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Analyzing the soybean transcriptome during autoregulation of mycorrhization identifies the transcription factors GmNF-YA1a/b as positive regulators of arbuscular mycorrhization
Sara Schaarschmidt, Peter M Gresshoff, Bettina Hause Genome Biology 2013, 14:R62 (18 June 2013)
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A transcriptomic analysis of changes in soybean gene expression in response to mycorrhization identifies GmNF-YA1a/b as positive regulators of arbuscular mycorrhization |
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User guide for mapping-by-sequencing in Arabidopsis
Geo Velikkakam James, Vipul Patel, Karl JV Nordstrom, Jonas R Klasen, Patrice A Salome, Detlef Weigel, Korbinian Schneeberger Genome Biology 2013, 14:R61 (17 June 2013)
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Method for mapping-by-sequencing in Arabidopsis, using the Pop-seq software, and application to barley and rice as well |
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Reference genomes and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis
Nicolas Sierro, James ND Battey, Sonia Ouadi, Lucien Bovet, Simon Goepfert, Nicolas Bakaher, Manuel C Peitsch, Nikolai V Ivanov Genome Biology 2013, 14:R60 (17 June 2013)
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Genome sequencing and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis show that differences in alkaloid production may regulate insect resistance |
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Hyperosmotic priming of Arabidopsis seedlings establishes a long-term somatic memory accompanied by specific changes of the epigenome
Emanuela Sani, Pawel Herzyk, Giorgio Perrella, Vincent Colot, Anna Amtmann Genome Biology 2013, 14:R59 (14 June 2013)
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Exposure of young seedlings to salt stress causes histone modifications and transcriptional changes, enhancing stress tolerance in mature plants |
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Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome
María Muñoz-Amatriaín, Steven R Eichten, Thomas Wicker, Todd A Richmond, Martin Mascher, Burkhard Steuernagel, Uwe Scholz, Ruvini Ariyadasa, Manuel Spannagl, Thomas Nussbaumer, Klaus FX Mayer, Stefan Taudien, Matthias Platzer, Jeffrey A Jeddeloh, Nathan M Springer, Gary J Muehlbauer, Nils Stein Genome Biology 2013, 14:R58 (12 June 2013)
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An analysis of copy number variations in 14 barley genomes shows that DNA repair and template slippage may have caused variations |
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Conservation and divergence of transcriptomic and epigenomic variation in maize hybrids
Guangming He, Beibei Chen, Xuncheng Wang, Xueyong Li, Jigang Li, Hang He, Mei Yang, Lu Lu, Yijun Qi, Xiping Wang, Xing Wang Deng Genome Biology 2013, 14:R57 (12 June 2013)
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An analysis of the effect of genotype and tissue type on transcriptional and epigenetic changes in maize inbred lines and hybrids |
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Identification of pathways directly regulated by SHORT VEGETATIVE PHASE during vegetative and reproductive development in Arabidopsis
Veronica Gregis, Fernando Andrés, Alice Sessa, Rosalinda F Guerra, Sara Simonini, Julieta L Mateos, Stefano Torti, Federico Zambelli, Gian Marco Prazzoli, Katrine N Bjerkan, Paul E Grini, Giulio Pavesi, Lucia Colombo, George Coupland, Martin M Kater Genome Biology 2013, 14:R56 (11 June 2013)
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An analysis of SVP-regulated pathways that control vegetative and floral meristem development |
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Comprehensive genotyping of the USA national maize inbred seed bank
Maria C Romay, Mark J Millard, Jeffrey C Glaubitz, Jason A Peiffer, Kelly L Swarts, Terry M Casstevens, Robert J Elshire, Charlotte B Acharya, Sharon E Mitchell, Sherry A Flint-Garcia, Michael D McMullen, James B Holland, Edward S Buckler, Candice A Gardner Genome Biology 2013, 14:R55 (11 June 2013)
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Genotyping-by-Sequencing analysis of maize inbred accessions, identifying candidate genes for kernel color, sweet corn, and flowering time |
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The plasticity of the grapevine berry transcriptome
Silvia Dal Santo, Giovanni Tornielli, Sara Zenoni, Marianna Fasoli, Lorenzo Farina, Andrea Anesi, Flavia Guzzo, Massimo Delledonne, Mario Pezzotti Genome Biology 2013, 14:r54 (7 June 2013)
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A transcriptomic and metabolomic analysis of the plasticity of grapevine berry gene expression in response to development and the environment |
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Plastic, fantastic! Phenotypic variance in the transcriptional landscape of the grape berry
Alisdair R Fernie, Takayuki Tohge Genome Biology 2013, 14:119 (7 June 2013)
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A Research Highlight covering Mario Pezzotti's research article analyzing the plasticity of grape berrys in response to environmental changes |
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The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color
Juan C Motamayor, Keithanne Mockaitis, Jeremy Schmutz, Niina Haiminen, Donald Livingstone, Omar Cornejo, Seth D Findley, Ping Zheng, Filippo Utro, Stefan Royaert, Christopher Saski, Jerry Jenkins, Ram Podicheti, Meixia Zhao, Brian E Scheffler, Joseph C Stack, Frank A Feltus, Guiliana M Mustiga, Freddy Amores, Wilbert Phillips, Jean Philippe Marelli, Gregory D May, Howard Shapiro, Jianxin Ma, Carlos D Bustamante, Raymond J Schnell, Dorrie Main, Don Gilbert, Laxmi Parida, David N Kuhn et al.
Genome Biology 2013, 14:R53 (3 June 2013)
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The genome sequence of Theobroma cacao Matina 1-6 allows the identification of a gene associated with pod color |
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Integrated analysis of recurrent properties of cancer genes to identify novel drivers
Matteo D'Antonio, Francesca D Ciccarelli Genome Biology 2013, 14:R52 (29 May 2013)
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A method to detect rare driver genes through integrated analysis of expression profiles, mutation effects and properties of known cancer genes |
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Characterizing and measuring bias in sequence data
Michael G Ross, Carsten Russ, Maura Costello, Andrew Hollinger, Niall J Lennon, Ryan Hegarty, Chad Nusbaum, David B Jaffe Genome Biology 2013, 14:R51 (29 May 2013)
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A comparison of the bias in sequencing data from four different platforms reveals that some human promoters are completelymissed |
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Machine learning and genome annotation: a match meant to be?
Kevin Y Yip, Chao Cheng, Mark Gerstein Genome Biology 2013, 14:205 (29 May 2013)
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Mark Gerstein, Kevin Yip and Chao Cheng present a beginner's guide to machine learning for genome annotation |
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Deep C diving: mapping the low-abundance modifications of the DNA demethylation pathway
John P Thomson, Jennifer M Hunter, Richard R Meehan Genome Biology 2013, 14:118 (29 May 2013)
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Richard Meehan and colleagues highlight recent insights into the 5th, 6th, 7th and 8th DNA bases: 5mC, 5hmC, 5fC and 5caC |
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DNA methylation dynamics during intestinal stem cell differentiation reveals enhancers driving gene expression in the villus
Lucas JT Kaaij, Marc van de Wetering, Fang Fang, Benjamin Decato, Antoine Molaro, Harmen JG van de Werken, Johan H van Es, Jurian Schuijers, Elzo de Wit, Wouter de Laat, Gregory J Hannon, Hans C Clevers, Andrew D Smith, Rene F Ketting Genome Biology 2013, 14:R50 (28 May 2013)
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Intriguingly, DNA methylation in mouse intestinal cells does not change much during differentiation |
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Genomic triumph meets clinical reality
Qasim Ayub, Yali Xue, Chris Tyler-Smith Genome Biology 2013, 14:307 (28 May 2013)
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A report on the 'Genomic Disorders 2013 - from 60 years of DNA to human genomes in the clinic' meeting, held at Homerton College, Hills Road, Cambridge, UK, April 10-12, 2013. |
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Rising from the crypt: decreasing DNA methylation during differentiation of the small intestine
Sean M Cullen, Margaret A Goodell Genome Biology 2013, 14:116 (28 May 2013)
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A Research Highlight examines why differentiation in the small intestine crypt bypasses the DNA methylation changes observed in other lineage progressions |
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Mutations within lncRNAs are effectively selected against in fruitfly but not in human
Wilfried Haerty, Chris P Ponting Genome Biology 2013, 14:R49 (27 May 2013)
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Analysis of lncRNA conservation in fruitfly and humans shows that these elements are well conserved in insects, but not in mammals |
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Genome-wide analysis of functional sirtuin chromatin targets in yeast
Mingguang Li, Veena Valsakumar, Kunal Poorey, Stefan Bekiranov, Jeffrey S Smith Genome Biology 2013, 14:R48 (27 May 2013)
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Sirtuins regulate both glycolytic gene expression and condensin/cohesin deposition, suggesting a mechanistic link between metabolism and chromatin architecture |
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REAPR: a universal tool for genome assembly evaluation
Martin Hunt, Taisei Kikuchi, Mandy Sanders, Chris Newbold, Matthew Berriman, Thomas D Otto Genome Biology 2013, 14:R47 (27 May 2013)
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A new user-friendly software tool for genome assembly evaluation |
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5-Hydroxymethylcytosine is an essential intermediate of active DNA demethylation processes in primary human monocytes
Maja Klug, Sandra Schmidhofer, Claudia Gebhard, Reinhard Andreesen, Michael Rehli Genome Biology 2013, 14:R46 (26 May 2013)
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TET2-mediated conversion of 5mC to 5hmC initiates active demethylation of the genome during monocyte differentiation |
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Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing
Shivendra Kishore, Andreas R Gruber, Dominik J Jedlinski, Afzal P Syed, Hadi Jorjani, Mihaela Zavolan Genome Biology 2013, 14:R45 (26 May 2013)
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PAR-CLIP of snoRNA-associated proteins reveals the existence of extensive human loci that are processed into snoRNAs |
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Adult monozygotic twins discordant for intra-uterine growth have indistinguishable genome-wide DNA methylation profiles
Nicole YP Souren, Pavlo Lutsik, Gilles Gasparoni, Sascha Tierling, Jasmin Gries, Matthias Riemenschneider, Jean-Pierre Fryns, Catherine Derom, Maurice P Zeegers, Jörn Walter Genome Biology 2013, 14:R44 (26 May 2013)
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Monozygotic twins discordant for birth weight have very similar DNA methylation profiles |
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Inactive or moderately active human promoters are enriched for inter-individual epialleles
Carolina Gemma, Sreeram V Ramagopalan, Thomas A Down, Huriya Beyan, Mohammed I Hawa, Michelle L Holland, Paul J Hurd, Gavin Giovannoni, R David Leslie, George C Ebers, Vardhman K Rakyan Genome Biology 2013, 14:R43 (25 May 2013)
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Epialleles between monozygotic twins are temporally stable, associated with chromatin changes and enriched in transcriptionally inactive regions |
