Replication timing alterations are associated with mutation acquisition during breast and lung cancer evolution
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DOI: 10.1038/s41467-024-50107-4
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- Hannah L. Harris & Huiya Gu & Moshe Olshansky & Ailun Wang & Irene Farabella & Yossi Eliaz & Achyuth Kalluchi & Akshay Krishna & Mozes Jacobs & Gesine Cauer & Melanie Pham & Suhas S. P. Rao & Olga Dud, 2023. "Chromatin alternates between A and B compartments at kilobase scale for subgenic organization," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
- Paz Polak & Rosa Karlić & Amnon Koren & Robert Thurman & Richard Sandstrom & Michael S. Lawrence & Alex Reynolds & Eric Rynes & Kristian Vlahoviček & John A. Stamatoyannopoulos & Shamil R. Sunyaev, 2015. "Cell-of-origin chromatin organization shapes the mutational landscape of cancer," Nature, Nature, vol. 518(7539), pages 360-364, February.
- Benjamin D. Pope & Tyrone Ryba & Vishnu Dileep & Feng Yue & Weisheng Wu & Olgert Denas & Daniel L. Vera & Yanli Wang & R. Scott Hansen & Theresa K. Canfield & Robert E. Thurman & Yong Cheng & Günhan G, 2014. "Topologically associating domains are stable units of replication-timing regulation," Nature, Nature, vol. 515(7527), pages 402-405, November.
- Yilong Li & Nicola D. Roberts & Jeremiah A. Wala & Ofer Shapira & Steven E. Schumacher & Kiran Kumar & Ekta Khurana & Sebastian Waszak & Jan O. Korbel & James E. Haber & Marcin Imielinski & Joachim We, 2020. "Patterns of somatic structural variation in human cancer genomes," Nature, Nature, vol. 578(7793), pages 112-121, February.
- Teh, Yee Whye & Jordan, Michael I. & Beal, Matthew J. & Blei, David M., 2006. "Hierarchical Dirichlet Processes," Journal of the American Statistical Association, American Statistical Association, vol. 101, pages 1566-1581, December.
- Fran Supek & Ben Lehner, 2015. "Differential DNA mismatch repair underlies mutation rate variation across the human genome," Nature, Nature, vol. 521(7550), pages 81-84, May.
- Serena Nik-Zainal & Helen Davies & Johan Staaf & Manasa Ramakrishna & Dominik Glodzik & Xueqing Zou & Inigo Martincorena & Ludmil B. Alexandrov & Sancha Martin & David C. Wedge & Peter Van Loo & Young, 2016. "Landscape of somatic mutations in 560 breast cancer whole-genome sequences," Nature, Nature, vol. 534(7605), pages 47-54, June.
- Ludmil B. Alexandrov & Serena Nik-Zainal & David C. Wedge & Samuel A. J. R. Aparicio & Sam Behjati & Andrew V. Biankin & Graham R. Bignell & Niccolò Bolli & Ake Borg & Anne-Lise Børresen-Dale & Sandri, 2013. "Correction: Corrigendum: Signatures of mutational processes in human cancer," Nature, Nature, vol. 502(7470), pages 258-258, October.
- Ludmil B. Alexandrov & Serena Nik-Zainal & David C. Wedge & Samuel A. J. R. Aparicio & Sam Behjati & Andrew V. Biankin & Graham R. Bignell & Niccolò Bolli & Ake Borg & Anne-Lise Børresen-Dale & Sandri, 2013. "Signatures of mutational processes in human cancer," Nature, Nature, vol. 500(7463), pages 415-421, August.
- Britny Blumenfeld & Hagit Masika & Marganit Farago & Yishai Yehuda & Lamia Halaseh & Oriya Vardi & Rachel Rapoport & Rena Levin-Klein & Howard Cedar & Yehudit Bergman & Itamar Simon, 2021. "Chromosomal coordination and differential structure of asynchronous replicating regions," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
- Sandro Morganella & Ludmil B. Alexandrov & Dominik Glodzik & Xueqing Zou & Helen Davies & Johan Staaf & Anieta M. Sieuwerts & Arie B. Brinkman & Sancha Martin & Manasa Ramakrishna & Adam Butler & Hyun, 2016. "The topography of mutational processes in breast cancer genomes," Nature Communications, Nature, vol. 7(1), pages 1-11, September.
- Lin Liu & Subhajyoti De & Franziska Michor, 2013. "DNA replication timing and higher-order nuclear organization determine single-nucleotide substitution patterns in cancer genomes," Nature Communications, Nature, vol. 4(1), pages 1-9, June.
- Jing Zhang & Donghoon Lee & Vineet Dhiman & Peng Jiang & Jie Xu & Patrick McGillivray & Hongbo Yang & Jason Liu & William Meyerson & Declan Clarke & Mengting Gu & Shantao Li & Shaoke Lou & Jinrui Xu &, 2020. "An integrative ENCODE resource for cancer genomics," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
- Yong H Woo & Wen-Hsiung Li, 2012. "DNA replication timing and selection shape the landscape of nucleotide variation in cancer genomes," Nature Communications, Nature, vol. 3(1), pages 1-8, January.
- Alexander M. Frankell & Michelle Dietzen & Maise Al Bakir & Emilia L. Lim & Takahiro Karasaki & Sophia Ward & Selvaraju Veeriah & Emma Colliver & Ariana Huebner & Abigail Bunkum & Mark S. Hill & Krist, 2023. "The evolution of lung cancer and impact of subclonal selection in TRACERx," Nature, Nature, vol. 616(7957), pages 525-533, April.
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