Signatures of mutational processes in human cancer

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1. Wenying Peng & Bin Li & Jin Li & Lianpeng Chang & Jing Bai & Yuting Yi & Rongrong Chen & Yanyan Zhang & Chen Chen & Xingxiang Pu & Meilin Jiang & Jia Li & Rui Zhong & Fang Xu & Bolin Chen & Li Xu & Ni, 2022. "Clinical and genomic features of Chinese lung cancer patients with germline mutations," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
2. Xing Cheng & Jing An & Jitong Lou & Qisheng Gu & Weimin Ding & Gaith Nabil Droby & Yilin Wang & Chenghao Wang & Yanzhe Gao & Jay Ramanlal Anand & Abigail Shelton & Andrew Benson Satterlee & Breanna Ma, 2024. "Trans-lesion synthesis and mismatch repair pathway crosstalk defines chemoresistance and hypermutation mechanisms in glioblastoma," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
3. Anna Luiza Silva Almeida Vicente & Alexei Novoloaca & Vincent Cahais & Zainab Awada & Cyrille Cuenin & Natália Spitz & André Lopes Carvalho & Adriane Feijó Evangelista & Camila Souza Crovador & Rui Ma, 2022. "Cutaneous and acral melanoma cross-OMICs reveals prognostic cancer drivers associated with pathobiology and ultraviolet exposure," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
4. Martin Boström & Erik Larsson, 2022. "Somatic mutation distribution across tumour cohorts provides a signal for positive selection in cancer," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
5. Mrinal M. Gounder & Narasimhan P. Agaram & Sally E. Trabucco & Victoria Robinson & Richard A. Ferraro & Sherri Z. Millis & Anita Krishnan & Jessica Lee & Steven Attia & Wassim Abida & Alexander Drilon, 2022. "Clinical genomic profiling in the management of patients with soft tissue and bone sarcoma," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
6. Lino Möhrmann & Maximilian Werner & Małgorzata Oleś & Andreas Mock & Sebastian Uhrig & Arne Jahn & Simon Kreutzfeldt & Martina Fröhlich & Barbara Hutter & Nagarajan Paramasivam & Daniela Richter & Kat, 2022. "Comprehensive genomic and epigenomic analysis in cancer of unknown primary guides molecularly-informed therapies despite heterogeneity," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
7. Teresa Maria Rosaria Noviello & Anna Maria Giacomo & Francesca Pia Caruso & Alessia Covre & Roberta Mortarini & Giovanni Scala & Maria Claudia Costa & Sandra Coral & Wolf H. Fridman & Catherine Sautès, 2023. "Guadecitabine plus ipilimumab in unresectable melanoma: five-year follow-up and integrated multi-omic analysis in the phase 1b NIBIT-M4 trial," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
8. Ye Cai & Huifen Cao & Fang Wang & Yufei Zhang & Philipp Kapranov, 2022. "Complex genomic patterns of abasic sites in mammalian DNA revealed by a high-resolution SSiNGLe-AP method," Nature Communications, Nature, vol. 13(1), pages 1-21, December.
9. Sijia Cui & Nicholas McGranahan & Jing Gao & Peng Chen & Wei Jiang & Lingrong Yang & Li Ma & Junfang Liao & Tian Xie & Congying Xie & Tariq Enver & Shixiu Wu, 2023. "Tracking the evolution of esophageal squamous cell carcinoma under dynamic immune selection by multi-omics sequencing," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
10. Maria Zhivagui & Areebah Hoda & Noelia Valenzuela & Yi-Yu Yeh & Jason Dai & Yudou He & Shuvro P. Nandi & Burcak Otlu & Bennett Houten & Ludmil B. Alexandrov, 2023. "DNA damage and somatic mutations in mammalian cells after irradiation with a nail polish dryer," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
11. Daan M. K. Soest & Paulien E. Polderman & Wytze T. F. Toom & Janneke P. Keijer & Markus J. Roosmalen & Tim M. F. Leyten & Johannes Lehmann & Susan Zwakenberg & Sasha Henau & Ruben Boxtel & Boudewijn M, 2024. "Mitochondrial H2O2 release does not directly cause damage to chromosomal DNA," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
12. Saptarshi Chakraborty & Colin B. Begg & Ronglai Shen, 2021. "Using the “Hidden” genome to improve classification of cancer types," Biometrics, The International Biometric Society, vol. 77(4), pages 1445-1455, December.
13. Marjan M. Naeini & Felicity Newell & Lauren G. Aoude & Vanessa F. Bonazzi & Kalpana Patel & Guy Lampe & Lambros T. Koufariotis & Vanessa Lakis & Venkateswar Addala & Olga Kondrashova & Rebecca L. John, 2023. "Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
14. Rebecca J. Austin & Jasmin Straube & Rohit Halder & Yashaswini Janardhanan & Claudia Bruedigam & Matthew Witkowski & Leanne Cooper & Amy Porter & Matthias Braun & Fernando Souza-Fonseca-Guimaraes & Si, 2023. "Oncogenic drivers dictate immune control of acute myeloid leukemia," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
15. Jurica Levatić & Marina Salvadores & Francisco Fuster-Tormo & Fran Supek, 2022. "Mutational signatures are markers of drug sensitivity of cancer cells," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
16. Celina Tretter & Niklas Andrade Krätzig & Matteo Pecoraro & Sebastian Lange & Philipp Seifert & Clara Frankenberg & Johannes Untch & Gabriela Zuleger & Mathias Wilhelm & Daniel P. Zolg & Florian S. Dr, 2023. "Proteogenomic analysis reveals RNA as a source for tumor-agnostic neoantigen identification," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
17. Hailiang Zhang & Lin Bai & Xin-Qiang Wu & Xi Tian & Jinwen Feng & Xiaohui Wu & Guo-Hai Shi & Xiaoru Pei & Jiacheng Lyu & Guojian Yang & Yang Liu & Wenhao Xu & Aihetaimujiang Anwaier & Yu Zhu & Da-Long, 2023. "Proteogenomics of clear cell renal cell carcinoma response to tyrosine kinase inhibitor," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
18. Heather E. Machado & Nina F. Øbro & Nicholas Williams & Shengjiang Tan & Ahmed Z. Boukerrou & Megan Davies & Miriam Belmonte & Emily Mitchell & E. Joanna Baxter & Nicole Mende & Anna Clay & Philip Anc, 2023. "Convergent somatic evolution commences in utero in a germline ribosomopathy," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
19. Amanda Fitzpatrick & Marjan Iravani & Adam Mills & David Vicente & Thanussuyah Alaguthurai & Ioannis Roxanis & Nicholas C. Turner & Syed Haider & Andrew N. J. Tutt & Clare M. Isacke, 2023. "Genomic profiling and pre-clinical modelling of breast cancer leptomeningeal metastasis reveals acquisition of a lobular-like phenotype," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
20. Sebastian Carrasco Pro & Heather Hook & David Bray & Daniel Berenzy & Devlin Moyer & Meimei Yin & Adam Thomas Labadorf & Ryan Tewhey & Trevor Siggers & Juan Ignacio Fuxman Bass, 2023. "Widespread perturbation of ETS factor binding sites in cancer," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
21. Francesca Menghi & Edison T. Liu, 2022. "Functional genomics of complex cancer genomes," Nature Communications, Nature, vol. 13(1), pages 1-4, December.
22. Kathiresan Selvam & Smitha Sivapragasam & Gregory M. K. Poon & John J. Wyrick, 2023. "Detecting recurrent passenger mutations in melanoma by targeted UV damage sequencing," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
23. Christopher Ruis & Aaron Weimann & Gerry Tonkin-Hill & Arun Prasad Pandurangan & Marta Matuszewska & Gemma G. R. Murray & Roger C. Lévesque & Tom L. Blundell & R. Andres Floto & Julian Parkhill, 2023. "Mutational spectra are associated with bacterial niche," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
24. Josefine Radke & Naveed Ishaque & Randi Koll & Zuguang Gu & Elisa Schumann & Lina Sieverling & Sebastian Uhrig & Daniel Hübschmann & Umut H. Toprak & Cristina López & Xavier Pastor Hostench & Simone B, 2022. "The genomic and transcriptional landscape of primary central nervous system lymphoma," Nature Communications, Nature, vol. 13(1), pages 1-20, December.
25. Ming Tang & Hussein A. Abbas & Marcelo V. Negrao & Maheshwari Ramineni & Xin Hu & Shawna Marie Hubert & Junya Fujimoto & Alexandre Reuben & Susan Varghese & Jianhua Zhang & Jun Li & Chi-Wan Chow & Xiz, 2021. "The histologic phenotype of lung cancers is associated with transcriptomic features rather than genomic characteristics," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
26. Qi Zhao & Feng Wang & Yan-Xing Chen & Shifu Chen & Yi-Chen Yao & Zhao-Lei Zeng & Teng-Jia Jiang & Ying-Nan Wang & Chen-Yi Wu & Ying Jing & You-Sheng Huang & Jing Zhang & Zi-Xian Wang & Ming-Ming He & , 2022. "Comprehensive profiling of 1015 patients’ exomes reveals genomic-clinical associations in colorectal cancer," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
27. Yasha Butt & Ramin Sakhtemani & Rukshana Mohamad-Ramshan & Michael S. Lawrence & Ashok S. Bhagwat, 2024. "Distinguishing preferences of human APOBEC3A and APOBEC3B for cytosines in hairpin loops, and reflection of these preferences in APOBEC-signature cancer genome mutations," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
28. Thomas G. Paulson & Patricia C. Galipeau & Kenji M. Oman & Carissa A. Sanchez & Mary K. Kuhner & Lucian P. Smith & Kevin Hadi & Minita Shah & Kanika Arora & Jennifer Shelton & Molly Johnson & Andre Co, 2022. "Somatic whole genome dynamics of precancer in Barrett’s esophagus reveals features associated with disease progression," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
29. Ming Chen & Runzhe Chen & Ying Jin & Jun Li & Xin Hu & Jiexin Zhang & Junya Fujimoto & Shawna M. Hubert & Carl M. Gay & Bo Zhu & Yanhua Tian & Nicholas McGranahan & Won-Chul Lee & Julie George & Xiao , 2021. "Cold and heterogeneous T cell repertoire is associated with copy number aberrations and loss of immune genes in small-cell lung cancer," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
30. Arthur Dondi & Ulrike Lischetti & Francis Jacob & Franziska Singer & Nico Borgsmüller & Ricardo Coelho & Viola Heinzelmann-Schwarz & Christian Beisel & Niko Beerenwinkel, 2023. "Detection of isoforms and genomic alterations by high-throughput full-length single-cell RNA sequencing in ovarian cancer," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
31. A. C. Katz-Summercorn & S. Jammula & A. Frangou & I. Peneva & M. O’Donovan & M. Tripathi & S. Malhotra & M. Pietro & S. Abbas & G. Devonshire & W. Januszewicz & A. Blasko & K. Nowicki-Osuch & S. MacRa, 2022. "Multi-omic cross-sectional cohort study of pre-malignant Barrett’s esophagus reveals early structural variation and retrotransposon activity," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
32. Mei Lin & Xiao-Long Zhang & Rui You & You-Ping Liu & Hong-Min Cai & Li-Zhi Liu & Xue-Fei Liu & Xiong Zou & Yu-Long Xie & Ru-Hai Zou & Yi-Nuan Zhang & Rui Sun & Wei-Yi Feng & Hai-Yan Wang & Gui-Hua Tao, 2023. "Evolutionary route of nasopharyngeal carcinoma metastasis and its clinical significance," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
33. Ankur Chakravarthy & Ian Reddin & Stephen Henderson & Cindy Dong & Nerissa Kirkwood & Maxmilan Jeyakumar & Daniela Rothschild Rodriguez & Natalia Gonzalez Martinez & Jacqueline McDermott & Xiaoping Su, 2022. "Integrated analysis of cervical squamous cell carcinoma cohorts from three continents reveals conserved subtypes of prognostic significance," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
34. Peter Georgeson & Tabitha A. Harrison & Bernard J. Pope & Syed H. Zaidi & Conghui Qu & Robert S. Steinfelder & Yi Lin & Jihoon E. Joo & Khalid Mahmood & Mark Clendenning & Romy Walker & Efrat L. Amita, 2022. "Identifying colorectal cancer caused by biallelic MUTYH pathogenic variants using tumor mutational signatures," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
35. Johann-Christoph Jann & Maximilian Mossner & Vladimir Riabov & Eva Altrock & Nanni Schmitt & Johanna Flach & Qingyu Xu & Verena Nowak & Julia Obländer & Iris Palme & Nadine Weimer & Alexander Streuer , 2021. "Bone marrow derived stromal cells from myelodysplastic syndromes are altered but not clonally mutated in vivo," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
36. Ezra Y. Rosen & Helen H. Won & Youyun Zheng & Emiliano Cocco & Duygu Selcuklu & Yixiao Gong & Noah D. Friedman & Ino Bruijn & Onur Sumer & Craig M. Bielski & Casey Savin & Caitlin Bourque & Christina , 2022. "The evolution of RET inhibitor resistance in RET-driven lung and thyroid cancers," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
37. Yonina R. Murciano-Goroff & Alison M. Schram & Ezra Y. Rosen & Helen Won & Yixiao Gong & Anne Marie Noronha & Yelena Y. Janjigian & Zsofia K. Stadler & Jason C. Chang & Soo-Ryum Yang & Diana Mandelker, 2022. "Reversion mutations in germline BRCA1/2-mutant tumors reveal a BRCA-mediated phenotype in non-canonical histologies," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
38. Bernard C. H. Lee & Philip S. Robinson & Tim H. H. Coorens & Helen H. N. Yan & Sigurgeir Olafsson & Henry Lee-Six & Mathijs A. Sanders & Hoi Cheong Siu & James Hewinson & Sarah S. K. Yue & Wai Yin Tsu, 2022. "Mutational landscape of normal epithelial cells in Lynch Syndrome patients," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
39. Sujath Abbas & Oriol Pich & Ginny Devonshire & Shahriar A. Zamani & Annalise Katz-Summercorn & Sarah Killcoyne & Calvin Cheah & Barbara Nutzinger & Nicola Grehan & Nuria Lopez-Bigas & Rebecca C. Fitzg, 2023. "Mutational signature dynamics shaping the evolution of oesophageal adenocarcinoma," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
40. Ambrocio Sanchez & Pedro Ortega & Ramin Sakhtemani & Lavanya Manjunath & Sunwoo Oh & Elodie Bournique & Alexandrea Becker & Kyumin Kim & Cameron Durfee & Nuri Alpay Temiz & Xiaojiang S. Chen & Reuben , 2024. "Mesoscale DNA features impact APOBEC3A and APOBEC3B deaminase activity and shape tumor mutational landscapes," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
41. Qingli Guo & Eszter Lakatos & Ibrahim Al Bakir & Kit Curtius & Trevor A. Graham & Ville Mustonen, 2022. "The mutational signatures of formalin fixation on the human genome," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
42. David Wang & Mathieu Quesnel-Vallieres & San Jewell & Moein Elzubeir & Kristen Lynch & Andrei Thomas-Tikhonenko & Yoseph Barash, 2023. "A Bayesian model for unsupervised detection of RNA splicing based subtypes in cancers," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
43. Caralyn Reisle & Laura M. Williamson & Erin Pleasance & Anna Davies & Brayden Pellegrini & Dustin W. Bleile & Karen L. Mungall & Eric Chuah & Martin R. Jones & Yussanne Ma & Eleanor Lewis & Isaac Beck, 2022. "A platform for oncogenomic reporting and interpretation," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
44. Pengfei Yu & Can Hu & Guangyu Ding & Xiaoliang Shi & Jingli Xu & Yang Cao & Xiangliu Chen & Wei Wu & Qi Xu & Jingquan Fang & Xingmao Huang & Shaohua Yuan & Hui Chen & Zhizheng Wang & Ling Huang & Fei , 2024. "Mutation characteristics and molecular evolution of ovarian metastasis from gastric cancer and potential biomarkers for paclitaxel treatment," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
45. Mischan Vali-Pour & Solip Park & Jose Espinosa-Carrasco & Daniel Ortiz-Martínez & Ben Lehner & Fran Supek, 2022. "The impact of rare germline variants on human somatic mutation processes," Nature Communications, Nature, vol. 13(1), pages 1-21, December.
46. Eleanor L. Woodward & Minjun Yang & Larissa H. Moura-Castro & Hilda Bos & Rebeqa Gunnarsson & Linda Olsson-Arvidsson & Diana C. J. Spierings & Anders Castor & Nicolas Duployez & Marketa Zaliova & Jan , 2023. "Clonal origin and development of high hyperdiploidy in childhood acute lymphoblastic leukaemia," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
47. Martin Lauss & Bengt Phung & Troels Holz Borch & Katja Harbst & Kamila Kaminska & Anna Ebbesson & Ingrid Hedenfalk & Joan Yuan & Kari Nielsen & Christian Ingvar & Ana Carneiro & Karolin Isaksson & Kri, 2024. "Molecular patterns of resistance to immune checkpoint blockade in melanoma," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
48. Antonio Rodriguez-Calero & John Gallon & Dilara Akhoundova & Sina Maletti & Alison Ferguson & Joanna Cyrta & Ursula Amstutz & Andrea Garofoli & Viola Paradiso & Scott A. Tomlins & Ekkehard Hewer & Ver, 2022. "Alterations in homologous recombination repair genes in prostate cancer brain metastases," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
49. Brittany N. Vandenberg & Marian F. Laughery & Cameron Cordero & Dalton Plummer & Debra Mitchell & Jordan Kreyenhagen & Fatimah Albaqshi & Alexander J. Brown & Piotr A. Mieczkowski & John J. Wyrick & S, 2023. "Contributions of replicative and translesion DNA polymerases to mutagenic bypass of canonical and atypical UV photoproducts," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
50. Yaodong Zhang & Zijian Ma & Changxian Li & Cheng Wang & Wangjie Jiang & Jiang Chang & Sheng Han & Zefa Lu & Zicheng Shao & Yirui Wang & Hongwei Wang & Chenyu Jiao & Dong Wang & Xiaofeng Wu & Hongbing , 2022. "The genomic landscape of cholangiocarcinoma reveals the disruption of post-transcriptional modifiers," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
51. Kakushadze, Zura & Yu, Willie, 2016. "Factor models for cancer signatures," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 462(C), pages 527-559.
52. Se Jin Park & Gwan Woo Ku & Su Yel Lee & Daeun Kang & Wan Jin Hwang & In Beom Jeong & Sun Jung Kwon & Jaeku Kang & Ji Woong Son, 2021. "Analysis of Single Nucleotide Variants (SNVs) Induced by Exposure to PM 10 in Lung Epithelial Cells Using Whole Genome Sequencing," IJERPH, MDPI, vol. 18(3), pages 1-11, January.
53. Jennifer B. Shah & Dana Pueschl & Bradley Wubbenhorst & Mengyao Fan & John Pluta & Kurt D’Andrea & Anna P. Hubert & Jake S. Shilan & Wenting Zhou & Adam A. Kraya & Alba Llop Guevara & Catherine Ruan &, 2022. "Analysis of matched primary and recurrent BRCA1/2 mutation-associated tumors identifies recurrence-specific drivers," Nature Communications, Nature, vol. 13(1), pages 1-19, December.