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Volume 14 Issue 8
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Comment |
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Astrogenomics: big data, old problems, old solutions?
Aaron Golden, S Djorgovski, John M Greally Genome Biology 2013, 14:129 (13 August 2013)
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Editor’s summary
Aaron Golden, George Djorgovski and John Greally on lessons from astronomy that might help genomicists stay afloat in the data deluge |
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Learning the language of post-transcriptional gene regulation
Stefanie Gerstberger, Markus Hafner, Thomas Tuschl Genome Biology 2013, 14:130 (23 August 2013)
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Editor’s summary
RNA-binding proteins: Stefanie Gerstberger, Markus Hafner and Thomas Tuschl on the language of post-transcriptional gene regulation |
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DNA methylation: an identity card for brain cells
Ambre Bender, Michael Weber Genome Biology 2013, 14:131 (27 August 2013)
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Editor’s summary
Ambre Bender and Michael Weber highlight recent work that delineates the dynamics of DNA (hydroxy)methylation during mammalian brain development |
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Report |
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Conquering computational challenges of omics data and post-ENCODE paradigms
Yves A Lussier, Haiquan Li, Mark Maienschein-Cline Genome Biology 2013, 14:310 (23 August 2013)
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Editor’s summary
A report on the 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 12th European Conference on Computational Biology (ECCB), held in Berlin, Germany, July 21-23, 2013 |
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Research |
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Ontogeny, distribution and potential roles of 5-hydroxymethylcytosine in human liver function
Maxim Ivanov, Mart Kals, Marina Kacevska, Isabel Barragan, Kie Kasuga, Anders Rane, Andres Metspalu, Lili Milani, Magnus Ingelman-Sundberg Genome Biology 2013, 14:R83 (19 August 2013)
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Editor’s summary
5-hydroxymethylcytosine distribution and abundance is different between adult and fetal human livers |
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Genome-wide analyses of Shavenbaby target genes reveals distinct features of enhancer organization
Delphine Menoret, Marc Santolini, Isabelle Fernandes, Rebecca Spokony, Jennifer Zanet, Ignacio Gonzalez, Yvan Latapie, Pierre Ferrer, Hervé Rouault, Kevin P White, Philippe Besse, Vincent Hakim, Stein Aerts, Francois Payre, Serge Plaza Genome Biology 2013, 14:R86 (23 August 2013)
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Editor’s summary
Shavenbaby, which induces terminal differentiation in Drosophila, binds to a set of enhancers that exhibit remarkable functional architectures |
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The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery
Roz Laing, Taisei Kikuchi, Axel Martinelli, Isheng J Tsai, Robin N Beech, Elizabeth Redman, Nancy Holroyd, David J Bartley, Helen Beasley, Collette Britton, David Curran, Eileen Devaney, Aude Gilabert, Martin Hunt, Frank Jackson, Stephanie L Johnston, Ivan Kryukov, Keyu Li, Alison A Morrison, Adam J Reid, Neil Sargison, Gary I Saunders, James D Wasmuth, Adrian Wolstenholme, Matthew Berriman, John S Gilleard, James A Cotton Genome Biology 2013, 14:R88 (28 August 2013)
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Editor’s summary
The genome and transcriptome of Haemonchus contortus, a nematode parasite of sheep, provides insights into antihelminthic resistance |
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The genome and developmental transcriptome of the strongylid nematode Haemonchus contortus
Erich M Schwarz, Pasi K Korhonen, Bronwyn E Campbell, Neil D Young, Aaron R Jex, Abdul Jabbar, Ross S Hall, Alinda Mondal, Adina C Howe, Jason Pell, Andreas Hofmann, Peter R Boag, Xing-Quan Zhu, T Gregory, Alex Loukas, Brian A Williams, Igor Antoshechkin, C Brown, Paul W Sternberg, Robin B Gasser Genome Biology 2013, 14:R89 (28 August 2013)
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Editor’s summary
Analysis of the Haemonchus contortus genome and developmental transcriptome provides insights into its RNAi machinery and identifies potential anthelmintic drug targets |
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Genome-wide analysis identifies a functional association of Tet1 and Polycomb repressive complex 2 in mouse embryonic stem cells
Francesco Neri, Danny Incarnato, Anna Krepelova, Stefania Rapelli, Andrea Pagnani, Riccardo Zecchina, Caterina Parlato, Salvatore Oliviero Genome Biology 2013, 14:R91 (29 August 2013)
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Editor’s summary
Genome-wide analysis of TET1 binding identifies an interaction between TET1 and PRC2 in ESCs, which recruits TET1 to regions of H3K27me3 |
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A global profiling of uncapped mRNAs under cold stress reveals specific decay patterns and endonucleolytic cleavages in Brachypodium distachyon
Jingyu Zhang, Zhiwei Mao, Kang Chong Genome Biology 2013, 14:R92 (30 August 2013)
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Editor’s summary
Genes regulating photosynthesis undergo rapid changes in transcript stability in response to cold treatment in Brachypodium distachyon |
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PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs
Annalisa Marsico, Matthew R Huska, Julia Lasserre, Haiyang Hu, Dubravka Vucicevic, Anne Musahl, Ulf Andersson Orom, Martin Vingron Genome Biology 2013, 14:R84 (19 August 2013)
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Editor’s summary
A new method for the detection of intronic microRNA promoters |
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Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits
Molly Megraw, Sayan Mukherjee, Uwe Ohler Genome Biology 2013, 14:R85 (23 August 2013)
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Editor’s summary
A new, rigorous algorithm for the generation of null models for identification of over-represented circuits in large networks |
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Virmid: accurate detection of somatic mutations with sample impurity inference
Sangwoo Kim, Kyowon Jeong, Kunal Bhutani, Jeong Lee, Anand Patel, Eric Scott, Hojung Nam, Hayan Lee, Joseph G Gleeson, Vineet Bafna Genome Biology 2013, 14:R90 (29 August 2013)
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Editor’s summary
Virmid is a method for estimating the proportion of healthy cells in a disease sample to facilitate variant calling |
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Measuring cell-type specific differential methylation in human brain tissue
Carolina M Montaño, Rafael A Irizarry, Walter E Kaufmann, Konrad Talbot, Raquel E Gur, Andrew P Feinberg, Margaret A Taub Genome Biology 2013, 14:R94 (30 August 2013)
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Editor’s summary
A method for deconvolving brain tissue into neuronal and non-neuronal populations using DNA methylation signatures to allow cell-type specific analysis |
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BreakTrans: uncovering the genomic architecture of gene fusions
Ken Chen, Nicholas E Navin, Yong Wang, Heather K Schmidt, John W Wallis, Beifang Niu, Xian Fan, Hao Zhao, Michael D McLellan, Katherine A Hoadley, Elaine R Mardis, Timothy J Ley, Charles M Perou, Richard K Wilson, Li Ding Genome Biology 2013, 14:R87 (23 August 2013)
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Editor’s summary
A new bioinformatic tool for the detection of cancer-related gene fusions and underlying genomic structural rearrangements |
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Web Apollo: a web-based genomic annotation editing platform
Eduardo Lee, Gregg A Helt, Justin T Reese, Monica C Munoz-Torres, Chris P Childers, Robert M Buels, Lincoln Stein, Ian H Holmes, Christine G Elsik, Suzanna E Lewis Genome Biology 2013, 14:R93 (30 August 2013)
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Editor’s summary
A new web-based tool for international collaborations on genome annotations |
