Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation

[1]  Mauno Vihinen,et al.  PON‐P: Integrated predictor for pathogenicity of missense variants , 2012, Human mutation.

[2]  A. Børresen-Dale,et al.  The landscape of cancer genes and mutational processes in breast cancer , 2012, Nature.

[3]  A. Kohlmann,et al.  Landscape of TET2 mutations in acute myeloid leukemia , 2012, Leukemia.

[4]  Jimmy Lin,et al.  Delving into somatic variation in sporadic melanoma , 2012, Pigment cell & melanoma research.

[5]  David T. W. Jones,et al.  Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma , 2012, Nature.

[6]  C. Sander,et al.  Mutual exclusivity analysis identifies oncogenic network modules. , 2012, Genome research.

[7]  David T. W. Jones,et al.  Genome Sequencing of Pediatric Medulloblastoma Links Catastrophic DNA Rearrangements with TP53 Mutations , 2012, Cell.

[8]  E. Giné,et al.  Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia , 2011, Nature Genetics.

[9]  L. Pasqualucci,et al.  Mutations of the SF3B1 splicing factor in chronic lymphocytic leukemia: association with progression and fludarabine-refractoriness. , 2011, Blood.

[10]  Syed Haider,et al.  International Cancer Genome Consortium Data Portal—a one-stop shop for cancer genomics data , 2011, Database J. Biol. Databases Curation.

[11]  Joel S Parker,et al.  Deep sequencing of gastric carcinoma reveals somatic mutations relevant to personalized medicine , 2011, Journal of Translational Medicine.

[12]  Juliane C. Dohm,et al.  Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia , 2011, Nature.

[13]  C. Sander,et al.  Predicting the functional impact of protein mutations: application to cancer genomics , 2011, Nucleic acids research.

[14]  Hannah Carter,et al.  CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer , 2011, Bioinform..

[15]  Benjamin J. Raphael,et al.  Integrated Genomic Analyses of Ovarian Carcinoma , 2011, Nature.

[16]  A. Gonzalez-Perez,et al.  Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel. , 2011, American journal of human genetics.

[17]  M. Vihinen,et al.  Performance of mutation pathogenicity prediction methods on missense variants , 2011, Human mutation.

[18]  D. Hanahan,et al.  Hallmarks of Cancer: The Next Generation , 2011, Cell.

[19]  Mary Goldman,et al.  The UCSC Genome Browser database: update 2011 , 2010, Nucleic Acids Res..

[20]  L. Holm,et al.  The Pfam protein families database , 2005, Nucleic Acids Res..

[21]  S. Gabriel,et al.  Advances in understanding cancer genomes through second-generation sequencing , 2010, Nature Reviews Genetics.

[22]  D. Altshuler,et al.  A map of human genome variation from population-scale sequencing , 2010, Nature.

[23]  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.

[24]  Daniel Rios,et al.  Bioinformatics Applications Note Databases and Ontologies Deriving the Consequences of Genomic Variants with the Ensembl Api and Snp Effect Predictor , 2022 .

[25]  P. Bork,et al.  A method and server for predicting damaging missense mutations , 2010, Nature Methods.

[26]  Gary D Bader,et al.  International network of cancer genome projects , 2010, Nature.

[27]  klaguia International Network of Cancer Genome Projects , 2010 .

[28]  Laurent Gil,et al.  Ensembl variation resources , 2010, BMC Genomics.

[29]  Leyla Isik,et al.  Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations. , 2009, Cancer research.

[30]  Andrew M. Jenkinson,et al.  Ensembl 2009 , 2008, Nucleic Acids Res..

[31]  S. Henikoff,et al.  Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm , 2009, Nature Protocols.

[32]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[33]  Brian H. Dunford-Shore,et al.  Somatic mutations affect key pathways in lung adenocarcinoma , 2008, Nature.

[34]  G. Parmigiani,et al.  Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses , 2008, Science.

[35]  D. Busam,et al.  An Integrated Genomic Analysis of Human Glioblastoma Multiforme , 2008, Science.

[36]  Joshua M. Korn,et al.  Comprehensive genomic characterization defines human glioblastoma genes and core pathways , 2008, Nature.

[37]  Desmond G. Higgins,et al.  Distinct Patterns in the Regulation and Evolution of Human Cancer Genes , 2008, Silico Biol..

[38]  Daniel Bayer,et al.  SNPtoGO: characterizing SNPs by enriched GO terms , 2008, Bioinform..

[39]  A. Sparks,et al.  The Genomic Landscapes of Human Breast and Colorectal Cancers , 2007, Science.

[40]  G. Parmigiani,et al.  A multidimensional analysis of genes mutated in breast and colorectal cancers. , 2007, Genome research.

[41]  Yan Zhang,et al.  CanPredict: a computational tool for predicting cancer-associated missense mutations , 2007, Nucleic Acids Res..

[42]  Pedro Larrañaga,et al.  A partially supervised classification approach to dominant and recessive human disease gene prediction , 2007, Comput. Methods Programs Biomed..

[43]  David Haussler,et al.  The UCSC genome browser database: update 2007 , 2006, Nucleic Acids Res..

[44]  G. Parmigiani,et al.  The Consensus Coding Sequences of Human Breast and Colorectal Cancers , 2006, Science.

[45]  Joost Schymkowitz,et al.  Bioinformatics Applications Note Snpeffect V2.0: a New Step in Investigating the Molecular Phenotypic Effects of Human Non-synonymous Snps , 2022 .

[46]  Núria López-Bigas,et al.  Differences in the evolutionary history of disease genes affected by dominant or recessive mutations , 2006, BMC Genomics.

[47]  Christos A. Ouzounis,et al.  Highly consistent patterns for inherited human diseases at the molecular level , 2006, Bioinform..

[48]  Peng Yue,et al.  SNPs3D: Candidate gene and SNP selection for association studies , 2006, BMC Bioinformatics.

[49]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[50]  T. Hubbard,et al.  A census of human cancer genes , 2004, Nature Reviews Cancer.

[51]  Steven Henikoff,et al.  SIFT: predicting amino acid changes that affect protein function , 2003, Nucleic Acids Res..

[52]  Alan F. Scott,et al.  Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders , 2002, Nucleic Acids Res..

[53]  P. Bork,et al.  Human non-synonymous SNPs: server and survey. , 2002, Nucleic acids research.

[54]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.