Genome Biology | Volume 11 Issue 8

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	Volume 11 Issue 8
	Comment
	Comment The past is a foreign country Gregory A Petsko Genome Biology 2010, 11:131 (27 August 2010) Full text \| PDF \| Editor’s summary The scientific worldview of someone starting graduate school today is very different from that of previous generations.
	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 highlight Transcription, one allele at a time Timothée Lionnet, Robert H Singer Genome Biology 2010, 11:129 (27 August 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new technique for the imaging of transcription from a single gene in living cells highlights the dynamic nature of transcriptional regulation.
	Research highlight Elucidating the molecular characteristics of organogenesis in human embryos Xin Geng, Guillermo Oliver Genome Biology 2010, 11:130 (27 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A transcriptomic analysis of early human organogenesis reveals the molecular signature of these processes.
	Review
	Review Dosage compensation and the global re-balancing of aneuploid genomes Matthias Prestel, Christian Feller, Peter B Becker Genome Biology 2010, 11:216 (26 August 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The dosage-compensation systems that equalize X-chromosome expression between sexes exemplify the intricacies of compensating for differences in gene copy number.
	Report
	Meeting report An illuminated view of molecular biology Yoseph Barash, Xinchen Wang Genome Biology 2010, 11:307 (26 August 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and the 7th Special Interest Group meeting on Alternative Splicing, Boston, USA, 9-13 July 2010.
	Research
	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.
	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 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 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 \| 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.
	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 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.
	Research Genomic acquisition of a capsular polysaccharide virulence cluster by non-pathogenic Burkholderia isolates Bernice Meng Qi Sim, Narisara Chantratita, Wen Fong Ooi, Tannistha Nandi, Ryan Tewhey, Vanaporn Wuthiekanun, Janjira Thaipadungpanit, Sarinna Tumapa, Pramila Ariyaratne, Wing-Kin Sung, Xiao Hui Sem, Hui Hoon Chua, Kalpana Ramnarayanan, Chi Ho Lin, Yichun Liu, Edward J Feil, Mindy B Glass, Gladys Tan, Sharon J Peacock, Patrick Tan Genome Biology 2010, 11:R89 (27 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Sequencing and microarray analyses of non-pathogenic and pathogenic Burkholderia isolates reveals insight into the factors underlying the acquisition of pathogenesis.
	Method A standard variation file format for human genome sequences Martin G Reese, Barry Moore, Colin Batchelor, Fidel Salas, Fiona Cunningham, Gabor T Marth, Lincoln Stein, Paul Flicek, Mark Yandell, Karen Eilbeck Genome Biology 2010, 11:R88 (26 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome variation format (GVF) and the 10Gen dataset provide a resource for the standardization of variant files and data analysis.
	Method Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites Doron Betel, Anjali Koppal, Phaedra Agius, Chris Sander, Christina Leslie Genome Biology 2010, 11:R90 (27 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary mirSVR is a method for miRNA target prediction that, unusually, takes into account non-canonical binding sequences and non-conserved sites
	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.
	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.

	Volume 11 Issue 8
	Comment
	Comment The past is a foreign country Gregory A Petsko Genome Biology 2010, 11:131 (27 August 2010) Full text \| PDF \| Editor’s summary The scientific worldview of someone starting graduate school today is very different from that of previous generations.
	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 highlight Transcription, one allele at a time Timothée Lionnet, Robert H Singer Genome Biology 2010, 11:129 (27 August 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new technique for the imaging of transcription from a single gene in living cells highlights the dynamic nature of transcriptional regulation.
	Research highlight Elucidating the molecular characteristics of organogenesis in human embryos Xin Geng, Guillermo Oliver Genome Biology 2010, 11:130 (27 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A transcriptomic analysis of early human organogenesis reveals the molecular signature of these processes.
	Review
	Review Dosage compensation and the global re-balancing of aneuploid genomes Matthias Prestel, Christian Feller, Peter B Becker Genome Biology 2010, 11:216 (26 August 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The dosage-compensation systems that equalize X-chromosome expression between sexes exemplify the intricacies of compensating for differences in gene copy number.
	Report
	Meeting report An illuminated view of molecular biology Yoseph Barash, Xinchen Wang Genome Biology 2010, 11:307 (26 August 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and the 7th Special Interest Group meeting on Alternative Splicing, Boston, USA, 9-13 July 2010.
	Research
	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.
	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 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 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 \| 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.
	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 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.
	Research Genomic acquisition of a capsular polysaccharide virulence cluster by non-pathogenic Burkholderia isolates Bernice Meng Qi Sim, Narisara Chantratita, Wen Fong Ooi, Tannistha Nandi, Ryan Tewhey, Vanaporn Wuthiekanun, Janjira Thaipadungpanit, Sarinna Tumapa, Pramila Ariyaratne, Wing-Kin Sung, Xiao Hui Sem, Hui Hoon Chua, Kalpana Ramnarayanan, Chi Ho Lin, Yichun Liu, Edward J Feil, Mindy B Glass, Gladys Tan, Sharon J Peacock, Patrick Tan Genome Biology 2010, 11:R89 (27 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Sequencing and microarray analyses of non-pathogenic and pathogenic Burkholderia isolates reveals insight into the factors underlying the acquisition of pathogenesis.
	Method A standard variation file format for human genome sequences Martin G Reese, Barry Moore, Colin Batchelor, Fidel Salas, Fiona Cunningham, Gabor T Marth, Lincoln Stein, Paul Flicek, Mark Yandell, Karen Eilbeck Genome Biology 2010, 11:R88 (26 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome variation format (GVF) and the 10Gen dataset provide a resource for the standardization of variant files and data analysis.
	Method Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites Doron Betel, Anjali Koppal, Phaedra Agius, Chris Sander, Christina Leslie Genome Biology 2010, 11:R90 (27 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary mirSVR is a method for miRNA target prediction that, unusually, takes into account non-canonical binding sequences and non-conserved sites
	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.
	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.

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Volume 11 Issue 8

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