Exploring background mutational processes to decipher cancer genetic heterogeneity
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Anna R. Panchenko | Minghui Li | Igor B. Rogozin | Alexander Goncearenco | Stephanie L. Rager | Qing-Xiang Sang | A. Panchenko | I. Rogozin | Minghui Li | A. Goncearenco | Q. Sang
[1] Steven A. Roberts,et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes , 2013 .
[2] D. Brash. UV Signature Mutations , 2015, Photochemistry and photobiology.
[3] C. Swanton. Intratumor heterogeneity: evolution through space and time. , 2012, Cancer research.
[4] P. Hainaut,et al. On the origin of G --> T transversions in lung cancer. , 2003, Mutation research.
[5] J. Mesirov,et al. The Molecular Signatures Database Hallmark Gene Set Collection , 2015 .
[6] David T. W. Jones,et al. Signatures of mutational processes in human cancer , 2013, Nature.
[7] I. Rogozin,et al. Theoretical analysis of mutation hotspots and their DNA sequence context specificity. , 2003, Mutation research.
[8] Serena Nik-Zainal,et al. Mechanisms underlying mutational signatures in human cancers , 2014, Nature Reviews Genetics.
[9] Mel Greaves,et al. Evolutionary determinants of cancer. , 2015, Cancer discovery.
[10] Nicholas C. Bauer,et al. The current state of eukaryotic DNA base damage and repair , 2015, Nucleic acids research.
[11] M. Lynch. Rate, molecular spectrum, and consequences of human mutation , 2010, Proceedings of the National Academy of Sciences.
[12] A. Børresen-Dale,et al. Mutational Processes Molding the Genomes of 21 Breast Cancers , 2012, Cell.
[13] Shamil R. Sunyaev,et al. Impact of deleterious passenger mutations on cancer progression , 2012, Proceedings of the National Academy of Sciences.
[14] J. Mesirov,et al. The Molecular Signatures Database (MSigDB) hallmark gene set collection. , 2015, Cell systems.
[15] M. Stratton,et al. Mutational signatures: the patterns of somatic mutations hidden in cancer genomes , 2014, Current opinion in genetics & development.
[16] Hanlee P. Ji,et al. Pan-cancer analysis of the extent and consequences of intratumor heterogeneity , 2015, Nature Medicine.
[17] A. Panchenko,et al. Annotating Mutational Effects on Proteins and Protein Interactions: Designing Novel and Revisiting Existing Protocols. , 2017, Methods in molecular biology.
[18] Joshua M. Stuart,et al. The Cancer Genome Atlas Pan-Cancer analysis project , 2013, Nature Genetics.
[19] Dietrich Lehmann,et al. Nonsmooth nonnegative matrix factorization (nsNMF) , 2006, IEEE Transactions on Pattern Analysis and Machine Intelligence.
[20] Serena Nik-Zainal,et al. A mutational signature in gastric cancer suggests therapeutic strategies , 2015, Nature Communications.
[21] Xavier Castells,et al. MutSpec: a Galaxy toolbox for streamlined analyses of somatic mutation spectra in human and mouse cancer genomes , 2016, BMC Bioinformatics.
[22] B. Vogelstein,et al. Variation in cancer risk among tissues can be explained by the number of stem cell divisions , 2015, Science.
[23] Faraz Hach,et al. Spatial genomic heterogeneity within localized, multifocal prostate cancer , 2015, Nature Genetics.
[24] Gregory D. Schuler,et al. Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.
[25] A. Morris,et al. Cancer etiology. Variation in cancer risk among tissues can be explained by the number of stem cell divisions , 2015, BDJ.
[26] Morris Swertz,et al. Genome-wide patterns and properties of de novo mutations in humans , 2015, Nature Genetics.
[27] Bin Tean Teh,et al. Mutation signatures implicate aristolochic acid in bladder cancer development , 2015, Genome Medicine.
[28] A. Agrawal,et al. Low Genetic Quality Alters Key Dimensions of the Mutational Spectrum , 2016, PLoS biology.
[29] Subhajyoti De,et al. The landscape of somatic mutations in protein coding genes in apparently benign human tissues carries signatures of relaxed purifying selection , 2016, Nucleic acids research.
[30] B. Taylor,et al. deconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution , 2016, Genome Biology.
[31] L. Alexandrov,et al. Understanding mutagenesis through delineation of mutational signatures in human cancer. , 2016, Carcinogenesis.
[32] Ke Ma,et al. Balancing Protein Stability and Activity in Cancer: A New Approach for Identifying Driver Mutations Affecting CBL Ubiquitin Ligase Activation. , 2016, Cancer research.
[33] Steven A. Roberts,et al. An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers , 2013, Nature Genetics.
[34] N. Socci,et al. Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity , 2015, Nature Biotechnology.
[35] 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.
[36] Evan Bolton,et al. Database resources of the National Center for Biotechnology Information , 2017, Nucleic Acids Res..
[37] Benjamin J. Raphael,et al. Mutational landscape and significance across 12 major cancer types , 2013, Nature.
[38] Mingming Jia,et al. COSMIC: exploring the world's knowledge of somatic mutations in human cancer , 2014, Nucleic Acids Res..
[39] Leyla Isik,et al. Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations. , 2009, Cancer research.
[40] L. Alexandrov,et al. Base changes in tumour DNA have the power to reveal the causes and evolution of cancer , 2016, Oncogene.
[41] Julian Gehring,et al. SomaticSignatures: inferring mutational signatures from single-nucleotide variants , 2014, bioRxiv.
[42] D. Haussler,et al. Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. , 2003, Molecular biology and evolution.
[43] Rainer Lehtonen,et al. Background mutation frequency in microsatellite-unstable colorectal cancer. , 2007, Cancer research.
[44] Zhongming Zhao,et al. Methylation-dependent transition rates are dependent on local sequence lengths and genomic regions. , 2007, Molecular biology and evolution.
[45] Jessica Zucman-Rossi,et al. Exome sequencing of hepatocellular carcinomas identifies new mutational signatures and potential therapeutic targets , 2015, Nature Genetics.
[46] M. Olivier,et al. Impact of mutant p53 functional properties on TP53 mutation patterns and tumor phenotype: lessons from recent developments in the IARC TP53 database , 2007, Human mutation.
[47] M. Lynch,et al. Asymmetric Context-Dependent Mutation Patterns Revealed through Mutation-Accumulation Experiments. , 2015, Molecular biology and evolution.
[48] Luciano Milanesi,et al. Computational analysis of mutation spectra , 2003, Briefings Bioinform..
[49] A. Børresen-Dale,et al. TP53 mutations in human cancers: functional selection and impact on cancer prognosis and outcomes , 2007, Oncogene.
[50] William H. Bisson,et al. Causes of genome instability: the effect of low dose chemical exposures in modern society. , 2015, Carcinogenesis.
[51] G. Pfeifer,et al. Mutational spectra of human cancer , 2009, Human Genetics.
[52] Gary D Bader,et al. Computational approaches to identify functional genetic variants in cancer genomes , 2013, Nature Methods.
[53] Subhajyoti De,et al. Activation induced deaminase mutational signature overlaps with CpG methylation sites in follicular lymphoma and other cancers , 2016, Scientific Reports.
[54] M. Stratton,et al. Deciphering Signatures of Mutational Processes Operative in Human Cancer , 2013, Cell reports.