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Breadcrumb Peter Van Loo Van Loo lab Cancer Genomics Laboratory : Publications Lab contentLab contentIn this section Overview Areas of research Publications Members Software Vacancies Zoom in of a ‘Circos plot’ showing genetic changes in cancer genomes. Toggle to view hero caption PublicationsYear published2023 (14)2022 (8)2021 (14)2020 (30)2019 (4)2018 (8)2017 (10)2016 (10)2015 (10)2014 (9)2013 (9)2012 (12)2011 (1)2010 (5) Facet Year publishedResearch topicsComputational & Systems Biology (101)Genetics & Genomics (101)Human Biology & Physiology (101)Tumour Biology (101)Chemical Biology & High Throughput (26)Genome Integrity & Repair (26)Signalling & Oncogenes (26)Structural Biology & Biophysics (16)Model Organisms (13)Cell Biology (10)Cell Cycle & Chromosomes (9)Immunology (9)Stem Cells (8)Gene Expression (7)Developmental Biology (4)Biochemistry & Proteomics (2)Infectious Disease (2)Imaging (1)Metabolism (1) Facet Research topicsCrick/Pre-CrickCrick publications (103)Pre-Crick publications (40) Facet Crick/Pre-CrickPublication typeJournal article (143)Primary research (130)Review (8)Commentary (3)Method (1) Facet Publication typeJournalNature Communications (24)Nature (19)Nature Genetics (15)Cell (7)Nature Biotechnology (6)Genome 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(1)Molecular Cancer (1)Molecular Oncology (1)Nature Methods (1)Nucleic Acids Research (1)Oncogene (1)PLoS Computational Biology (1)PLOS Genetics (1) Facet Journal Publications Displaying 1 - 20 of 144Last updated : 30 November 2023 02:18 Spatiotemporal genomic profiling of intestinal metaplasia reveals clonal dynamics of gastric cancer progression Authors (34) Kie Kyon Huang Haoran Ma Roxanne Hui Heng Chong Tomoyuki Uchihara Benedict Shi Xiang Lian Feng Zhu[...] Hyunsoo Chung Jimmy Bok Yan So Khay Guan Yeoh Patrick Tan Singapore Gastric Cancer Consortium Cancer Cell Published 26 October 2023 Crick labsPeter Van LooFull 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 origin tracing and timing in two high-risk prostate cancers using multisample whole genome analysis: prospects for personalized medicine Authors (25) Anssi Nurminen Serafiina Jaatinen Sinja Taavitsainen Gunilla HögnäsTom Lesluyes Naser Ansari-Pour[...] Tapio Visakorpi Matti Nykter David C WedgePeter Van Loo G Steven Bova Genome Medicine Published 12 October 2023 Crick labsPeter Van LooFull 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 The clinicogenomic landscape of induction failure in childhood and young adult T-cell acute lymphoblastic leukemia Authors (18) David O'ConnorJonas Demeulemeester Lucia Conde Amy Kirkwood Kent FungFoteini Papaleonidopoulou[...] Javier HerreroPeter Van Loo Anthony V Moorman Ajay Vora Marc R Mansour Journal of Clinical Oncology Published 1 July 2023 Crick labsPeter Van LooFull details Tracking early lung cancer metastatic dissemination in TRACERx using ctDNA Authors (55) Christopher AbboshAlexander Frankell Thomas Harrison Judit Kisistok Aaron Garnett Laura Johnson[...] Mariam Jamal-Hanjani TRACERx ConsortiumNicolai Birkbak Nicholas McGranahanCharles Swanton Nature Published 20 April 2023 Crick labs/ facilitiesPeter Van LooCharles SwantonGeorge KassiotisGerard EvanFlow CytometryExperimental HistopathologyBioinformatics and BiostatisticsAdvanced SequencingScientific computingFull details Antibodies against endogenous retroviruses promote lung cancer immunotherapy Authors (51)Kevin NgJesse BoumelhaKatey EnfieldJorge Almagro Hongui Cha Oriol Pich[...] Se-Hoon LeeSamra TurajlicCharles SwantonJulian DownwardGeorge Kassiotis Nature Published 20 April 2023 Crick labs/ facilitiesRobert J WilkinsonPeter Van LooSamra TurajlicCharles SwantonGeorge KassiotisJulian DownwardAxel BehrensFlow CytometryExperimental HistopathologyBioinformatics and BiostatisticsAdvanced SequencingScientific computingProteomicsLight MicroscopyCell ServicesBiological Research FacilityFull details Body composition and lung cancer-associated cachexia in TRACERx Authors (44)Othman Al-Sawaf Jakob Weiss Marcin Skrzypski Jie Min LamTakahiro Karasaki Francisco Zambrana[...]Nicolai Birkbak Hugo JWL Aerts TRACERx Consortium Mariam Jamal-HanjaniCharles Swanton Nature Medicine Published 1 April 2023 Crick labs/ facilitiesPeter Van LooCharles SwantonGeorge KassiotisFlow CytometryExperimental HistopathologyBioinformatics and BiostatisticsAdvanced SequencingScientific computingFull details Evolutionary characterization of lung adenocarcinoma morphology in TRACERx Authors (53)Takahiro Karasaki David A Moore Selvaraju Veeriah Cristina Naceur-Lombardelli Antonia Toncheva Neil Magno[...] Andrew G Nicholson TRACERx Consortium Nicholas McGranahanCharles Swanton Mariam Jamal-Hanjani Nature Medicine Published 1 April 2023 Crick labs/ facilitiesPeter Van LooCharles SwantonGeorge KassiotisFlow CytometryExperimental HistopathologyBioinformatics and BiostatisticsAdvanced SequencingScientific computingFull details Genomic-transcriptomic evolution in lung cancer and metastasis Authors (47) Carlos Martínez-Ruiz James RM Black Clare Puttick Mark S HillJonas DemeulemeesterElizabeth Larose Cadieux[...] Peter Van Loo Mariam Jamal-Hanjani TRACERx Consortium Charles Swanton Nicholas McGranahan Nature Published 20 April 2023 Crick labs/ facilitiesPeter Van LooCharles SwantonGeorge KassiotisJulian DownwardFlow CytometryExperimental HistopathologyBioinformatics and BiostatisticsAdvanced SequencingScientific computingFull details The evolution of lung cancer and impact of subclonal selection in TRACERx Authors (81)Alexander FrankellMichelle DietzenMaise Al BakirEmilia LimTakahiro KarasakiSophie Ward[...] Simone Zaccaria TRACERx Consortium Mariam Jamal-Hanjani Nicholas McGranahanCharles Swanton Nature Published 20 April 2023 Crick labs/ facilitiesPeter Van LooCharles SwantonGeorge KassiotisFlow CytometryExperimental HistopathologyBioinformatics and BiostatisticsAdvanced SequencingScientific computingFull details The evolution of non-small cell lung cancer metastases in TRACERx Authors (66)Maise Al BakirAriana Huebner Carlos Martínez-Ruiz Kristiana GrigoriadisTom Watkins Oriol Pich[...] Simone Zaccaria TRACERx Consortium Mariam Jamal-Hanjani Nicholas McGranahanCharles Swanton Nature Published 20 April 2023 Crick labs/ facilitiesPeter Van LooCharles SwantonGeorge KassiotisFlow CytometryExperimental HistopathologyBioinformatics and BiostatisticsAdvanced SequencingScientific computingFull details Lung adenocarcinoma promotion by air pollutants Authors (72)William HillEmilia LimClare Weeden Claudia Lee Marcellus Augustine Kezhong Chen[...] Kevin Litchfield TRACERx Consortium James DeGregori Mariam Jamal-HanjaniCharles Swanton Nature Published 6 April 2023 Crick labs/ facilitiesPeter Van LooCharles SwantonIlaria MalanchiGeorge KassiotisJulian DownwardFlow CytometryExperimental HistopathologyBioinformatics and BiostatisticsAdvanced SequencingScientific computingLight MicroscopyBiological Research FacilityFull details Analyses of non-coding somatic drivers in 2,658 cancer whole genomes Authors (97) Esther Rheinbay Morten Muhlig Nielsen Federico Abascal Jeremiah A Wala Ofer Shapira Grace Tiao[...] Rameen Beroukhim Iñigo Martincorena Jakob Skou Pedersen Gad Getz PCAWG Consortium Nature Published 6 February 2020 Crick labsPeter Van LooDavid JonesFull details MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution Authors (13) Tom L Kaufmann Marina PetkovicTom Watkins Emma C Colliver Sofya Laskina Nisha Thapa[...]Charles SwantonPeter Van Loo Kerstin HaaseMaxime Tarabichi Roland F Schwarz Genome Biology Published 14 November 2022 Crick labsPeter Van LooCharles SwantonFull details Mutually exclusive genetic interactions and gene essentiality shape the genomic landscape of primary melanoma Authors (18) Sofia Birkeälv Mark Harland Larissa Satiko Alcântara Sekimoto Matsuyama Mamun Rashid Ishan Mehta Jonathan P Laye[...] Patricia A Possik Silvya Stuchi Maria Engler D Timothy Bishop Julia Newton-Bishop David J Adams Journal of Pathology Published 1 January 2023 Crick labsPeter Van LooFull details The architecture of clonal expansions in morphologically normal tissue from cancerous and non-cancerous prostates Authors (27) Claudia Buhigas Anne Y Warren Wing-Kit Leung Hayley C Whitaker Hayley J Luxton Steve Hawkins[...] Andy G Lynch Rosalind A Eeles Colin S Cooper David C Wedge Daniel S Brewer Molecular Cancer Published 22 September 2022 Crick labsPeter Van LooFull details A genetic model for central chondrosarcoma evolution correlates with patient outcome Authors (23) William Cross Iben LyskjærTom LesluyesSteven Hargreaves Anna-Christina Strobl Christopher Davies[...] Genomics England Research Consortium Paul Cool Nischalan Pillay Peter Van Loo Adrienne M Flanagan Genome Medicine Published 30 August 2022 Crick labsPeter Van LooFull details A pan-cancer compendium of chromosomal instability Authors (14) Ruben M Drews Barbara HernandoMaxime TarabichiKerstin HaaseTom Lesluyes Philip S Smith[...] Michael Schneider James D BrentonPeter Van Loo Geoff Macintyre Florian Markowetz Nature Published 30 June 2022 Crick labsPeter Van LooFull details Signatures of copy number alterations in human cancer Authors (24) Christopher D Steele Ammal Abbasi SM Ashiqul IslamAmy Bowes Azhar KhandekarKerstin Haase[...] Adrienne M FlanaganMaxime TarabichiPeter Van Loo Ludmil B Alexandrov Nischalan Pillay Nature Published 30 June 2022 Crick labsPeter Van LooFull details Pagination Current page 1 Page 2 Page 3 Page 4 Page 5 Page 6 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Spatiotemporal genomic profiling of intestinal metaplasia reveals clonal dynamics of gastric cancer progression Authors (34) Kie Kyon Huang Haoran Ma Roxanne Hui Heng Chong Tomoyuki Uchihara Benedict Shi Xiang Lian Feng Zhu[...] Hyunsoo Chung Jimmy Bok Yan So Khay Guan Yeoh Patrick Tan Singapore Gastric Cancer Consortium Cancer Cell Published 26 October 2023 Crick labsPeter Van LooFull 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 origin tracing and timing in two high-risk prostate cancers using multisample whole genome analysis: prospects for personalized medicine Authors (25) Anssi Nurminen Serafiina Jaatinen Sinja Taavitsainen Gunilla HögnäsTom Lesluyes Naser Ansari-Pour[...] Tapio Visakorpi Matti Nykter David C WedgePeter Van Loo G Steven Bova Genome Medicine Published 12 October 2023 Crick labsPeter Van LooFull 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
The clinicogenomic landscape of induction failure in childhood and young adult T-cell acute lymphoblastic leukemia Authors (18) David O'ConnorJonas Demeulemeester Lucia Conde Amy Kirkwood Kent FungFoteini Papaleonidopoulou[...] Javier HerreroPeter Van Loo Anthony V Moorman Ajay Vora Marc R Mansour Journal of Clinical Oncology Published 1 July 2023 Crick labsPeter Van LooFull details
Tracking early lung cancer metastatic dissemination in TRACERx using ctDNA Authors (55) Christopher AbboshAlexander Frankell Thomas Harrison Judit Kisistok Aaron Garnett Laura Johnson[...] Mariam Jamal-Hanjani TRACERx ConsortiumNicolai Birkbak Nicholas McGranahanCharles Swanton Nature Published 20 April 2023 Crick labs/ facilitiesPeter Van LooCharles SwantonGeorge KassiotisGerard EvanFlow CytometryExperimental HistopathologyBioinformatics and BiostatisticsAdvanced SequencingScientific computingFull details
Antibodies against endogenous retroviruses promote lung cancer immunotherapy Authors (51)Kevin NgJesse BoumelhaKatey EnfieldJorge Almagro Hongui Cha Oriol Pich[...] Se-Hoon LeeSamra TurajlicCharles SwantonJulian DownwardGeorge Kassiotis Nature Published 20 April 2023 Crick labs/ facilitiesRobert J WilkinsonPeter Van LooSamra TurajlicCharles SwantonGeorge KassiotisJulian DownwardAxel BehrensFlow CytometryExperimental HistopathologyBioinformatics and BiostatisticsAdvanced SequencingScientific computingProteomicsLight MicroscopyCell ServicesBiological Research FacilityFull details
Body composition and lung cancer-associated cachexia in TRACERx Authors (44)Othman Al-Sawaf Jakob Weiss Marcin Skrzypski Jie Min LamTakahiro Karasaki Francisco Zambrana[...]Nicolai Birkbak Hugo JWL Aerts TRACERx Consortium Mariam Jamal-HanjaniCharles Swanton Nature Medicine Published 1 April 2023 Crick labs/ facilitiesPeter Van LooCharles SwantonGeorge KassiotisFlow CytometryExperimental HistopathologyBioinformatics and BiostatisticsAdvanced SequencingScientific computingFull details
Evolutionary characterization of lung adenocarcinoma morphology in TRACERx Authors (53)Takahiro Karasaki David A Moore Selvaraju Veeriah Cristina Naceur-Lombardelli Antonia Toncheva Neil Magno[...] Andrew G Nicholson TRACERx Consortium Nicholas McGranahanCharles Swanton Mariam Jamal-Hanjani Nature Medicine Published 1 April 2023 Crick labs/ facilitiesPeter Van LooCharles SwantonGeorge KassiotisFlow CytometryExperimental HistopathologyBioinformatics and BiostatisticsAdvanced SequencingScientific computingFull details
Genomic-transcriptomic evolution in lung cancer and metastasis Authors (47) Carlos Martínez-Ruiz James RM Black Clare Puttick Mark S HillJonas DemeulemeesterElizabeth Larose Cadieux[...] Peter Van Loo Mariam Jamal-Hanjani TRACERx Consortium Charles Swanton Nicholas McGranahan Nature Published 20 April 2023 Crick labs/ facilitiesPeter Van LooCharles SwantonGeorge KassiotisJulian DownwardFlow CytometryExperimental HistopathologyBioinformatics and BiostatisticsAdvanced SequencingScientific computingFull details
The evolution of lung cancer and impact of subclonal selection in TRACERx Authors (81)Alexander FrankellMichelle DietzenMaise Al BakirEmilia LimTakahiro KarasakiSophie Ward[...] Simone Zaccaria TRACERx Consortium Mariam Jamal-Hanjani Nicholas McGranahanCharles Swanton Nature Published 20 April 2023 Crick labs/ facilitiesPeter Van LooCharles SwantonGeorge KassiotisFlow CytometryExperimental HistopathologyBioinformatics and BiostatisticsAdvanced SequencingScientific computingFull details
The evolution of non-small cell lung cancer metastases in TRACERx Authors (66)Maise Al BakirAriana Huebner Carlos Martínez-Ruiz Kristiana GrigoriadisTom Watkins Oriol Pich[...] Simone Zaccaria TRACERx Consortium Mariam Jamal-Hanjani Nicholas McGranahanCharles Swanton Nature Published 20 April 2023 Crick labs/ facilitiesPeter Van LooCharles SwantonGeorge KassiotisFlow CytometryExperimental HistopathologyBioinformatics and BiostatisticsAdvanced SequencingScientific computingFull details
Lung adenocarcinoma promotion by air pollutants Authors (72)William HillEmilia LimClare Weeden Claudia Lee Marcellus Augustine Kezhong Chen[...] Kevin Litchfield TRACERx Consortium James DeGregori Mariam Jamal-HanjaniCharles Swanton Nature Published 6 April 2023 Crick labs/ facilitiesPeter Van LooCharles SwantonIlaria MalanchiGeorge KassiotisJulian DownwardFlow CytometryExperimental HistopathologyBioinformatics and BiostatisticsAdvanced SequencingScientific computingLight MicroscopyBiological Research FacilityFull details
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes Authors (97) Esther Rheinbay Morten Muhlig Nielsen Federico Abascal Jeremiah A Wala Ofer Shapira Grace Tiao[...] Rameen Beroukhim Iñigo Martincorena Jakob Skou Pedersen Gad Getz PCAWG Consortium Nature Published 6 February 2020 Crick labsPeter Van LooDavid JonesFull details
MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution Authors (13) Tom L Kaufmann Marina PetkovicTom Watkins Emma C Colliver Sofya Laskina Nisha Thapa[...]Charles SwantonPeter Van Loo Kerstin HaaseMaxime Tarabichi Roland F Schwarz Genome Biology Published 14 November 2022 Crick labsPeter Van LooCharles SwantonFull details
Mutually exclusive genetic interactions and gene essentiality shape the genomic landscape of primary melanoma Authors (18) Sofia Birkeälv Mark Harland Larissa Satiko Alcântara Sekimoto Matsuyama Mamun Rashid Ishan Mehta Jonathan P Laye[...] Patricia A Possik Silvya Stuchi Maria Engler D Timothy Bishop Julia Newton-Bishop David J Adams Journal of Pathology Published 1 January 2023 Crick labsPeter Van LooFull details
The architecture of clonal expansions in morphologically normal tissue from cancerous and non-cancerous prostates Authors (27) Claudia Buhigas Anne Y Warren Wing-Kit Leung Hayley C Whitaker Hayley J Luxton Steve Hawkins[...] Andy G Lynch Rosalind A Eeles Colin S Cooper David C Wedge Daniel S Brewer Molecular Cancer Published 22 September 2022 Crick labsPeter Van LooFull details
A genetic model for central chondrosarcoma evolution correlates with patient outcome Authors (23) William Cross Iben LyskjærTom LesluyesSteven Hargreaves Anna-Christina Strobl Christopher Davies[...] Genomics England Research Consortium Paul Cool Nischalan Pillay Peter Van Loo Adrienne M Flanagan Genome Medicine Published 30 August 2022 Crick labsPeter Van LooFull details
A pan-cancer compendium of chromosomal instability Authors (14) Ruben M Drews Barbara HernandoMaxime TarabichiKerstin HaaseTom Lesluyes Philip S Smith[...] Michael Schneider James D BrentonPeter Van Loo Geoff Macintyre Florian Markowetz Nature Published 30 June 2022 Crick labsPeter Van LooFull details
Signatures of copy number alterations in human cancer Authors (24) Christopher D Steele Ammal Abbasi SM Ashiqul IslamAmy Bowes Azhar KhandekarKerstin Haase[...] Adrienne M FlanaganMaxime TarabichiPeter Van Loo Ludmil B Alexandrov Nischalan Pillay Nature Published 30 June 2022 Crick labsPeter Van LooFull details