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		Research Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species Moran Yassour, Jenna Pfiffner, Joshua Z Levin, Xian Adiconis, Andreas Gnirke, Chad Nusbaum, Dawn-Anne Thompson, Nir Friedman, Aviv Regev Genome Biology 2010, 11:R87 (26 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Strand-specific RNA sequencing in yeast species reveals antisense transcripts and their conserved expression across multiple species.
		Software Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences Jeremy Goecks, Anton Nekrutenko, James Taylor, The Galaxy Team Genome Biology 2010, 11:R86 (25 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Galaxy computing platform allows researchers to share data and data analysis workflows, facilitating easily reproducible analyses.
		Research Digital expression profiling of novel diatom transcripts provides insight into their biological functions Uma Maheswari, Kamel Jabbari, Jean-Louis Petit, Betina M Porcel, Andrew E Allen, Jean-Paul Cadoret, Alessandra De Martino, Marc Heijde, Raymond Kaas, Julie La Roche, Pascal J Lopez, Véronique Martin-Jézéquel, Agnès Meichenin, Thomas Mock, Micaela Schnitzler Parker, Assaf Vardi, E Virginia Armbrust, Jean Weissenbach, Michaël Katinka, Chris Bowler Genome Biology 2010, 11:R85 (25 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Digital expression profiling of the diatom transcriptome under varying environmental conditions provides insights into the roles of novel diatom genes.
		Research highlight The missing graphical user interface for genomics Michael C Schatz Genome Biology 2010, 11:128 (25 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Galaxy package for genomic analysis empowers regular users through a much-needed and user-friendly graphical web interface.
		Research Intronic motif pairs cooperate across exons to promote pre-mRNA splicing Shengdong Ke, Lawrence A Chasin Genome Biology 2010, 11:R84 (12 August 2010) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary New motifs are found to act synergistically across exons to define exon boundaries and promote pre-RNA splicing in the human genome.
		Software Cloud-scale RNA-sequencing differential expression analysis with Myrna Ben Langmead, Kasper D Hansen, Jeffrey T Leek Genome Biology 2010, 11:R83 (11 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Myrna is a software pipeline for calculating differential gene expression from large RNA-seq data sets in the cloud.
		Research Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors Steven JM Jones, Janessa Laskin, Yvonne Y Li, Obi L Griffith, Jianghong An, Mikhail Bilenky, Yaron S Butterfield, Timothee Cezard, Eric Chuah, Richard Corbett, Anthony P Fejes, Malachi Griffith, John Yee, Montgomery Martin, Michael Mayo, Nataliya Melnyk, Ryan D Morin, Trevor J Pugh, Tesa Severson, Sohrab P Shah, Margaret Sutcliffe, Angela Tam, Jefferson Terry, Nina Thiessen, Thomas Thomson, Richard Varhol, Thomas Zeng, Yongjun Zhao, Richard A Moore, David G Huntsman, Inanc Birol, Martin Hirst, Robert A Holt, Marco A Marra et al. Genome Biology 2010, 11:R82 (9 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genomes of a primary tumor and two metastases were sequenced, and the information used to guide treatment
		Research Multiple distinct small RNAs originate from the same microRNA precursors Weixiong Zhang, Shang Gao, Xuefeng Zhou, Jing Xia, Padmanabhan Chellappan, Xiang Zhou, Xiaoming Zhang, Hailing Jin Genome Biology 2010, 11:R81 (9 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Deep sequencing of Arabidopsis small RNAs reveals the existence of novel miRNA-like RNAs generated from miRNA precursor hairpins.
		Research Comprehensive transcriptome analysis of mouse embryonic stem cell adipogenesis unravels new processes of adipocyte development Nathalie Billon, Raivo Kolde, Jüri Reimand, Miguel C Monteiro, Meelis Kull, Hedi Peterson, Konstantin Tretyakov, Priit Adler, Brigitte Wdziekonski, Jaak Vilo, Christian Dani Genome Biology 2010, 11:R80 (3 August 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A combined in silico and experimental analysis of mouse embryonic stem cell to adipocyte differentiation reveals new pathway dynamics and regulatory insights.
		Comment When the pie is too small Gregory A Petsko Genome Biology 2010, 11:127 (30 July 2010) Full text \| PDF \| PubMed \| Editor’s summary The NIH science funding pie has many mouths to feed; can a little go a long way?
		Review Nuclear transcription factors in mammalian mitochondria Sarah Leigh-Brown, José Enriquez, Duncan T Odom Genome Biology 2010, 11:215 (29 July 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Some nuclear-encoded transcription factors also act within mitochondria to regulate mitochondrial function.
		Research Paternally biased X inactivation in mouse neonatal brain Xu Wang, Paul D Soloway, Andrew G Clark Genome Biology 2010, 11:R79 (27 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Pyrosequencing of X-linked genes in embryonic mouse brains reveals a small but statistically significant preference for inactivating the paternal X chromosome.
		Correspondence Genomic information infrastructure after the deluge Julian Parkhill, Ewan Birney, Paul Kersey Genome Biology 2010, 11:402 (26 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Maintaining up-to-date annotation on reference genomes is becoming more important, not less, as the ability to rapidly and cheaply resequence genomes expands.
		Research Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing Anna Wetterbom, Adam Ameur, Lars Feuk, Ulf Gyllensten, Lucia Cavelier Genome Biology 2010, 11:R78 (23 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Sequencing of chimpanzee transcriptomes from different tissues and individuals using RNA-seq reveals novel transcribed regions.
		Research Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering Dwight Kuo, Kai Tan, Guy Zinman, Timothy Ravasi, Ziv Bar-Joseph, Trey Ideker Genome Biology 2010, 11:R77 (23 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Three yeast species respond to azole drugs in different ways and show different sensitivities to fluconazole
		Research highlight Annotating conserved and novel features of primate transcriptomes using sequencing Philipp Khaitovich Genome Biology 2010, 11:125 (23 July 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparison of chimpanzee and human transcripts reveals transcripts lost in humans and highlights the incompleteness of non-human primate genome annotations.
		Method Analysis of the copy number profiles of several tumor samples from the same patient reveals the successive steps in tumorigenesis Eric Letouzé, Yves Allory, Marc A Bollet, François Radvanyi, Frédéric Guyon Genome Biology 2010, 11:R76 (22 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary TuMult is a method for reconstructing the history of cancer progression from copy number variations in several samples from a patient
		Research RNA polymerase mapping during stress responses reveals widespread nonproductive transcription in yeast Tae Soo Kim, Chih Long Liu, Moran Yassour, John Holik, Nir Friedman, Stephen Buratowski, Oliver J Rando Genome Biology 2010, 11:R75 (16 July 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary ChIP-chip for RNA PolII occupancy and transcription analysis reveals that mRNA levels in yeast do not correlate with PolII abundance on genes.
		Research Quantifying the mechanisms of domain gain in animal proteins Marija Buljan, Adam Frankish, Alex Bateman Genome Biology 2010, 11:R74 (15 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The main mechanism of domain gain in metazoan proteins is shown to be the joining of exons from adjacent genes.
		Research highlight How do proteins gain new domains? Joseph A Marsh, Sarah A Teichmann Genome Biology 2010, 11:126 (15 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire C André Lévesque, Henk Brouwer, Liliana Cano, John P Hamilton, Carson Holt, Edgar Huitema, Sylvain Raffaele, Gregg P Robideau, Marco Thines, Joe Win, Marcelo M Zerillo, Gordon W Beakes, Jeffrey L Boore, Dana Busam, Bernard Dumas, Steve Ferriera, Susan I Fuerstenberg, Claire MM Gachon, Elodie Gaulin, Francine Govers, Laura Grenville-Briggs, Neil Horner, Jessica Hostetler, Rays HY Jiang, Justin Johnson, Theerapong Krajaejun, Haining Lin, Harold JG Meijer, Barry Moore, Paul Morris et al. Genome Biology 2010, 11:R73 (13 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome sequence of the plant pathogenic oomycete, Pythium ultimum and a comparison with the related potato blight pathogen genome reveals differences in pathogenicity.
		Research Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes Rebecca A Chodroff, Leo Goodstadt, Tamara M Sirey, Peter L Oliver, Kay E Davies, Eric D Green, Zoltán Molnár, Chris P Ponting Genome Biology 2010, 11:R72 (12 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Long non-coding RNAs are shown to have conserved sequence and expression in brain tissue across amniotes, suggesting a conserved functional role.
		Research Experimental annotation of the human pathogen Candida albicans coding and noncoding transcribed regions using high-resolution tiling arrays Adnane Sellam, Hervé Hogues, Christopher Askew, Faiza Tebbji, Marco van het Hoog, Hugo Lavoie, Carol A Kumamoto, Malcolm Whiteway, André Nantel Genome Biology 2010, 11:R71 (9 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Candida albicans transcriptional landscape reveals antisense transcription, novel open reading frames and non-coding RNAs, whose expression is correlated with RNA polymerase occupancy.
		Research Contrasting chromatin organization of CpG islands and exons in the human genome Jung Kyoon Choi Genome Biology 2010, 11:R70 (5 July 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An analysis of CpG methylation and histone positioning finds that these both help to define exons.
		Comment Hand-made biology Gregory A Petsko Genome Biology 2010, 11:124 (30 June 2010) Full text \| PDF \| PubMed \| Editor’s summary The genomics era Shelley, Craig Venter, has refocused attention on synthetic biology by creating a bacterium.

	All
		Research Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species Moran Yassour, Jenna Pfiffner, Joshua Z Levin, Xian Adiconis, Andreas Gnirke, Chad Nusbaum, Dawn-Anne Thompson, Nir Friedman, Aviv Regev Genome Biology 2010, 11:R87 (26 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Strand-specific RNA sequencing in yeast species reveals antisense transcripts and their conserved expression across multiple species.
		Software Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences Jeremy Goecks, Anton Nekrutenko, James Taylor, The Galaxy Team Genome Biology 2010, 11:R86 (25 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Galaxy computing platform allows researchers to share data and data analysis workflows, facilitating easily reproducible analyses.
		Research Digital expression profiling of novel diatom transcripts provides insight into their biological functions Uma Maheswari, Kamel Jabbari, Jean-Louis Petit, Betina M Porcel, Andrew E Allen, Jean-Paul Cadoret, Alessandra De Martino, Marc Heijde, Raymond Kaas, Julie La Roche, Pascal J Lopez, Véronique Martin-Jézéquel, Agnès Meichenin, Thomas Mock, Micaela Schnitzler Parker, Assaf Vardi, E Virginia Armbrust, Jean Weissenbach, Michaël Katinka, Chris Bowler Genome Biology 2010, 11:R85 (25 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Digital expression profiling of the diatom transcriptome under varying environmental conditions provides insights into the roles of novel diatom genes.
		Research highlight The missing graphical user interface for genomics Michael C Schatz Genome Biology 2010, 11:128 (25 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Galaxy package for genomic analysis empowers regular users through a much-needed and user-friendly graphical web interface.
		Research Intronic motif pairs cooperate across exons to promote pre-mRNA splicing Shengdong Ke, Lawrence A Chasin Genome Biology 2010, 11:R84 (12 August 2010) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary New motifs are found to act synergistically across exons to define exon boundaries and promote pre-RNA splicing in the human genome.
		Software Cloud-scale RNA-sequencing differential expression analysis with Myrna Ben Langmead, Kasper D Hansen, Jeffrey T Leek Genome Biology 2010, 11:R83 (11 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Myrna is a software pipeline for calculating differential gene expression from large RNA-seq data sets in the cloud.
		Research Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors Steven JM Jones, Janessa Laskin, Yvonne Y Li, Obi L Griffith, Jianghong An, Mikhail Bilenky, Yaron S Butterfield, Timothee Cezard, Eric Chuah, Richard Corbett, Anthony P Fejes, Malachi Griffith, John Yee, Montgomery Martin, Michael Mayo, Nataliya Melnyk, Ryan D Morin, Trevor J Pugh, Tesa Severson, Sohrab P Shah, Margaret Sutcliffe, Angela Tam, Jefferson Terry, Nina Thiessen, Thomas Thomson, Richard Varhol, Thomas Zeng, Yongjun Zhao, Richard A Moore, David G Huntsman, Inanc Birol, Martin Hirst, Robert A Holt, Marco A Marra et al. Genome Biology 2010, 11:R82 (9 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genomes of a primary tumor and two metastases were sequenced, and the information used to guide treatment
		Research Multiple distinct small RNAs originate from the same microRNA precursors Weixiong Zhang, Shang Gao, Xuefeng Zhou, Jing Xia, Padmanabhan Chellappan, Xiang Zhou, Xiaoming Zhang, Hailing Jin Genome Biology 2010, 11:R81 (9 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Deep sequencing of Arabidopsis small RNAs reveals the existence of novel miRNA-like RNAs generated from miRNA precursor hairpins.
		Research Comprehensive transcriptome analysis of mouse embryonic stem cell adipogenesis unravels new processes of adipocyte development Nathalie Billon, Raivo Kolde, Jüri Reimand, Miguel C Monteiro, Meelis Kull, Hedi Peterson, Konstantin Tretyakov, Priit Adler, Brigitte Wdziekonski, Jaak Vilo, Christian Dani Genome Biology 2010, 11:R80 (3 August 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A combined in silico and experimental analysis of mouse embryonic stem cell to adipocyte differentiation reveals new pathway dynamics and regulatory insights.
		Comment When the pie is too small Gregory A Petsko Genome Biology 2010, 11:127 (30 July 2010) Full text \| PDF \| PubMed \| Editor’s summary The NIH science funding pie has many mouths to feed; can a little go a long way?
		Review Nuclear transcription factors in mammalian mitochondria Sarah Leigh-Brown, José Enriquez, Duncan T Odom Genome Biology 2010, 11:215 (29 July 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Some nuclear-encoded transcription factors also act within mitochondria to regulate mitochondrial function.
		Research Paternally biased X inactivation in mouse neonatal brain Xu Wang, Paul D Soloway, Andrew G Clark Genome Biology 2010, 11:R79 (27 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Pyrosequencing of X-linked genes in embryonic mouse brains reveals a small but statistically significant preference for inactivating the paternal X chromosome.
		Correspondence Genomic information infrastructure after the deluge Julian Parkhill, Ewan Birney, Paul Kersey Genome Biology 2010, 11:402 (26 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Maintaining up-to-date annotation on reference genomes is becoming more important, not less, as the ability to rapidly and cheaply resequence genomes expands.
		Research Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing Anna Wetterbom, Adam Ameur, Lars Feuk, Ulf Gyllensten, Lucia Cavelier Genome Biology 2010, 11:R78 (23 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Sequencing of chimpanzee transcriptomes from different tissues and individuals using RNA-seq reveals novel transcribed regions.
		Research Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering Dwight Kuo, Kai Tan, Guy Zinman, Timothy Ravasi, Ziv Bar-Joseph, Trey Ideker Genome Biology 2010, 11:R77 (23 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Three yeast species respond to azole drugs in different ways and show different sensitivities to fluconazole
		Research highlight Annotating conserved and novel features of primate transcriptomes using sequencing Philipp Khaitovich Genome Biology 2010, 11:125 (23 July 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparison of chimpanzee and human transcripts reveals transcripts lost in humans and highlights the incompleteness of non-human primate genome annotations.
		Method Analysis of the copy number profiles of several tumor samples from the same patient reveals the successive steps in tumorigenesis Eric Letouzé, Yves Allory, Marc A Bollet, François Radvanyi, Frédéric Guyon Genome Biology 2010, 11:R76 (22 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary TuMult is a method for reconstructing the history of cancer progression from copy number variations in several samples from a patient
		Research RNA polymerase mapping during stress responses reveals widespread nonproductive transcription in yeast Tae Soo Kim, Chih Long Liu, Moran Yassour, John Holik, Nir Friedman, Stephen Buratowski, Oliver J Rando Genome Biology 2010, 11:R75 (16 July 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary ChIP-chip for RNA PolII occupancy and transcription analysis reveals that mRNA levels in yeast do not correlate with PolII abundance on genes.
		Research Quantifying the mechanisms of domain gain in animal proteins Marija Buljan, Adam Frankish, Alex Bateman Genome Biology 2010, 11:R74 (15 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The main mechanism of domain gain in metazoan proteins is shown to be the joining of exons from adjacent genes.
		Research highlight How do proteins gain new domains? Joseph A Marsh, Sarah A Teichmann Genome Biology 2010, 11:126 (15 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire C André Lévesque, Henk Brouwer, Liliana Cano, John P Hamilton, Carson Holt, Edgar Huitema, Sylvain Raffaele, Gregg P Robideau, Marco Thines, Joe Win, Marcelo M Zerillo, Gordon W Beakes, Jeffrey L Boore, Dana Busam, Bernard Dumas, Steve Ferriera, Susan I Fuerstenberg, Claire MM Gachon, Elodie Gaulin, Francine Govers, Laura Grenville-Briggs, Neil Horner, Jessica Hostetler, Rays HY Jiang, Justin Johnson, Theerapong Krajaejun, Haining Lin, Harold JG Meijer, Barry Moore, Paul Morris et al. Genome Biology 2010, 11:R73 (13 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome sequence of the plant pathogenic oomycete, Pythium ultimum and a comparison with the related potato blight pathogen genome reveals differences in pathogenicity.
		Research Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes Rebecca A Chodroff, Leo Goodstadt, Tamara M Sirey, Peter L Oliver, Kay E Davies, Eric D Green, Zoltán Molnár, Chris P Ponting Genome Biology 2010, 11:R72 (12 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Long non-coding RNAs are shown to have conserved sequence and expression in brain tissue across amniotes, suggesting a conserved functional role.
		Research Experimental annotation of the human pathogen Candida albicans coding and noncoding transcribed regions using high-resolution tiling arrays Adnane Sellam, Hervé Hogues, Christopher Askew, Faiza Tebbji, Marco van het Hoog, Hugo Lavoie, Carol A Kumamoto, Malcolm Whiteway, André Nantel Genome Biology 2010, 11:R71 (9 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Candida albicans transcriptional landscape reveals antisense transcription, novel open reading frames and non-coding RNAs, whose expression is correlated with RNA polymerase occupancy.
		Research Contrasting chromatin organization of CpG islands and exons in the human genome Jung Kyoon Choi Genome Biology 2010, 11:R70 (5 July 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An analysis of CpG methylation and histone positioning finds that these both help to define exons.
		Comment Hand-made biology Gregory A Petsko Genome Biology 2010, 11:124 (30 June 2010) Full text \| PDF \| PubMed \| Editor’s summary The genomics era Shelley, Craig Venter, has refocused attention on synthetic biology by creating a bacterium.