Deciphering oncogenic drivers: from single genes to integrated pathways
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[1] Steven A. Roberts,et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes , 2013 .
[2] Christopher A. Miller,et al. Discovering functional modules by identifying recurrent and mutually exclusive mutational patterns in tumors , 2011, BMC Medical Genomics.
[3] Steven A. Roberts,et al. Mutational heterogeneity in cancer and the search for new cancer genes , 2014 .
[4] Alfonso Valencia,et al. EnrichNet: network-based gene set enrichment analysis , 2012, Bioinform..
[5] Eli Upfal,et al. Algorithms for Detecting Significantly Mutated Pathways in Cancer , 2010, RECOMB.
[6] Trevor J Pugh,et al. Initial genome sequencing and analysis of multiple myeloma , 2011, Nature.
[7] David L. Masica,et al. Correlation of somatic mutation and expression identifies genes important in human glioblastoma progression and survival. , 2011, Cancer research.
[8] Michael Krawczak,et al. Where genotype is not predictive of phenotype: towards an understanding of the molecular basis of reduced penetrance in human inherited disease , 2013, Human Genetics.
[9] Stefan Fröhling,et al. Identification of driver and passenger mutations of FLT3 by high-throughput DNA sequence analysis and functional assessment of candidate alleles. , 2007, Cancer cell.
[10] F. McCormick,et al. Signalling networks that cause cancer. , 1999, Trends in cell biology.
[11] A. Valencia,et al. From cancer genomes to cancer models: bridging the gaps , 2009, EMBO reports.
[12] A. Gonzalez-Perez,et al. Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation , 2012, Genome Medicine.
[13] David Haussler,et al. Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM , 2010, Bioinform..
[14] Eli Upfal,et al. De Novo Discovery of Mutated Driver Pathways in Cancer , 2011, RECOMB.
[15] D. Busam,et al. An Integrated Genomic Analysis of Human Glioblastoma Multiforme , 2008, Science.
[16] Leyla Isik,et al. Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations. , 2009, Cancer research.
[17] Brian H. Dunford-Shore,et al. Somatic mutations affect key pathways in lung adenocarcinoma , 2008, Nature.
[18] D. Hanahan,et al. Hallmarks of Cancer: The Next Generation , 2011, Cell.
[19] Hiroyuki Ogata,et al. KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..
[20] P. Ng,et al. Predicting the effects of frameshifting indels , 2012, Genome Biology.
[21] Yuedong Yang,et al. DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels , 2013, Genome Biology.
[22] K. Kinzler,et al. Cancer genes and the pathways they control , 2004, Nature Medicine.
[23] Gary D Bader,et al. Computational approaches to identify functional genetic variants in cancer genomes , 2013, Nature Methods.
[24] J. Ptak,et al. High Frequency of Mutations of the PIK3CA Gene in Human Cancers , 2004, Science.
[25] Joshua F. McMichael,et al. Genome Remodeling in a Basal-like Breast Cancer Metastasis and Xenograft , 2010, Nature.
[26] Atul J. Butte,et al. Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges , 2012, PLoS Comput. Biol..
[27] C. Sander,et al. Automated Network Analysis Identifies Core Pathways in Glioblastoma , 2010, PloS one.
[28] P. Stenson,et al. The Human Gene Mutation Database: 2008 update , 2009, Genome Medicine.
[29] David Haussler,et al. Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE) , 2013, Bioinform..
[30] Matthew B. Callaway,et al. MuSiC: Identifying mutational significance in cancer genomes , 2012, Genome research.
[31] Joe W. Gray,et al. Translating insights from the cancer genome into clinical practice , 2008, Nature.
[32] Gary D Bader,et al. Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers , 2013 .
[33] Bairong Shen,et al. Post genome-wide association studies functional characterization of prostate cancer risk loci , 2013, BMC Genomics.
[34] S. Henikoff,et al. Predicting deleterious amino acid substitutions. , 2001, Genome research.
[35] Anaïs Mottaz,et al. Bioinformatics Applications Note Databases and Ontologies Easy Retrieval of Single Amino-acid Polymorphisms and Phenotype Information Using Swissvar , 2022 .
[36] C. Sander,et al. Mutual exclusivity analysis identifies oncogenic network modules. , 2012, Genome research.
[37] P. Ng,et al. SIFT Indel: Predictions for the Functional Effects of Amino Acid Insertions/Deletions in Proteins , 2013, PloS one.
[38] B. Peters,et al. Distinguishing cancer-associated missense mutations from common polymorphisms. , 2007, Cancer research.
[39] G. Parmigiani,et al. Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses , 2008, Science.
[40] P. Bork,et al. A method and server for predicting damaging missense mutations , 2010, Nature Methods.
[41] C. Sander,et al. Predicting the functional impact of protein mutations: application to cancer genomics , 2011, Nucleic acids research.
[42] Benjamin J. Raphael,et al. Integrated Genomic Analyses of Ovarian Carcinoma , 2011, Nature.
[43] Shi-Hua Zhang,et al. Efficient methods for identifying mutated driver pathways in cancer , 2012, Bioinform..
[44] Kenneth H. Buetow,et al. PID: the Pathway Interaction Database , 2008, Nucleic Acids Res..
[45] Tao Xie,et al. Inferring causal genomic alterations in breast cancer using gene expression data , 2011, BMC Systems Biology.
[46] Kenneth H. Buetow,et al. Large-scale analysis of non-synonymous coding region single nucleotide polymorphisms , 2004, Bioinform..
[47] Yin Li,et al. Identifying novel glioma associated pathways based on systems biology level meta-analysis , 2013, BMC Systems Biology.
[48] N. Schork,et al. Identification of rare cancer driver mutations by network reconstruction. , 2009, Genome research.
[49] D. Hanahan,et al. The Hallmarks of Cancer , 2000, Cell.
[50] Laurent Farinelli,et al. Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes. , 2010, Genome research.
[51] C. Yeang,et al. Combinatorial patterns of somatic gene mutations in cancer , 2008, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.
[52] P. A. Futreal,et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. , 2012, The New England journal of medicine.
[53] A. McKenna,et al. The Mutational Landscape of Head and Neck Squamous Cell Carcinoma , 2011, Science.
[54] Deanna M. Church,et al. ClinVar: public archive of relationships among sequence variation and human phenotype , 2013, Nucleic Acids Res..
[55] J. Hicks,et al. Insight into the heterogeneity of breast cancer through next-generation sequencing. , 2011, The Journal of clinical investigation.
[56] Jae K. Lee,et al. Utilizing the molecular gateway: the path to personalized cancer management. , 2009, Clinical chemistry.
[57] A. Nicholson,et al. Mutations of the BRAF gene in human cancer , 2002, Nature.
[58] R. Hruban,et al. Prioritization of driver mutations in pancreatic cancer using cancer-specific high-throughput annotation of somatic mutations (CHASM) , 2010, Cancer biology & therapy.
[59] Dana Pe'er,et al. JISTIC: Identification of Significant Targets in Cancer , 2010, BMC Bioinformatics.
[60] M. Stratton,et al. Statistical Analysis of Pathogenicity of Somatic Mutations in Cancer , 2006, Genetics.
[61] E. Lander,et al. Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma , 2007, Proceedings of the National Academy of Sciences.
[62] Christopher D. Brown,et al. Rapid growth of a hepatocellular carcinoma and the driving mutations revealed by cell-population genetic analysis of whole-genome data , 2011, Proceedings of the National Academy of Sciences.
[63] Elaine R. Mardis,et al. A decade’s perspective on DNA sequencing technology , 2011, Nature.
[64] Benjamin J. Raphael,et al. Identifying driver mutations in sequenced cancer genomes: computational approaches to enable precision medicine , 2014, Genome Medicine.
[65] Xiaobo Zhou,et al. A novel missense-mutation-related feature extraction scheme for 'driver' mutation identification , 2012, Bioinform..
[66] Kei-Hoi Cheung,et al. A graph theoretic approach to utilizing protein structure to identify non-random somatic mutations , 2013, BMC Bioinformatics.
[67] Derek Y. Chiang,et al. The landscape of somatic copy-number alteration across human cancers , 2010, Nature.
[68] Ling Lin,et al. PathScan: a tool for discerning mutational significance in groups of putative cancer genes , 2011, Bioinform..
[69] Alan F. Scott,et al. McKusick's Online Mendelian Inheritance in Man (OMIM®) , 2008, Nucleic Acids Res..
[70] Jiajia Chen,et al. Identification of novel microRNA regulatory pathways associated with heterogeneous prostate cancer , 2013, BMC Systems Biology.
[71] Lincoln Stein,et al. Reactome: a knowledgebase of biological pathways , 2004, Nucleic Acids Res..
[72] Joshua M. Korn,et al. Comprehensive genomic characterization defines human glioblastoma genes and core pathways , 2008, Nature.
[73] Yan Zhang,et al. CanPredict: a computational tool for predicting cancer-associated missense mutations , 2007, Nucleic Acids Res..
[74] A. Sparks,et al. The Genomic Landscapes of Human Breast and Colorectal Cancers , 2007, Science.
[75] Allan Balmain,et al. Mutually exclusive mutations of the Pten and ras pathways in skin tumor progression. , 2004, Genes & development.
[76] J. Tchinda,et al. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. , 2006, Science.
[77] G. Parmigiani,et al. The Consensus Coding Sequences of Human Breast and Colorectal Cancers , 2006, Science.
[78] G. Getz,et al. GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers , 2011, Genome Biology.
[79] Roded Sharan,et al. Simultaneous Identification of Multiple Driver Pathways in Cancer , 2013, PLoS Comput. Biol..
[80] J. Miller,et al. Predicting the Functional Effect of Amino Acid Substitutions and Indels , 2012, PloS one.
[81] G. Parmigiani,et al. Integrated analysis of homozygous deletions, focal amplifications, and sequence alterations in breast and colorectal cancers , 2008, Proceedings of the National Academy of Sciences.
[82] N. Schork,et al. Prediction of cancer driver mutations in protein kinases. , 2008, Cancer research.
[83] D. Pe’er,et al. An Integrated Approach to Uncover Drivers of Cancer , 2010, Cell.