Pan-cancer Convergence to a Small-Cell Neuroendocrine Phenotype that Shares Susceptibilities with Hematological Malignancies.

[1]  M. Mino‐Kenudson,et al.  EGFR-Mutant Adenocarcinomas That Transform to Small-Cell Lung Cancer and Other Neuroendocrine Carcinomas: Clinical Outcomes. , 2019, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[2]  T. Graeber,et al.  Reprogramming normal human epithelial tissues to a common, lethal neuroendocrine cancer lineage , 2018, Science.

[3]  A. Kundaje,et al.  Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin. , 2018, Cancer discovery.

[4]  C. Mullighan,et al.  Safety and Efficacy of the BCL Inhibitors Venetoclax and Navitoclax in Combination with Chemotherapy in Patients with Relapsed/Refractory Acute Lymphoblastic Leukemia and Lymphoblastic Lymphoma: ALL‐131 , 2018, Clinical Lymphoma Myeloma and Leukemia.

[5]  K. Sheu,et al.  A Human Adult Stem Cell Signature Marks Aggressive Variants across Epithelial Cancers. , 2018, Cell reports.

[6]  Vinicius S. Chagas,et al.  Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer , 2018, Cell.

[7]  P. Kiely,et al.  Unusual Sites of High-Grade Neuroendocrine Carcinomas: A Case Series and Review of the Literature , 2018, The American journal of case reports.

[8]  Paul A Clemons,et al.  A precision oncology approach to the pharmacological targeting of mechanistic dependencies in neuroendocrine tumors , 2018, Nature Genetics.

[9]  T. Graeber,et al.  Multi-stage Differentiation Defines Melanoma Subtypes with Differential Vulnerability to Drug-Induced Iron-Dependent Oxidative Stress. , 2018, Cancer cell.

[10]  Joshua M. Stuart,et al.  Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer , 2018, Cell.

[11]  Joshua M. Stuart,et al.  Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation. , 2018, Cell.

[12]  Marco Montillo,et al.  Venetoclax–Rituximab in Relapsed or Refractory Chronic Lymphocytic Leukemia , 2018, The New England journal of medicine.

[13]  C. Creighton,et al.  Pan-Cancer Molecular Classes Transcending Tumor Lineage Across 32 Cancer Types, Multiple Data Platforms, and over 10,000 Cases , 2018, Clinical Cancer Research.

[14]  A. Iafrate,et al.  Polyclonal RB1 mutations and acquired resistance to CDK 4/6 inhibitors in patients with metastatic breast cancer , 2017, Annals of oncology : official journal of the European Society for Medical Oncology.

[15]  P. Hinds.  Faculty Opinions recommendation of Palbociclib (PD-0332991), a selective CDK4/6 inhibitor, restricts tumour growth in preclinical models of hepatocellular carcinoma. , 2017 .

[16]  Roman K. Thomas,et al.  Targeting a non-oncogene addiction to the ATR/CHK1 axis for the treatment of small cell lung cancer , 2017, Scientific Reports.

[17]  Julia M. Lewis,et al.  Synergy of BCL2 and histone deacetylase inhibition against leukemic cells from cutaneous T-cell lymphoma patients. , 2017, Blood.

[18]  Krista M. Powell,et al.  Venetoclax Is Effective in Small-Cell Lung Cancers with High BCL-2 Expression , 2017, Clinical Cancer Research.

[19]  P. Ma,et al.  Nothing But NET: A Review of Neuroendocrine Tumors and Carcinomas , 2017, Neoplasia.

[20]  A. Roulston,et al.  Novel NAPRT specific antibody identifies small cell lung cancer and neuronal cancers as promising clinical indications for a NAMPT inhibitor/niacin co-administration strategy , 2017, Oncotarget.

[21]  Phillip G. Montgomery,et al.  Defining a Cancer Dependency Map , 2017, Cell.

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

[23]  M. Rubin,et al.  Biology and evolution of poorly differentiated neuroendocrine tumors , 2017, Nature Medicine.

[24]  P. Park,et al.  Clonal History and Genetic Predictors of Transformation Into Small-Cell Carcinomas From Lung Adenocarcinomas. , 2017, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[25]  Kim-Anh Lê Cao,et al.  mixOmics: An R package for ‘omics feature selection and multiple data integration , 2017, bioRxiv.

[26]  Mary Goldman,et al.  Toil enables reproducible, open source, big biomedical data analyses , 2017, Nature Biotechnology.

[27]  K. Garcia,et al.  Intratumoral heterogeneity generated by Notch signaling promotes small cell lung cancer , 2017, Nature.

[28]  G. Miller,et al.  Alternative REST Splicing Underappreciated , 2017, eNeuro.

[29]  Geet Duggal,et al.  Salmon: fast and bias-aware quantification of transcript expression using dual-phase inference , 2017, Nature Methods.

[30]  Yiling Lu,et al.  Characterization of Human Cancer Cell Lines by Reverse-phase Protein Arrays. , 2017, Cancer cell.

[31]  N. Gray,et al.  THZ1 targeting CDK7 suppresses STAT transcriptional activity and sensitizes T-cell lymphomas to BCL2 inhibitors , 2017, Nature Communications.

[32]  Ximing J. Yang,et al.  FOXA1 inhibits prostate cancer neuroendocrine differentiation , 2017, Oncogene.

[33]  Henry W. Long,et al.  Rb1 and Trp53 cooperate to suppress prostate cancer lineage plasticity, metastasis, and antiandrogen resistance , 2017, Science.

[34]  M. Rubin,et al.  SOX2 promotes lineage plasticity and antiandrogen resistance in TP53- and RB1-deficient prostate cancer , 2017, Science.

[35]  S. Cho,et al.  Cervical small cell neuroendocrine tumor mutation profiles via whole exome sequencing , 2016, Oncotarget.

[36]  Camille Stephan-Otto Attolini,et al.  Targeting metastasis-initiating cells through the fatty acid receptor CD36 , 2016, Nature.

[37]  Emanuel J. V. Gonçalves,et al.  A Landscape of Pharmacogenomic Interactions in Cancer , 2016, Cell.

[38]  J. Taipale,et al.  The role of enhancers in cancer , 2016, Nature Reviews Cancer.

[39]  Mariano J. Alvarez,et al.  Network-based inference of protein activity helps functionalize the genetic landscape of cancer , 2016, Nature Genetics.

[40]  Andrea Califano,et al.  ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information , 2016, Bioinform..

[41]  Matteo Benelli,et al.  Divergent clonal evolution of castration resistant neuroendocrine prostate cancer , 2016, Nature Medicine.

[42]  V. Arora,et al.  Emerging mechanisms of resistance to androgen receptor inhibitors in prostate cancer , 2015, Nature Reviews Cancer.

[43]  C. Shaw,et al.  Mutations in the transcriptional repressor REST predispose to Wilms tumor , 2015, Nature Genetics.

[44]  Anders Isaksson,et al.  Rawcopy: Improved copy number analysis with Affymetrix arrays , 2015, Scientific Reports.

[45]  D. Metz,et al.  Consensus on biomarkers for neuroendocrine tumour disease. , 2015, The Lancet. Oncology.

[46]  D. Price,et al.  THZ1 Reveals Roles for Cdk7 in Co-transcriptional Capping and Pausing. , 2015, Molecular cell.

[47]  M. Pappalardi,et al.  A DNA Hypomethylation Signature Predicts Antitumor Activity of LSD1 Inhibitors in SCLC. , 2015, Cancer cell.

[48]  Martin Vingron,et al.  Comprehensive genomic profiles of small cell lung cancer , 2015, Nature.

[49]  K. McVary,et al.  Contemporary Incidence and Mortality Rates of Neuroendocrine Prostate Cancer. , 2015, Anticancer research.

[50]  P. Nelson,et al.  SRRM4 Expression and the Loss of REST Activity May Promote the Emergence of the Neuroendocrine Phenotype in Castration-Resistant Prostate Cancer , 2015, Clinical Cancer Research.

[51]  H. Beltran,et al.  The spectrum of neuroendocrine tumors: histologic classification, unique features and areas of overlap. , 2015, American Society of Clinical Oncology educational book. American Society of Clinical Oncology. Annual Meeting.

[52]  Max Kuhn,et al.  caret: Classification and Regression Training , 2015 .

[53]  G. Getz,et al.  RB loss in resistant EGFR mutant lung adenocarcinomas that transform to small-cell lung cancer , 2015, Nature Communications.

[54]  J. Bradner,et al.  Targeting transcriptional addictions in small cell lung cancer with a covalent CDK7 inhibitor. , 2014, Cancer cell.

[55]  Bandana Sharma,et al.  CDK7 Inhibition Suppresses Super-Enhancer-Linked Oncogenic Transcription in MYCN-Driven Cancer , 2014, Cell.

[56]  Yun Wu,et al.  Invasive neuroendocrine carcinoma of the breast: a population-based study from the surveillance, epidemiology and end results (SEER) database , 2014, BMC Cancer.

[57]  J. Epstein,et al.  Small cell carcinoma of the prostate , 2014, Nature Reviews Urology.

[58]  Brent S. Pedersen,et al.  Fast and accurate alignment of long bisulfite-seq reads , 2014, 1401.1129.

[59]  J. Saltz,et al.  Cancer Digital Slide Archive: an informatics resource to support integrated in silico analysis of TCGA pathology data. , 2013, Journal of the American Medical Informatics Association : JAMIA.

[60]  G. Getz,et al.  A Genomics-Based Classification of Human Lung Tumors , 2013, Science Translational Medicine.

[61]  Robert Gentleman,et al.  Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer , 2012, Nature Genetics.

[62]  Adam A. Margolin,et al.  The Cancer Cell Line Encyclopedia enables predictive modeling of anticancer drug sensitivity , 2012, Nature.

[63]  Laura H. Tang,et al.  Small Cell and Large Cell Neuroendocrine Carcinomas of the Pancreas are Genetically Similar and Distinct From Well-differentiated Pancreatic Neuroendocrine Tumors , 2012, The American journal of surgical pathology.

[64]  D. Zaykin,et al.  Optimally weighted Z‐test is a powerful method for combining probabilities in meta‐analysis , 2011, Journal of evolutionary biology.

[65]  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.

[66]  Xavier Robin,et al.  pROC: an open-source package for R and S+ to analyze and compare ROC curves , 2011, BMC Bioinformatics.

[67]  R. Taschereau,et al.  Rank–rank hypergeometric overlap: identification of statistically significant overlap between gene-expression signatures , 2010, Nucleic acids research.

[68]  Ben S. Wittner,et al.  Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1 , 2009, Nature.

[69]  Karine Gilbert,et al.  The Small Molecule GMX1778 Is a Potent Inhibitor of NAD+ Biosynthesis: Strategy for Enhanced Therapy in Nicotinic Acid Phosphoribosyltransferase 1-Deficient Tumors , 2009, Molecular and Cellular Biology.

[70]  A. Giordano,et al.  Cell cycle kinases as therapeutic targets for cancer , 2009, Nature Reviews Drug Discovery.

[71]  Y. Wong,et al.  The epidemiology and survival of extrapulmonary small cell carcinoma in South East England, 1970–2004 , 2009, BMC Cancer.

[72]  Herb Chen,et al.  The HDAC inhibitor trichostatin A inhibits growth of small cell lung cancer cells. , 2007, The Journal of surgical research.

[73]  Joachim Selbig,et al.  pcaMethods - a bioconductor package providing PCA methods for incomplete data , 2007, Bioinform..

[74]  J. Mesirov,et al.  From the Cover: Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005 .

[75]  P. Hermonat,et al.  A morphologic and statistical comparative study of small‐cell carcinoma and non‐Hodgkin's lymphoma in fine‐needle aspiration biopsy material from lymph nodes , 2004, Diagnostic cytopathology.

[76]  R. Gray.  Modeling Survival Data: Extending the Cox Model , 2002 .

[77]  P. Grambsch,et al.  Modeling Survival Data: Extending the Cox Model , 2000 .

[78]  N. Harris,et al.  Precursor B-Lymphoblastic lymphoma presenting as a solitary bone tumor and mimicking Ewing's sarcoma: a report of four cases and review of the literature. , 1998, The American journal of surgical pathology.

[79]  D. Ruysscher,et al.  Small-cell lung cancer , 1980, The Lancet.

[80]  T. Graeber,et al.  Abstract A113: Recurrent patterns of DNA copy number alterations in tumors reflect metabolic selection pressures , 2018 .

[81]  Jiaoti Huang,et al.  Alternative Splicing Provides a Novel Molecular Mechanism for Prostatic Small-cell Neuroendocrine Carcinoma. , 2017, European urology.

[82]  G. Zamboni,et al.  Neuroendocrine Carcinoma of the Breast: Current Evidence and Future Perspectives. , 2016, The oncologist.

[83]  Cedric E. Ginestet.  ggplot2: Elegant Graphics for Data Analysis , 2011 .

[84]  D. Lucas,et al.  Ewing sarcoma vs lymphoblastic lymphoma. A comparative immunohistochemical study. , 2001, American journal of clinical pathology.