Genome Biology | Volume 10 Issue 5

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	Volume 10 Issue 5
	Comment
	Comment Render unto Darwin Gregory A Petsko Genome Biology 2009, 10:106 (1 June 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Science and religion; never the twain shall meet.
	Review
	Review Learning to get along despite struggling to get by Elizabeth A Ostrowski, Gad Shaulsky Genome Biology 2009, 10:218 (26 May 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A review of evolutionary theories for cooperation, with emphasis on the mechanisms that can favor cooperation and reduce conflict within multicellular organisms, enabling the transition from unicellular to multicellular life.
	Minireview Induced pluripotent stem cells free of exogenous reprogramming factors Ramzey Abujarour, Sheng Ding Genome Biology 2009, 10:220 (6 May 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The search continues to find ways of efficiently generating induced pluripotent stem cells free of vectors and transgenes.
	Minireview Rare protection against type 1 diabetes Robert M Plenge Genome Biology 2009, 10:219 (15 May 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Next-generation DNA sequencing reveals rare alleles protective from type 1 diabetes.
	Opinion The 1001 Genomes Project for Arabidopsis thaliana Detlef Weigel, Richard Mott Genome Biology 2009, 10:107 (27 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The 1001 Genomes project for Arabidopsis thaliana could provide an enormous boost for plant research for a modest financial investment.
	Report
	Meeting report Genome duality Silvia Kocanova, Kerstin Bystricky Genome Biology 2009, 10:308 (28 May 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on 'Higher Order Genome Architecture', the third meeting of the Marie Curie Conferences and Training Courses (MC-GARD), Edinburgh, UK, 1-5 April 2009.
	Research
	Research Systemic analysis of the response of Aspergillus niger to ambient pH Mikael R Andersen, Linda Lehmann, Jens Nielsen Genome Biology 2009, 10:R47 (1 May 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Systems modeling of Aspergillus niger under different pH conditions reveals novel pH-regulated metabolic genes and signaling genes in the pal/pacC pathway.
	Research Co-evolutionary networks of genes and cellular processes across fungal species Tamir Tuller, Martin Kupiec, Eytan Ruppin Genome Biology 2009, 10:R48 (5 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Two new measures of evolution are used to study co-evolutionary networks of fungal genes and cellular processes; links between co-evolution and co-functionality are revealed.
	Research Origin of nascent lineages and the mechanisms used to prime second-strand DNA synthesis in the R1 and R2 retrotransposons of Drosophila Deborah E Stage, Thomas H Eickbush Genome Biology 2009, 10:R49 (5 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative analysis of 12 Drosophila genomes reveals insights into the evolution and mechanism of integration of R1 and R2 retrotransposons.
	Research Insights into the regulation of intrinsically disordered proteins in the human proteome by analyzing sequence and gene expression data Yvonne JK Edwards, Anna E Lobley, Melissa M Pentony, David T Jones Genome Biology 2009, 10:R50 (11 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Signals for microRNA targeting and ubiquitination are enriched in intrinsically disordered proteins, but some highly disordered proteins can escape rapid degradation.
	Research Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens Mark W Silby, Ana M Cerdeño-Tárraga, Georgios S Vernikos, Stephen R Giddens, Robert W Jackson, Gail M Preston, Xue-Xian Zhang, Christina D Moon, Stefanie M Gehrig, Scott AC Godfrey, Christopher G Knight, Jacob G Malone, Zena Robinson, Andrew J Spiers, Simon Harris, Gregory L Challis, Alice M Yaxley, David Harris, Kathy Seeger, Lee Murphy, Simon Rutter, Rob Squares, Michael A Quail, Elizabeth Saunders, Konstantinos Mavromatis, Thomas S Brettin, Stephen D Bentley, Joanne Hothersall, Elton Stephens, Christopher M Thomas, Julian Parkhill, Stuart B Levy, Paul B Rainey, Nicholas R Thomson et al. Genome Biology 2009, 10:R51 (11 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of the genome sequences of three Pseudomonas fluorescens strains reveals a heterogeneity reminiscent of a species complex rather than a single species
	Research Conserved features of cohesin binding along fission yeast chromosomes Christine K Schmidt, Neil Brookes, Frank Uhlmann Genome Biology 2009, 10:R52 (19 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary High-resolution analysis of cohesin localization on fission yeast chromosomes reveals that several determinants, previously thought to be organism-specific, come together to shape overall distribution.
	Research Whole genome sequencing of a natural recombinant Toxoplasma gondii strain reveals chromosome sorting and local allelic variants Irene Bontell, Neil Hall, Kevin E Ashelford, JP Dubey, Jon P Boyle, Johan Lindh, Judith E Smith Genome Biology 2009, 10:R53 (20 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Extensive sequence analysis of eight Toxoplasma gondii isolates from Uganda has revealed chromosome sorting and local allelic variants.
	Research Dynamic expression of small non-coding RNAs, including novel microRNAs and piRNAs/21U-RNAs, during Caenorhabditis elegans development Masaomi Kato, Alexandre de Lencastre, Zachary Pincus, Frank J Slack Genome Biology 2009, 10:R54 (21 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A deep-sequencing approach to profiling gender-specific developmental regulation of small non-coding RNA expression in C. elegans reveals dynamic temporal expression and novel miRNAs and 21U RNAs.
	Research Multi-tissue coexpression networks reveal unexpected subnetworks associated with disease Radu Dobrin, Jun Zhu, Cliona Molony, Carmen Argman, Mark L Parrish, Sonia Carlson, Mark F Allan, Daniel Pomp, Eric E Schadt Genome Biology 2009, 10:R55 (22 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Tissue-to-tissue coexpression networks between genes in hypothalamus, liver or adipose tissue enable identification of obesity-specific genes.
	Research Phylogenetic classification of Escherichia coli O157:H7 strains of human and bovine origin using a novel set of nucleotide polymorphisms Michael L Clawson, James E Keen, Timothy PL Smith, Lisa M Durso, Tara G McDaneld, Robert E Mandrell, Margaret A Davis, James L Bono Genome Biology 2009, 10:R56 (22 May 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Novel SNPs from human and bovine O157:H7 E. coli isolates are mapped, revealing that the majority of human disease is caused by a bovine subset of this strain.
	Research The histone deacetylase Rpd3p is required for transient changes in genomic expression in response to stress Adriana L Alejandro-Osorio, Dana J Huebert, Dominic T Porcaro, Megan E Sonntag, Songdet Nillasithanukroh, Jessica L Will, Audrey P Gasch Genome Biology 2009, 10:R57 (26 May 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Chromatin-immunoprecipitation and computational analysis implicate Rpd3p as an important co-factor in the network of genes regulating the yeast environmental stress response.
	Software MotifAdjuster: a tool for computational reassessment of transcription factor binding site annotations Jens Keilwagen, Jan Baumbach, Thomas A Kohl, Ivo Grosse Genome Biology 2009, 10:R46 (1 May 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary MotifAdjuster helps to detect errors in binding site annotations.
	Software The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process Erick Antezana, Mikel Egaña, Ward Blondé, Aitzol Illarramendi, Iñaki Bilbao, Bernard De Baets, Robert Stevens, Vladimir Mironov, Martin Kuiper Genome Biology 2009, 10:R58 (29 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A software resource for the analysis of cell cycle related molecular networks.

	Volume 10 Issue 5
	Comment
	Comment Render unto Darwin Gregory A Petsko Genome Biology 2009, 10:106 (1 June 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Science and religion; never the twain shall meet.
	Review
	Review Learning to get along despite struggling to get by Elizabeth A Ostrowski, Gad Shaulsky Genome Biology 2009, 10:218 (26 May 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A review of evolutionary theories for cooperation, with emphasis on the mechanisms that can favor cooperation and reduce conflict within multicellular organisms, enabling the transition from unicellular to multicellular life.
	Minireview Induced pluripotent stem cells free of exogenous reprogramming factors Ramzey Abujarour, Sheng Ding Genome Biology 2009, 10:220 (6 May 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The search continues to find ways of efficiently generating induced pluripotent stem cells free of vectors and transgenes.
	Minireview Rare protection against type 1 diabetes Robert M Plenge Genome Biology 2009, 10:219 (15 May 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Next-generation DNA sequencing reveals rare alleles protective from type 1 diabetes.
	Opinion The 1001 Genomes Project for Arabidopsis thaliana Detlef Weigel, Richard Mott Genome Biology 2009, 10:107 (27 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The 1001 Genomes project for Arabidopsis thaliana could provide an enormous boost for plant research for a modest financial investment.
	Report
	Meeting report Genome duality Silvia Kocanova, Kerstin Bystricky Genome Biology 2009, 10:308 (28 May 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on 'Higher Order Genome Architecture', the third meeting of the Marie Curie Conferences and Training Courses (MC-GARD), Edinburgh, UK, 1-5 April 2009.
	Research
	Research Systemic analysis of the response of Aspergillus niger to ambient pH Mikael R Andersen, Linda Lehmann, Jens Nielsen Genome Biology 2009, 10:R47 (1 May 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Systems modeling of Aspergillus niger under different pH conditions reveals novel pH-regulated metabolic genes and signaling genes in the pal/pacC pathway.
	Research Co-evolutionary networks of genes and cellular processes across fungal species Tamir Tuller, Martin Kupiec, Eytan Ruppin Genome Biology 2009, 10:R48 (5 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Two new measures of evolution are used to study co-evolutionary networks of fungal genes and cellular processes; links between co-evolution and co-functionality are revealed.
	Research Origin of nascent lineages and the mechanisms used to prime second-strand DNA synthesis in the R1 and R2 retrotransposons of Drosophila Deborah E Stage, Thomas H Eickbush Genome Biology 2009, 10:R49 (5 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative analysis of 12 Drosophila genomes reveals insights into the evolution and mechanism of integration of R1 and R2 retrotransposons.
	Research Insights into the regulation of intrinsically disordered proteins in the human proteome by analyzing sequence and gene expression data Yvonne JK Edwards, Anna E Lobley, Melissa M Pentony, David T Jones Genome Biology 2009, 10:R50 (11 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Signals for microRNA targeting and ubiquitination are enriched in intrinsically disordered proteins, but some highly disordered proteins can escape rapid degradation.
	Research Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens Mark W Silby, Ana M Cerdeño-Tárraga, Georgios S Vernikos, Stephen R Giddens, Robert W Jackson, Gail M Preston, Xue-Xian Zhang, Christina D Moon, Stefanie M Gehrig, Scott AC Godfrey, Christopher G Knight, Jacob G Malone, Zena Robinson, Andrew J Spiers, Simon Harris, Gregory L Challis, Alice M Yaxley, David Harris, Kathy Seeger, Lee Murphy, Simon Rutter, Rob Squares, Michael A Quail, Elizabeth Saunders, Konstantinos Mavromatis, Thomas S Brettin, Stephen D Bentley, Joanne Hothersall, Elton Stephens, Christopher M Thomas, Julian Parkhill, Stuart B Levy, Paul B Rainey, Nicholas R Thomson et al. Genome Biology 2009, 10:R51 (11 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of the genome sequences of three Pseudomonas fluorescens strains reveals a heterogeneity reminiscent of a species complex rather than a single species
	Research Conserved features of cohesin binding along fission yeast chromosomes Christine K Schmidt, Neil Brookes, Frank Uhlmann Genome Biology 2009, 10:R52 (19 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary High-resolution analysis of cohesin localization on fission yeast chromosomes reveals that several determinants, previously thought to be organism-specific, come together to shape overall distribution.
	Research Whole genome sequencing of a natural recombinant Toxoplasma gondii strain reveals chromosome sorting and local allelic variants Irene Bontell, Neil Hall, Kevin E Ashelford, JP Dubey, Jon P Boyle, Johan Lindh, Judith E Smith Genome Biology 2009, 10:R53 (20 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Extensive sequence analysis of eight Toxoplasma gondii isolates from Uganda has revealed chromosome sorting and local allelic variants.
	Research Dynamic expression of small non-coding RNAs, including novel microRNAs and piRNAs/21U-RNAs, during Caenorhabditis elegans development Masaomi Kato, Alexandre de Lencastre, Zachary Pincus, Frank J Slack Genome Biology 2009, 10:R54 (21 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A deep-sequencing approach to profiling gender-specific developmental regulation of small non-coding RNA expression in C. elegans reveals dynamic temporal expression and novel miRNAs and 21U RNAs.
	Research Multi-tissue coexpression networks reveal unexpected subnetworks associated with disease Radu Dobrin, Jun Zhu, Cliona Molony, Carmen Argman, Mark L Parrish, Sonia Carlson, Mark F Allan, Daniel Pomp, Eric E Schadt Genome Biology 2009, 10:R55 (22 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Tissue-to-tissue coexpression networks between genes in hypothalamus, liver or adipose tissue enable identification of obesity-specific genes.
	Research Phylogenetic classification of Escherichia coli O157:H7 strains of human and bovine origin using a novel set of nucleotide polymorphisms Michael L Clawson, James E Keen, Timothy PL Smith, Lisa M Durso, Tara G McDaneld, Robert E Mandrell, Margaret A Davis, James L Bono Genome Biology 2009, 10:R56 (22 May 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Novel SNPs from human and bovine O157:H7 E. coli isolates are mapped, revealing that the majority of human disease is caused by a bovine subset of this strain.
	Research The histone deacetylase Rpd3p is required for transient changes in genomic expression in response to stress Adriana L Alejandro-Osorio, Dana J Huebert, Dominic T Porcaro, Megan E Sonntag, Songdet Nillasithanukroh, Jessica L Will, Audrey P Gasch Genome Biology 2009, 10:R57 (26 May 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Chromatin-immunoprecipitation and computational analysis implicate Rpd3p as an important co-factor in the network of genes regulating the yeast environmental stress response.
	Software MotifAdjuster: a tool for computational reassessment of transcription factor binding site annotations Jens Keilwagen, Jan Baumbach, Thomas A Kohl, Ivo Grosse Genome Biology 2009, 10:R46 (1 May 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary MotifAdjuster helps to detect errors in binding site annotations.
	Software The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process Erick Antezana, Mikel Egaña, Ward Blondé, Aitzol Illarramendi, Iñaki Bilbao, Bernard De Baets, Robert Stevens, Vladimir Mironov, Martin Kuiper Genome Biology 2009, 10:R58 (29 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A software resource for the analysis of cell cycle related molecular networks.

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Volume 10 Issue 5

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