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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 published2024 (5)2023 (14)2022 (8)2021 (14)2020 (33)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 (109)Genetics & Genomics (109)Human Biology & Physiology (109)Tumour Biology (109)Chemical Biology & High Throughput (27)Genome Integrity & Repair (27)Signalling & Oncogenes (27)Structural Biology & Biophysics (19)Model Organisms (14)Cell Biology (11)Cell Cycle & Chromosomes (10)Immunology (10)Stem Cells (9)Gene Expression (7)Developmental Biology (4)Biochemistry & Proteomics (2)Imaging (2)Infectious Disease (2)Metabolism (1) Facet Research topicsCrick/Pre-CrickCrick publications (111)Pre-Crick publications (40) Facet Crick/Pre-CrickPublication typeJournal article (151)Primary research (137)Review (9)Commentary (3)Method (1) Facet Publication typeJournalNature Communications (24)Nature (22)Nature Genetics (15)Cell (7)Nature Biotechnology (6)Genome Biology (5)Genome Medicine (5)Science (5)Cancer Cell (4)Nature Cancer (4)Cell Reports (3)Journal of Pathology (3)Nature Medicine (3)New England Journal of Medicine (3)Blood (2)Cancer Research (2)Communications Biology (2)Journal of Clinical Oncology (2)PLOS ONE (2)Proceedings of the National Academy of Sciences of the United States of America (2)Acta Neuropathologica Communications (1)Alzheimer's & Dementia (1)American Journal of Human Genetics (1)American Journal of Transplantation (1)Annals of Oncology (1)Bioinformatics (1)BMC Genomics (1)British Journal of Cancer (1)British Journal of Haematology (1)Cell Genomics (1)Cell systems (1)Clinical cancer research (1)Cold Spring Harbor Perspectives in Medicine (1)Current Opinion in Genetics & Development (1)Current Protocols in Bioinformatics (1)Endocrine-Related Cancer (1)Frontiers in Oncology (1)Genes, Chromosomes & Cancer (1)Haematologica (1)Journal of Clinical Investigation (1)Leukemia & Lymphoma (1)Methods in Molecular Biology (1)Modern pathology (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 152Last updated : 19 April 2024 03:53 Evolution of chromosome-arm aberrations in breast cancer through genetic network rewiring Authors (29) Elena KuzminToby BakerTom Lesluyes Jean Monlong Kento T Abe Paula P Coelho[...] Anne-Claude Gingras Jiannis Ragoussis Guillaume BourquePeter Van Loo Morag Park Cell Reports Published 22 March 2024 Crick labsPeter Van LooFull details Genomic evolution shapes prostate cancer disease type Authors (37) Dan J Woodcock Atef Sahli Ruxandra Teslo Vinayak Bhandari Andreas J Gruber Aleksandra Ziubroniewicz[...] Andy G Lynch Daniel S Brewer Rosalind A Eeles Colin S Cooper David C Wedge Cell Genomics Published 13 March 2024 Crick labsPeter Van LooFull details Aneuploidy and complex genomic rearrangements in cancer evolution Authors (4)Toby BakerSara WaiseMaxime TarabichiPeter Van Loo Nature Cancer Published 1 February 2024 Crick labsPeter Van LooFull details Tumor- and circulating-free DNA methylation identifies clinically relevant small cell lung cancer subtypes Authors (42) Simon Heeke Carl M Gay Marcos R Estecio Hai Tran Benjamin B Morris Bingnan Zhang[...]Peter Van Loo Jing Wang Ignacio I Wistuba Lauren A Byers John V Heymach Cancer Cell Published 12 February 2024 Crick labsPeter Van LooFull 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 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 11 December 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 Pagination Current page 1 Page 2 Page 3 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Evolution of chromosome-arm aberrations in breast cancer through genetic network rewiring Authors (29) Elena KuzminToby BakerTom Lesluyes Jean Monlong Kento T Abe Paula P Coelho[...] Anne-Claude Gingras Jiannis Ragoussis Guillaume BourquePeter Van Loo Morag Park Cell Reports Published 22 March 2024 Crick labsPeter Van LooFull details
Genomic evolution shapes prostate cancer disease type Authors (37) Dan J Woodcock Atef Sahli Ruxandra Teslo Vinayak Bhandari Andreas J Gruber Aleksandra Ziubroniewicz[...] Andy G Lynch Daniel S Brewer Rosalind A Eeles Colin S Cooper David C Wedge Cell Genomics Published 13 March 2024 Crick labsPeter Van LooFull details
Aneuploidy and complex genomic rearrangements in cancer evolution Authors (4)Toby BakerSara WaiseMaxime TarabichiPeter Van Loo Nature Cancer Published 1 February 2024 Crick labsPeter Van LooFull details
Tumor- and circulating-free DNA methylation identifies clinically relevant small cell lung cancer subtypes Authors (42) Simon Heeke Carl M Gay Marcos R Estecio Hai Tran Benjamin B Morris Bingnan Zhang[...]Peter Van Loo Jing Wang Ignacio I Wistuba Lauren A Byers John V Heymach Cancer Cell Published 12 February 2024 Crick labsPeter Van LooFull 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
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 11 December 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