cran: deconstructSigs | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0239197

Effects of germline and somatic events in candidate BRCA-like genes on breast-tumor signatures
Cited by: 13
Author(s): Weston R. Bodily, Brian H. Shirts, Tom Walsh, Süleyman Gülsüner, Mary‐Claire King, Alyssa Parker, Moom R. Roosan, Stephen R. Piccolo
Software Mentions: 12
Published: about 4 years ago

10.1016/j.cell.2016.08.041

A Biobank of Breast Cancer Explants with Preserved Intra-tumor Heterogeneity to Screen Anticancer Compounds
Cited by: 359
Author(s): Alejandra Bruna, Oscar M. Rueda, Wendy Greenwood, Ankita Batra, Maurizio Callari, R N Batra, Katherine Pogrebniak, José Luís Sandoval, John W. Cassidy, Ana Tufegdžić Vidaković, Stephen‐John Sammut, Linda Jones, Elena Provenzano, Richard D. Baird, Peter Eirew, James Hadfield, Matthew Eldridge, Anne McLaren-Douglas, Andrew Barthorpe, Howard Lightfoot, Mark J. O’Connor, Joe W. Gray, Javier Cortés, José Baselga, Elisabetta Marangoni, Alana L. Welm, Samuel Aparicio, Violeta Serra, Mathew J. Garnett, Carlos Caldas
Software Mentions: 11
Published: about 8 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: about 5 years ago

10.3390/cancers12051076

Tumor-Infiltrating CD8 T Cells Predict Clinical Breast Cancer Outcomes in Young Women
Cited by: 31
Author(s): Yong Won Jin, Pingzhao Hu
Software Mentions: 9
Published: over 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: almost 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: almost 5 years ago

10.3389/fmolb.2020.00053

Intrinsic Genetic and Transcriptomic Patterns Reflect Tumor Immune Subtypes Facilitating Exploring Possible Combinatory Therapy
Cited by: 1
Author(s): Yong Xu, Daixi Li, Zhenhao Liu, David L. Gibbs, Lu Xie, Guangrong Qin
Software Mentions: 7
Published: over 4 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

10.1136/jitc-2021-002467

Tumor microenvironment evaluation promotes precise checkpoint immunotherapy of advanced gastric cancer
Cited by: 75
Author(s): Dongqiang Zeng, Jiani Wu, Hongyu Luo, Yong Li, Jian Xiao, Jianjun Peng, Zilan Ye, Rui Zhou, Yunfang Yu, Gaofeng Wang, Na Huang, Jianhua Wu, Xiaoxiang Rong, Li Sun, Huiying Sun, Wenjun Qiu, Yuting Xue, Jianping Bin, Yulin Liao, Li N, Min Shi, Kyoung‐Mee Kim, Wangjun Liao
Software Mentions: 7
Published: over 3 years ago

10.1186/s12864-018-5264-y

Helmsman: fast and efficient mutation signature analysis for massive sequencing datasets
Cited by: 18
Author(s): Jedidiah Carlson, Jun Z. Li, Sebastian Zöllner
Software Mentions: 6
Published: almost 6 years ago

10.1002/1878-0261.12755

The benefits of smoking cessation on survival in cancer patients by integrative analysis of multi‐omics data
Cited by: 7
Author(s): Sheng Yang, Tong Liu, Geyu Liang
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pcbi.1009119

De novo mutational signature discovery in tumor genomes using SparseSignatures
Cited by: 21
Author(s): Avantika Lal, Keli Liu, Robert Tibshirani, Arend Sidow, Daniele Ramazzotti
Software Mentions: 6
Published: over 3 years ago

10.1186/s12920-020-00819-5

Genomic profile of MYCN non-amplified neuroblastoma and potential for immunotherapeutic strategies in neuroblastoma
Cited by: 6
Author(s): Eun-Jin Lee, Ji Won Lee, Boram Lee, Kyunghee Park, Joon Ho Shim, Keon Hee Yoo, Hong Hoe Koo, Ki Woong Sung, Woong-Yang Park
Software Mentions: 6
Published: about 4 years ago

10.1007/s13577-021-00492-5

Establishment and characterization of 38 novel patient-derived primary cancer cell lines using multi-region sampling revealing intra-tumor heterogeneity of gallbladder carcinoma
Cited by: 5
Author(s): Feiling Feng, Qiang Cheng, Bin Li, Chen Liu, Huizhen Wang, Xiang Xu, Yang Yu, Zishuo Chen, Xiaobing Wu, Dong Hua, Kai-Jian Chu, Zhenghua Xie, Qingxiang Gao, Lei Xiong, Fugen Li, Bin Yi, Dadong Zhang, Xiaoqing Jiang
Software Mentions: 5
Published: over 3 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

10.1186/s13059-020-02175-0

Multiomics profiling of primary lung cancers and distant metastases reveals immunosuppression as a common characteristic of tumor cells with metastatic plasticity
Cited by: 32
Author(s): Won‐Chul Lee, Alexandre Reuben, Xin Hu, Nicholas McGranahan, Runzhe Chen, Ali Jalali, Marcelo V. Negrão, Shawna M. Hubert, Chad Tang, Chia-Chin Wu, Anthony San Lucas, Whijae Roh, Kenichi Suda, Jihye Kim, Aik-Choon Tan, David H. Peng, Wei Lü, Ximing Tang, Chi-Wan Chow, Junya Fujimoto, Carmen Behrens, Neda Kalhor, Kazutaka Fukumura, Marcus Coyle, Rebecca Thornton, Curtis Gumbs, Jun Li, Chang-Jiun Wu, Latasha Little, Emily Roarty, Xingzhi Song, J. Jack Lee, Erik P. Sulman, Ganesh Rao, Stephen G. Swisher, Lixia Diao, Jing Wang, John V. Heymach, Jason T. Huse, Paul Scheet, Ignacio I. Wistuba, Don L. Gibbons, P. Andrew Futreal, Jianhua Zhang, Daniel R. Gomez, Jianjun Zhang
Software Mentions: 5
Published: about 4 years ago

10.1038/s41598-020-75062-0

MutSignatures: an R package for extraction and analysis of cancer mutational signatures
Cited by: 27
Author(s): Damiano Fantini, Vania Vidimar, Yu Yu, Salvatore Condello, Joshua J. Meeks
Software Mentions: 5
Published: about 4 years ago

10.1186/s13059-020-02192-z

The evolution of relapse of adult T cell acute lymphoblastic leukemia
Cited by: 9
Author(s): Inés Sentís, Santiago González, Eulàlia Genescà, Violeta García-Hernández, Ferran Muiños, Celia Guadalupe Morales González, Erika López-Arribillaga, Jéssica González, Lierni Fernández‐Ibarrondo, Loris Mularoni, Lluís Espinosa, Beatríz Bellosillo, Josep‐María Ribera, Anna Bigas, Abel González-Pérez, Núria López‐Bigas
Software Mentions: 5
Published: almost 4 years ago

10.1002/cam4.3481

Integrated genomic analysis identifies a genetic mutation model predicting response to immune checkpoint inhibitors in melanoma
Cited by: 22
Author(s): Junjie Jiang, Yongfeng Ding, Mengjie Wu, Yanyan Chen, Xiadong Lyu, Jun Lü, Haiyong Wang, Lisong Teng
Software Mentions: 5
Published: about 4 years ago

10.1186/s13073-021-00826-w

Comprehensive molecular characterization of gastric cancer patients from phase II second-line ramucirumab plus paclitaxel therapy trial
Cited by: 16
Author(s): Seung Tae Kim, K. Jason, Sung Yong Oh, Kyung Kim, Jung Yong Hong, Won Ki Kang, Jeeyun Lee
Software Mentions: 4
Published: almost 4 years ago

10.1038/s12276-021-00583-1

High prevalence of TP53 loss and whole-genome doubling in early-onset colorectal cancer
Cited by: 11
Author(s): Jeong Eun Kim, Jaeyong Choi, Chang Ohk Sung, Yong Sang Hong, Sun Young Kim, Hyunjung Lee, Tae Won Kim, Jong‐Il Kim
Software Mentions: 4
Published: over 3 years ago

10.1186/s40425-019-0609-x

Paired whole exome and transcriptome analyses for the Immunogenomic changes during concurrent chemoradiotherapy in esophageal squamous cell carcinoma
Cited by: 22
Author(s): Sehhoon Park, Je‐Gun Joung, Min Ye, Jae‐Yong Nam, Daeun Ryu, Dongryul Oh, Woong-Yang Park, Sehoon Lee, Yoon La Choi, Jin Seok Ahn, Myung‐Ju Ahn, Keunchil Park, Jong‐Mu Sun
Software Mentions: 4
Published: over 5 years ago

10.1186/s13058-019-1170-8

Claudin-low-like mouse mammary tumors show distinct transcriptomic patterns uncoupled from genomic drivers
Cited by: 17
Author(s): Christian Fougner, Helga Bergholtz, Raoul V. Kuiper, Jens Henrik Norum, Thérese Sørlie
Software Mentions: 4
Published: over 5 years ago

10.18632/oncotarget.26352

Genomic characterization of metastatic ultra-hypermutated interdigitating dendritic cell sarcoma through rapid research autopsy
Cited by: 6
Author(s): Hui-Zi Chen, Russell Bonneville, Lianbo Yu, Michele R. Wing, Julie W. Reeser, Melanie A. Krook, Jharna Miya, Eric Samorodnitsky, Amy M. Smith, Dorrelyn M. Martin, Thuy Dao, Qishan Guo, David A. Liebner, Aharon G. Freud, Patricia Allenby, Sameek Roychowdhury
Software Mentions: 4
Published: almost 6 years ago

10.1002/cam4.3649

Integration of comprehensive genomic profiling, tumor mutational burden, and PD‐L1 expression to identify novel biomarkers of immunotherapy in non‐small cell lung cancer
Cited by: 43
Author(s): Yunfei Shi, Youming Lei, Li Liu, Shiyue Zhang, Wenjing Wang, Juan Zhao, Shuaiguo Zhao, Xiaowei Dong, Ming Yao, Kai Wang, Qing Zhou
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pmed.1002204

The Subclonal Architecture of Metastatic Breast Cancer: Results from a Prospective Community-Based Rapid Autopsy Program “CASCADE”
Cited by: 111
Author(s): Peter Savas, Zhi L. Teo, Christophe Lefèvre, Christoffer Flensburg, Franco Caramia, Kathryn Alsop, Mariam Mansour, Prudence A. Francis, Heather Thorne, Maria João Silva, Nnennaya Kanu, Michelle Dietzen, Andrew Rowan, Maik Kschischo, Stephen B. Fox, David D.L. Bowtell, Sarah-Jane Dawson, Terence P. Speed, Charles Swanton, Sherene Loi
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pmed.1002309

Contribution of systemic and somatic factors to clinical response and resistance to PD-L1 blockade in urothelial cancer: An exploratory multi-omic analysis
Cited by: 231
Author(s): Alexandra Snyder, Tavi Nathanson, Samuel A. Funt, Arun Ahuja, Jacqueline L. Buros, Matthew D. Hellmann, Eliza Chang, Bülent Arman Aksoy, Hikmat Al‐Ahmadie, Erik Yusko, Marissa Vignali, Sharon Benzeno, Mariel Elena Boyd, Meredith Maisie Moran, Gopa Iyer, Harlan Robins, Elaine R. Mardis, Taha Merghoub, Jeff Hammerbacher, Jonathan E. Rosenberg, Dean F. Bajorin
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0246443

Unraveling the chaotic genomic landscape of primary and metastatic canine appendicular osteosarcoma with current sequencing technologies and bioinformatic approaches
Cited by: 4
Author(s): Shirley Chu, Zachary L. Skidmore, Jason Kunisaki, Jason Walker, Malachi Griffith, Obi L. Griffith, Jeffrey N. Bryan
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12864-019-6041-2

SigProfilerMatrixGenerator: a tool for visualizing and exploring patterns of small mutational events
Cited by: 142
Author(s): Erik N. Bergstrom, Huang Mi, Uma Mahto, Mark Barnes, Michael R. Stratton, Steven G. Rozen, Ludmil B. Alexandrov
Software Mentions: 4
Published: about 5 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

10.1186/s12967-020-02235-w

Poor clinical outcome in metastatic melanoma is associated with a microRNA-modulated immunosuppressive tumor microenvironment
Cited by: 25
Author(s): Natasha Andressa Nogueira Jorge, Jéssica Gonçalves Vieira da Cruz, Marco Antônio M. Pretti, Martín Bonamino, Patrícia A. Possik, Mariana Boroni
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-021-94064-0

Exome sequencing identifies novel somatic variants in African American esophageal squamous cell carcinoma
Cited by: 3
Author(s): Hayriye V. Erkizan, Shrey Sukhadia, Thanemozhi G. Natarajan, Gustavo Mariño, Vicente Notario, Jack H. Lichy, Robert G. Wadleigh
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-018-33396-w

The genetic landscape of 5T models for multiple myeloma
Cited by: 13
Author(s): Ken Maes, Bram Boeckx, Philip Vlummens, Kim De Veirman, Eline Menu, Karin Vanderkerken, Diether Lambrechts, Elke De Bruyne
Software Mentions: 3
Published: about 6 years ago

10.1186/s40425-019-0660-7

Epigenetic alterations are associated with tumor mutation burden in non-small cell lung cancer
Cited by: 28
Author(s): Lun Cai, Hua Bai, Jianchun Duan, Zhijie Wang, Shugeng Gao, Di Wang, Shuhang Wang, Jun Jiang, Jiefei Han, Yanhua Tian, Xue Zhang, Yue Hao, Minghui Li, Bingding Huang, Jie He, Jie Wang
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.61082

Supervised mutational signatures for obesity and other tissue-specific etiological factors in cancer
Cited by: 9
Author(s): Bahman Afsari, Albert Kuo, Yifan Zhang, Lu Li, Kamel Lahouel, Ludmila Danilova, Alexander V. Favorov, Thomas A. Rosenquist, Arthur P. Grollman, Ken W Kinzler, Leslie Cope, Bert Vogelstein, Cristian Tomasetti
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pgen.1008641

Integrative comparison of the genomic and transcriptomic landscape between prostate cancer patients of predominantly African or European genetic ancestry
Cited by: 73
Author(s): Jiao Yuan, Kevin H. Kensler, Zhongyi Hu, Youyou Zhang, Tianli Zhang, Junjie Jiang, Mu Xu, Yongsheng Pan, Meixiao Long, Kathleen T. Montone, János L. Tanyi, Yi Fan, Rugang Zhang, Xiaowen Hu, Timothy R. Rebbeck, Lin Zhang
Software Mentions: 3
Published: almost 5 years ago

10.3390/genes11111367

Comprehensive Genomic Profile of Heterogeneous Long Follow-Up Triple-Negative Breast Cancer and Its Clinical Characteristics Shows DNA Repair Deficiency Has Better Prognostic
Cited by: 5
Author(s): Ernesto Rojas Jiménez, Javier Mejia-Gomez, Clara Díaz-Velásquez, Rosalía Quezada-Urbán, Héctor Martínez Gregorio, Fernando Vallejo-Lecuona, Aldo de la Cruz-Montoya, Fany Iris Porras Reyes, Víctor Manuel Pérez-Sánchez, Héctor Aquiles Maldonado-Martínez, Maybelline Robles-Estrada, Enrique Bargalló-Rocha, Paula Cabrera‐Galeana, Maritza Ramos‐Ramírez, Yolanda I. Chirino, Luis A. Herrera, Luis I. Terrazas, Javier Oliver, Cecilia Frecha, Sandra Pérdomo, Felipe Vaca-Paniagua
Software Mentions: 3
Published: about 4 years ago

10.1186/s12885-020-6684-z

Mutational landscape differences between young-onset and older-onset breast cancer patients
Cited by: 9
Author(s): Nicole E. Mealey, Dylan E. O’Sullivan, Joy Pader, Yibing Ruan, Edwin Wang, May Lynn Quan, Darren R. Brenner
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-020-58107-2

CANCERSIGN: a user-friendly and robust tool for identification and classification of mutational signatures and patterns in cancer genomes
Cited by: 17
Author(s): Masroor Bayati, Hamid R. Rabiee, Mehrdad Mehrbod, Fatemeh Vafaee, Diako Ebrahimi, Alistair R.R. Forrest, Hamid Alinejad‐Rokny
Software Mentions: 3
Published: almost 5 years ago

10.1038/s42003-019-0476-5

Paternal exposure to benzo(a)pyrene induces genome-wide mutations in mouse offspring
Cited by: 22
Author(s): Marc A. Beal, Matthew J. Meier, Andrew Williams, Andrea Rowan-Carroll, Rémi Gagné, Sarah Lindsay, Tomas Fitzgerald, Matthew E. Hurles, Francesco Marchetti, Carole L. Yauk
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-018-26967-4

Molecular profiling and sequential somatic mutation shift in hypermutator tumours harbouring POLE mutations
Cited by: 24
Author(s): Keiichi Hatakeyama, Keiichi Ohshima, Takeshi Nagashima, Shumpei Ohnami, Sumiko Ohnami, Masakuni Serizawa, Yuji Shimoda, Koji Maruyama, Yasuto Akiyama, Kenichi Urakami, Masatoshi Kusuhara, Tohru Mochizuki, Ken Yamaguchi
Software Mentions: 2
Published: over 6 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/s12885-018-4977-2

Predominance of triple wild-type and IGF2R mutations in mucosal melanomas
Cited by: 15
Author(s): Yuuki Iida, Matthew P. Salomon, Keisuke Hata, Kevin Tran, Shuichi Ohe, Chester F Griffiths, Sandy C. Hsu, Nellie Nelson, Dave S. B. Hoon
Software Mentions: 2
Published: about 6 years ago

10.1186/s12885-017-3825-0

Chemotherapy weakly contributes to predicted neoantigen expression in ovarian cancer
Cited by: 32
Author(s): Timothy J. O’Donnell, Elizabeth L. Christie, Arun Ahuja, Jacqueline Buros, Bülent Arman Aksoy, David D.L. Bowtell, Alexandra Snyder, Jeff Hammerbacher
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12919-020-00185-1

Abstracts from the 9th International Conference for Healthcare and Medical Students (ICHAMS)
Cited by: 0
Author(s):
Software Mentions: 2
Published: over 4 years ago

10.1002/cam4.3426

Genomic, transcriptomic, and viral integration profiles associated with recurrent/metastatic progression in high‐risk human papillomavirus cervical carcinomas
Cited by: 3
Author(s): Jing Jing Liu, Jung Ho, Jung Eum Lee, Soo Young Hur, Jinseon Yoo, Kyu Ryung Kim, Daeun Ryu, Tae Min Kim, Youn Jin Choi
Software Mentions: 2
Published: about 4 years ago

10.1002/cam4.2120

Tumor mutation burden and recurrent tumors in hereditary lung cancer
Cited by: 13
Author(s): Yi Chiung Hsu, Yun‐chien Chang, Gee Chen Chang, Bing-Ching Ho, Shin Sheng Yuan, Yu Cheng Li, Jhih Wun Zeng, Sung-Liang Yu, Ker Chau Li, Pan Chyr Yang, Hsuan Yu Chen
Software Mentions: 2
Published: over 5 years ago

10.1002/cam4.2146

Prognostic implications of a molecular classifier derived from whole‐exome sequencing in nasopharyngeal carcinoma
Cited by: 12
Author(s): Hai–Yun Wang, Fugen Li, Na Liu, Xiao‐Yun Liu, Xinhua Yang, Yun‐Miao Guo, Jin‐Xin Bei, Yi‐Xin Zeng, Jian Yong Shao
Software Mentions: 2
Published: over 5 years ago

10.3390/cancers12071799

Comprehensive Constitutional Genetic and Epigenetic Characterization of Lynch-Like Individuals
Cited by: 12
Author(s): Estela Dámaso, Maribel González‐Acosta, Gardenia Vargas-Parra, Matilde Navarro, Judith Balmañà, Teresa Ramón y Cajal, N Tuset, Bryony A. Thompson, Fátima Marín, Anna Fernández, Carolina Gómez, Àngela Velasco, Ares Solanes, Sílvia Iglesias, Gisela Urgel, Consol López, Jesús Del Valle, Olga Campos, Maria Santacana, Xavier Matías‐Guiu, Conxi Lázaro, Laura Valle, Joan Brunet, Marta Pineda, Gabriel Capellá
Software Mentions: 2
Published: over 4 years ago

10.18632/aging.102099

Better prognostic determination and feature characterization of cutaneous melanoma through integrative genomic analysis
Cited by: 8
Author(s): Xia Li, Yunpeng Cai
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-020-75753-8

CaMuS: simultaneous fitting and de novo imputation of cancer mutational signature
Cited by: 5
Author(s): Maria Cartolano, Nima Abedpour, Viktor Achter, Tsun-Po Yang, Sandra Ackermann, Matthias Fischer, Martin Peifer
Software Mentions: 2
Published: about 4 years ago

10.1155/2017/2029315

Whole-Exome Sequencing-Based Mutational Profiling of Hepatitis B Virus-Related Early-Stage Hepatocellular Carcinoma
Cited by: 12
Author(s): Hao Zhan, Jiahao Jiang, Qiqing Sun, Ai–Wu Ke, Jinwu Hu, Zhiqiang Hu, Kai Zhu, Chu-Bin Luo, Ning Ren, Jia Fan, Jian Zhou, Xiaowu Huang
Software Mentions: 1
Published: almost 8 years ago

10.3389/fgene.2020.00829

Germline PALB2 Mutations in Cancers and Its Distinction From Somatic PALB2 Mutations in Breast Cancers
Cited by: 7
Author(s): Zhe Hu, Liping Liu, Ning Xie, Jun Lü, Zhentian Liu, Yu Tang, Yikai Wang, Jianbo Yang, Qi Ouyang
Software Mentions: 1
Published: about 4 years ago

10.1186/s13059-016-0893-4

deconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution
Cited by: 865
Author(s): Rachel Rosenthal, Nicholas McGranahan, Javier Herrero, Barry S. Taylor, Charles Swanton
Software Mentions: 1
Published: over 8 years ago

10.3389/fgene.2018.00002

Genomic Analysis Revealed New Oncogenic Signatures in TP53-Mutant Hepatocellular Carcinoma
Cited by: 29
Author(s): Venkatesh Kancherla, Samir Abdullazade, Matthias S. Matter, Manuela Lanzafame, Luca Quagliata, Guglielmo Roma, Yujin Hoshida, Luigi Terracciano, Charlotte K.Y. Ng, Salvatore Piscuoglio
Software Mentions: 1
Published: almost 7 years ago

10.3389/fcell.2021.698659

Pan-Cancer Survey of Tumor Mass Dormancy and Underlying Mutational Processes
Cited by: 3
Author(s): Anna Julia Wiecek, Daniel Hadar Jacobson, Wojciech Lason, Maria Secrier
Software Mentions: 1
Published: over 3 years ago

10.1186/s13073-018-0520-y

NSAID use and somatic exomic mutations in Barrett’s esophagus
Cited by: 14
Author(s): Patricia C. Galipeau, Kenji Oman, Thomas G. Paulson, Carissa A. Sanchez, Qing Zhang, Jerry A. Marty, Jeffrey J. Delrow, Mary K. Kuhner, Thomas L. Vaughan, Brian J. Reid, Xiaohong Li
Software Mentions: 1
Published: over 6 years ago

10.1038/s42003-021-01938-0

mmsig: a fitting approach to accurately identify somatic mutational signatures in hematological malignancies
Cited by: 15
Author(s): Even H Rustad, Ferran Nadeu, Nicos Angelopoulos, Bachisio Ziccheddu, Niccolò Bolli, Xosé S. Puente, Elı́as Campo, Ola Landgren, Francesco Maura
Software Mentions: 1
Published: over 3 years ago

10.1038/s42003-018-0182-8

Whole-genome sequencing of esophageal adenocarcinoma in Chinese patients reveals distinct mutational signatures and genomic alterations
Cited by: 5
Author(s): James Y. Dai, Xiaoyu Wang, Matthew F. Buas, Chengjuan Zhang, Jie Ma, Bing Wei, Yin Li, Baosheng Zhao, Teresa S. Hyun, Xueyan Chen, Keith R. Loeb, Robert D. Odze, Lena Yao, Xin Sun, Steve Self, Thomas L. Vaughan, Yongjun Guo
Software Mentions: 1
Published: about 6 years ago

10.1038/s42003-020-01119-5

Mutational signature SBS8 predominantly arises due to late replication errors in cancer
Cited by: 30
Author(s): V. P. Singh, Arnav Rastogi, Xiaoju Hu, Yaqun Wang, Subhajyoti De
Software Mentions: 1
Published: over 4 years ago

10.3390/cancers12102938

Clonal Evolution and Timing of Metastatic Colorectal Cancer
Cited by: 7
Author(s): Sarah Siraj, Tariq Masoodi, Abdul K. Siraj, Saud Azam, Zeeshan Qadri, Suhaib Ahmed, Wafaa N. Albalawy, Khadija Alobaisi, Sandeep Kumar Parvathareddy, Hadeel Almanea, Hussah F AlHussaini, Alaa Abduljabbar, Samar Alhomoud, Fouad Al‐Dayel, Fowzan S. Alkuraya, Khawla S. Al‐Kuraya
Software Mentions: 1
Published: about 4 years ago

10.3390/cancers12061568

Well-Differentiated Papillary Mesothelioma of the Peritoneum Is Genetically Distinct from Malignant Mesothelioma
Cited by: 18
Author(s): Raunak Shrestha, Noushin Nabavi, Stanislav V. Volik, Shawn Anderson, Anne Haegert, Brian McConeghy, Funda Sar, Sonal Brahmbhatt, Robert H. Bell, Stéphane Le Bihan, Yuzhuo Wang, Colin C. Collins, Andrew Churg
Software Mentions: 1
Published: over 4 years ago

10.3390/cancers13081762

Tumor Signature Analysis Implicates Hereditary Cancer Genes in Endometrial Cancer Development
Cited by: 5
Author(s): Olga Kondrashova, Jannah Shamsani, Tracy A. O’Mara, Felicity Newell, Amy E. McCart Reed, Sunil R. Lakhani, Judy Kirk, John V. Pearson, Nicola Waddell, Amanda B. Spurdle
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-017-07888-0

A pooled mutational analysis identifies ionizing radiation-associated mutational signatures conserved between mouse and human malignancies
Cited by: 22
Author(s): Philip R. Davidson, Amy L. Sherborne, Barry S. Taylor, Alice Nakamura, Jean L. Nakamura
Software Mentions: 1
Published: over 7 years ago

10.1093/annonc/mdw686

Complex chromosomal rearrangements by single catastrophic pathogenesis in NUT midline carcinoma
Cited by: 44
Author(s): Jake June-Koo Lee, Sandra Louzada, Yu An, S.Y. Kim, S. Kim, Jeonghwan Youk, S. Park, Sun Hoe Koo, Bhumsuk Keam, Yoon Kyung Jeon, Ja Lok Ku, Fengtang Yang, T.M. Kim, Young Seok Ju
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0215381

Association of BRCA1- and BRCA2-deficiency with mutation burden, expression of PD-L1/PD-1, immune infiltrates, and T cell-inflamed signature in breast cancer
Cited by: 67
Author(s): Wei Wen, Chee‐Onn Leong
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-019-55352-y

Mutation signature analysis identifies increased mutation caused by tobacco smoke associated DNA adducts in larynx squamous cell carcinoma compared with oral cavity and oropharynx
Cited by: 16
Author(s): Andrew P. South, Nicoline Y. den Breems, Tony Richa, Uche Nwagu, Tingting Zhan, Shiv Poojan, Ubaldo Martinez‐Outschoorn, Jennifer M. Johnson, Adam Luginbuhl, Joseph Curry
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0201546

Genetic heterogeneity and mutational signature in Chinese Epstein-Barr virus-positive diffuse large B-cell lymphoma
Cited by: 7
Author(s): Fang Liu, Zhe Wang, Xiaoge Zhou, Qing Liu, Gang Chen, Hualiang Xiao, Wenwu Yin, Shigeo Nakamura, Hui‐Lan Rao
Software Mentions: 1
Published: over 6 years ago

10.1002/mgg3.810

Integrative genomic analysis identifies associations of molecular alterations to APOBEC and BRCA1/2 mutational signatures in breast cancer
Cited by: 6
Author(s): Víctor Treviño
Software Mentions: 1
Published: over 5 years ago

10.1186/s12967-020-02607-2

Genomic profile of metastatic breast cancer patient-derived xenografts established using percutaneous biopsy
Cited by: 0
Author(s): Seongyeong Kim, Dong-Jin Shin, Ahrum Min, Minjung Kim, Deukchae Na, Han Byeol Lee, Han Suk Ryu, Yaewon Yang, Gwang Hoon Woo, Kyung Hun Lee, Dae Won Lee, Tae Yong Kim, Charles Lee, Seock Ah Im, Jong‐Il Kim
Software Mentions: 1
Published: almost 4 years ago

10.1002/cam4.2344

Clinicopathological and mutational analyses of colorectal cancer with mutations in the <i>POLE</i> gene
Cited by: 22
Author(s): Hitoshi Hino, Akio Shiomi, Masatoshi Kusuhara, Hiroyasu Kagawa, Yushi Yamakawa, Keiichi Hatakeyama, Takanori Kawabata, Takuma Oishi, Kenichi Urakami, Takeshi Nagashima, Yusuke Kinugasa, Ken Yamaguchi
Software Mentions: 1
Published: over 5 years ago

10.7150/thno.45311

Identification of second primary tumors from lung metastases in patients with esophageal squamous cell carcinoma using whole-exome sequencing
Cited by: 4
Author(s): Liyan Xue, Weihua Li, Xinyi Fan, Zitong Zhao, Wei Zhou, Zhihui Feng, Linxiu Liu, Lin Hua, Liang-In Lin, Xuemin Xue, Xuanlin Huang, Peide Huang, Jia Guo, Peina Du, Ning Lü, Qimin Zhan, Yongmei Song
Software Mentions: 1
Published: almost 5 years ago

10.1002/cam4.1612

Germline genetic variants were interactively associated with somatic alterations in gastric cancer
Cited by: 5
Author(s): Xu Zhang, Yuzhuo Wang, Tian Tian, Gangqiao Zhou, Guangfu Jin
Software Mentions: 1
Published: over 6 years ago

10.1038/s41408-020-0315-4

Impact of mitochondrial DNA mutations in multiple myeloma
Cited by: 8
Author(s): Phuc H. Hoang, Alex J. Cornish, Daniel Chubb, Graham Jackson, Martin Kaiser, Richard S. Houlston
Software Mentions: 1
Published: over 4 years ago

10.1038/s41408-020-00367-2

An enhanced genetic model of relapsed IGH-translocated multiple myeloma evolutionary dynamics
Cited by: 12
Author(s): Phuc H. Hoang, Alex J. Cornish, Amy L. Sherborne, Daniel Chubb, Scott Kimber, Graham Jackson, Gareth J. Morgan, Gordon Cook, Ben Kinnersley, Martin Kaiser, Richard S. Houlston
Software Mentions: 1
Published: about 4 years ago

10.1038/s41388-018-0657-6

APOBEC-induced mutations and their cancer effect size in head and neck squamous cell carcinoma
Cited by: 75
Author(s): Vincent L. Cannataro, Stephen G. Gaffney, Tomoaki Sasaki, Natalia Issaeva, Nicholas Grewal, Jennifer R. Grandis, Wendell G. Yarbrough, Barbara Burtness, Karen S. Anderson, Jeffrey P. Townsend
Software Mentions: 1
Published: almost 6 years ago

10.1186/s13256-021-02685-w

Elevated APOBEC mutational signatures implicate chronic injury in etiology of an aggressive head-and-neck squamous cell carcinoma: a case report
Cited by: 0
Author(s): Jena Patel, Nicoline Y. den Breems, Madalina Tuluc, Jennifer M. Johnson, Joseph Curry, Andrew P. South, Raymond J. Cho
Software Mentions: 1
Published: over 3 years ago

10.1186/s12885-019-6227-7

Validation of computational determination of microsatellite status using whole exome sequencing data from colorectal cancer patients
Cited by: 15
Author(s): Amanda Frydendahl, Christine Gaasdal Kassentoft, Michael Knudsen, Maria Bach Laursen, Anders Husted Madsen, Lene Hjerrild Iversen, Kåre Andersson Gotschalck, Mads Heilskov Rasmussen, Claus Lindbjerg Andersen
Software Mentions: 1
Published: about 5 years ago

10.18632/oncotarget.22862

Molecular-genetic profiling and high-throughput <i>in vitro</i> drug screening in NUT midline carcinoma—an aggressive and fatal disease
Cited by: 24
Author(s): Anja Stirnweiß, Joyce Oommen, Rishi S. Kotecha, Ursula R. Kees, Alex H. Beesley
Software Mentions: 1
Published: almost 7 years ago

10.18632/oncotarget.23066

Exome sequencing reveals aberrant signalling pathways as hallmark of treatment-naive anal squamous cell carcinoma
Cited by: 21
Author(s): Wulfran Cacheux, Virginie Dangles‐Marie, Étienne Rouleau, Julien Lazartigues, Elodie Girard, Adrien Briaux, Pascale Mariani, Sophie Richon, Sophie Vacher, Benedetto Bruno, Marion Richard‐Molard, Emmanuelle Jeannot, Nicolas Servant, Fereshteh Farkhondeh, Odette Mariani, Thomas Rio-Frio, Sergio Román-Román, Emmanuel Mitry, Ivan Bièche, Astrid Lièvre
Software Mentions: 1
Published: almost 7 years ago

10.18632/oncotarget.25041

Genetic heterogeneity and actionable mutations in HER2-positive primary breast cancers and their brain metastases
Cited by: 35
Author(s): Leticia De Mattos-Arruda, Charlotte K.Y. Ng, Salvatore Piscuoglio, María González‐Cao, Raymond S. Lim, Maria Rosaria De Filippo, Nicola Fusco, Anne M. Schultheis, Carolina Ortiz, Santiago Viteri, Alexandra Arias, Gabriel S. Macedo, Mafalda Oliveira, Patricia Gómez, Cristina Teixidó, Paolo Nuciforo, Vicente Peg, Cristina Saura, Santiago Ramón y Cajal, Francesc Casas, Britta Weigelt, Javier Cortés, Joan Seoane, Jorge S. Reis‐Filho
Software Mentions: 1
Published: over 6 years ago

10.1186/s12859-020-3451-8

pyCancerSig: subclassifying human cancer with comprehensive single nucleotide, structural and microsatellite mutational signature deconstruction from whole genome sequencing
Cited by: 6
Author(s): Jessada Thutkawkorapin, Jesper Eisfeldt, Emma Tham, Daniel Nilsson
Software Mentions: 1
Published: over 4 years ago

10.18632/oncotarget.27538

Does breast carcinoma belong to the Lynch syndrome tumor spectrum? – Somatic mutational profiles vs. ovarian and colorectal carcinomas
Cited by: 10
Author(s): Noora Porkka, Alisa Olkinuora, Teijo Kuopio, Maarit Ahtiainen, Samuli Eldfors, Henrikki Almusa, Jukka–Pekka Mecklin∥, Païvi Peltomäki
Software Mentions: 1
Published: over 4 years ago

10.3389/fonc.2019.00288

Germline Predisposition and Copy Number Alteration in Pre-stage Lung Adenocarcinomas Presenting as Ground-Glass Nodules
Cited by: 15
Author(s): Yijiu Ren, Shujun Huang, Chenyang Dai, Dong Xie, Laura Zheng, Huikang Xie, Hui Zheng, Yunlang She, Fangyu Zhou, Yue Wang, Pengpeng Li, Ke Fei, Gening Jiang, Yang Zhang, Bo Su, E. Alejandro Sweet-Cordero, Nhan L. Tran, Yanan Yang, Jai N. Patel, Christian Rolfo, Gaetano Rocco, Andrés Felipe Cardona, Alessandro Tuzi, Matteo B. Suter, Ping Yang, Wayne Xu, Chen Chang
Software Mentions: 1
Published: over 5 years ago

10.3389/fonc.2021.621422

Next-Generation Sequencing Reveals High Uncommon EGFR Mutations and Tumour Mutation Burden in a Subgroup of Lung Cancer Patients
Cited by: 8
Author(s): Gang Guo, Gaofeng Li, Yinqiang Liu, Heng Li, Qi Guo, Jun Li, Yang Xiao-sheng, Tao Shou, Yunfei Shi
Software Mentions: 1
Published: over 3 years ago

Projects: cran: deconstructSigs

Papers Mentioning deconstructSigs 85