and targeted cancer therapy resistance Authors (85)Deborah Caswell Philippe Gui Manasi K Mayekar Emily K Law Oriol Pich Chris Bailey[...] Nnennaya Kanu Reuben S HarrisJulian Downward Trever G BivonaCharles Swanton Nature Genetics Published 1 January 2024 Crick labs/ facilitiesKaren VousdenCharles SwantonJulian DownwardExperimental HistopathologyBiological Research FacilityFull details CONIPHER: a computational framework for scalable phylogenetic reconstruction with error correction Authors (11) Kristiana GrigoriadisAriana Huebner Abigail Bunkum Emma ColliverAlexander Frankell Mark S Hill Kerstin TholNicolai BirkbakCharles Swanton Simone Zaccaria Nicholas McGranahan Nature Protocols Published 1 January 2024 Crick labsCharles SwantonFull details Quantifying the impact of immunotherapy on RNA dynamics in cancer Authors (16) Ieva UsaiteDhruva BiswasKrijn Dijkstra Thomas BK Watkins Oriol Pich Clare Puttick[...] Simone Zaccaria Yin Wu Kevin LitchfieldCharles Swanton Nnennaya Kanu Journal for ImmunoTherapy of Cancer Published 1 November 2023 Crick labsCharles SwantonFull details Turning a failing PhD around Authors (1)Charles Swanton Nature Cancer Published 1 October 2023 Crick labsCharles SwantonFull details Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity Authors (11)Tom Watkins Emma C Colliver Matthew R Huska Tom L KaufmannEmilia Lim Cody B Duncan Kerstin HaasePeter Van LooCharles Swanton Nicholas McGranahan Roland F Schwarz PLoS Computational Biology Published 23 October 2023 Crick labsPeter Van LooCharles SwantonFull details Cancer cell-intrinsic mechanisms driving acquired immune tolerance Authors (3) Ehsan GhoraniCharles Swanton Sergio A Quezada Immunity Published 10 October 2023 Crick labsCharles SwantonFull details MyPathway human epidermal growth factor receptor 2 basket study: Pertuzumab + trastuzumab treatment of a tissue-agnostic cohort of patients with human epidermal growth factor receptor 2-altered advanced solid tumors Authors (17) Christopher J Sweeney John D Hainsworth Ron Bose Howard A Burris Razelle KurzrockCharles Swanton[...] Amy A Lo Jonathan Levy Yong Wang Wei Yu Funda Meric-Bernstam Journal of Clinical Oncology Published 20 January 2024 Crick labsCharles SwantonFull details Tumor heterogeneity impairs immunogenicity in mismatch repair deficient tumors Authors (3) James L ReadingDeborah CaswellCharles Swanton Nature Genetics Published 1 October 2023 Crick labsCharles SwantonFull details Placing the patient at the heart of discovery science Authors (4) Mihaela Aldea Elsa BernardCharles Swanton Fabrice Andre European Journal of Cancer Published 1 November 2023 Crick labsCharles SwantonFull details Copy number architectures define treatment-mediated selection of lethal prostate cancer clones Authors (24) AM Mahedi Hasan Paolo Cremaschi Daniel Wetterskog Anuradha Jayaram Stephen Q Wong Scott Williams[...]Charles Swanton Mariam Jamal-Hanjani Stefano Lise Shahneen Sandhu Gerhardt Attard Nature Communications Published 10 August 2023 Crick labs/ facilitiesPeter Van LooSamra TurajlicCharles SwantonPeter ParkerExperimental HistopathologyBiological Research FacilityAdvanced SequencingFull details Independent SARS-CoV-2 staff testing protected academic and health-care institutions in northwest London Authors (54) Chris BaileyTheo Sanderson Hermaleigh Townsley Jacki Goldman James RM BlackGeorge Young[...]Jerome NicodSonia GandhiDavid LV Bauer Emma C WallCharles Swanton The Lancet Published 1 July 2023 Crick labs/ facilitiesSamra TurajlicCharles SwantonSam RodriquesSonia GandhiSteve GamblinMike BlackmanRupert BealeDavid LV BauerWorldwide Influenza CentreStructural BiologyMetabolomicsHigh Throughput ScreeningFlow CytometryBioinformatics and BiostatisticsAdvanced SequencingScientific computingBiological Research FacilityFull details Neutralising immunity to omicron sublineages BQ.1.1, XBB, and XBB.1.5 in healthy adults is boosted by bivalent BA.1-containing mRNA vaccination and previous Omicron infection Authors (36)Edward CarrMary Wu Joshua Gahir Ruth Harvey Hermaleigh Townsley Chris Bailey[...]Charles SwantonSonia GandhiDavid LV Bauer Emma C Wall Crick COVID Serology Consortium Lancet Infectious Diseases Published 1 July 2023 Crick labs/ facilitiesCharles SwantonGeorge KassiotisSonia GandhiSteve GamblinRupert BealeDavid LV BauerWorldwide Influenza CentreHigh Throughput ScreeningBiological Research FacilityAdvanced SequencingScientific computingFull details Phenotyping of lymphoproliferative tumours generated in xenografts of non-small cell lung cancer Authors (16) David R Pearce Ayse U Akarca Roel PH De Maeyer Emily KostinaAriana Huebner Monica Sivakumar[...] Arne N Akbar David A Moore Teresa MarafiotiCharles SwantonRob Hynds Frontiers in Oncology Published 5 June 2023 Crick labsCharles SwantonFull details Pan-cancer T cell atlas links a cellular stress response state to immunotherapy resistance Authors (45) Yanshuo Chu Enyu Dai Yating Li Guangchun Han Guangsheng Pei Davis R Ingram[...] Michael GreenKevin Litchfield Humam Kadara Cassian Yee Linghua Wang Nature Medicine Published 1 June 2023 Crick labsCharles SwantonFull details Pagination Current page 1 Page 2 Page 3 Page 4 Page 5 Page 6 Page 7 Page 8 Page 9 … Next page Next Last page Last Share the page Share on Twitter Share on Facebook Share on LinkedIn Share on 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COVID-19 in non-hospitalised adults caused by either SARS-CoV-2 sub-variants Omicron BA.1, BA.2, BA.4/5 or Delta associates with similar illness duration, symptom severity and viral kinetics, irrespective of vaccination history Authors (37) Hermaleigh Townsley Joshua Gahir Timothy W Russell David GreenwoodEdward Carr Matala Dyke[...]Sonia Gandhi Adam J KucharskiCharles SwantonDavid LV Bauer Emma C Wall PLOS ONE Published 21 March 2024 Crick labs/ facilitiesRobert J WilkinsonCharles SwantonGeorge KassiotisSonia GandhiSteve GamblinRupert BealeDavid LV BauerBiological Research FacilityBioinformatics and BiostatisticsAdvanced SequencingFull details
Divergent performance of vaccines in the UK autumn 2023 COVID-19 booster campaign Authors (22) Marianne Shawe-Taylor David Greenwood Agnieszka Hobbs Giulia DowgierBecky PennTheo Sanderson[...]Sonia GandhiEdward CarrMary WuDavid LV Bauer Emma C Wall The Lancet Published 11 March 2024 Crick labs/ facilitiesCharles SwantonGeorge KassiotisSonia GandhiSteve GamblinMike BlackmanRupert BealeDavid LV BauerWorldwide Influenza CentreStructural BiologyHigh Throughput ScreeningBioinformatics and BiostatisticsAdvanced SequencingScientific computingFull details
Combined analyses of within-host SARS-CoV-2 viral kinetics and information on past exposures to the virus in a human cohort identifies intrinsic differences of Omicron and Delta variants Authors (26) Timothy W Russell Hermaleigh Townsley Sam Abbott Joel HellewellEdward Carr Lloyd AC Chapman[...]Charles SwantonRupert BealeDavid LV Bauer Emma C Wall Adam J Kucharski PLOS Biology Published 30 January 2024 Crick labs/ facilitiesCharles SwantonSonia GandhiSteve GamblinRupert BealeDavid LV BauerWorldwide Influenza CentreBiological Research FacilityAdvanced SequencingFull details
The artificial intelligence-based model ANORAK improves histopathological grading of lung adenocarcinoma Authors (20) Xiaoxi Pan Khalid AbdulJabbar Jose Coelho-Lima Anca-Ioana Grapa Hanyun Zhang Alvin Ho Kwan Cheung[...] TRACERx ConsortiumCharles Swanton Yinyin Yuan John Le Quesne David A Moore Nature Cancer Published 1 February 2024 Crick labs/ facilitiesPeter Van LooSamra TurajlicCharles SwantonErik SahaiGeorge KassiotisFlow CytometryExperimental HistopathologyBiological Research FacilityBioinformatics and BiostatisticsAdvanced SequencingScientific computingFull details
Breaking the performance ceiling for neoantigen immunogenicity prediction Authors (12) Hugh O'Brien Max Salm Laura Morton Maciej Szukszto Felix O'Farrell Charlotte Boulton[...] Yardena SamuelsCharles Swanton Marc R Mansour Sine Reker Hadrup Sergio A Quezada Nature Cancer Published 1 December 2023 Crick labsCharles SwantonFull details
SARS-CoV-2 mucosal neutralising immunity after vaccination Authors (38)Edward Carr Guilia Dowgier David Greenwood Lou S Herman Agnieszka Hobbs Martina Ragno[...]Charles SwantonSonia GandhiDavid LV Bauer Emma WallMary Wu Lancet Infectious Diseases Published 1 January 2024 Crick labs/ facilitiesCharles SwantonGeorge KassiotisSonia GandhiSteve GamblinRupert BealeDavid LV BauerWorldwide Influenza CentreHigh Throughput ScreeningBiological Research FacilityAdvanced SequencingFull details
The role of APOBEC3B in lung tumor evolution and targeted cancer therapy resistance Authors (85)Deborah Caswell Philippe Gui Manasi K Mayekar Emily K Law Oriol Pich Chris Bailey[...] Nnennaya Kanu Reuben S HarrisJulian Downward Trever G BivonaCharles Swanton Nature Genetics Published 1 January 2024 Crick labs/ facilitiesKaren VousdenCharles SwantonJulian DownwardExperimental HistopathologyBiological Research FacilityFull details
CONIPHER: a computational framework for scalable phylogenetic reconstruction with error correction Authors (11) Kristiana GrigoriadisAriana Huebner Abigail Bunkum Emma ColliverAlexander Frankell Mark S Hill Kerstin TholNicolai BirkbakCharles Swanton Simone Zaccaria Nicholas McGranahan Nature Protocols Published 1 January 2024 Crick labsCharles SwantonFull details
Quantifying the impact of immunotherapy on RNA dynamics in cancer Authors (16) Ieva UsaiteDhruva BiswasKrijn Dijkstra Thomas BK Watkins Oriol Pich Clare Puttick[...] Simone Zaccaria Yin Wu Kevin LitchfieldCharles Swanton Nnennaya Kanu Journal for ImmunoTherapy of Cancer Published 1 November 2023 Crick labsCharles SwantonFull details
Turning a failing PhD around Authors (1)Charles Swanton Nature Cancer Published 1 October 2023 Crick labsCharles SwantonFull details
Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity Authors (11)Tom Watkins Emma C Colliver Matthew R Huska Tom L KaufmannEmilia Lim Cody B Duncan Kerstin HaasePeter Van LooCharles Swanton Nicholas McGranahan Roland F Schwarz PLoS Computational Biology Published 23 October 2023 Crick labsPeter Van LooCharles SwantonFull details
Cancer cell-intrinsic mechanisms driving acquired immune tolerance Authors (3) Ehsan GhoraniCharles Swanton Sergio A Quezada Immunity Published 10 October 2023 Crick labsCharles SwantonFull details
MyPathway human epidermal growth factor receptor 2 basket study: Pertuzumab + trastuzumab treatment of a tissue-agnostic cohort of patients with human epidermal growth factor receptor 2-altered advanced solid tumors Authors (17) Christopher J Sweeney John D Hainsworth Ron Bose Howard A Burris Razelle KurzrockCharles Swanton[...] Amy A Lo Jonathan Levy Yong Wang Wei Yu Funda Meric-Bernstam Journal of Clinical Oncology Published 20 January 2024 Crick labsCharles SwantonFull details
Tumor heterogeneity impairs immunogenicity in mismatch repair deficient tumors Authors (3) James L ReadingDeborah CaswellCharles Swanton Nature Genetics Published 1 October 2023 Crick labsCharles SwantonFull details
Placing the patient at the heart of discovery science Authors (4) Mihaela Aldea Elsa BernardCharles Swanton Fabrice Andre European Journal of Cancer Published 1 November 2023 Crick labsCharles SwantonFull details
Copy number architectures define treatment-mediated selection of lethal prostate cancer clones Authors (24) AM Mahedi Hasan Paolo Cremaschi Daniel Wetterskog Anuradha Jayaram Stephen Q Wong Scott Williams[...]Charles Swanton Mariam Jamal-Hanjani Stefano Lise Shahneen Sandhu Gerhardt Attard Nature Communications Published 10 August 2023 Crick labs/ facilitiesPeter Van LooSamra TurajlicCharles SwantonPeter ParkerExperimental HistopathologyBiological Research FacilityAdvanced SequencingFull details
Independent SARS-CoV-2 staff testing protected academic and health-care institutions in northwest London Authors (54) Chris BaileyTheo Sanderson Hermaleigh Townsley Jacki Goldman James RM BlackGeorge Young[...]Jerome NicodSonia GandhiDavid LV Bauer Emma C WallCharles Swanton The Lancet Published 1 July 2023 Crick labs/ facilitiesSamra TurajlicCharles SwantonSam RodriquesSonia GandhiSteve GamblinMike BlackmanRupert BealeDavid LV BauerWorldwide Influenza CentreStructural BiologyMetabolomicsHigh Throughput ScreeningFlow CytometryBioinformatics and BiostatisticsAdvanced SequencingScientific computingBiological Research FacilityFull details
Neutralising immunity to omicron sublineages BQ.1.1, XBB, and XBB.1.5 in healthy adults is boosted by bivalent BA.1-containing mRNA vaccination and previous Omicron infection Authors (36)Edward CarrMary Wu Joshua Gahir Ruth Harvey Hermaleigh Townsley Chris Bailey[...]Charles SwantonSonia GandhiDavid LV Bauer Emma C Wall Crick COVID Serology Consortium Lancet Infectious Diseases Published 1 July 2023 Crick labs/ facilitiesCharles SwantonGeorge KassiotisSonia GandhiSteve GamblinRupert BealeDavid LV BauerWorldwide Influenza CentreHigh Throughput ScreeningBiological Research FacilityAdvanced SequencingScientific computingFull details
Phenotyping of lymphoproliferative tumours generated in xenografts of non-small cell lung cancer Authors (16) David R Pearce Ayse U Akarca Roel PH De Maeyer Emily KostinaAriana Huebner Monica Sivakumar[...] Arne N Akbar David A Moore Teresa MarafiotiCharles SwantonRob Hynds Frontiers in Oncology Published 5 June 2023 Crick labsCharles SwantonFull details
Pan-cancer T cell atlas links a cellular stress response state to immunotherapy resistance Authors (45) Yanshuo Chu Enyu Dai Yating Li Guangchun Han Guangsheng Pei Davis R Ingram[...] Michael GreenKevin Litchfield Humam Kadara Cassian Yee Linghua Wang Nature Medicine Published 1 June 2023 Crick labsCharles SwantonFull details