bioconductor: SomaticSignatures | Projects

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

10.1016/j.celrep.2019.11.077

Integrated Epigenome, Exome, and Transcriptome Analyses Reveal Molecular Subtypes and Homeotic Transformation in Uterine Fibroids
Cited by: 42
Author(s): Jitu W. George, Huihui Fan, Benjamin K. Johnson, Tyler J. Carpenter, Kelly K. Foy, Anindita Chatterjee, Amanda L. Patterson, Julie Koeman, Marie Adams, Zachary Madaj, David Chesla, Erica E. Marsh, Timothy J. Triche, Hui Shen, Jose Teixeira
Software Mentions: 9
Published: almost 5 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

10.1038/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/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

10.1128/mBio.02079-16

Merkel Cell Polyomavirus Exhibits Dominant Control of the Tumor Genome and Transcriptome in Virus-Associated Merkel Cell Carcinoma
Cited by: 87
Author(s): Gabriel J. Starrett, Christina Marcelus, Paul G. Cantalupo, Joshua P. Katz, Jingwei Cheng, Keiko Akagi, Manisha Thakuria, Guilherme Rabinowits, Linda C. Wang, David E. Symer, James M. Pipas, Reuben S. Harris, James A. DeCaprio
Software Mentions: 5
Published: over 7 years ago

10.1242/dmm.049044

Comparison of the oncogenomic landscape of canine and feline hemangiosarcoma shows novel parallels with human angiosarcoma
Cited by: 16
Author(s): Kim Wong, Latasha Ludwig, Oscar Krijgsman, David J. Adams, Geoffrey A. Wood, Louise van der Weyden
Software Mentions: 4
Published: over 3 years ago

10.1186/s40246-018-0170-6

Forward and reverse mutations in stages of cancer development
Cited by: 11
Author(s): Taobo Hu, Yogesh Kumar, Shazia Iram, Si Duan, Yang Li, Lei Chen, Jinfei Chen, Rong Yin, Ava Kwong, Gilberto Ka Kit Leung, Wai Kin Mat, Zhenggang Wu, Xi Long, Colin Chan, Si Chen, Peggy Lee, Siu Kin Ng, Timothy Y. C. Ho, Jianfeng Yang, Xueliang Ding, Suk Ying Tsang, Xinrui Zhou, Danhua Zhang, Enbo Zhou, Lin Xu, Wai-sang Poon, Hongyang Wang, Hong Xue
Software Mentions: 4
Published: over 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

10.3390/cancers10120500

Mitochondrial RNA Expression and Single Nucleotide Variants in Association with Clinical Parameters in Primary Breast Cancers
Cited by: 6
Author(s): Marjolein J.A. Weerts, Marcel Smid, John A. Foekens, Stefan Sleijfer, John W.M. Martens
Software Mentions: 4
Published: almost 6 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

10.1186/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/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

10.3390/cancers12051178

The Impact of Whole Genome Data on Therapeutic Decision-Making in Metastatic Prostate Cancer: A Retrospective Analysis
Cited by: 10
Author(s): Megan Crumbaker, Eva Chan, Ting-Ting Gong, Niall M. Corcoran, Weerachai Jaratlerdsiri, Ruth J. Lyons, Anne‐Maree Haynes, Anna Kulidjian, Anton M.F. Kalsbeek, Desiree C. Petersen, Phillip D. Stricker, Christina Jamieson, Peter I. Croucher, Christopher M. Hovens, Anthony M. Joshua, Vanessa M. Hayes
Software Mentions: 3
Published: over 4 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

10.3389/fgene.2020.565341

Multi-Omics Analysis Reveals Novel Subtypes and Driver Genes in Glioblastoma
Cited by: 11
Author(s): Yuan Yang, Qi Pan, Xiang Wang, Yan‐Hui Liu, Li Yu, Qing Mao
Software Mentions: 2
Published: almost 4 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

10.3390/cancers13174376

Whole-Genome Analysis of De Novo Somatic Point Mutations Reveals Novel Mutational Biomarkers in Pancreatic Cancer
Cited by: 9
Author(s): Amin Ghareyazi, Amir Mohseni, Hamed Dashti, Amin Beheshti, Abdollah Dehzangi, Hamid R. Rabiee, Hamid Alinejad‐Rokny
Software Mentions: 2
Published: about 3 years ago

10.1172/JCI121924

Immunogenomic analyses associate immunological alterations with mismatch repair defects in prostate cancer
Cited by: 148
Author(s): Daniel Nava Rodrigues, Pasquale Rescigno, David Liu, Wei Yuan, Suzanne Carreira, Maryou Lambros, George Seed, Joaquín Mateo, Ruth Riisnaes, Stephanie A. Mullane, Claire A. Margolis, Diana Miao, Susana Miranda, David Dolling, Matthew Clarke, Claudia Bertan, Mateus Crespo, Gunther Boysen, Ana Ferreira, Adam Sharp, Ines Figueiredo, Daniel Keliher, Saud H. AlDubayan, Kelly P. Burke, Semini Sumanasuriya, Mariane Fontes, Diletta Bianchini, Zafeiris Zafeiriou, Larissa Sena Teixeira Mendes, Kent W. Mouw, Michael T. Schweizer, Colin C. Pritchard, Stephen J. Salipante, Mary‐Ellen Taplin, Himisha Beltran, Mark A. Rubin, Marcin Cieślik, Dan R. Robinson, E. Heath, Nikolaus Schultz, Joshua Armenia, Wassim Abida, Howard I. Scher, Christopher J. Lord, Alan D. D’Andrea, Charles L. Sawyers, Arul M. Chinnaiyan, Andrea Alimonti, Peter S. Nelson, Charles G. Drake, Eliezer M. Van Allen, Johann S. de Bono
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-018-21844-6

Somatic Mitochondrial DNA Mutations in Diffuse Large B-Cell Lymphoma
Cited by: 4
Author(s): Andy G.X. Zeng, Andy Leung, Angela Brooks‐Wilson
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-017-17162-y

Whole exome sequencing identified sixty-five coding mutations in four neuroblastoma tumors
Cited by: 7
Author(s): Aubrey L. Miller, Patrick L. Garcia, Joseph G. Pressey, Elizabeth A. Beierle, David R. Kelly, David K. Crossman, Richard Daniel, Raymond G. Watts, Stewart F. Cramer, Karina J. Yoon
Software Mentions: 1
Published: almost 7 years ago

10.18632/oncotarget.22321

The ubiquitous ‘cancer mutational signature’ 5 occurs specifically in cancers with deleted <i>FHIT</i> alleles
Cited by: 16
Author(s): Stefano Volinia, Teresa Druck, Carolyn Paisie, Morgan S. Schrock, Kay Huebner
Software Mentions: 1
Published: about 7 years ago

10.3389/fgene.2021.598304

Identification of Potential Driver Genes Based on Multi-Genomic Data in Cervical Cancer
Cited by: 13
Author(s): Yuexun Xu, Hui Luo, Hu Qin, Haiyan Zhu
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-018-38315-7

Establishment, molecular and biological characterization of HCB-514: a novel human cervical cancer cell line
Cited by: 13
Author(s): Marcela Nunes Rosa, Adriane Feijó Evangelista, Letícia Ferro Leal, Cristina Mendes de Oliveira, Viviane Aline Oliveira Silva, Carla Carolina Munari, Fernanda Franco Munari, Graziela de Macêdo Matsushita, Ricardo dos Reis, Carlos Eduardo Mattos da Cunha Andrade, Cristiano de Pádua Souza, Rui Manuel Reis
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-019-54773-z

Somatic mutation signatures in primary liver tumors of workers exposed to ionizing radiation
Cited by: 7
Author(s): David Goerlitz, Jan Blancato, Archana Ramesh, Mohammad Islam, Garrett T. Graham, Valentina Revina, Bhaskar Kallakury, Jay Zeck, Е. В. Кириллова, Christopher A. Loffredo
Software Mentions: 1
Published: almost 5 years ago

10.14814/phy2.14993

Whole genome sequencing of low input circulating cell‐free DNA obtained from normal human subjects
Cited by: 1
Author(s): Julie F. Foley, Brian Elgart, B. Alex Merrick, Dhiral Phadke, Molly E. Cook, Jason Malphurs, Greg Solomon, Ruchir Shah, Michael B. Fessler, Frederick W. Miller, Kevin Gerrish
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-021-81106-w

Investigating the causal role of MRE11A p.E506* in breast and ovarian cancer
Cited by: 5
Author(s): Islam Elkholi, Massimo Di Iorio, Somayyeh Fahiminiya, Suzanna L. Arcand, Hyerim Han, Clara Nogué, Supriya Behl, Nancy Hamel, Sylvie Giroux, Manon de Ladurantaye, Olga Aleynikova, Walter H. Gotlieb, Jean‐François Côté, François Rousseau, Patricia N. Tonin, Diane Provencher, Anne‐Marie Mes‐Masson, Mohammad Reza Akbari, Bárbara Rivera, William D. Foulkes
Software Mentions: 1
Published: almost 4 years ago

10.1093/bioinformatics/btv408

SomaticSignatures: inferring mutational signatures from single-nucleotide variants
Cited by: 250
Author(s): Julian Gehring, Bernd Fischer, Michael Lawrence, Wolfgang Huber
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-018-4858-8

Whole exome sequencing in the rat
Cited by: 5
Author(s): Julie F. Foley, Dhiral Phadke, Owen Hardy, Sara Hardy, Victor F. Miller, Anup Madan, Kellie Howard, Kimberly Kruse, Cara Lord, Sreenivasa Ramaiahgari, Greg Solomon, Ruchir Shah, Arun R. Pandiri, Ronald A. Herbert, Robert C. Sills, B. Alex Merrick
Software Mentions: 1
Published: over 6 years ago

10.3389/fonc.2020.01457

Mutational Landscape of Esophageal Squamous Cell Carcinoma in an Indian Cohort
Cited by: 17
Author(s): Kiran K. Mangalaparthi, Krishna Patel, Aafaque Ahmad Khan, Malini Manoharan, Karunakaran Coral, Sakthivel Murugan, Ravi Gupta, Rohit Gupta, Arati Khanna-Gupta, Amitabha Chaudhuri, Prashant Kumar, Bipin Nair, Rekha V. Kumar, T. S. Keshava Prasad, Aditi Chatterjee, Akhilesh Pandey, Harsha Gowda
Software Mentions: 1
Published: over 4 years ago

10.18632/oncotarget.20515

Genomic profiles of a hepatoblastoma from a patient with Beckwith-Wiedemann syndrome with uniparental disomy on chromosome 11p15 and germline mutation of APC and PALB2
Cited by: 13
Author(s): Shinn Young Kim, Seung‐Hyun Jung, Min Sung Kim, Mi Seon Han, Hyeon-Chun Park, Eun Sun Jung, Sung Hak Lee, Sug Hyung Lee, Yeun‐Jun Chung
Software Mentions: 1
Published: about 7 years ago

Ecosyste.ms: Papers

Projects: bioconductor: SomaticSignatures

Papers Mentioning SomaticSignatures 32