bioconductor: MutationalPatterns | Projects

10.3389/fonc.2021.619242

The Identification and Validation of Two Heterogenous Subtypes and a Risk Signature Based on Ferroptosis in Hepatocellular Carcinoma
Cited by: 40
Author(s): Xinwei Han, Libo Wang, Long Liu, Taoyuan Lu, Dechao Jiao, Yuling Sun, Xinwei Han
Software Mentions: 9
Published: almost 4 years ago

10.7150/jca.56005

Integrated Genomic and Transcriptomic Analysis reveals key genes for predicting dual-phenotype Hepatocellular Carcinoma Prognosis
Cited by: 6
Author(s): Yaobang Wang, Xi Wang, Xiaoliang Huang, Jie Zhang, Jinwen Hu, Yinliang Qi, Bang‐De Xiang, Qiuyan Wang
Software Mentions: 9
Published: about 4 years ago

10.1371/journal.pone.0221235

Computational tools to detect signatures of mutational processes in DNA from tumours: A review and empirical comparison of performance
Cited by: 42
Author(s): Hanane Omichessan, Gianluca Severi, Vittorio Perduca
Software Mentions: 9
Published: over 5 years ago

10.3389/fimmu.2021.651056

Immune Infiltration Subtypes Characterization and Identification of Prognosis-Related lncRNAs in Adenocarcinoma of the Esophagogastric Junction
Cited by: 12
Author(s): Xin Hu, Liuxing Wu, Ben Liu, Kexin Chen
Software Mentions: 8
Published: over 3 years ago

10.1038/s42003-020-01174-y

Chemically induced mutations in a MutaMouse reporter gene inform mechanisms underlying human cancer mutational signatures
Cited by: 12
Author(s): Marc A. Beal, Matthew J. Meier, Danielle P. LeBlanc, Clotilde Maurice, Jason M. O’Brien, Carole L. Yauk, Francesco Marchetti
Software Mentions: 7
Published: over 4 years ago

10.1186/s13073-019-0695-x

FIREVAT: finding reliable variants without artifacts in human cancer samples using etiologically relevant mutational signatures
Cited by: 7
Author(s): Hyunbin Kim, Andy Jinseok Lee, Jongkeun Lee, Hyonho Chun, Young Seok Ju, Dong Ho Hong
Software Mentions: 7
Published: about 5 years ago

10.1038/s41598-021-98414-w

Integrated genomics point to immune vulnerabilities in pleural mesothelioma
Cited by: 7
Author(s): Anca Năstase, Amit Kumar Mandal, Shir Kiong Lu, Hima Anbunathan, Deborah Morris-Rosendahl, Yu Zhi Zhang, Xiaoming Sun, Spyridon Gennatas, Robert C. Rintoul, Matthew Edwards, Alex Bowman, Tatyana Chernova, T. Benepal, Eric Lim, Alison Taylor, Andrew G. Nicholson, Sanjay Popat, Anne E. Willis, Marion MacFarlane, Mark Lathrop, Anne M. Bowcock, Miriam F. Moffatt, William Cookson
Software Mentions: 6
Published: over 3 years ago

10.15252/emmm.202012118

The mutational landscape of the <scp>SCAN</scp> ‐B real‐world primary breast cancer transcriptome
Cited by: 30
Author(s): Christian Brueffer, Sergii Gladchuk, Christof Winter, Johan Vallon‐Christersson, Cecilia Hegardt, Jari Häkkinen, Anthony George, Yilun Chen, Anna Ehinger, Christer Larsson, Niklas Loman, Martin Malmberg, Lisa Rydén, Åke Borg, Lao H. Saal
Software Mentions: 6
Published: over 4 years ago

10.1186/s13073-018-0539-0

MutationalPatterns: comprehensive genome-wide analysis of mutational processes
Cited by: 459
Author(s): Francis Blokzijl, Roel Janssen, Ruben van Boxtel, Edwin Cuppen
Software Mentions: 5
Published: over 6 years ago

10.1530/ERC-19-0474

A xenograft and cell line model of SDH-deficient pheochromocytoma derived from Sdhb+/− rats
Cited by: 15
Author(s): James F. Powers, Brent Cochran, James D. Baleja, Hadley D. Sikes, Andrew Pattison, Xue Zhang, Inna Lomakin, Annette Shepard-Barry, Karel Pacák, Sun Jin Moon, Troy F. Langford, Kassi T. Stein, Richard W. Tothill, Ying-Bin Ouyang, Arthur S. Tischler
Software Mentions: 5
Published: over 4 years ago

10.1186/s13014-021-01853-y

Complete response to neoadjuvant chemoradiotherapy in rectal cancer is associated with RAS/AKT mutations and high tumour mutational burden
Cited by: 4
Author(s): Joanne Stockton, Louise Tee, Celina M. Whalley, Jonathan James, Mark Dilworth, Rachel Wheat, Thomas Nieto, Ian Geh, João D. Barros-Silva, Andrew D Beggs
Software Mentions: 4
Published: over 3 years ago

10.1172/jci.insight.150203

Genomic and epigenomic evolution of acquired resistance to combination therapy in esophageal squamous cell carcinoma
Cited by: 6
Author(s): Qingjie Min, Yan Wang, Qingnan Wu, Xianfeng Li, Huajing Teng, Jingyuan Fan, Yiren Cao, Pingsheng Fan, Qimin Zhan
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pgen.1009526

Expression of the cancer-associated DNA polymerase ε P286R in fission yeast leads to translesion synthesis polymerase dependent hypermutation and defective DNA replication
Cited by: 5
Author(s): Ignacio Soriano, Enrique Vázquez, Nagore de León, Sibyl Bertrand, Ellen Heitzer, Sophia Toumazou, Zhihan Bo, Claire Palles, Chen-Chun Pai, Timothy C. Humphrey, Ian Tomlinson, Sue Cotterill, Stephen Kearsey
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pgen.1009302

UV-exposure, endogenous DNA damage, and DNA replication errors shape the spectra of genome changes in human skin
Cited by: 24
Author(s): Natalie Saini, Camille K. Giacobone, Leszek J. Klimczak, Brian N. Papas, Adam Burkholder, Jianliang Li, David C. Fargo, Re Bai, Kevin Gerrish, Cynthia L. Innes, Shepherd H. Schurman, Dmitry A. Gordenin
Software Mentions: 4
Published: about 4 years ago

10.26508/lsa.202101135

UVB mutagenesis differs in <i>Nras</i>- and <i>Braf</i>-mutant mouse models of melanoma
Cited by: 7
Author(s): Robert L. Bowman, Rebecca C. Hennessey, Tirzah J. Weiss, David Tallman, Emma R. Crawford, Brandon Murphy, Amy Webb, Souhui Zhang, Krista M. La Perle, Craig J. Burd, Ross L. Levine, A. Hunter Shain
Software Mentions: 4
Published: over 3 years ago

10.1093/gigascience/giab036

MesKit: a tool kit for dissecting cancer evolution of multi-region tumor biopsies through somatic alterations
Cited by: 10
Author(s): Mengni Liu, Jianyu Chen, Xin Wang, Chengwei Wang, Xiaolong Zhang, Yubin Xie, Zhixiang Zuo, Qi Zhao
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-021-95109-0

Mutational patterns and clonal evolution from diagnosis to relapse in pediatric acute lymphoblastic leukemia
Cited by: 4
Author(s): Shumaila Sayyab, Anders Lundmark, Malin Larsson, Markus Ringnér, Sara Nystedt, Yanara Marincevic-Zuniga, Katja Pokrovskaja Tamm, Jonas Abrahamsson, Linda Fogelstrand, Mats Heyman, Ulrika Norén‐Nyström, Gudmar Lönnerholm, Arja Harila‐Saari, Eva Berglund, Jessica Nordlund, Ann‐Christine Syvänen
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-019-50805-w

Identification of somatic alterations in lipoma using whole exome sequencing
Cited by: 4
Author(s): Deepika Kanojia, Pushkar Dakle, Anand Mayakonda, Rajeev Parameswaran, Mark E. Puhaindran, Victor Kwan Min Lee, Vikas Madan, Phillip Koeffler
Software Mentions: 3
Published: over 5 years ago

10.3390/jpm11050330

The Quandary of DNA-Based Treatment Assessment in De Novo Metastatic Prostate Cancer in the Era of Precision Oncology
Cited by: 1
Author(s): Sigve Nakken, Wolfgang Lilleby, Marta D. Switlyk, Karen E. Knudsen, Oscar Lilleby, Sen Zhao, Fatemeh Kaveh, Per Olaf Ekstrøm, Alfonso Urbanucci, Eivind Hovig
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12920-021-01032-8

Somatic mutations in benign breast disease tissues and association with breast cancer risk
Cited by: 2
Author(s): Stacey J. Winham, Chen Wang, Ethan P. Heinzen, Aditya Bhagwate, Yuanhang Liu, Samantha J. McDonough, Melody Stallings-Mann, Marlene H. Frost, Robert A. Vierkant, Lori A. Denison, Jodi M. Carter, Mark E. Sherman, Derek C. Radisky, Amy C. Degnim, Julie M. Cunningham
Software Mentions: 2
Published: over 3 years ago

10.1186/s12920-021-01017-7

Frequent POLE-driven hypermutation in ovarian endometrioid cancer revealed by mutational signatures in RNA sequencing
Cited by: 8
Author(s): Jaime Davila, Pritha Chanana, Vivekananda Sarangi, Zachary Fogarty, S. John Weroha, Ruifeng Guo, Ellen L. Goode, Yajue Huang, Chen Wang
Software Mentions: 2
Published: over 3 years ago

10.3390/cancers12123869

Breast Cancer Organoids Model Patient-Specific Response to Drug Treatment
Cited by: 38
Author(s): Elena Campaner, Alessandro Zannini, Mariangela Santorsola, Deborah Bonazza, Cristina Bottin, Valeria Cancila, Claudio Tripodo, Marina Bortul, Fabrizio Zanconati, Stefan Schoeftner, Giannino Del Sal
Software Mentions: 2
Published: about 4 years ago

10.1038/s42003-021-02597-x

Differential whole-genome doubling and homologous recombination deficiencies across breast cancer subtypes from the Taiwanese population
Cited by: 2
Author(s): Chia-Hsin Wu, Chia Shan Hsieh, Yo Cheng Chang, Chi Cheng Huang, Hsien Tang Yeh, Ming‐Feng Hou, Yuan Chiang Chung, Shih Hsin Tu, Kang‐Tsung Chang, Amrita Chattopadhyay, Liang‐Chuan Lai, Tzu-Pin Lu, Yung Hua Li, Mong‐Hsun Tsai, Eric Y. Chuang
Software Mentions: 2
Published: over 3 years ago

10.3390/genes12020214

Unravelling the Sequential Interplay of Mutational Mechanisms during Clonal Evolution in Relapsed Pediatric Acute Lymphoblastic Leukemia
Cited by: 6
Author(s): Željko Antić, Stefan H. Lelieveld, Cédric G. van der Ham, Edwin Sonneveld, Peter M. Hoogerbrugge, Roland P. Kuiper
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41598-020-69822-1

Mutation accumulation and developmental lineages in normal and Down syndrome human fetal haematopoiesis
Cited by: 19
Author(s): Karlijn Hasaart, Freek Manders, Marie-Louise van der Hoorn, Mark Verheul, Tomasz Poplonski, Ewart Kuijk, Susana M. Chuva de Sousa Lopes, Ruben van Boxtel
Software Mentions: 2
Published: over 4 years ago

10.7150/thno.43251

Aristolochic acid mutational signature defines the low-risk subtype in upper tract urothelial carcinoma
Cited by: 31
Author(s): Huan Lü, Liang Yuan, Bao Guan, Yue Shi, Yanqing Gong, Juan Li, Wenwen Kong, Jin Liu, Dong Fang, Libo Li, Qun He, Muhammad Shakeel, Xuesong Li, Liqun Zhou, Weimin Ci
Software Mentions: 2
Published: about 5 years ago

10.1186/s12859-018-2234-y

Mutational Signatures in Cancer (MuSiCa): a web application to implement mutational signatures analysis in cancer samples
Cited by: 73
Author(s): Marcos Díaz‐Gay, María Vila-Casadesús, Sebastià Franch‐Expósito, Eva Hernández‐Illán, Juan José Lozano, Sergi Castellví–Bel
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-019-6056-8

Bioinformatics and DNA-extraction strategies to reliably detect genetic variants from FFPE breast tissue samples
Cited by: 34
Author(s): Aditya Bhagwate, Yuanhang Liu, Stacey J. Winham, Samantha J. McDonough, Melody Stallings-Mann, Ethan P. Heinzen, Jaime Davila, Robert A. Vierkant, Tanya L. Hoskin, Marlene H. Frost, Jodi M. Carter, Derek C. Radisky, Julie M. Cunningham, Amy C. Degnim, Chen Wang
Software Mentions: 1
Published: over 5 years ago

10.1186/s12935-020-01268-x

Genomic characterization of a newly established esophageal squamous cell carcinoma cell line from China and published esophageal squamous cell carcinoma cell lines
Cited by: 5
Author(s): Xiang Li, Dan Tian, Yi Guo, Shiyue Qiu, Zexin Xu, Wen Deng, Min Shu
Software Mentions: 1
Published: over 4 years ago

10.1073/pnas.2011332117

Trajectory and uniqueness of mutational signatures in yeast mutators
Cited by: 27
Author(s): Sophie Loeillet, Mareike Herzog, Fabio Puddu, Patricia Legoix, Sylvain Baulande, Stephen Jackson, Alain Nicolas
Software Mentions: 1
Published: over 4 years ago

10.3390/cancers13081821

Evolutionary Trajectories and Genomic Divergence in Localized Breast Cancers after Ipsilateral Breast Tumor Recurrence
Cited by: 3
Author(s): Chia-Hsin Wu, Hsien-Tang Yeh, Chia-Shan Hsieh, Chi‐Cheng Huang, Amrita Chattopadhyay, Yuan‐Chiang Chung, Shih Hsin Tu, Yung-Hua Li, Tzu-Pin Lu, Liang‐Chuan Lai, Ming‐Feng Hou, King‐Jen Chang, Mong‐Hsun Tsai, Eric Y. Chuang
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pcbi.1007469

Uncovering and characterizing splice variants associated with survival in lung cancer patients
Cited by: 9
Author(s): Sean West, Sushil Kumar, Surinder K. Batra, Hesham Ali, Dario Ghersi
Software Mentions: 1
Published: about 5 years ago

Ecosyste.ms: Papers

Projects: bioconductor: MutationalPatterns

Papers Mentioning MutationalPatterns 32