Literature DB >> 25431938

The era of integrative genomics: more data or better methods?

Devin C Koestler1, Meaghan J Jones, Meaghan Jones, Michael S Kobor, Michael Kobor.   

Abstract

Entities:  

Keywords:  DNA methylation; epigenetic silencing; integrative genomics; protein–protein interaction (PPI) networks

Year:  2014        PMID： 25431938      PMCID： PMC4414242          DOI： 10.2217/epi.14.44

Source DB:  PubMed          Journal:  Epigenomics        ISSN： 1750-192X            Impact factor:   4.778


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  19 in total

1.  Comprehensive high-throughput arrays for relative methylation (CHARM).

Authors:  Rafael A Irizarry; Christine Ladd-Acosta; Benilton Carvalho; Hao Wu; Sheri A Brandenburg; Jeffrey A Jeddeloh; Bo Wen; Andrew P Feinberg
Journal:  Genome Res       Date:  2008-03-03       Impact factor: 9.043

Review 2.  CpG islands--'a rough guide'.

Authors:  Robert S Illingworth; Adrian P Bird
Journal:  FEBS Lett       Date:  2009-04-18       Impact factor: 4.124

3.  A systems-level integrative framework for genome-wide DNA methylation and gene expression data identifies differential gene expression modules under epigenetic control.

Authors:  Yinming Jiao; Martin Widschwendter; Andrew E Teschendorff
Journal:  Bioinformatics       Date:  2014-05-02       Impact factor: 6.937

4.  NCBI GEO: archive for high-throughput functional genomic data.

Authors:  Tanya Barrett; Dennis B Troup; Stephen E Wilhite; Pierre Ledoux; Dmitry Rudnev; Carlos Evangelista; Irene F Kim; Alexandra Soboleva; Maxim Tomashevsky; Kimberly A Marshall; Katherine H Phillippy; Patti M Sherman; Rolf N Muertter; Ron Edgar
Journal:  Nucleic Acids Res       Date:  2008-10-21       Impact factor: 16.971

5.  Pathway Commons, a web resource for biological pathway data.

Authors:  Ethan G Cerami; Benjamin E Gross; Emek Demir; Igor Rodchenkov; Ozgün Babur; Nadia Anwar; Nikolaus Schultz; Gary D Bader; Chris Sander
Journal:  Nucleic Acids Res       Date:  2010-11-10       Impact factor: 16.971

6.  An integrative network algorithm identifies age-associated differential methylation interactome hotspots targeting stem-cell differentiation pathways.

Authors:  James West; Stephan Beck; Xiangdong Wang; Andrew E Teschendorff
Journal:  Sci Rep       Date:  2013       Impact factor: 4.379

7.  Passive and active DNA methylation and the interplay with genetic variation in gene regulation.

Authors:  Maria Gutierrez-Arcelus; Tuuli Lappalainen; Stephen B Montgomery; Alfonso Buil; Halit Ongen; Alisa Yurovsky; Julien Bryois; Thomas Giger; Luciana Romano; Alexandra Planchon; Emilie Falconnet; Deborah Bielser; Maryline Gagnebin; Ismael Padioleau; Christelle Borel; Audrey Letourneau; Periklis Makrythanasis; Michel Guipponi; Corinne Gehrig; Stylianos E Antonarakis; Emmanouil T Dermitzakis
Journal:  Elife       Date:  2013-06-04       Impact factor: 8.140

8.  ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression.

Authors:  Helen Parkinson; Misha Kapushesky; Nikolay Kolesnikov; Gabriella Rustici; Mohammad Shojatalab; Niran Abeygunawardena; Hugo Berube; Miroslaw Dylag; Ibrahim Emam; Anna Farne; Ele Holloway; Margus Lukk; James Malone; Roby Mani; Ekaterina Pilicheva; Tim F Rayner; Faisal Rezwan; Anjan Sharma; Eleanor Williams; Xiangqun Zheng Bradley; Tomasz Adamusiak; Marco Brandizi; Tony Burdett; Richard Coulson; Maria Krestyaninova; Pavel Kurnosov; Eamonn Maguire; Sudeshna Guha Neogi; Philippe Rocca-Serra; Susanna-Assunta Sansone; Nataliya Sklyar; Mengyao Zhao; Ugis Sarkans; Alvis Brazma
Journal:  Nucleic Acids Res       Date:  2008-11-10       Impact factor: 16.971

9.  Role of DNA methylation and epigenetic silencing of HAND2 in endometrial cancer development.

Authors:  Allison Jones; Andrew E Teschendorff; Quanxi Li; Jane D Hayward; Athilakshmi Kannan; Tim Mould; James West; Michal Zikan; David Cibula; Heidi Fiegl; Shih-Han Lee; Elisabeth Wik; Richard Hadwin; Rupali Arora; Charlotte Lemech; Henna Turunen; Päivi Pakarinen; Ian J Jacobs; Helga B Salvesen; Milan K Bagchi; Indrani C Bagchi; Martin Widschwendter
Journal:  PLoS Med       Date:  2013-11-12       Impact factor: 11.069

10.  DNA methylation, genotype and gene expression: who is driving and who is along for the ride?

Authors:  Meaghan J Jones; Anthony P Fejes; Michael S Kobor
Journal:  Genome Biol       Date:  2013-07-29       Impact factor: 13.583
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  2 in total

1.  Computational challenges in modeling gene regulatory events.

Authors:  Abhijeet Pataskar; Vijay K Tiwari
Journal:  Transcription       Date:  2016-07-08

2.  SMITE: an R/Bioconductor package that identifies network modules by integrating genomic and epigenomic information.

Authors:  N Ari Wijetunga; Andrew D Johnston; Ryo Maekawa; Fabien Delahaye; Netha Ulahannan; Kami Kim; John M Greally
Journal:  BMC Bioinformatics       Date:  2017-01-18       Impact factor: 3.169
  2 in total

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