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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 (9)2023 (44)2022 (26)2021 (40)2020 (43)2019 (26)2018 (27)2017 (36)2016 (24)2015 (28)2014 (28)2013 (24)2012 (18)2011 (11)2010 (12) Facet Year publishedResearch topicsTumour Biology (293)Genetics & Genomics (292)Computational & Systems Biology (291)Genome Integrity & Repair (291)Human Biology & Physiology (290)Signalling & Oncogenes (290)Chemical Biology & High Throughput (289)Model Organisms (59)Cell Biology (57)Immunology (47)Stem Cells (46)Cell Cycle & Chromosomes (42)Infectious Disease (35)Structural Biology & Biophysics (32)Metabolism (31)Neurosciences (30)Biochemistry & Proteomics (25)Gene Expression (21)Imaging (20)Developmental Biology (19)Synthetic Biology (4)Microfabrication & Bioengineering (2) Facet Research topicsPublication typeJournal article (396)Primary research (218)Review (109)Commentary (31)Letter (18)Editorial (10)Method (5)Biography (1)Book review (1)Obituary (1)Policy letter (1) Facet Publication typeJournalAnnals of Oncology (39)Nature (18)Cancer Discovery (17)Cancer Cell (14)Cell (14)Nature Communications (14)Cancer Research (13)Nature Cancer (11)Nature Medicine (11)Nature Reviews Clinical Oncology (10)The Lancet (10)Lancet Oncology (9)Journal of Pathology (8)Nature Genetics (8)British Journal of Cancer (7)Genome Biology (7)New England Journal of Medicine (7)EPMA Journal (5)Journal of Clinical Oncology (5)Science (5)Science Translational Medicine (5)Lancet (4)npj Breast Cancer (4)Oncogene (4)PLOS ONE (4)Cell Reports (3)Clinical cancer research (3)Cold Spring Harbor Perspectives in Medicine (3)European Journal of Cancer (3)European Urology (3)Frontiers in Oncology (3)Nature Biotechnology (3)PLOS Medicine (3)The Lancet Oncology (3)Annual Review of Cancer Biology (2)ASCO Educational Book (2)Autophagy (2)Breast Cancer Research (2)Breast Cancer Research and Treatment (2)Cancer Prevention Research (2)Gastroenterology (2)Genome Medicine (2)Immunity (2)Journal of Cell Science (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)Nature Reviews Urology (2)Oncologist (2)Oncotarget (2)PLOS Biology (2)Trends in Cancer (2)American Journal of Pathology (1)Annals of the New York Academy of Sciences (1)Annals of Translational Medicine (1)Annual Review of Genetics (1)Biochemical Pharmacology (1)Biochemical Society Transactions (1)Biochimica et Biophysica Acta (1)BJU international (1)BMC Bioinformatics (1)BMC Medical Genomics (1)BMC Medicine (1)BMJ (1)Breast (1)CA: a cancer journal for clinicians (1)Cancer Epidemiology, Biomarkers & Prevention (1)Cancer Immunology, Immunotherapy (1)Cancer Letters (1)Cancers (Basel) (1)Cell Cycle (1)Cell Reports Medicine (1)Clinical Chemistry (1)Clinical Medicine (1)Clinical Oncology (1)Current Biology (1)Current Cancer Drug Targets (1)Current Opinion in Genetics & Development (1)Current Opinion in Pharmacology (1)Current Opinion in Systems Biology (1)Current Opinion in Urology (1)Disease Models & Mechanisms (1)Drugs (1)eLife (1)EMBO Molecular Medicine (1)EMBO Reports (1)Epilepsy and Behavior (1)ESMO Open (1)Evolutionary Applications (1)Expert Review of Anticancer Therapy (1)Frontiers in Pharmacology (1)G3 (1)Immuno-Oncology and Technology (1)Immunological Reviews (1)International Journal of Cancer (1)Investigational New Drugs (1)Journal for ImmunoTherapy of Cancer (1)Journal of Cellular Biochemistry (1)Journal of hepatology (1)Journal of the Royal Society of Medicine (1)Molecular & Cellular Oncology (1)Molecular and Cellular Oncology (1)Molecular 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)Neuro-Oncology (1)Nucleic Acids Research (1)Open Biology (1)Orvosi Hetilap (1)PLoS Computational Biology (1)Preventive Medicine (1)Proceedings of the National Academy of Sciences of USA (1)Scientific Reports (1)Seminars in Cancer Biology (1)Stem Cell Reports (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 396Last updated : 23 April 2024 02:56 Spatial architecture of myeloid and T cells orchestrates immune evasion and clinical outcome in lung cancer Authors (35)Katey Enfield Emma Colliver Claudia Lee Alastair Magness David A Moore Monica Sivakumar[...]Crispin HileyJulian DownwardErik SahaiCharles SwantonMihaela Angelova Cancer Discovery Published 6 April 2024 Crick labs/ facilitiesCharles SwantonErik SahaiJulian DownwardFlow CytometryExperimental HistopathologyScientific computingProteomicsLight MicroscopyCell ServicesBiological Research FacilityAdvanced SequencingFull details Research autopsy programmes in oncology: shared experience from 14 centres across the world Authors (46) Tatjana Geukens Marion Maetens Jody E Hooper Steffi Oesterreich Adrian V Lee Lori Miller[...] A Marcell Szasz Anna-Mária Tőkés Wouter Van Den Bogaert Giuseppe Floris Christine Desmedt Journal of Pathology Published 29 March 2024 Crick labsCharles SwantonFull details Cancer biomarkers: Emerging trends and clinical implications for personalized treatment Authors (10) Antonio PassaroMaise Al Bakir Emily G Hamilton Maximilian Diehn Fabrice André Sinchita Roy-Chowdhuri Giannis Mountzios Ignacio I WistubaCharles Swanton Solange Peters Cell Published 28 March 2024 Crick labsCharles SwantonFull details Embracing cancer complexity: Hallmarks of systemic disease Authors (33)Charles Swanton Elsa Bernard Chris Abbosh Fabrice André Johan Auwerx Allan Balmain[...] Eileen White Frank Winkler John N WoodKaren Vousden Douglas Hanahan Cell Published 28 March 2024 Crick labsKaren VousdenCharles SwantonIlaria MalanchiGerard EvanFull details Oncogenic extrachromosomal DNA identification using whole-genome sequencing from formalin-fixed glioblastomas Authors (11)Imran Noorani Jens LuebeckAndrew RowanEva Gronroos Vittorio Barbe Mark Fabian James Nicoll Delphine Boche Vineet Bafna Paul S MischelCharles Swanton Annals of Oncology Published 28 March 2024 Crick labsCharles SwantonFull details 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 23 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 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 Email
Spatial architecture of myeloid and T cells orchestrates immune evasion and clinical outcome in lung cancer Authors (35)Katey Enfield Emma Colliver Claudia Lee Alastair Magness David A Moore Monica Sivakumar[...]Crispin HileyJulian DownwardErik SahaiCharles SwantonMihaela Angelova Cancer Discovery Published 6 April 2024 Crick labs/ facilitiesCharles SwantonErik SahaiJulian DownwardFlow CytometryExperimental HistopathologyScientific computingProteomicsLight MicroscopyCell ServicesBiological Research FacilityAdvanced SequencingFull details
Research autopsy programmes in oncology: shared experience from 14 centres across the world Authors (46) Tatjana Geukens Marion Maetens Jody E Hooper Steffi Oesterreich Adrian V Lee Lori Miller[...] A Marcell Szasz Anna-Mária Tőkés Wouter Van Den Bogaert Giuseppe Floris Christine Desmedt Journal of Pathology Published 29 March 2024 Crick labsCharles SwantonFull details
Cancer biomarkers: Emerging trends and clinical implications for personalized treatment Authors (10) Antonio PassaroMaise Al Bakir Emily G Hamilton Maximilian Diehn Fabrice André Sinchita Roy-Chowdhuri Giannis Mountzios Ignacio I WistubaCharles Swanton Solange Peters Cell Published 28 March 2024 Crick labsCharles SwantonFull details
Embracing cancer complexity: Hallmarks of systemic disease Authors (33)Charles Swanton Elsa Bernard Chris Abbosh Fabrice André Johan Auwerx Allan Balmain[...] Eileen White Frank Winkler John N WoodKaren Vousden Douglas Hanahan Cell Published 28 March 2024 Crick labsKaren VousdenCharles SwantonIlaria MalanchiGerard EvanFull details
Oncogenic extrachromosomal DNA identification using whole-genome sequencing from formalin-fixed glioblastomas Authors (11)Imran Noorani Jens LuebeckAndrew RowanEva Gronroos Vittorio Barbe Mark Fabian James Nicoll Delphine Boche Vineet Bafna Paul S MischelCharles Swanton Annals of Oncology Published 28 March 2024 Crick labsCharles SwantonFull details
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 23 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