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Genome-wide analysis of condensin binding in Caenorhabditis elegans
Anna-Lena Kranz, Chen-Yu Jiao, Lara Heermans Winterkorn, Sarah Elizabeth Albritton, Maxwell Kramer, Sevinç Ercan Genome Biology 2013, 14:R112 (14 October 2013)
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A genome-wide analysis of condensin binding in the model organism Caenorhabditis elegans |
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Cell-cycle regulated transcription associates with DNA replication timing in yeast and human
Hunter B Fraser Genome Biology 2013, 14:R111 (7 October 2013)
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Genes transcribed during S-phase are found to replicate early in human, budding yeast and fission yeast |
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High-efficiency RNA cloning enables accurate quantification of miRNA expression by deep sequencing
Zhaojie Zhang, Jerome E Lee, Kent Riemondy, Emily M Anderson, Rui Yi Genome Biology 2013, 14:R109 (7 October 2013)
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An efficient sRNA cloning method from Rui Yi's lab overcomes ligation biases and enables accurate quantification over a wide dynamic range |
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Cytosine methylation changes in enhancer regions of core pro-fibrotic genes characterize kidney fibrosis development
Yi-An Ko, Davoud Mohtat, Masako Suzuki, Ae Seo Park, Maria Concepcion Izquierdo, Sang Youb Han, Hyun Mi Kang, Han Si, Thomas Hostetter, James M Pullman, Melissa Fazzari, Amit Verma, Deyou Zheng, John M Greally, Katalin Susztak Genome Biology 2013, 14:R108 (7 October 2013)
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The enhancers of genes involved in fibrosis exhibit DNA methylation in chronically diseased kidneys, with correlated changes in gene expression |
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Mechanisms of eukaryotic transcription
Miles A Pufall, Craig D Kaplan Genome Biology 2013, 14:311 (30 September 2013)
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A report on the Cold Spring Harbor Laboratory Mechanisms of Eukaryotic Transcription meeting, Cold Spring Harbor, New York, USA, August 27–31, 2013 |
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Toward knowledge support for analysis and interpretation of complex traits
Nigel Collier, Anika Oellrich, Tudor Groza Genome Biology 2013, 14:214 (30 September 2013)
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Nigel Collier reviews how algorithmic advances are set to enhance the description of complex traits through high-throughput phenotype analysis |
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Neurexins
Carsten Reissner, Fabian Runkel, Markus Missler Genome Biology 2013, 14:213 (30 September 2013)
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A Protein Family Review by Markus Missler and colleagues considers the role of neurexins in synaptic function and, consequently, neurological conditions |
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Crowdfunding genomics and bioinformatics
Pamela Cameron, David W Corne, Christopher E Mason, Jeffrey Rosenfeld Genome Biology 2013, 14:134 (30 September 2013)
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How to bypass traditional research funding routes and seek pennies from the people |
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Runaway transcription
Jiannan Guo, Tiandao Li, David H Price Genome Biology 2013, 14:133 (30 September 2013)
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David Price proposes that 7SK snRNA is a key barrier to runaway transcription - in contrast to the inept engineer Casey Jones |
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PINTing for p53
Ramin Shiekhattar Genome Biology 2013, 14:132 (30 September 2013)
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Ramin Sheikhattar discusses new findings, published in Genome Biology, about a novel lncRNA ('PINT'), p53 and cancer |
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Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus
Laurent AF Frantz, Joshua G Schraiber, Ole Madsen, Hendrik-Jan Megens, Mirte Bosse, Yogesh Paudel, Gono Semiadi, Erik Meijaard, Ning Li, Richard PMA Crooijmans, Alan L Archibald, Montgomery Slatkin, Lawrence B Schook, Greger Larson, Martien AM Groenen Genome Biology 2013, 14:R107 (26 September 2013)
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Genome sequencing points to climatic fluctuations and human mediated translocations as factors impacting upon Sus speciation in Southeast Asia |
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Pint lincRNA connects the p53 pathway with epigenetic silencing by the Polycomb repressive complex 2
Oskar Marin-Bejar, Francesco P Marchese, Alejandro Athie, Yolanda Sanchez, Jovanna Gonzalez, Victor Segura, Lulu Huang, Isabel Moreno, Alfons Navarro, Mariano Monzo, Jesus Garcia-Foncillas, John L Rinn, Shuling Guo, Maite Huarte Genome Biology 2013, 14:R104 (26 September 2013)
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A novel lincRNA, PINT, connects p53 activation with epigenetic silencing by PRC2 and is identified as a candidate tumor suppressor |
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The mutational landscape of chromatin regulatory factors across 4623 tumor samples
Abel Gonzalez-Perez, Alba Jene-Sanz, Nuria Lopez-Bigas Genome Biology 2013, 14:r106 (24 September 2013)
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Identification of mutations in chromatin regulatory factors and their potential role in tumorigenesis |
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Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia
Jessica Nordlund, Christofer L Bäcklin, Per Wahlberg, Stephan Busche, Eva C Berglund, Maija-Leena Eloranta, Trond Flaegstad, Erik Forestier, Britt-Marie Frost, Arja Harila-Saari, Mats Heyman, Ólafur G Jónsson, Rolf Larsson, Josefine Palle, Lars Rönnblom, Kjeld Schmiegelow, Daniel Sinnett, Stefan Söderhäll, Tomi Pastinen, Mats G Gustafsson, Gudmar Lönnerholm, Ann-Christine Syvänen Genome Biology 2013, 14:r105 (24 September 2013)
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DNA methylation signatures associated with subtype, relapse and gene expression in pediatric acute lymphoblastic leukemia |
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Intraspecific variation of recombination rate in maize
Eva Bauer, Matthieu Falque, Hildrun Walter, Cyril Bauland, Christian Camisan, Laura Campo, Nina Meyer, Nicolas Ranc, Renaud Rincent, Wolfgang Schipprack, Thomas Altmann, Pascal Flament, Albrecht E Melchinger, Monica Menz, Jesús Moreno-González, Milena Ouzunova, Pedro Revilla, Alain Charcosset, Olivier C Martin, Chris-Carolin Schön Genome Biology 2013, 14:R103 (19 September 2013)
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A large-scale analysis of recombination rates between 22 European maize inbred lines reveals significant differences in recombination between populations |
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The non-coding snRNA 7SK controls transcriptional termination, poising and bidirectionality in embryonic stem cells
Gonçalo Castelo-Branco, Paulo P Amaral, Pär G Engström, Samuel C Robson, Sueli C Marques, Paul Bertone, Tony Kouzarides Genome Biology 2013, 14:r98 (17 September 2013)
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Editor’s summary
A study in ESCs finds that 7SK promotes transcriptional termination and poising, and regulates bidirectional transcription |
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Differential DNA methylation with age displays both common and dynamic features across human tissues that are influenced by CpG landscape
Kenneth Day, Lindsay L Waite, Anna Thalacker-Mercer, Andrew West, Marcas M Bamman, James D Brooks, Richard M Myers, Devin Absher Genome Biology 2013, 14:R102 (13 September 2013)
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A study of DNA methylation changes in four tissues during aging finds both tissue-specific and universal age-associated methylation changes |
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Reducing assembly complexity of microbial genomes with single-molecule sequencing
Sergey Koren, Gregory P Harhay, Timothy PL Smith, James L Bono, Dayna M Harhay, Scott D Mcvey, Diana Radune, Nicholas H Bergman, Adam M Phillippy Genome Biology 2013, 14:R101 (13 September 2013)
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PacBio sequencing alone is capable of generating finished bacterial genomes in the majority of cases at reasonably low cost |
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On the design of clone-based haplotyping
Christine Lo, Rui Liu, Jehyuk Lee, Kimberly Robasky, Susan Byrne, Carolina Lucchesi, John Aach, George Church, Vineet Bafna, Kun Zhang Genome Biology 2013, 14:R100 (12 September 2013)
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Practical guidelines for the development and design of clone-based methods to achieve long range, high-resolution and accurate haplotypes |
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PU.1 target genes undergo Tet2-coupled demethylation and DNMT3b-mediated methylation in monocyte-to-osteoclast differentiation
Lorenzo de la Rica, Javier Rodríguez-Ubreva, Mireia García, Abul BMMK Islam, José M Urquiza, Henar Hernando, Jesper Christensen, Kristian Helin, Carmen Gómez-Vaquero, Esteban Ballestar Genome Biology 2013, 14:R99 (12 September 2013)
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Tet2 and DNMT3b act in concert with the transcription factor PU.1 to remodel the epigenome during monocyte-to-osteoclast differentiation |
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Assembly of a phased diploid Candida albicans genome facilitates allele-specific measurements and provides a simple model for repeat and indel structure
Dale Muzzey, Katja Schwartz, Jonathan S Weissman, Gavin Sherlock Genome Biology 2013, 14:R97 (11 September 2013)
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An assembly of a diploid Candida albicans phased genome helps detect allele-specific events and significantly expands the number of known polymorphisms |
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An ENU mutagenesis screen identifies novel and known genes involved in epigenetic processes in the mouse
Lucia Daxinger, Sarah K Harten, Harald Oey, Trevor Epp, Luke Isbel, Edward Huang, Nadia Whitelaw, Anwyn Apedaile, Anabel Sorolla, Joan Yong, Vandhana Bharti, Joanne Sutton, Alyson Ashe, Zhenyi Pang, Nathan Wallace, Daniel J Gerhardt, Marnie E Blewitt, Jeffrey A Jeddeloh, Emma Whitelaw Genome Biology 2013, 14:R96 (11 September 2013)
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A full characterization of the Momme screen for mouse genes regulating epigenetic processes includes three novel epigenetic regulators |
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Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data
Franck Rapaport, Raya Khanin, Yupu Liang, Mono Pirun, Azra Krek, Paul Zumbo, Christopher E Mason, Nicholas D Socci, Doron Betel Genome Biology 2013, 14:R95 (10 September 2013)
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An evaluation of differential gene expression analysis methods for RNA-seq data using the SEQC gold standard dataset |
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Are there unequivocal criteria to label a given protein as a toxin? Permissive versus conservative annotation processes
Yves Terrat, Frédéric Ducancel Genome Biology 2013, 14:406 (3 September 2013)
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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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A method for deconvolving brain tissue into neuronal and non-neuronal populations using DNA methylation signatures to allow cell-type specific analysis |
