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		Research 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 Dunigan, James Gurnon, Istvan Ladunga, Erika Lindquist, Susan Lucas, Jasmyn Pangilinan, Thomas Proschold, Asaf Salamov, Jeremy Schmutz, Donald Weeks, Takashi Yamada, Jean-Michel Claverie, Igor Grigoriev, James Van Etten, Alexandre Lomsadze, Mark Borodovsky Genome Biology 2012, 13:R39 (25 May 2012) Abstract \| Provisional PDF \| Editor’s summary The first genome of a polar eukaryotic microorganism, an alga called Coccomyxa subellipsoidea C-169, reveals universal strategies for cold adaptation
		Research Genomic diversity of the human intestinal parasite Entamoeba histolytica Gareth D Weedall, Graham Clarck, Pia Koldkjaer, Suzanne Kay, Iris Bruchhaus, Egbert Tannich, Steve Patterson, Neil Hall Genome Biology 2012, 13:R38 (25 May 2012) Abstract \| Provisional PDF \| Editor’s summary Ten strains of Entamoeba histolytica are sequenced. Low levels of genetic diversity are found, and evidence for sexual reproduction is uncovered
		Research Comparative multi-omics systems analysis of Escherichia coli strains B and K-12 Sung Ho Yoon, Mee-Jung Han, Haeyoung Jeong, Choong Hoon Lee, Xiao-Xia Xia, Dae-Hee Lee, Ji Hoon Shim, Sang Yup Lee, Tae Kwang Oh, Jihyun F Kim Genome Biology 2012, 13:R37 (25 May 2012) Abstract \| Provisional PDF \| Editor’s summary An analysis of multi-omics data and the generation of a genome-scale metabolic network to determine the phenotypic characteristics of E. coli
		Meeting report A Keystone for ncRNA Ezgi Hacisuleyman, Moran N Cabili, John L Rinn Genome Biology 2012, 13:315 (25 May 2012) Abstract \| Full text \| PDF \| Editor’s summary 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.
		Research 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A screen for regulators of the G2/M transition in fission yeast reveals novel regulators of cell cycle control
		Research Mammalian tissues defective in nonsense-mediated mRNA decay display highly aberrant splicing patterns Joachim Weischenfeldt, Johannes E Waage, Geng Tian, Jing Zhao, Inge Damgaard, Janus S Jakobsen, Karsten Kristiansen, Anders Krogh, Jun Wang, Bo T Porse Genome Biology 2012, 13:R35 (24 May 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary An extensive in vivo analysis of how nonsense mediated mRNA decay regulates alternative splicing in two mouse tissues
		Method 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A method is presented for differentiating mutations present at low level in a sample from sequencing errors
		Research highlight Enhancer dysfunction: how the main regulators of gene expression contribute to cancer Siavash K Kurdistani Genome Biology 2012, 13:156 (23 May 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Research Highlight on the role of variant epigenetics in establishing an enhancer element-mediated oncogenic transcriptional program
		Research highlight Layer cake: the first bite at gene expression diversity in the human brain Philipp Khaitovich Genome Biology 2012, 13:157 (22 May 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Philipp Khaitovich highlights research by Allan Jones and colleagues that assesses regional gene expression in the human brain neocortex
		Comment Goodbye, Columbus Gregory A Petsko Genome Biology 2012, 13:155 (18 May 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Guaranteeing experimental outcomes and findings: funding then and now
		Research 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 Chapkin Genome Biology 2012, 13:R32 (30 April 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A novel host-microbiome analysis method reveals a transcriptional immune response in the breast-fed infant gut associated with diet-specific microbiota
		Review Genetic architecture of body size in mammals Kathryn E Kemper, Peter M Visscher, Michael E Goddard Genome Biology 2012, 13:244 (30 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Peter Visscher and colleagues survey the current known mutations affecting body size in humans, mice, dogs and livestock species
		Comment Economies of scale Gregory A Petsko Genome Biology 2012, 13:154 (30 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The current glut of postdoctoral and graduate scientists can be addressed by applying economic principles.
		Research highlight We are what we eat: how the diet of infants affects their gut microbiome Mihai Pop Genome Biology 2012, 13:152 (30 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary We are what we eat: Mihai Pop highlights our Research article investigating the impact of diet on an infant's gut
		Research 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary The genome and transcriptome sequences of the founder strains of the HXB/BXH panel of recombinant inbred rat strains
		Review 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Michael Schatz and colleagues assess challenges in de novo plant genome assembly and review the best practices for the plant community
		Research highlight The Arabidopsis clock: time for an about-face? David E Somers Genome Biology 2012, 13:153 (27 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary David Somers highlights three recent papers that arrive at a surprising conclusion about how TOC1 functions in the plant circadian clock
		Research 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 Kolsto, Nicolas J Tourasse, Timothy D Read, Ole Andreas Okstad Genome Biology 2012, 13:R30 (26 April 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary RNA-seq is used to determine mRNA decay rates to single nucleotide resolution in the Gram positive bacterium Bacillus cereus
		Software 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method for visualizing complex, large-scale networks that combines R/Bioconductor with Java, and allows the incorporation of plug-ins
		Research 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A comprehensive RNA-seq analysis of autosomal dosage effects and compensation in 21 autosomal deficiency Drosophila lines
		Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Single-molecule deep sequencing and comparative genomics in three Schizosaccharomyces species sheds light on the nature of replication origins
		Research 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, 13:26 (23 April 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary An extensive, genome-wide analysis of RNA editing in the brain transcriptomes of 15 mouse strains
		Research Regulation of transcriptome, translation, and proteome in response to environmental stress in fission yeast Daniel H Lackner, Michael W Schmidt, Shuangding Wu, Dieter A Wolf, Jürg Bähler Genome Biology 2012, 13:R25 (18 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Changes in transcription and translation are measured in fission yeast exposed to different stresses to elucidate layers of gene expression control
		Comment Apocalypse now? Gregory A Petsko Genome Biology 2012, 13:151 (30 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Greg Petsko identifies some signs of the coming end of the world and, in that context, urges readers to pay close attention to the coming US presidential election
		Software The Transcription Factor Encyclopedia Dimas Yusuf, Stefanie L Butland, Magdalena I Swanson, Eugene Bolotin, Amy Ticoll, Warren A Cheung, Xiao YC Zhang, Christopher TD Dickman, Debra L Fulton, Jonathan S Lim, Jake M Schnabl, Oscar HP Ramos, Mireille Vasseur-Cognet, Charles N de Leeuw, Elizabeth M Simpson, Gerhart U Ryffel, Eric W-F Lam, Ralf Kist, Miranda SC Wilson, Raquel Marco-Ferreres, Jan J Brosens, Leonardo L Beccari, Paola Bovolenta, Berenice A Benayoun, Lara J Monteiro, Helma DC Schwenen, Lars Grontved, Elizabeth Wederell, Susanne Mandrup, Reiner A Veitia et al. Genome Biology 2012, 13:R24 (29 March 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A high quality compendium of transcription factor data that allows researchers to add new data via a peer-review system

	All
		Research 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 Dunigan, James Gurnon, Istvan Ladunga, Erika Lindquist, Susan Lucas, Jasmyn Pangilinan, Thomas Proschold, Asaf Salamov, Jeremy Schmutz, Donald Weeks, Takashi Yamada, Jean-Michel Claverie, Igor Grigoriev, James Van Etten, Alexandre Lomsadze, Mark Borodovsky Genome Biology 2012, 13:R39 (25 May 2012) Abstract \| Provisional PDF \| Editor’s summary The first genome of a polar eukaryotic microorganism, an alga called Coccomyxa subellipsoidea C-169, reveals universal strategies for cold adaptation
		Research Genomic diversity of the human intestinal parasite Entamoeba histolytica Gareth D Weedall, Graham Clarck, Pia Koldkjaer, Suzanne Kay, Iris Bruchhaus, Egbert Tannich, Steve Patterson, Neil Hall Genome Biology 2012, 13:R38 (25 May 2012) Abstract \| Provisional PDF \| Editor’s summary Ten strains of Entamoeba histolytica are sequenced. Low levels of genetic diversity are found, and evidence for sexual reproduction is uncovered
		Research Comparative multi-omics systems analysis of Escherichia coli strains B and K-12 Sung Ho Yoon, Mee-Jung Han, Haeyoung Jeong, Choong Hoon Lee, Xiao-Xia Xia, Dae-Hee Lee, Ji Hoon Shim, Sang Yup Lee, Tae Kwang Oh, Jihyun F Kim Genome Biology 2012, 13:R37 (25 May 2012) Abstract \| Provisional PDF \| Editor’s summary An analysis of multi-omics data and the generation of a genome-scale metabolic network to determine the phenotypic characteristics of E. coli
		Meeting report A Keystone for ncRNA Ezgi Hacisuleyman, Moran N Cabili, John L Rinn Genome Biology 2012, 13:315 (25 May 2012) Abstract \| Full text \| PDF \| Editor’s summary 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.
		Research 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A screen for regulators of the G2/M transition in fission yeast reveals novel regulators of cell cycle control
		Research Mammalian tissues defective in nonsense-mediated mRNA decay display highly aberrant splicing patterns Joachim Weischenfeldt, Johannes E Waage, Geng Tian, Jing Zhao, Inge Damgaard, Janus S Jakobsen, Karsten Kristiansen, Anders Krogh, Jun Wang, Bo T Porse Genome Biology 2012, 13:R35 (24 May 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary An extensive in vivo analysis of how nonsense mediated mRNA decay regulates alternative splicing in two mouse tissues
		Method 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A method is presented for differentiating mutations present at low level in a sample from sequencing errors
		Research highlight Enhancer dysfunction: how the main regulators of gene expression contribute to cancer Siavash K Kurdistani Genome Biology 2012, 13:156 (23 May 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Research Highlight on the role of variant epigenetics in establishing an enhancer element-mediated oncogenic transcriptional program
		Research highlight Layer cake: the first bite at gene expression diversity in the human brain Philipp Khaitovich Genome Biology 2012, 13:157 (22 May 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Philipp Khaitovich highlights research by Allan Jones and colleagues that assesses regional gene expression in the human brain neocortex
		Comment Goodbye, Columbus Gregory A Petsko Genome Biology 2012, 13:155 (18 May 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Guaranteeing experimental outcomes and findings: funding then and now
		Research 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 Chapkin Genome Biology 2012, 13:R32 (30 April 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A novel host-microbiome analysis method reveals a transcriptional immune response in the breast-fed infant gut associated with diet-specific microbiota
		Review Genetic architecture of body size in mammals Kathryn E Kemper, Peter M Visscher, Michael E Goddard Genome Biology 2012, 13:244 (30 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Peter Visscher and colleagues survey the current known mutations affecting body size in humans, mice, dogs and livestock species
		Comment Economies of scale Gregory A Petsko Genome Biology 2012, 13:154 (30 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The current glut of postdoctoral and graduate scientists can be addressed by applying economic principles.
		Research highlight We are what we eat: how the diet of infants affects their gut microbiome Mihai Pop Genome Biology 2012, 13:152 (30 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary We are what we eat: Mihai Pop highlights our Research article investigating the impact of diet on an infant's gut
		Research 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary The genome and transcriptome sequences of the founder strains of the HXB/BXH panel of recombinant inbred rat strains
		Review 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Michael Schatz and colleagues assess challenges in de novo plant genome assembly and review the best practices for the plant community
		Research highlight The Arabidopsis clock: time for an about-face? David E Somers Genome Biology 2012, 13:153 (27 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary David Somers highlights three recent papers that arrive at a surprising conclusion about how TOC1 functions in the plant circadian clock
		Research 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 Kolsto, Nicolas J Tourasse, Timothy D Read, Ole Andreas Okstad Genome Biology 2012, 13:R30 (26 April 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary RNA-seq is used to determine mRNA decay rates to single nucleotide resolution in the Gram positive bacterium Bacillus cereus
		Software 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method for visualizing complex, large-scale networks that combines R/Bioconductor with Java, and allows the incorporation of plug-ins
		Research 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) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A comprehensive RNA-seq analysis of autosomal dosage effects and compensation in 21 autosomal deficiency Drosophila lines
		Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Single-molecule deep sequencing and comparative genomics in three Schizosaccharomyces species sheds light on the nature of replication origins
		Research 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, 13:26 (23 April 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary An extensive, genome-wide analysis of RNA editing in the brain transcriptomes of 15 mouse strains
		Research Regulation of transcriptome, translation, and proteome in response to environmental stress in fission yeast Daniel H Lackner, Michael W Schmidt, Shuangding Wu, Dieter A Wolf, Jürg Bähler Genome Biology 2012, 13:R25 (18 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Changes in transcription and translation are measured in fission yeast exposed to different stresses to elucidate layers of gene expression control
		Comment Apocalypse now? Gregory A Petsko Genome Biology 2012, 13:151 (30 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Greg Petsko identifies some signs of the coming end of the world and, in that context, urges readers to pay close attention to the coming US presidential election
		Software The Transcription Factor Encyclopedia Dimas Yusuf, Stefanie L Butland, Magdalena I Swanson, Eugene Bolotin, Amy Ticoll, Warren A Cheung, Xiao YC Zhang, Christopher TD Dickman, Debra L Fulton, Jonathan S Lim, Jake M Schnabl, Oscar HP Ramos, Mireille Vasseur-Cognet, Charles N de Leeuw, Elizabeth M Simpson, Gerhart U Ryffel, Eric W-F Lam, Ralf Kist, Miranda SC Wilson, Raquel Marco-Ferreres, Jan J Brosens, Leonardo L Beccari, Paola Bovolenta, Berenice A Benayoun, Lara J Monteiro, Helma DC Schwenen, Lars Grontved, Elizabeth Wederell, Susanne Mandrup, Reiner A Veitia et al. Genome Biology 2012, 13:R24 (29 March 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A high quality compendium of transcription factor data that allows researchers to add new data via a peer-review system