Insights into beta cell regeneration for diabetes via integration of molecular landscapes in human insulinomas

[1]  J. Flowers,et al.  Origins and geographic diversification of African rice (Oryza glaberrima) , 2018, bioRxiv.

[2]  Shivashankar H. Nagaraj,et al.  Whole-genome landscape of pancreatic neuroendocrine tumours , 2017, Nature.

[3]  G. Rutter,et al.  Beta Cell Hubs Dictate Pancreatic Islet Responses to Glucose , 2016, Cell metabolism.

[4]  Jonathan Schug,et al.  Human islets contain four distinct subtypes of β cells , 2016, Nature Communications.

[5]  Olle Korsgren,et al.  Identification of proliferative and mature β-cells in the islets of Langerhans , 2016, Nature.

[6]  Benjamin S. Glicksberg,et al.  Development and clinical application of an integrative genomic approach to personalized cancer therapy , 2016, Genome Medicine.

[7]  Howard Y. Chang,et al.  Age-Dependent Pancreatic Gene Regulation Reveals Mechanisms Governing Human β Cell Function. , 2016, Cell metabolism.

[8]  S. Itzkovitz,et al.  The Genetic Program of Pancreatic β-Cell Replication In Vivo , 2016, Diabetes.

[9]  D. E. Olson,et al.  Inhibition of DYRK1A Stimulates Human β-Cell Proliferation , 2016, Diabetes.

[10]  C. Stanley,et al.  Histologic and Molecular Profile of Pediatric Insulinomas: Evidence of a Paternal Parent-of-Origin Effect. , 2016, The Journal of clinical endocrinology and metabolism.

[11]  Zhongyang Zhang,et al.  SAAS-CNV: A Joint Segmentation Approach on Aggregated and Allele Specific Signals for the Identification of Somatic Copy Number Alterations with Next-Generation Sequencing Data , 2015, PLoS Comput. Biol..

[12]  Austin D. Swafford,et al.  Inhibition of DYRK1A and GSK3B induces human β-cell proliferation , 2015, Nature Communications.

[13]  Michael B. Stadler,et al.  Aging-Dependent Demethylation of Regulatory Elements Correlates with Chromatin State and Improved β Cell Function. , 2015, Cell metabolism.

[14]  Nathaniel H. Boyd,et al.  Polycomb recruitment at the Class II transactivator gene. , 2015, Molecular immunology.

[15]  R. Paro,et al.  Trithorax and Polycomb group-dependent regulation: a tale of opposing activities , 2015, Development.

[16]  Rezvan Ehsani,et al.  EpiFactors: a comprehensive database of human epigenetic factors and complexes , 2015, Database J. Biol. Databases Curation.

[17]  Emily K. Tsang,et al.  Effect of predicted protein-truncating genetic variants on the human transcriptome , 2015, Science.

[18]  Dale L. Greiner,et al.  Novel Observations From Next-Generation RNA Sequencing of Highly Purified Human Adult and Fetal Islet Cell Subsets , 2015, Diabetes.

[19]  Annabelle L. Fonseca,et al.  Neomorphic effects of recurrent somatic mutations in Yin Yang 1 in insulin-producing adenomas , 2015, Proceedings of the National Academy of Sciences.

[20]  T. Wieland,et al.  Frequency and clinical correlates of somatic Ying Yang 1 mutations in sporadic insulinomas. , 2015, The Journal of clinical endocrinology and metabolism.

[21]  Doron Betel,et al.  Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution , 2015, Journal of visualized experiments : JoVE.

[22]  P. Wang,et al.  Diabetes mellitus—advances and challenges in human β-cell proliferation , 2015, Nature Reviews Endocrinology.

[23]  Peng Wang,et al.  Induction of human pancreatic beta cell replication by inhibitors of dual specificity tyrosine regulated kinase , 2015, Nature Medicine.

[24]  Brian T. Lee,et al.  The UCSC Genome Browser database: 2015 update , 2014, Nucleic Acids Research.

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

[26]  Alessandro Vullo,et al.  Ensembl 2015 , 2014, Nucleic Acids Res..

[27]  L. Groop,et al.  Global genomic and transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolism , 2014, Proceedings of the National Academy of Sciences.

[28]  A. Kasarskis,et al.  Analytical validation of whole exome and whole genome sequencing for clinical applications , 2014, BMC Medical Genomics.

[29]  K. Kaestner,et al.  Targeting the cell cycle inhibitor p57Kip2 promotes adult human β cell replication. , 2014, The Journal of clinical investigation.

[30]  Charity W. Law,et al.  voom: precision weights unlock linear model analysis tools for RNA-seq read counts , 2014, Genome Biology.

[31]  J. Gaglia,et al.  Soluble Factors Secreted by T Cells Promote β-Cell Proliferation , 2013, Diabetes.

[32]  Jiaqian Wang,et al.  Whole exome sequencing of insulinoma reveals recurrent T372R mutations in YY1 , 2013, Nature Communications.

[33]  Y. Schwartz,et al.  A new world of Polycombs: unexpected partnerships and emerging functions , 2013, Nature Reviews Genetics.

[34]  R. Bottino,et al.  Combined modulation of polycomb and trithorax genes rejuvenates β cell replication. , 2013, The Journal of clinical investigation.

[35]  Mauricio O. Carneiro,et al.  From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline , 2013, Current protocols in bioinformatics.

[36]  Hongen Zhang,et al.  RCircos: an R package for Circos 2D track plots , 2013, BMC Bioinformatics.

[37]  Robert Gentleman,et al.  Software for Computing and Annotating Genomic Ranges , 2013, PLoS Comput. Biol..

[38]  G. Rutter,et al.  When less is more: the forbidden fruits of gene repression in the adult β‐cell , 2013, Diabetes, obesity & metabolism.

[39]  B. Reva.  Revealing selection in cancer using the predicted functional impact of cancer mutations. Application to nomination of cancer drivers , 2013, BMC Genomics.

[40]  Halit Ongen,et al.  Cell-type, allelic, and genetic signatures in the human pancreatic beta cell transcriptome , 2013, Genome research.

[41]  W. Shi,et al.  The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote , 2013, Nucleic acids research.

[42]  J. Schug,et al.  Epigenomic plasticity enables human pancreatic α to β cell reprogramming. , 2013, The Journal of clinical investigation.

[43]  A. Sivachenko,et al.  Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples , 2013, Nature Biotechnology.

[44]  Bernhard Mlecnik,et al.  CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data , 2013, Bioinform..

[45]  S. Gabriel,et al.  Analysis of 6,515 exomes reveals a recent origin of most human protein-coding variants , 2012, Nature.

[46]  Kenny Q. Ye,et al.  An integrated map of genetic variation from 1,092 human genomes , 2012, Nature.

[47]  F. Schuit.  Response to Comment on: Schuit et al. β-Cell–Specific Gene Repression: A Mechanism to Protect Against Inappropriate or Maladjusted Insulin Secretion? Diabetes 2012;61:969–975 , 2012, Diabetes.

[48]  D. Cook,et al.  ggbio: an R package for extending the grammar of graphics for genomic data , 2012, Genome Biology.

[49]  J. Gregg,et al.  Molecular pathology of pancreatic neuroendocrine tumors. , 2012, Journal of gastrointestinal oncology.

[50]  M. Granvik,et al.  β-Cell–Specific Gene Repression: A Mechanism to Protect Against Inappropriate or Maladjusted Insulin Secretion? , 2012, Diabetes.

[51]  W. Huber,et al.  Detecting differential usage of exons from RNA-seq data , 2012, Genome research.

[52]  Christopher A. Miller,et al.  VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. , 2012, Genome research.

[53]  David G. Knowles,et al.  Fast Computation and Applications of Genome Mappability , 2012, PloS one.

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

[55]  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.

[56]  M. DePristo,et al.  A framework for variation discovery and genotyping using next-generation DNA sequencing data , 2011, Nature Genetics.

[57]  Michael A. Choti,et al.  DAXX/ATRX, MEN1, and mTOR Pathway Genes Are Frequently Altered in Pancreatic Neuroendocrine Tumors , 2011, Science.

[58]  M. Fraga,et al.  Beckwith–Wiedemann syndrome and uniparental disomy 11p: fine mapping of the recombination breakpoints and evaluation of several techniques , 2011, European Journal of Human Genetics.

[59]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[60]  A. F. Stewart,et al.  Induction of Human β-Cell Proliferation and Engraftment Using a Single G1/S Regulatory Molecule, cdk6 , 2010, Diabetes.

[61]  M. Palassini,et al.  Derepression of Polycomb targets during pancreatic organogenesis allows insulin-producing beta-cells to adopt a neural gene activity program. , 2010, Genome research.

[62]  Matthew D. Young,et al.  Gene ontology analysis for RNA-seq: accounting for selection bias , 2010, Genome Biology.

[63]  I. Gut,et al.  Hypermethylation of the IGF2 differentially methylated region 2 is a specific event in insulinomas leading to loss-of-imprinting and overexpression. , 2009, Endocrine-related cancer.

[64]  A. Tarakhovsky,et al.  Polycomb protein Ezh2 regulates pancreatic beta-cell Ink4a/Arf expression and regeneration in diabetes mellitus. , 2009, Genes & development.

[65]  L. Miller,et al.  CDKN1C (p57KIP2) Is a Direct Target of EZH2 and Suppressed by Multiple Epigenetic Mechanisms in Breast Cancer Cells , 2009, PloS one.

[66]  Pornpimol Charoentong,et al.  ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks , 2009, Bioinform..

[67]  S. Horvath,et al.  WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.

[68]  Jun Dong,et al.  Geometric Interpretation of Gene Coexpression Network Analysis , 2008, PLoS Comput. Biol..

[69]  P. Ferrari,et al.  Familial Beckwith–Wiedemann syndrome due to CDKN1C mutation manifesting with recurring omphalocele , 2008, Prenatal diagnosis.

[70]  R. Thakker,et al.  Multiple endocrine neoplasia type 1 (MEN1): analysis of 1336 mutations reported in the first decade following identification of the gene , 2008, Human mutation.

[71]  Camillo Ricordi,et al.  The unique cytoarchitecture of human pancreatic islets has implications for islet cell function , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[72]  Alvin C. Powers,et al.  Assessment of Human Pancreatic Islet Architecture and Composition by Laser Scanning Confocal Microscopy , 2005, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.

[73]  Gordon K Smyth,et al.  Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments , 2004, Statistical applications in genetics and molecular biology.

[74]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[75]  D. Hanahan,et al.  Of Mice and MEN1: Insulinomas in a Conditional Mouse Knockout , 2003, Molecular and Cellular Biology.

[76]  M. Seto,et al.  Overexpression of cyclin D1 occurs frequently in human pancreatic endocrine tumors. , 2000, The Journal of clinical endocrinology and metabolism.

[77]  B. Glaser,et al.  Beta-cell proliferation and apoptosis in the developing normal human pancreas and in hyperinsulinism of infancy. , 2000, Diabetes.

[78]  R. Jensen,et al.  Localization of putative tumor suppressor loci by genome-wide allelotyping in human pancreatic endocrine tumors. , 1998, Cancer research.

[79]  C. Junien,et al.  Somatic deletion of the imprinted 11p15 region in sporadic persistent hyperinsulinemic hypoglycemia of infancy is specific of focal adenomatous hyperplasia and endorses partial pancreatectomy. , 1997, The Journal of clinical investigation.

[80]  R. Simes,et al.  An improved Bonferroni procedure for multiple tests of significance , 1986 .

[81]  R. Thakker.  Chapter 148 – Multiple Endocrine Neoplasia Type 1 , 2016 .

[82]  Clemons,et al.  Inhibition of DYRK1A stimulates human beta-cell proliferation , 2016 .

[83]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[84]  Elizabeth M. Smigielski,et al.  dbSNP: the NCBI database of genetic variation , 2001, Nucleic Acids Res..

[85]  G. Benson,et al.  Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.

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