Genome Biology | Volume 13 Issue 10

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	Volume 13 Issue 10 Epigenomics special issue Guest Editor: Alexander Meissner In this issue of Genome Biology we present a special collection of Research, Review, Opinion, Research Highlight and Editorial articles focusing on epigenomics. The issue provides a variety of new insights into the biology of DNA methylation, histone modifications and chromatin organization, and includes perspectives on epigenomics past, present and future from leaders in the field.
	Comment
	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
	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
	Comment Hypothesis-driven genomics pays off Gregory A Petsko Genome Biology 2012, 13:176 (30 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Greg Petsko on deCode's rocky road to AD drug discovery
	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
	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
	Review
	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
	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
	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
	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
	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
	Report
	Meeting report Bioinformatics: living on the edge Evangelos Bellos, Lachlan JM Coin, Myrsini Kaforou Genome Biology 2012, 13:321 (26 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 11th European Conference on Computational Biology (ECCB), held at Basel, Switzerland, September 9-12, 2012
	Research
	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
	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
	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
	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
	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
	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 \| Cited on BioMed Central \| Editor’s summary Inherited changes in transcriptional networks associated with epimutations in rats treated with the fungicide vinclozolin
	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
	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
	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
	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
	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
	Research Differential DNA methylation in discrete developmental stages of the parasitic nematode Trichinella spiralis Fei Gao, Xiaolei Liu, Xiu-Ping Wu, Xue-Lin Wang, Desheng Gong, Hanlin Lu, Yudong Xia, Yanxia Song, Junwen Wang, Jing Du, Siyang Liu, Xu Han, Yizhi Tang, Huanming Yang, Qi Jin, Xiuqing Zhang, Mingyuan Liu Genome Biology 2012, 13:R100 (17 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The discovery of DNA methylation in the parasitic worm Trichinella spiralis, a human pathogen, challenges the prevailing dogma of nematode epigenetics
	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
	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
	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 \| Cited on BioMed Central \| Editor’s summary An extremely sensitive, high-throughput mass spectrometry platform for the unambiguous identification of histone post-translational modifications
	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
	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
	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
	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

	Volume 13 Issue 10 Epigenomics special issue Guest Editor: Alexander Meissner In this issue of Genome Biology we present a special collection of Research, Review, Opinion, Research Highlight and Editorial articles focusing on epigenomics. The issue provides a variety of new insights into the biology of DNA methylation, histone modifications and chromatin organization, and includes perspectives on epigenomics past, present and future from leaders in the field.
	Comment
	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
	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
	Comment Hypothesis-driven genomics pays off Gregory A Petsko Genome Biology 2012, 13:176 (30 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Greg Petsko on deCode's rocky road to AD drug discovery
	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
	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
	Review
	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
	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
	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
	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
	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
	Report
	Meeting report Bioinformatics: living on the edge Evangelos Bellos, Lachlan JM Coin, Myrsini Kaforou Genome Biology 2012, 13:321 (26 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 11th European Conference on Computational Biology (ECCB), held at Basel, Switzerland, September 9-12, 2012
	Research
	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
	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
	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
	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
	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
	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 \| Cited on BioMed Central \| Editor’s summary Inherited changes in transcriptional networks associated with epimutations in rats treated with the fungicide vinclozolin
	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
	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
	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
	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
	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
	Research Differential DNA methylation in discrete developmental stages of the parasitic nematode Trichinella spiralis Fei Gao, Xiaolei Liu, Xiu-Ping Wu, Xue-Lin Wang, Desheng Gong, Hanlin Lu, Yudong Xia, Yanxia Song, Junwen Wang, Jing Du, Siyang Liu, Xu Han, Yizhi Tang, Huanming Yang, Qi Jin, Xiuqing Zhang, Mingyuan Liu Genome Biology 2012, 13:R100 (17 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The discovery of DNA methylation in the parasitic worm Trichinella spiralis, a human pathogen, challenges the prevailing dogma of nematode epigenetics
	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
	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
	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 \| Cited on BioMed Central \| Editor’s summary An extremely sensitive, high-throughput mass spectrometry platform for the unambiguous identification of histone post-translational modifications
	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
	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
	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
	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

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Volume 13 Issue 10

Epigenomics special issue

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