Cancer subtype identification using somatic mutation data

[1]  Maximillian G. Marin,et al.  A Massively Parallel Fluorescence Assay to Characterize the Effects of Synonymous Mutations on TP53 Expression , 2017, Molecular Cancer Research.

[2]  Jean-Philippe Vert,et al.  NetNorM: Capturing cancer-relevant information in somatic exome mutation data with gene networks for cancer stratification and prognosis , 2017, PLoS Comput. Biol..

[3]  Jun Li,et al.  Widespread position-specific conservation of synonymous rare codons within coding sequences , 2017, PLoS Comput. Biol..

[4]  S. Rafii,et al.  A proangiogenic signaling axis in myeloid cells promotes malignant progression of glioma , 2017, The Journal of clinical investigation.

[5]  AACR Project GENIE: Powering Precision Medicine through an International Consortium. , 2017, Cancer discovery.

[6]  C. Stratakis,et al.  PKA inhibits WNT signalling in adrenal cortex zonation and prevents malignant tumour development , 2016, Nature Communications.

[7]  Steven J. M. Jones,et al.  Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma , 2016, Cell.

[8]  Benjamin J Raphael,et al.  Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma. , 2016, Cancer cell.

[9]  M. Fassnacht,et al.  Notch1 pathway in adrenocortical carcinomas: correlations with clinical outcome. , 2015, Endocrine-related cancer.

[10]  Gary D Bader,et al.  Pathway and network analysis of cancer genomes , 2015, Nature Methods.

[11]  T. Haferlach,et al.  Downregulation of the Wnt inhibitor CXXC5 predicts a better prognosis in acute myeloid leukemia. , 2015, Blood.

[12]  Michael P. Schroeder,et al.  In silico prescription of anticancer drugs to cohorts of 28 tumor types reveals targeting opportunities. , 2015, Cancer cell.

[13]  Mingming Jia,et al.  COSMIC: exploring the world's knowledge of somatic mutations in human cancer , 2014, Nucleic Acids Res..

[14]  Benjamin J. Raphael,et al.  Pan-Cancer Network Analysis Identifies Combinations of Rare Somatic Mutations across Pathways and Protein Complexes , 2014, Nature Genetics.

[15]  M. Samur.  RTCGAToolbox: A New Tool for Exporting TCGA Firehose Data , 2014, PloS one.

[16]  Benjamin J. Raphael,et al.  Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin , 2014, Cell.

[17]  J. Valcárcel,et al.  Synonymous Mutations Frequently Act as Driver Mutations in Human Cancers , 2014, Cell.

[18]  Michael P. Schroeder,et al.  IntOGen-mutations identifies cancer drivers across tumor types , 2013, Nature Methods.

[19]  Andrew M. Gross,et al.  Network-based stratification of tumor mutations , 2013, Nature Methods.

[20]  Steven A. Roberts,et al.  Mutational heterogeneity in cancer and the search for new cancer genes , 2014 .

[21]  Man Tsuey Tse.  Cancer: Activating Notch ameliorates AML , 2013, Nature Reviews Drug Discovery.

[22]  Steven J. M. Jones,et al.  Comprehensive molecular portraits of human breast tumours , 2013 .

[23]  Steven A. Roberts,et al.  Mutational heterogeneity in cancer and the search for new cancer-associated genes , 2013 .

[24]  Peter Bouwman,et al.  The effects of deregulated DNA damage signalling on cancer chemotherapy response and resistance , 2012, Nature Reviews Cancer.

[25]  Steven J. M. Jones,et al.  Comprehensive molecular portraits of human breast tumors , 2012, Nature.

[26]  John Quackenbush,et al.  A three-gene model to robustly identify breast cancer molecular subtypes. , 2012, Journal of the National Cancer Institute.

[27]  Soniya priyadharishni,et al.  Network-based Identification of Novel Cancer Genes , 2012 .

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

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

[30]  R. Wilson,et al.  Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma. , 2010, Cancer cell.

[31]  Eli Upfal,et al.  Algorithms for Detecting Significantly Mutated Pathways in Cancer , 2010, RECOMB.

[32]  S. Gabriel,et al.  Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. , 2010, Cancer cell.

[33]  E. Sonnhammer,et al.  Network-based Identification of Novel Cancer Genes , 2009, Molecular & Cellular Proteomics.

[34]  Paul A Clemons,et al.  The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease , 2006, Science.

[35]  G. Collins.  The next generation. , 2006, Scientific American.

[36]  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.

[37]  Y. Barde,et al.  Neurotrophins: key regulators of cell fate and cell shape in the vertebrate nervous system. , 2000, Genes & development.

[38]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .