Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation.

[1]  Jonghwan Kim,et al.  Embryonic stem cell-specific signatures in cancer: insights into genomic regulatory networks and implications for medicine , 2011, Genome Medicine.

[2]  Adrian V. Lee,et al.  Epigenomic Deconvolution of Breast Tumors Reveals Metabolic Coupling between Constituent Cell Types. , 2016, Cell reports.

[3]  Ash A. Alizadeh,et al.  Abstract PR09: The prognostic landscape of genes and infiltrating immune cells across human cancers , 2015 .

[4]  Stuart H. Orkin,et al.  A Myc Network Accounts for Similarities between Embryonic Stem and Cancer Cell Transcription Programs , 2010, Cell.

[5]  Robert J. Lonigro,et al.  Integrative Clinical Genomics of Metastatic Cancer , 2017, Nature.

[6]  F. Schmitt,et al.  Prognostic value of stromal tumour infiltrating lymphocytes and programmed cell death-ligand 1 expression in breast cancer , 2017, Journal of Clinical Pathology.

[7]  Dan Roth,et al.  Generalization Bounds for the Area Under the ROC Curve , 2005, J. Mach. Learn. Res..

[8]  Daniel V. Oliveira,et al.  StemChecker: a web-based tool to discover and explore stemness signatures in gene sets , 2015, Nucleic Acids Res..

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

[10]  A. Regev,et al.  An embryonic stem cell–like gene expression signature in poorly differentiated aggressive human tumors , 2008, Nature Genetics.

[11]  C. Chai,et al.  Overexpression of annexin 1 in the development and differentiation of urothelial carcinoma , 2012, The Kaohsiung journal of medical sciences.

[12]  S. Tsai,et al.  The miR‐200b–ZEB1 circuit regulates diverse stemness of human hepatocellular carcinoma , 2017, Molecular carcinogenesis.

[13]  Gianluca Bontempi,et al.  Moonlight: a tool for biological interpretation and driver genes discovery , 2018, bioRxiv.

[14]  J. Ko,et al.  Suberoylanilide hydroxamic acid (SAHA) causes tumor growth slowdown and triggers autophagy in glioblastoma stem cells , 2013, Autophagy.

[15]  Claude Preudhomme,et al.  A 17-gene stemness score for rapid determination of risk in acute leukaemia , 2016, Nature.

[16]  Mariella G. Filbin,et al.  Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma , 2016, Nature.

[17]  D. Friedmann-Morvinski,et al.  Dedifferentiation and reprogramming: origins of cancer stem cells , 2014, EMBO reports.

[18]  Mark M. Davis,et al.  Autologous iPSC-Based Vaccines Elicit Anti-tumor Responses In Vivo. , 2018, Cell stem cell.

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

[20]  P. Royston,et al.  Regression using fractional polynomials of continuous covariates: parsimonious parametric modelling. , 1994 .

[21]  S. Leng,et al.  EMT and stem cell-like properties associated with miR-205 and miR-200 epigenetic silencing are early manifestations during carcinogen-induced transformation of human lung epithelial cells. , 2011, Cancer research.

[22]  J. Uhm IDH1 mutation is sufficient to establish the glioma hypermethylator phenotype , 2012 .

[23]  Gianluca Bontempi,et al.  TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data , 2015, Nucleic acids research.

[24]  Angela N. Brooks,et al.  A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles , 2017, Cell.

[25]  Sean C. Bendall,et al.  Systemic Immunity Is Required for Effective Cancer Immunotherapy , 2017, Cell.

[26]  R. Weinberg,et al.  EMT, CSCs, and drug resistance: the mechanistic link and clinical implications , 2017, Nature Reviews Clinical Oncology.

[27]  Hong-Yang Wang,et al.  Acetyl‐coenzyme A carboxylase alpha promotion of glucose‐mediated fatty acid synthesis enhances survival of hepatocellular carcinoma in mice and patients , 2016, Hepatology.

[28]  Adam A. Margolin,et al.  Integrated Genomic Analysis of Diverse Induced Pluripotent Stem Cells from the Progenitor Cell Biology Consortium , 2016, Stem cell reports.

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

[30]  J. Gingold,et al.  Modeling Cancer with Pluripotent Stem Cells. , 2016, Trends in cancer.

[31]  Angelo J. Canty,et al.  Stem cell gene expression programs influence clinical outcome in human leukemia , 2011, Nature Medicine.

[32]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[33]  T. Graeber,et al.  Mutations Associated with Acquired Resistance to PD-1 Blockade in Melanoma. , 2016, The New England journal of medicine.

[34]  Richard A Young,et al.  Control of the Embryonic Stem Cell State , 2011, Cell.

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

[36]  C-Y Lin,et al.  Identification of thioridazine, an antipsychotic drug, as an antiglioblastoma and anticancer stem cell agent using public gene expression data , 2015, Cell Death and Disease.

[37]  B. Bao,et al.  Over‐expression of FoxM1 leads to epithelial–mesenchymal transition and cancer stem cell phenotype in pancreatic cancer cells , 2011, Journal of cellular biochemistry.

[38]  A. Brivanlou,et al.  Molecular signature of human embryonic stem cells and its comparison with the mouse. , 2003, Developmental biology.

[39]  S. Plevritis,et al.  Identification of ovarian cancer driver genes by using module network integration of multi-omics data , 2013, Interface Focus.

[40]  Jeong Eon Lee,et al.  Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer , 2017, Nature Communications.

[41]  Dylan M. Marchione,et al.  Impaired H3K36 methylation defines a subset of head and neck squamous cell carcinomas , 2017, Nature Genetics.

[42]  Julie V. Harness,et al.  Recurrent variations in DNA methylation in human pluripotent stem cells and their differentiated derivatives. , 2012, Cell stem cell.

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

[44]  Alexander R. Pico,et al.  Molecular, phenotypic, and sample-associated data to describe pluripotent stem cell lines and derivatives , 2017, Scientific Data.

[45]  Lijing Yao,et al.  Inferring regulatory element landscapes and transcription factor networks from cancer methylomes , 2015, Genome Biology.

[46]  D. Medici,et al.  Signaling mechanisms of the epithelial-mesenchymal transition , 2014, Science Signaling.

[47]  P. Grambsch,et al.  Estimating the Survival and Hazard Functions , 2000 .

[48]  J. Visvader,et al.  Cancer stem cells: current status and evolving complexities. , 2012, Cell stem cell.

[49]  Gary D Bader,et al.  Inhibition of Dopamine Receptor D4 Impedes Autophagic Flux, Proliferation, and Survival of Glioblastoma Stem Cells. , 2016, Cancer cell.

[50]  Radu Dobrin,et al.  Dissecting self-renewal in stem cells with RNA interference , 2006, Nature.

[51]  R. Ferris,et al.  Immunotherapy for Head and Neck Squamous Cell Carcinoma , 2018, Current Oncology Reports.

[52]  F. Bertucci,et al.  PDL1 expression is an independent prognostic factor in localized GIST , 2015, Oncoimmunology.

[53]  I. Ng,et al.  MiR-200b/200c/429 subfamily negatively regulates Rho/ROCK signaling pathway to suppress hepatocellular carcinoma metastasis , 2015, Oncotarget.

[54]  Michele Ceccarelli,et al.  TCGAbiolinksGUI: A graphical user interface to analyze GDC cancer molecular and clinical data , 2017, bioRxiv.

[55]  A. Psyrri,et al.  The emerging role of immunotherapy in head and neck squamous cell carcinoma (HNSCC): anti-tumor immunity and clinical applications. , 2016, Annals of translational medicine.

[56]  G. Goodall,et al.  The miR-200 family and miR-205 regulate epithelial to mesenchymal transition by targeting ZEB1 and SIP1 , 2008, Nature Cell Biology.

[57]  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.

[58]  Olivier Elemento,et al.  Stem Cell Lineage Infidelity Drives Wound Repair and Cancer , 2017, Cell.

[59]  K. Tomczak,et al.  The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge , 2015, Contemporary oncology.

[60]  E. Hurt,et al.  Gossypol Induces Apoptosis by Activating p53 in Prostate Cancer Cells and Prostate Tumor–Initiating Cells , 2010, Molecular Cancer Therapeutics.

[61]  Jaime Rodriguez-Canales,et al.  A Patient-Derived, Pan-Cancer EMT Signature Identifies Global Molecular Alterations and Immune Target Enrichment Following Epithelial-to-Mesenchymal Transition , 2015, Clinical Cancer Research.

[62]  Fang Liu,et al.  Overexpression of annexin 1 in pancreatic cancer and its clinical significance. , 2004, World journal of gastroenterology.

[63]  A. Kimmelman,et al.  Metabolic Interactions in the Tumor Microenvironment. , 2017, Trends in cell biology.

[64]  Yan Shi,et al.  Roles of dopamine receptors and their antagonist thioridazine in hepatoma metastasis , 2015, OncoTargets and Therapy.

[65]  R. Young,et al.  Transcriptional Addiction in Cancer , 2017, Cell.

[66]  Alexey Sergushichev,et al.  An algorithm for fast preranked gene set enrichment analysis using cumulative statistic calculation , 2016 .

[67]  T. Mikkelsen,et al.  A Distinct DNA Methylation Shift in a Subset of Glioma CpG Island Methylator Phenotypes during Tumor Recurrence , 2018, Cell reports.

[68]  D. Gifford,et al.  Analysis of the mouse embryonic stem cell regulatory networks obtained by ChIP-chip and ChIP-PET , 2008, Genome Biology.

[69]  I. Mellman,et al.  Oncology meets immunology: the cancer-immunity cycle. , 2013, Immunity.

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

[71]  Bonnie Berger,et al.  A gene expression profile of stem cell pluripotentiality and differentiation is conserved across diverse solid and hematopoietic cancers , 2012, Genome Biology.

[72]  A. Viale,et al.  Remodeling of the Methylation Landscape in Breast Cancer Metastasis , 2014, PloS one.

[73]  David T. W. Jones,et al.  Hotspot mutations in H3F3A and IDH1 define distinct epigenetic and biological subgroups of glioblastoma. , 2012, Cancer cell.

[74]  Nathan D Price,et al.  A CD133-related gene expression signature identifies an aggressive glioblastoma subtype with excessive mutations , 2011, Proceedings of the National Academy of Sciences.

[75]  Yi Wang,et al.  Overexpression of FOXM1 predicts poor prognosis and promotes cancer cell proliferation, migration and invasion in epithelial ovarian cancer , 2014, Journal of Translational Medicine.

[76]  C. Shaw,et al.  Molecular Signatures of Proliferation and Quiescence in Hematopoietic Stem Cells , 2004, PLoS biology.

[77]  Liang Xu,et al.  WNT pathway inhibitor pyrvinium pamoate inhibits the self-renewal and metastasis of breast cancer stem cells. , 2016, International journal of oncology.

[78]  Ash A. Alizadeh,et al.  Association of a leukemic stem cell gene expression signature with clinical outcomes in acute myeloid leukemia. , 2010, JAMA.

[79]  Min Liu,et al.  Overexpression of FoxM1 is associated with tumor progression in patients with clear cell renal cell carcinoma , 2012, Journal of Translational Medicine.

[80]  L. Qin,et al.  Targeting Lung Cancer Stem Cells with Antipsychological Drug Thioridazine , 2016, BioMed research international.

[81]  S. Berger,et al.  IDH mutation impairs histone demethylation and results in a block to cell differentiation , 2012, Nature.

[82]  I. Fabregat,et al.  New Insights into the Crossroads between EMT and Stemness in the Context of Cancer , 2016, Journal of clinical medicine.

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

[84]  Artem Sokolov,et al.  One-Class Detection of Cell States in Tumor Subtypes , 2016, PSB.

[85]  Michael Q. Zhang,et al.  Integrative analysis of 111 reference human epigenomes , 2015, Nature.