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The multidrug-resistant PMEN1 pneumococcus is a paradigm for genetic success
Kelly L Wyres, Lotte M Lambertsen, Nicholas J Croucher, Lesley McGee, Anne von Gottberg, Josefina Liñares, Michael R Jacobs, Karl G Kristinsson, Bernard W Beall, Keith P Klugman, Julian Parkhill, Regine Hakenbeck, Stephen D Bentley, Angela B Brueggemann Genome Biology 2012, 13:R103 (16 November 2012)
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Sequencing of a collection of isolates of Streptococcus pneumoniae reveals extensive gene transfer between the virulent strain PMEN1 and other strains
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Evidence for conserved post-transcriptional roles of unitary pseudogenes and for frequent bifunctionality of mRNAs
Ana C Marques, Jennifer Tan, Sheena Lee, Lesheng Kong, Andreas Heger, Chris P Ponting Genome Biology 2012, 13:R102 (15 November 2012)
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Analysis of pseudogenes in the mouse genome shows that some transcripts have a regulatory role separate from their protein coding potential
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Microbiome dynamics of human epidermis following skin barrier disruption
Patrick LJM Zeeuwen, Jos Boekhorst, Ellen H van den Bogaard, Heleen D de Koning, Peter MC van de Kerkhof, Delphine M Saulnier, Iris I van Swam, Sacha AFT van Hijum, Michiel Kleerebezem, Joost Schalkwijk, Harro M Timmerman Genome Biology 2012, 13:R101 (15 November 2012)
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An analysis of the microbiota of the surface and deeper layers of skin, and how it changes following skin barrier disruption
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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)
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First came genomics, and then epigenomics. But is epitranscriptomics the future? A picture is emerging of RNA methylation's functional importance
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Hypothesis-driven genomics pays off
Gregory A Petsko Genome Biology 2012, 13:176 (30 October 2012)
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Greg Petsko on deCode's rocky road to AD drug discovery
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Bioinformatics: living on the edge
Evangelos Bellos, Lachlan JM Coin, Myrsini Kaforou Genome Biology 2012, 13:321 (26 October 2012)
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A report on the 11th European Conference on Computational Biology (ECCB), held at Basel, Switzerland, September 9-12, 2012
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What can epigenomics do for you?
Alexander Meissner Genome Biology 2012, 13:420 (23 October 2012)
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Alexander Meissner asks not what you can do for epigenomics, but what epigenomics can do for you
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The allure of the epigenome
Naomi Attar Genome Biology 2012, 13:419 (23 October 2012)
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A guide to the articles published in our special issue on epigenomics
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Balance of DNA methylation and demethylation in cancer development
Chun-Xiao Song, Chuan He Genome Biology 2012, 13:173 (23 October 2012)
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How this issue's research article on 5hmC, together with other recent work, adds to our understanding of methylation processes in cancer
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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)
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How a dramatic reorganization of the epigenome ultimately results in the induced pluripotent stem cell state
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Surveying the epigenomic landscape, one base at a time
Gabriel E Zentner, Steven Henikoff Genome Biology 2012, 13:250 (22 October 2012)
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New methods for mapping histones at higher resolution open many new doors in epigenomics research
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DNA methylation studies using twins: what are they telling us?
Jordana T Bell, Tim D Spector Genome Biology 2012, 13:172 (18 October 2012)
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Jordana Bell and Tim Spector on what twin studies can teach us about human epigenetics
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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)
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DNA hydroxymethylation, via an initial cytosine methylation step, marks loci for genome elimination in the ciliate Oxytricha trifallax
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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)
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The discovery of DNA methylation in the parasitic worm Trichinella spiralis, a human pathogen, challenges the prevailing dogma of nematode epigenetics
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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)
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Why this issue's research articles on DNA methylation in nematodes and ciliates are surprising, and what we can learn from them
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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)
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A user friendly graphical software package with multiple tools for quality assessment of ChIP-seq data
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Epialleles in plant evolution
Detlef Weigel, Vincent Colot Genome Biology 2012, 13:249 (11 October 2012)
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Detlef Weigel and Vincent Colot review the role of epialleles in plant biology and evolution
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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)
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An age-related co-methylation module in human brain and blood tissue includes genes associated with Alzheimer's disease
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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)
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A text indexing algorithm enables extremely rapid, global analysis of large epigenomic datasets
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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)
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Multiple approaches are used to identify high-confidence methylation biomarkers for predicting prognosis in neuroblastoma
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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)
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H3K27me3 is linked to lower expression divergence yet higher coding sequence divergence following Arabidopsis thaliana's recent whole genome duplication
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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)
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5hmC had been hypothesized to function as an intermediate of active demethylation in carcinogenesis; a rodent model now provides confirmation
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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)
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A protocol for gel-free multiplexed reduced representation bisulfite sequencing increases the throughput and reduces the cost of large-scale DNA methylation profiling
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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)
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Inherited changes in transcriptional networks associated with epimutations in rats treated with the fungicide vinclozolin
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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)
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An analysis of repeat families in human heart failure finds satellite repeat elements to be specifically hypomethylated and transcriptionally upregulated
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