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High-throughput sequencing to decipher the genetic heterogeneity of deafness
Zippora Brownstein, Yoni Bhonker, Karen B Avraham Genome Biology 2012, 13:245 (29 May 2012)
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High-throughput sequencing approaches have accelerated the discovery of genes related to hearing loss, and may reshape clinical diagnosis of deafness
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A high-throughput approach to identify genomic variants of bacterial metabolite producers at the single-cell level
Stephan Binder, Georg Schendzielorz, Norma Stäbler, Karin Krumbach, Kristina Hoffmann, Michael Bott, Lothar Eggeling Genome Biology 2012, 13:R40 (28 May 2012)
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A novel high-throughput method that uses in vivo metabolite sensors to identify bacterial metabolite producers
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The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation
Guillaume Blanc, Irina Agarkova, Jane Grimwood, Alan Kuo, Andrew Brueggeman, David D Dunigan, James Gurnon, Istvan Ladunga, Erika Lindquist, Susan Lucas, Jasmyn Pangilinan, Thomas Pröschold, Asaf Salamov, Jeremy Schmutz, Donald Weeks, Takashi Yamada, Alexandre Lomsadze, Mark Borodovsky, Jean-Michel Claverie, Igor V Grigoriev, James L Van Etten Genome Biology 2012, 13:R39 (25 May 2012)
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The first genome of a polar eukaryotic microorganism, an alga called Coccomyxa subellipsoidea C-169, reveals universal strategies for cold adaptation
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Genomic diversity of the human intestinal parasite Entamoeba histolytica
Gareth D Weedall, C Graham Clark, Pia Koldkjaer, Suzanne Kay, Iris Bruchhaus, Egbert Tannich, Steve Paterson, Neil Hall Genome Biology 2012, 13:R38 (25 May 2012)
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Ten strains of Entamoeba histolytica are sequenced. Low levels of genetic diversity are found, and evidence for sexual reproduction is uncovered
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Comparative multi-omics systems analysis of Escherichia coli strains B and K-12
Sung Yoon, Mee-Jung Han, Haeyoung Jeong, Choong Lee, Xiao-Xia Xia, Dae-Hee Lee, Ji Shim, Sang Lee, Tae Oh, Jihyun F Kim Genome Biology 2012, 13:R37 (25 May 2012)
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An analysis of multi-omics data and the generation of a genome-scale metabolic network to determine the phenotypic characteristics of E. coli
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A Keystone for ncRNA
Ezgi Hacisuleyman, Moran N Cabili, John L Rinn Genome Biology 2012, 13:315 (25 May 2012)
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John Rinn and colleagues give a report on the Keystone symposium 'Non-coding RNAs' held at Snowbird, Utah, USA, 31 March to 5 April 2012.
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A systematic screen reveals new elements acting at the G2/M cell cycle control
Francisco J Navarro, Paul Nurse Genome Biology 2012, 13:R36 (24 May 2012)
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A screen for regulators of the G2/M transition in fission yeast reveals novel regulators of cell cycle control
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Mammalian tissues defective in nonsense-mediated mRNA decay display highly aberrant splicing patterns
Joachim Weischenfeldt, Johannes Waage, Geng Tian, Jing Zhao, Inge Damgaard, Janus Jakobsen, Karsten Kristiansen, Anders Krogh, Jun Wang, Bo T Porse Genome Biology 2012, 13:R35 (24 May 2012)
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An extensive in vivo analysis of how nonsense mediated mRNA decay regulates alternative splicing in two mouse tissues
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A new approach for detecting low-level mutations in next-generation sequence data
Mingkun Li, Mark Stoneking Genome Biology 2012, 13:R34 (23 May 2012)
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A method is presented for differentiating mutations present at low level in a sample from sequencing errors
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Enhancer dysfunction: how the main regulators of gene expression contribute to cancer
Siavash K Kurdistani Genome Biology 2012, 13:156 (23 May 2012)
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A Research Highlight on the role of variant epigenetics in establishing an enhancer element-mediated oncogenic transcriptional program
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Layer cake: the first bite at gene expression diversity in the human brain
Philipp Khaitovich Genome Biology 2012, 13:157 (22 May 2012)
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Philipp Khaitovich highlights research by Allan Jones and colleagues that assesses regional gene expression in the human brain neocortex
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Goodbye, Columbus
Gregory A Petsko Genome Biology 2012, 13:155 (18 May 2012)
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Guaranteeing experimental outcomes and findings: funding then and now
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A quantitative literature-curated gold standard for kinase-substrate pairs
Sara Sharifpoor, Alex N Nguyen Ba, Ji-Young Youn, Dewald van Dyk, Helena Friesen, Alison C Douglas, Christoph F Kurat, Yolanda T Chong, Karen Founk, Alan M Moses, Brenda J Andrews Genome Biology 2012, 13:417 (10 May 2012)
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A metagenomic study of diet-dependent interaction between gut microbiota and host in infants reveals differences in immune response
Scott Schwartz, Iddo Friedberg, Ivan V Ivanov, Laurie A Davidson, Jennifer S Goldsby, David B Dahl, Damir Herman, Mei Wang, Sharon M Donovan, Robert S Chapkin Genome Biology 2012, 13:r32 (30 April 2012)
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A novel host-microbiome analysis method reveals a transcriptional immune response in the breast-fed infant gut associated with diet-specific microbiota
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Genetic architecture of body size in mammals
Kathryn E Kemper, Peter M Visscher, Michael E Goddard Genome Biology 2012, 13:244 (30 April 2012)
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Peter Visscher and colleagues survey the current known mutations affecting body size in humans, mice, dogs and livestock species
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Economies of scale
Gregory A Petsko Genome Biology 2012, 13:154 (30 April 2012)
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The current glut of postdoctoral and graduate scientists can be addressed by applying economic principles.
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We are what we eat: how the diet of infants affects their gut microbiome
Mihai Pop Genome Biology 2012, 13:152 (30 April 2012)
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We are what we eat: Mihai Pop highlights our Research article investigating the impact of diet on an infant's gut
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Genetic basis of transcriptome differences between the founder strains of the rat HXB/BXH recombinant inbred panel
Marieke Simonis, Santosh S Atanur, Sam Linsen, Victor Guryev, Frans-Paul Ruzius, Laurence Game, Nico Lansu, Ewart de Bruijn, Sebastiaan van Heesch, Steven JM Jones, Michal Pravenec, Tim J Aitman, Edwin Cuppen Genome Biology 2012, 13:r31 (27 April 2012)
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The genome and transcriptome sequences of the founder strains of the HXB/BXH panel of recombinant inbred rat strains
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Current challenges in de novo plant genome sequencing and assembly
Michael C Schatz, Jan Witkowski, W Richard McCombie Genome Biology 2012, 13:243 (27 April 2012)
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Michael Schatz and colleagues assess challenges in de novo plant genome assembly and review the best practices for the plant community
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The Arabidopsis clock: time for an about-face?
David E Somers Genome Biology 2012, 13:153 (27 April 2012)
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David Somers highlights three recent papers that arrive at a surprising conclusion about how TOC1 functions in the plant circadian clock
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Global mRNA decay analysis at single nucleotide resolution reveals segmental and positional degradation patterns in a Gram-positive bacterium
Simen M Kristoffersen, Chad Haase, M Ryan Weil, Karla D Passalacqua, Faheem Niazi, Stephen K Hutchison, Brian Desany, Anne-Brit Kolstø, Nicolas J Tourasse, Timothy D Read, Ole Økstad Genome Biology 2012, 13:R30 (26 April 2012)
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RNA-seq is used to determine mRNA decay rates to single nucleotide resolution in the Gram positive bacterium Bacillus cereus
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RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations
Mauro AA Castro, Xin Wang, Michael NC Fletcher, Kerstin B Meyer, Florian Markowetz Genome Biology 2012, 13:R29 (24 April 2012)
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A method for visualizing complex, large-scale networks that combines R/Bioconductor with Java, and allows the incorporation of plug-ins
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Mediation of Drosophila autosomal dosage effects and compensation by network interactions
John H Malone, Dong-Yeon Cho, Nicolas R Mattiuzzo, Carlo G Artieri, Lichun Jiang, Ryan K Dale, Harold E Smith, Jennifer McDaniel, Sarah Munro, Marc Salit, Justen Andrews, Teresa M Przytycka, Brian Oliver Genome Biology 2012, 13:R28 (24 April 2012)
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A comprehensive RNA-seq analysis of autosomal dosage effects and compensation in 21 autosomal deficiency Drosophila lines
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Genome-wide identification and characterization of replication origins by deep sequencing
Jia Xu, Yoshimi Yanagisawa, Alexander M Tsankov, Christopher Hart, Keita Aoki, Naveen Kommajosyula, Kathleen E Steinmann, James Bochicchio, Carsten Russ, Aviv Regev, Oliver J Rando, Chad Nusbaum, Hironori Niki, Patrice Milos, Zhiping Weng, Nicholas Rhind Genome Biology 2012, 13:R27 (24 April 2012)
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Single-molecule deep sequencing and comparative genomics in three Schizosaccharomyces species sheds light on the nature of replication origins
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High levels of RNA-editing site conservation amongst 15 laboratory mouse strains
Petr Danecek, Christoffer Nellåker, Rebecca E McIntyre, Jorge E Buendia-Buendia, Suzannah Bumpstead, Chris P Ponting, Jonathan Flint, Richard Durbin, Thomas M Keane, David J Adams Genome Biology 2012, 13:r26 (23 April 2012)
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An extensive, genome-wide analysis of RNA editing in the brain transcriptomes of 15 mouse strains
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