De novo mutational signature discovery in tumor genomes using SparseSignatures
暂无分享,去创建一个
Robert Tibshirani | Daniele Ramazzotti | Arend Sidow | Avantika Lal | R. Tibshirani | A. Sidow | D. Ramazzotti | Keli Liu | Avantika Lal | Keli Liu | Daniele Ramazzotti
[1] S. Lindsay,et al. Signatures of Mutational Processes in Human DNA Evolution , 2021, bioRxiv.
[2] M. Stratton,et al. The mutational landscape of human somatic and germline cells , 2020, Nature.
[3] A. Balmain,et al. The mutational signature profile of known and suspected human carcinogens in mice , 2020, Nature genetics.
[4] M. Stratton,et al. Characterizing Mutational Signatures in Human Cancer Cell Lines Reveals Episodic APOBEC Mutagenesis , 2019, Cell.
[5] Ville Mustonen,et al. The repertoire of mutational signatures in human cancer , 2018, Nature.
[6] Peter J. Campbell,et al. Somatic mutant clones colonize the human esophagus with age , 2018, Science.
[7] Z. Weng,et al. Comprehensive genomic characterization of breast tumors with BRCA1 and BRCA2 mutations , 2018, BMC Medical Genomics.
[8] Adrian Baez-Ortega,et al. sigfit: flexible Bayesian inference of mutational signatures , 2018, bioRxiv.
[9] S. Shariat,et al. Association of Smoking Status With Recurrence, Metastasis, and Mortality Among Patients With Localized Prostate Cancer Undergoing Prostatectomy or Radiotherapy: A Systematic Review and Meta-analysis , 2018, JAMA oncology.
[10] M. Jia,et al. APOBEC3B and APOBEC mutational signature as potential predictive markers for immunotherapy response in non-small cell lung cancer , 2018, Oncogene.
[11] Daniele Ramazzotti,et al. Multi-omic tumor data reveal diversity of molecular mechanisms that correlate with survival , 2018, Nature Communications.
[12] Junjie Zhu,et al. SIMLR: A Tool for Large‐Scale Genomic Analyses by Multi‐Kernel Learning , 2018, Proteomics.
[13] Mary Goldman,et al. Online resources for PCAWG data exploration, visualization, and discovery , 2017 .
[14] Lei Zhang,et al. Differences between germline and somatic mutation rates in humans and mice , 2017, Nature Communications.
[15] Anna R. Panchenko,et al. Exploring background mutational processes to decipher cancer genetic heterogeneity , 2017, Nucleic Acids Res..
[16] Heidi Ledford. DNA typos to blame for most cancer mutations , 2017, Nature.
[17] J. Asara,et al. Chromatin association of XRCC5/6 in the absence of DNA damage depends on the XPE gene product DDB2 , 2017, Molecular biology of the cell.
[18] Bo Wang,et al. Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning , 2016, Nature Methods.
[19] Rafael Rosales,et al. signeR: an empirical Bayesian approach to mutational signature discovery , 2017, Bioinform..
[20] Hans Clevers,et al. Tissue-specific mutation accumulation in human adult stem cells during life , 2016, Nature.
[21] M. Stratton,et al. Mutational signatures associated with tobacco smoking in human cancer , 2016, Science.
[22] David C. Jones,et al. Landscape of somatic mutations in 560 breast cancer whole genome sequences , 2016, Nature.
[23] B. Taylor,et al. deconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution , 2016, Genome Biology.
[24] Eve Shinbrot,et al. Mutation signatures reveal biological processes in human cancer , 2016, bioRxiv.
[25] Arthur Wuster,et al. Timing, rates and spectra of human germline mutation , 2015, Nature Genetics.
[26] C. Tyler-Smith,et al. Ancient DNA and the rewriting of human history: be sparing with Occam’s razor , 2016, Genome Biology.
[27] M. Stratton,et al. Clock-like mutational processes in human somatic cells , 2015, Nature Genetics.
[28] M. Stratton,et al. The genome as a record of environmental exposure , 2015, Mutagenesis.
[29] M. Stephens,et al. A Simple Model-Based Approach to Inferring and Visualizing Cancer Mutation Signatures , 2015, bioRxiv.
[30] Jessica Zucman-Rossi,et al. Exome sequencing of hepatocellular carcinomas identifies new mutational signatures and potential therapeutic targets , 2015, Nature Genetics.
[31] Julian Gehring,et al. SomaticSignatures: inferring mutational signatures from single-nucleotide variants , 2014, bioRxiv.
[32] D. Brash. UV Signature Mutations , 2015, Photochemistry and photobiology.
[33] M. Puigt,et al. Non-negative Matrix Factorization under equality constraints—a study of industrial source identification , 2014 .
[34] Serena Nik-Zainal,et al. Mechanisms underlying mutational signatures in human cancers , 2014, Nature Reviews Genetics.
[35] G. Parmigiani,et al. Heterogeneity of genomic evolution and mutational profiles in multiple myeloma , 2014, Nature Communications.
[36] David T. W. Jones,et al. Signatures of mutational processes in human cancer , 2013, Nature.
[37] P. Campbell,et al. EMu: probabilistic inference of mutational processes and their localization in the cancer genome , 2013, Genome Biology.
[38] K. Kinzler,et al. Cancer Genome Landscapes , 2013, Science.
[39] Peter W. Laird,et al. Interplay between the Cancer Genome and Epigenome , 2013, Cell.
[40] A. McKenna,et al. Exome and whole genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity , 2013, Nature Genetics.
[41] M. Stratton,et al. Deciphering Signatures of Mutational Processes Operative in Human Cancer , 2013, Cell reports.
[42] Vincent Y. F. Tan,et al. Automatic Relevance Determination in Nonnegative Matrix Factorization with the /spl beta/-Divergence , 2011, IEEE Transactions on Pattern Analysis and Machine Intelligence.
[43] Robert Tibshirani,et al. Spectral Regularization Algorithms for Learning Large Incomplete Matrices , 2010, J. Mach. Learn. Res..
[44] Trevor Hastie,et al. Regularization Paths for Generalized Linear Models via Coordinate Descent. , 2010, Journal of statistical software.
[45] Renaud Gaujoux,et al. A flexible R package for nonnegative matrix factorization , 2010, BMC Bioinformatics.
[46] Patrick O. Perry,et al. Bi-cross-validation of the SVD and the nonnegative matrix factorization , 2009, 0908.2062.
[47] Hyunsoo Kim,et al. Sparse Non-negative Matrix Factorizations via Alternating Non-negativity-constrained Least Squares , 2006 .
[48] Dietrich Lehmann,et al. Nonsmooth nonnegative matrix factorization (nsNMF) , 2006, IEEE Transactions on Pattern Analysis and Machine Intelligence.
[49] H. Zou,et al. Regularization and variable selection via the elastic net , 2005 .
[50] Pablo Tamayo,et al. Metagenes and molecular pattern discovery using matrix factorization , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[51] P. Green,et al. Transcription-associated mutational asymmetry in mammalian evolution , 2003, Nature Genetics.
[52] N. Tretyakova,et al. Tobacco smoke carcinogens, DNA damage and p53 mutations in smoking-associated cancers , 2002, Oncogene.
[53] J. Essigmann,et al. The chemistry and biology of aflatoxin B(1): from mutational spectrometry to carcinogenesis. , 2001, Carcinogenesis.
[54] P. Boffetta,et al. Risk of childhood cancer and adult lung cancer after childhood exposure to passive smoke: A meta-analysis. , 1999, Environmental health perspectives.
[55] R. Tibshirani. Regression Shrinkage and Selection via the Lasso , 1996 .