Machine learning-based extrachromosomal DNA identification in large-scale cohorts reveals its clinical implications in cancer
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DOI: 10.1038/s41467-024-45479-6
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- Erik N. Bergstrom & Jens Luebeck & Mia Petljak & Azhar Khandekar & Mark Barnes & Tongwu Zhang & Christopher D. Steele & Nischalan Pillay & Maria Teresa Landi & Vineet Bafna & Paul S. Mischel & Reuben , 2022. "Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA," Nature, Nature, vol. 602(7897), pages 510-517, February.
- Viraj Deshpande & Jens Luebeck & Nam-Phuong D. Nguyen & Mehrdad Bakhtiari & Kristen M. Turner & Richard Schwab & Hannah Carter & Paul S. Mischel & Vineet Bafna, 2019. "Exploring the landscape of focal amplifications in cancer using AmpliconArchitect," Nature Communications, Nature, vol. 10(1), pages 1-14, December.
- Heyang Cui & Yong Zhou & Fang Wang & Caixia Cheng & Weimin Zhang & Ruifang Sun & Ling Zhang & Yanghui Bi & Min Guo & Yan Zhou & Xinhui Wang & Jiaxin Ren & Ruibing Bai & Ning Ding & Chen Cheng & Longlo, 2022. "Characterization of somatic structural variations in 528 Chinese individuals with Esophageal squamous cell carcinoma," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
- Rameen Beroukhim & Craig H. Mermel & Dale Porter & Guo Wei & Soumya Raychaudhuri & Jerry Donovan & Jordi Barretina & Jesse S. Boehm & Jennifer Dobson & Mitsuyoshi Urashima & Kevin T. Mc Henry & Reid M, 2010. "The landscape of somatic copy-number alteration across human cancers," Nature, Nature, vol. 463(7283), pages 899-905, February.
- Kosuke Yoshihara & Maria Shahmoradgoli & Emmanuel Martínez & Rahulsimham Vegesna & Hoon Kim & Wandaliz Torres-Garcia & Victor Treviño & Hui Shen & Peter W. Laird & Douglas A. Levine & Scott L. Carter , 2013. "Inferring tumour purity and stromal and immune cell admixture from expression data," Nature Communications, Nature, vol. 4(1), pages 1-11, December.
- Mahmoud Ghandi & Franklin W. Huang & Judit Jané-Valbuena & Gregory V. Kryukov & Christopher C. Lo & E. Robert McDonald & Jordi Barretina & Ellen T. Gelfand & Craig M. Bielski & Haoxin Li & Kevin Hu & , 2019. "Next-generation characterization of the Cancer Cell Line Encyclopedia," Nature, Nature, vol. 569(7757), pages 503-508, May.
- Jens Luebeck & Ceyda Coruh & Siavash R. Dehkordi & Joshua T. Lange & Kristen M. Turner & Viraj Deshpande & Dave A. Pai & Chao Zhang & Utkrisht Rajkumar & Julie A. Law & Paul S. Mischel & Vineet Bafna, 2020. "AmpliconReconstructor integrates NGS and optical mapping to resolve the complex structures of focal amplifications," Nature Communications, Nature, vol. 11(1), pages 1-14, December.
- Sihan Wu & Kristen M. Turner & Nam Nguyen & Ramya Raviram & Marcella Erb & Jennifer Santini & Jens Luebeck & Utkrisht Rajkumar & Yarui Diao & Bin Li & Wenjing Zhang & Nathan Jameson & M. Ryan Corces &, 2019. "Circular ecDNA promotes accessible chromatin and high oncogene expression," Nature, Nature, vol. 575(7784), pages 699-703, November.
- King L. Hung & Kathryn E. Yost & Liangqi Xie & Quanming Shi & Konstantin Helmsauer & Jens Luebeck & Robert Schöpflin & Joshua T. Lange & Rocío Chamorro González & Natasha E. Weiser & Celine Chen & Mar, 2021. "ecDNA hubs drive cooperative intermolecular oncogene expression," Nature, Nature, vol. 600(7890), pages 731-736, December.
- Yael Cohen-Sharir & James M. McFarland & Mai Abdusamad & Carolyn Marquis & Sara V. Bernhard & Mariya Kazachkova & Helen Tang & Marica R. Ippolito & Kathrin Laue & Johanna Zerbib & Heidi L. H. Malaby &, 2021. "Aneuploidy renders cancer cells vulnerable to mitotic checkpoint inhibition," Nature, Nature, vol. 590(7846), pages 486-491, February.
- Jens Luebeck & Alvin Wei Tian Ng & Patricia C. Galipeau & Xiaohong Li & Carissa A. Sanchez & Annalise C. Katz-Summercorn & Hoon Kim & Sriganesh Jammula & Yudou He & Scott M. Lippman & Roel G. W. Verha, 2023. "Extrachromosomal DNA in the cancerous transformation of Barrett’s oesophagus," Nature, Nature, vol. 616(7958), pages 798-805, April.
- Christopher D. Steele & Ammal Abbasi & S. M. Ashiqul Islam & Amy L. Bowes & Azhar Khandekar & Kerstin Haase & Shadi Hames-Fathi & Dolapo Ajayi & Annelien Verfaillie & Pawan Dhami & Alex McLatchie & Ma, 2022. "Signatures of copy number alterations in human cancer," Nature, Nature, vol. 606(7916), pages 984-991, June.
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