The Consensus Molecular Subtypes of Colorectal Cancer

[1]  S. Rigatti.  Random Forest. , 2017, Journal of insurance medicine.

[2]  B. Vogelstein,et al.  PD-1 blockade in tumors with mismatch repair deficiency. , 2015, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[3]  James Stephen Marron,et al.  Distance‐weighted discrimination , 2015 .

[4]  D. Sargent,et al.  Molecular markers identify subtypes of stage III colon cancer associated with patient outcomes. , 2015, Gastroenterology.

[5]  K. Kinzler,et al.  The vigorous immune microenvironment of microsatellite instable colon cancer is balanced by multiple counter-inhibitory checkpoints , 2015, Journal of Immunotherapy for Cancer.

[6]  M. Esteller,et al.  A comprehensive DNA methylation profile of epithelial-to-mesenchymal transition. , 2014, Cancer research.

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

[8]  D. Dill,et al.  MYC through miR-17-92 suppresses specific target genes to maintain survival, autonomous proliferation, and a neoplastic state. , 2014, Cancer cell.

[9]  Steven J. M. Jones,et al.  Comprehensive molecular characterization of gastric adenocarcinoma , 2014, Nature.

[10]  Jeffrey R. Whiteaker,et al.  Proteogenomic characterization of human colon and rectal cancer , 2014, Nature.

[11]  B. Jiang,et al.  MiR-143 acts as a tumor suppressor by targeting N-RAS and enhances temozolomide-induced apoptosis in glioma , 2014, OncoTarget.

[12]  M. Broggini,et al.  Capturing the metabolomic diversity of KRAS mutants in non-small-cell lung cancer cells , 2014, Oncotarget.

[13]  D. Bentrem,et al.  β-Catenin Promotes Colitis and Colon Cancer Through Imprinting of Proinflammatory Properties in T Cells , 2014, Science Translational Medicine.

[14]  Andreas Schlicker,et al.  Colorectal cancer intrinsic subtypes predict chemotherapy benefit, deficient mismatch repair and epithelial-to-mesenchymal transition , 2013, International journal of cancer.

[15]  G. Getz,et al.  Inferring tumour purity and stromal and immune cell admixture from expression data , 2013, Nature Communications.

[16]  Gary D Bader,et al.  Comprehensive identification of mutational cancer driver genes across 12 tumor types , 2013, Scientific Reports.

[17]  M. Delorenzi,et al.  Context-dependent interpretation of the prognostic value of BRAF and KRAS mutations in colorectal cancer , 2013, BMC Cancer.

[18]  Bin Tean Teh,et al.  Identification of molecular subtypes of gastric cancer with different responses to PI3-kinase inhibitors and 5-fluorouracil. , 2013, Gastroenterology.

[19]  Sabine Tejpar,et al.  Gene expression patterns unveil a new level of molecular heterogeneity in colorectal cancer , 2013, The Journal of pathology.

[20]  Benjamin Haibe-Kains,et al.  CD4⁺ follicular helper T cell infiltration predicts breast cancer survival. , 2013, The Journal of clinical investigation.

[21]  F. Marincola,et al.  Molecular signatures mostly associated with NK cells are predictive of relapse free survival in breast cancer patients , 2013, Journal of Translational Medicine.

[22]  E. White,et al.  Hypoxic and Ras-transformed cells support growth by scavenging unsaturated fatty acids from lysophospholipids , 2013, Proceedings of the National Academy of Sciences.

[23]  Jeffrey J Meyer,et al.  Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature 2012. (5) , 2013 .

[24]  Mira Ayadi,et al.  Gene Expression Classification of Colon Cancer into Molecular Subtypes: Characterization, Validation, and Prognostic Value , 2013, PLoS medicine.

[25]  Florian Markowetz,et al.  Poor-prognosis colon cancer is defined by a molecularly distinct subtype and develops from serrated precursor lesions , 2013, Nature Medicine.

[26]  Lewis C Cantley,et al.  A colorectal cancer classification system that associates cellular phenotype and responses to therapy , 2013, Nature Medicine.

[27]  John M. Asara,et al.  Glutamine supports pancreatic cancer growth through a Kras-regulated metabolic pathway , 2013, Nature.

[28]  Jared S. Murray,et al.  Bayesian Gaussian Copula Factor Models for Mixed Data , 2011, Journal of the American Statistical Association.

[29]  G. Orphanides,et al.  Subtypes of primary colorectal tumors correlate with response to targeted treatment in colorectal cell lines , 2012, BMC Medical Genomics.

[30]  Sabine Tejpar,et al.  A robust genomic signature for the detection of colorectal cancer patients with microsatellite instability phenotype and high mutation frequency# , 2012, The Journal of pathology.

[31]  Greg Yothers,et al.  Mutation Profiling and Microsatellite Instability in Stage II and III Colon Cancer: An Assessment of Their Prognostic and Oxaliplatin Predictive Value , 2012, Clinical Cancer Research.

[32]  Steven J. M. Jones,et al.  Comprehensive molecular characterization of human colon and rectal cancer , 2012, Nature.

[33]  X. Chen,et al.  Random forests for genomic data analysis. , 2012, Genomics.

[34]  A. McKenna,et al.  Absolute quantification of somatic DNA alterations in human cancer , 2012, Nature Biotechnology.

[35]  Gerald C. Chu,et al.  Oncogenic Kras Maintains Pancreatic Tumors through Regulation of Anabolic Glucose Metabolism , 2012, Cell.

[36]  S. Singhal,et al.  Transcriptomic Analysis Comparing Tumor-Associated Neutrophils with Granulocytic Myeloid-Derived Suppressor Cells and Normal Neutrophils , 2012, PloS one.

[37]  S. Friend,et al.  Developing predictive molecular maps of human disease through community-based modeling , 2011, Nature Genetics.

[38]  Javier Sastre,et al.  Colon cancer molecular subtypes identified by expression profiling and associated to stroma, mucinous type and different clinical behavior , 2012, BMC Cancer.

[39]  P. Gibbs,et al.  Impact of BRAF mutation and microsatellite instability on the pattern of metastatic spread and prognosis in metastatic colorectal cancer , 2011, Cancer.

[40]  Colin N. Dewey,et al.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.

[41]  Hans Clevers,et al.  The intestinal stem cell signature identifies colorectal cancer stem cells and predicts disease relapse. , 2011, Cell stem cell.

[42]  Tae Jin Lee,et al.  p53 regulates epithelial–mesenchymal transition through microRNAs targeting ZEB1 and ZEB2 , 2011, The Journal of experimental medicine.

[43]  J. Galon,et al.  Clinical impact of different classes of infiltrating T cytotoxic and helper cells (Th1, th2, treg, th17) in patients with colorectal cancer. , 2011, Cancer research.

[44]  David B Jackson,et al.  EMT is the dominant program in human colon cancer , 2011, BMC Medical Genomics.

[45]  Rafael A Irizarry,et al.  Frozen robust multiarray analysis (fRMA). , 2010, Biostatistics.

[46]  Zlatko Trajanoski,et al.  Biomolecular network reconstruction identifies T-cell homing factors associated with survival in colorectal cancer. , 2010, Gastroenterology.

[47]  R. Greil,et al.  Randomized phase III trial comparing biweekly infusional fluorouracil/leucovorin alone or with irinotecan in the adjuvant treatment of stage III colon cancer: PETACC-3. , 2009, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[48]  P. Coulie,et al.  Comparison of stable human Treg and Th clones by transcriptional profiling , 2009, European journal of immunology.

[49]  David B Dunson,et al.  Default Prior Distributions and Efficient Posterior Computation in Bayesian Factor Analysis , 2009, Journal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America.

[50]  Audrey Kauffmann,et al.  Bioinformatics Applications Note Arrayqualitymetrics—a Bioconductor Package for Quality Assessment of Microarray Data , 2022 .

[51]  Sun-Mi Park,et al.  The miR-200 family determines the epithelial phenotype of cancer cells by targeting the E-cadherin repressors ZEB1 and ZEB2. , 2008, Genes & development.

[52]  Stijn van Dongen,et al.  Graph Clustering Via a Discrete Uncoupling Process , 2008, SIAM J. Matrix Anal. Appl..

[53]  R. Irizarry,et al.  A gene expression bar code for microarray data , 2007, Nature Methods.

[54]  Suet Yi Leung,et al.  Gene expression patterns of human colon tops and basal crypts and BMP antagonists as intestinal stem cell niche factors , 2007, Proceedings of the National Academy of Sciences.

[55]  H. Clevers,et al.  The Intestinal Wnt/TCF Signature. , 2007, Gastroenterology.

[56]  Cheng Li,et al.  Adjusting batch effects in microarray expression data using empirical Bayes methods. , 2007, Biostatistics.

[57]  R. Tibshirani,et al.  On testing the significance of sets of genes , 2006, math/0610667.

[58]  Z. Trajanoski,et al.  Type, Density, and Location of Immune Cells Within Human Colorectal Tumors Predict Clinical Outcome , 2006, Science.

[59]  P. Laird,et al.  CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer , 2006, Nature Genetics.

[60]  F. Slack,et al.  RAS Is Regulated by the let-7 MicroRNA Family , 2005, Cell.

[61]  C. Burge,et al.  Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets , 2005, Cell.

[62]  Jean YH Yang,et al.  Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.

[63]  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.

[64]  Sudhir Srivastava,et al.  Revised Bethesda Guidelines for hereditary nonpolyposis colorectal cancer (Lynch syndrome) and microsatellite instability. , 2004, Journal of the National Cancer Institute.

[65]  Benjamin M. Bolstad,et al.  affy - analysis of Affymetrix GeneChip data at the probe level , 2004, Bioinform..

[66]  Leo Breiman,et al.  Random Forests , 2001, Machine Learning.

[67]  Kathryn A. O’Donnell,et al.  An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets , 2003, Genome Biology.

[68]  R. Tibshirani,et al.  Diagnosis of multiple cancer types by shrunken centroids of gene expression , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[69]  Anton J. Enright,et al.  An efficient algorithm for large-scale detection of protein families. , 2002, Nucleic acids research.

[70]  Daniel J Sargent,et al.  Immunohistochemistry versus microsatellite instability testing in phenotyping colorectal tumors. , 2002, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[71]  R. Tibshirani,et al.  Significance analysis of microarrays applied to the ionizing radiation response , 2001, Proceedings of the National Academy of Sciences of the United States of America.