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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
	26.	Method Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling Patrick Boyle, Kendell Clement, Hongcang Gu, Zachary D Smith, Michael Ziller, Jennifer L Fostel, Laurie Holmes, Jim Meldrim, Fontina Kelley, Andreas Gnirke, Alexander Meissner Genome Biology 2012, 13:R92 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A protocol for gel-free multiplexed reduced representation bisulfite sequencing increases the throughput and reduces the cost of large-scale DNA methylation profiling
	27.	Research Epigenetic transgenerational inheritance of somatic transcriptomes and epigenetic control regions Michael K Skinner, Mohan Manikkam, Md M Haque, Bin Zhang, Marina I Savenkova Genome Biology 2012, 13:R91 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Inherited changes in transcriptional networks associated with epimutations in rats treated with the fungicide vinclozolin
	28.	Research The landscape of DNA repeat elements in human heart failure Syed Haider, Lina Cordeddu, Emma Robinson, Mehregan Movassagh, Lee Siggens, Ana Vujic, Mun-Kit Choy, Martin Goddard, Pietro Lio, Roger Foo Genome Biology 2012, 13:R90 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of repeat families in human heart failure finds satellite repeat elements to be specifically hypomethylated and transcriptionally upregulated
	29.	Research Epigenetic interplay between mouse endogenous retroviruses and host genes Rita Rebollo, Katharine Miceli-Royer, Ying Zhang, Sharareh Farivar, Liane Gagnier, Dixie L Mager Genome Biology 2012, 13:R89 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genes proximal to mouse endogenous retroviral elements defend against the invasion of silencing methylation using both buffer regions and euchromatin propagation
	30.	Research Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity Alok K Tewari, Galip Yardimci, Yoichiro Shibata, Nathan C Sheffield, Lingyun Song, Barry S Taylor, Stoyan G Georgiev, Gerhard A Coetzee, Uwe Ohler, Terrence S Furey, Gregory E Crawford, Phillip G Febbo Genome Biology 2012, 13:R88 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Androgen receptor binding to the genome occurs by multiple mechanisms and is associated with an increase in chromatin accessibility
	31.	Software methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles Altuna Akalin, Matthias Kormaksson, Sheng Li, Francine E Garrett-Bakelman, Maria E Figueroa, Ari Melnick, Christopher E Mason Genome Biology 2012, 13:R87 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An R package (incorporating multiple analysis tools) automates and simplifies the characterization of methylation datasets
	32.	Method Enhanced top-down characterization of histone post-translational modifications Zhixin Tian, Nikola Tolić, Rui Zhao, Ronald J Moore, Shawna M Hengel, Errol W Robinson, David L Stenoien, Si Wu, Richard D Smith, Ljiljana Paša-Tolić Genome Biology 2012, 13:R86 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An extremely sensitive, high-throughput mass spectrometry platform for the unambiguous identification of histone post-translational modifications
	33.	Research H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions Manching Ku, Jacob D Jaffe, Richard P Koche, Esther Rheinbay, Mitsuhiro Endoh, Haruhiko Koseki, Steven A Carr, Bradley E Bernstein Genome Biology 2012, 13:R85 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The landscape of H2A.Z, including a novel post-transcriptionally modified variant, in ES and neural progenitor cells
	34.	Research Tissue of origin determines cancer-associated CpG island promoter hypermethylation patterns Duncan Sproul, Robert R Kitchen, Colm E Nestor, J Michael Dixon, Andrew H Sims, David J Harrison, Bernard H Ramsahoye, Richard R Meehan Genome Biology 2012, 13:R84 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Aberrant promoter hypermethylation in cancer does not promote tumorigenesis, but instead reinforces repression inherited from pre-cancerous tissue
	35.	Method BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions Kasper D Hansen, Benjamin Langmead, Rafael A Irizarry Genome Biology 2012, 13:R83 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An alignment, quality control and analysis pipeline for bisulfite sequencing data
	36.	Method BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation Jing-Quan Lim, Chandana Tennakoon, Guoliang Li, Eleanor Wong, Yijun Ruan, Chia-Lin Wei, Wing-Kin Sung Genome Biology 2012, 13:R82 (3 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary BatMeth is a fast, accurate tool for mapping Illumina or SOLiD bisulfite sequencing reads
	37.	Research Modeling gene expression using chromatin features in various cellular contexts Xianjun Dong, Melissa C Greven, Anshul Kundaje, Sarah Djebali, James B Brown, Chao Cheng, Thomas R Gingeras, Mark Gerstein, Roderic Guigó, Ewan Birney, Zhiping Weng Genome Biology 2012, 13:R53 (5 September 2012) This article is part of a collection on The ENCODE project Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Models for linking gene expression with chromatin features vary according to cellular context and RNA measurement method
	38.	Research Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase Eun-Ang Raiber, Dario Beraldi, Gabriella Ficz, Heather E Burgess, Miguel R Branco, Pierre Murat, David Oxley, Michael J Booth, Wolf Reik, Shankar Balasubramanian Genome Biology 2012, 13:R69 (17 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genome-wide mapping of 5-formylcytosine in ES cells reveals an enrichment in promoter and exon CpG islands, and an association with transcription
	39.	Research Proteogenomic characterization and mapping of nucleosomes decoded by Brd and HP1 proteins Gary LeRoy, Iouri Chepelev, Peter A DiMaggio, Mario A Blanco, Barry M Zee, Keji Zhao, Benjamin A Garcia Genome Biology 2012, 13:R68 (16 August 2012) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary A novel proteogenomic strategy links the histone reader proteins Brd3 and Brd4 to HOX gene regulation
	40.	Research highlight The aging epigenome: DNA methylation from the cradle to the grave Marc Winnefeld, Frank Lyko Genome Biology 2012, 13:165 (30 July 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Frank Lyko and Marc Winnefeld highlight a new survey of age-related epigenetic changes in newborn and centenarian methylomes
	41.	Research Developmental features of DNA methylation during activation of the embryonic zebrafish genome Ingrid S Andersen, Andrew H Reiner, Håvard Aanes, Peter Aleström, Philippe Collas Genome Biology 2012, 13:R65 (25 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary DNA methylation patterning at developmental genes is assayed before, during and after zygotic genome activation
	42.	Research highlight *piRNAs and siRNAs collaborate in Caenorhabditis elegans* genome defense** Allison C Billi, Mallory A Freeberg, John K Kim Genome Biology 2012, 13:164 (20 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary John Kim and colleagues discuss transgenerational genome surveillance and the recognition of non-self by the worm piRNA system
	43.	Method Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data Yaping Liu, Kimberly D Siegmund, Peter W Laird, Benjamin P Berman Genome Biology 2012, 13:R61 (11 July 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A model-based SNP caller for bisulfite sequencing data improves methylation estimates and imprinting analysis
	44.	Review The role of longitudinal cohort studies in epigenetic epidemiology: challenges and opportunities Jane WY Ng, Laura M Barrett, Andrew Wong, Diana Kuh, George Smith, Caroline L Relton Genome Biology 2012, 13:246 (29 June 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Longitudinal cohort studies provide an opportunity to study how changes in epigenetic patterns occur in response to diverse factors
	45.	Method SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips Jovana Maksimovic, Lavinia Gordon, Alicia Oshlack Genome Biology 2012, 13:R44 (15 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for normalizing the Illumina 450k methylation array data, allowing analysis of the genome-wide methylation status of the human genome
	46.	Research Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood Matthew N Davies, Manuela Volta, Ruth Pidsley, Katie Lunnon, Abhishek Dixit, Simon Lovestone, Cristian Coarfa, R Alan Harris, Aleksandar Milosavljevic, Claire Troakes, Safa Al-Sarraj, Richard Dobson, Leonard C Schalkwyk, Jonathan Mill Genome Biology 2012, 13:R43 (15 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Differentially methylated regions are annotated using matched blood and brain samples from multiple individuals
	47.	Research highlight Enhancer dysfunction: how the main regulators of gene expression contribute to cancer Siavash K Kurdistani Genome Biology 2012, 13:156 (23 May 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Research Highlight on the role of variant epigenetics in establishing an enhancer element-mediated oncogenic transcriptional program
	48.	Research Genome-wide identification and characterization of replication origins by deep sequencing Jia Xu, Yoshimi Yanagisawa, Alexander M Tsankov, Christopher Hart, Keita Aoki, Naveen Kommajosyula, Kathleen E Steinmann, James Bochicchio, Carsten Russ, Aviv Regev, Oliver J Rando, Chad Nusbaum, Hironori Niki, Patrice Milos, Zhiping Weng, Nicholas Rhind Genome Biology 2012, 13:R27 (24 April 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Single-molecule deep sequencing and comparative genomics in three Schizosaccharomyces species sheds light on the nature of replication origins
	49.	Meeting report Epigenomics and chromatin dynamics Veronika Akopian, Michelle M Chan, Kendell Clement, Christina Galonska, Casey A Gifford, Elizabeth Lehtola, Jing Liao, Payman Samavarchi-Tehrani, Camille Sindhu, Zachary D Smith, Alexander M Tsankov, Jamie Webster, Yingying Zhang, Michael J Ziller, Alexander Meissner Genome Biology 2012, 13:313 (24 February 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Joint Keystone Symposium on Epigenomics and Chromatin Dynamics, Keystone, Colorado, 17-22 January 2012
	50.	Research Population-specificity of human DNA methylation Hunter B Fraser, Lucia L Lam, Sarah M Neumann, Michael S Kobor Genome Biology 2012, 13:R8 (9 February 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Measurement of TSS-proximal DNA methylation in CEU and YRI genomes reveals significant population specificity