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#epigenomics

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	1.	Research Longitudinal, genome-scale analysis of DNA methylation in twins from birth to 18 months of age reveals rapid epigenetic change in early life and pair-specific effects of discordance David Martino, Yuk Jin Loke, Lavinia Gordon, Miina Ollikainen, Mark N Cruickshank, Richard Saffery, Jeffrey M Craig Genome Biology 2013, 14:R42 (22 May 2013) Abstract \| Provisional PDF \| Editor’s summary A longitudinal study of DNA methylation in twins at birth and 18 months finds that some loci drift in methylation status
	2.	Method jMOSAiCS: joint analysis of multiple ChIP-seq datasets Xin Zeng, Rajendran Sanalkumar, Emery H Bresnick, Hongda Li, Qiang Chang, Sunduz Keles Genome Biology 2013, 14:R38 (29 April 2013) Abstract \| Provisional PDF \| Editor’s summary A novel probabilistic method for jointly analyzing multiple ChIP-seq datasets offers an improvement over chromHMM
	3.	Research Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of Polycomb-target genes James P Reddington, Sara M Perricone, Colm E Nestor, Judith Reichmann, Neil A Youngson, Masako Suzuki, Diana Reinhardt, Donncha S Dunican, James G Prendegast, Heidi Mjoseng, Bernard H Ramsahoye, Emma Whitelaw, John M Greally, Ian R Adams, Wendy A Bickmore, Richard R Meehan Genome Biology 2013, 14:R25 (25 March 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary An intact DNA methylome is required for appropriate Polycomb-mediated gene repression, as revealed by H3K4me3 and PRC2 mapping in hypomethylated cells
	4.	Research DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes Dvir Aran, Sivan Sabato, Asaf Hellman Genome Biology 2013, 14:R21 (12 March 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A new study using an innovative machine learning approach finds that distal gene regulatory sites are hypermethylated in cancers
	5.	Research The BET protein FSH functionally interacts with ASH1 to orchestrate global gene activity in Drosophila Tobias Kockmann, Moritz Gerstung, Tommy Schlumpf, Zhu Xhinzhou, Daniel Hess, Niko Beerenwinkel, Christian Beisel, Renato Paro Genome Biology 2013, 14:R18 (25 February 2013) Abstract \| Provisional PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Trithorax group members ASH1 and FSH act as general coactivators of transcription rather than by blocking Polycomb group repression
	6.	Research The B cell transcription program mediates hypomethylation and overexpression of key genes in Epstein-Barr virus-associated proliferative conversion Henar Hernando, Claire Shannon-Lowe, Abul B Islam, Fatima Al-Shahrour, Javier Rodríguez-Ubreva, Virginia C Rodríguez-Cortez, Biola M Javierre, Cristina Mangas, Agustín F Fernández, Maribel Parra, Henri-Jacques Delecluse, Manel Esteller, Eduardo López-Granados, Mario F Fraga, Nuria López-Bigas, Esteban Ballestar Genome Biology 2013, 14:R3 (15 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary DNA hypomethylation is a key feature of Epstein-Barr virus-associated B cell proliferative transformation, and occurs via a passive demethylation process
	7.	Research *Natural variation of H3K27me3 distribution between two Arabidopsis* accessions and its association with flanking transposable elements** Xue Dong, Julia Reimer, Ulrike Göbel, Julia Engelhorn, Fei He, Heiko Schoof, Franziska Turck Genome Biology 2012, 13:R117 (19 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An analysis of natural variation of H3K27me3 in 2 Arabidopsis thaliana accessions and in their F1 hybrids
	8.	Research Human genes with CpG island promoters have a distinct transcription-associated chromatin organization Tanya Vavouri, Ben Lehner Genome Biology 2012, 13:R110 (27 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A study of the chromatin architecture at promoters reveals different histone modifications at those with CpG islands and those without
	9.	Research Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling Mariona Nadal-Ribelles, Núria Conde, Oscar Flores, Juan González-Vallinas, Eduardo Eyras, Modesto Orozco, Eulàlia de Nadal, Francesc Posas Genome Biology 2012, 13:R106 (18 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Hog1 bypasses gene expression regulation by targeting RNA polymerase II machinery and inducing chromatin remodeling at stress-responsive loci
	10.	Opinion The birth of the Epitranscriptome: deciphering the function of RNA modifications Yogesh Saletore, Kate Meyer, Jonas Korlach, Igor D Vilfan, Samie Jaffrey, Christopher E Mason Genome Biology 2012, 13:175 (31 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary First came genomics, and then epigenomics. But is epitranscriptomics the future? A picture is emerging of RNA methylation's functional importance
	11.	Editorial What can epigenomics do for you? Alexander Meissner Genome Biology 2012, 13:420 (23 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Alexander Meissner asks not what you can do for epigenomics, but what epigenomics can do for you
	12.	Editorial The allure of the epigenome Naomi Attar Genome Biology 2012, 13:419 (23 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A guide to the articles published in our special issue on epigenomics
	13.	Research highlight Balance of DNA methylation and demethylation in cancer development Chun-Xiao Song, Chuan He Genome Biology 2012, 13:173 (23 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary How this issue's research article on 5hmC, together with other recent work, adds to our understanding of methylation processes in cancer
	14.	Review The roles of the reprogramming factors Oct4, Sox2 and Klf4 in resetting the somatic cell epigenome during induced pluripotent stem cell generation Ryan Schmidt, Kathrin Plath Genome Biology 2012, 13:251 (22 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary How a dramatic reorganization of the epigenome ultimately results in the induced pluripotent stem cell state
	15.	Review Surveying the epigenomic landscape, one base at a time Gabriel E Zentner, Steven Henikoff Genome Biology 2012, 13:250 (22 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary New methods for mapping histones at higher resolution open many new doors in epigenomics research
	16.	Opinion DNA methylation studies using twins: what are they telling us? Jordana T Bell, Tim D Spector Genome Biology 2012, 13:172 (18 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Jordana Bell and Tim Spector on what twin studies can teach us about human epigenetics
	17.	Research highlight Birds do it, bees do it, worms and ciliates do it too: DNA methylation from unexpected corners of the tree of life Soojin V Yi Genome Biology 2012, 13:174 (17 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Why this issue's research articles on DNA methylation in nematodes and ciliates are surprising, and what we can learn from them
	18.	Research Cytosine methylation and hydroxymethylation mark DNA for elimination in Oxytricha trifallax John R Bracht, David H Perlman, Laura F Landweber Genome Biology 2012, 13:R99 (17 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary DNA hydroxymethylation, via an initial cytosine methylation step, marks loci for genome elimination in the ciliate Oxytricha trifallax
	19.	Software CHANCE: comprehensive software for quality control and validation of ChIP-seq data Aaron Diaz, Abhinav Nellore, Jun S Song Genome Biology 2012, 13:R98 (15 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A user friendly graphical software package with multiple tools for quality assessment of ChIP-seq data
	20.	Review Epialleles in plant evolution Detlef Weigel, Vincent Colot Genome Biology 2012, 13:249 (11 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Detlef Weigel and Vincent Colot review the role of epialleles in plant biology and evolution
	21.	Research Aging effects on DNA methylation modules in human brain and blood tissue Steve Horvath, Yafeng Zhang, Peter Langfelder, René S Kahn, Marco PM Boks, Kristel van Eijk, Leonard H van den Berg, Roel A Ophoff Genome Biology 2012, 13:R97 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An age-related co-methylation module in human brain and blood tissue includes genes associated with Alzheimer's disease
	22.	Software EpiExplorer: live exploration and global analysis of large epigenomic datasets Konstantin Halachev, Hannah Bast, Felipe Albrecht, Thomas Lengauer, Christoph Bock Genome Biology 2012, 13:R96 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A text indexing algorithm enables extremely rapid, global analysis of large epigenomic datasets
	23.	Research Genome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkers Anneleen Decock, Maté Ongenaert, Jasmien Hoebeeck, Katleen De Preter, Gert Van Peer, Wim Van Criekinge, Ruth Ladenstein, Johannes H Schulte, Rosa Noguera, Raymond L Stallings, An Van Damme, Geneviève Laureys, Joëlle Vermeulen, Tom Van Maerken, Frank Speleman, Jo Vandesompele Genome Biology 2012, 13:R95 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Multiple approaches are used to identify high-confidence methylation biomarkers for predicting prognosis in neuroblastoma
	24.	Research Contribution of the epigenetic mark H3K27me3 to functional divergence after whole genome duplication in Arabidopsis Lidija Berke, Gabino F Sanchez-Perez, Berend Snel Genome Biology 2012, 13:R94 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary H3K27me3 is linked to lower expression divergence yet higher coding sequence divergence following Arabidopsis thaliana's recent whole genome duplication
	25.	Research Non-genotoxic carcinogen exposure induces defined changes in the 5-hydroxymethylome John P Thomson, Harri Lempiäinen, Jamie A Hackett, Colm E Nestor, Arne Müller, Federico Bolognani, Edward J Oakeley, Dirk Schübeler, Rémi Terranova, Diana Reinhardt, Jonathan G Moggs, Richard R Meehan Genome Biology 2012, 13:R93 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary 5hmC had been hypothesized to function as an intermediate of active demethylation in carcinogenesis; a rodent model now provides confirmation