Genome Biology | Volume 9 Issue 4

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	Volume 9 Issue 4
	Comment
	Comment Not debatable Gregory A Petsko Genome Biology 2008, 9:104 (30 April 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Science is essential to the economic future and national security. The next US President needs to understand the importance of science, communicate that to the public, and use scientific information properly.
	Review
	Review Genetic determinants of phenotypic diversity in humans Nazli G Rahim, Olivier Harismendy, Eric J Topol, Kelly A Frazer Genome Biology 2008, 9:215 (24 April 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary New techniques are enabling the identification of genetic variants underlying complex diseases and phenotypic traits.
	Review The AAA+ superfamily of functionally diverse proteins Jamie Snider, Guillaume Thibault, Walid A Houry Genome Biology 2008, 9:216 (30 April 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The AAA+ superfamily is a large superfamily of ATPases that are characterized by a conserved catalytic module, the AAA+ module. Members are involved in an astonishing range of different cellular processes.
	Minireview Lifting the veil on the transcriptome Kevin P Callahan, J Butler Genome Biology 2008, 9:218 (24 April 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Inhibition of the cellular RNA surveillance system in Arabidopsis reveals a normally hidden transcriptome of small noncoding RNAs.
	Minireview New tricks for old NODs Eric M Pietras, Genhong Cheng Genome Biology 2008, 9:217 (25 April 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The mammalian NOD-like receptor NLRX1 appears to have a role as a regulator of antiviral response pathways.
	Minireview The topless plant developmental phenotype explained! Karen S Osmont, Christian S Hardtke Genome Biology 2008, 9:219 (30 April 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary TOPLESS acts as a corepressor of auxin-mediated gene expresssion in plant development.
	Report
	Meeting report Maize genome in motion Virginia Walbot Genome Biology 2008, 9:303 (7 April 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the Maize Genetics Conference held in Washington DC, USA, 27 February-1 March, 2008.
	Meeting report Plant immunity from A to Z Silke Robatzek, Yusuke Saijo Genome Biology 2008, 9:304 (9 April 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of The Keystone Symposium on Plant Innate Immunity, Keystone, USA, 10-15 February 2008.
	Meeting report Chromatin organization and expression Elaine Sanij, Ross D Hannan Genome Biology 2008, 9:305 (14 April 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 29th Lorne Genome Conference on the Organization and Expression of the Genome, Lorne, Australia, 17-21 February 2008.
	Research
	Research Histone deacetylase inhibition accelerates the early events of stem cell differentiation: transcriptomic and epigenetic analysis Efthimia Karantzali, Herbert Schulz, Oliver Hummel, Norbert Hubner, AK Hatzopoulos, Androniki Kretsovali Genome Biology 2008, 9:R65 (4 April 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A gene profiling study of mouse embryonic stem cells treated with the histone deacetylase inhibitor trichostatin A shows that inhibition of histone deacetylases accelerates the early events of differentiation, by regulating the expression of pluripotency- and differentiation-associated in an opposite manner.
	Research Membrane transporters and protein traffic networks differentially affecting metal tolerance: a genomic phenotyping study in yeast Roberta Ruotolo, Gessica Marchini, Simone Ottonello Genome Biology 2008, 9:R67 (7 April 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genomic phenotyping was used to assess the role of all non-essential S. cerevisiae proteins in modulating cell viability after exposure to cadmium, nickel and other metals.
	Research Natural selection of protein structural and functional properties: a single nucleotide polymorphism perspective Jinfeng Liu, Yan Zhang, Xingye Lei, Zemin Zhang Genome Biology 2008, 9:R69 (8 April 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A large-scale survey using single nucleotide polymorphism data from dbSNP provides insights into the evolutionary selection constraints on human proteins of different structural and functional categories.
	Research Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes Sandip Paul, Sumit K Bag, Sabyasachi Das, Eric T Harvill, Chitra Dutta Genome Biology 2008, 9:R70 (9 April 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comparative genomic and proteomic study of halophilic and non-halophilic prokaryotes identifies specific genomic and proteomic features typical of halophilic species that are independent from genomic GC-content and taxonomic position.
	Research Genomic context analysis in Archaea suggests previously unrecognized links between DNA replication and translation Jonathan Berthon, Diego Cortez, Patrick Forterre Genome Biology 2008, 9:R71 (9 April 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Specific functional interactions of proteins involved in DNA replication and/or DNA repair or transcription might occur in Archaea, suggesting a previously unrecognized regulatory network coupling DNA replication and translation, which might also exist in Eukarya.
	Research Perceiving molecular evolution processes in Escherichia coli by comprehensive metabolite and gene expression profiling Chandran Vijayendran, Aiko Barsch, Karl Friehs, Karsten Niehaus, Anke Becker, Erwin Flaschel Genome Biology 2008, 9:R72 (10 April 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcript and metabolite abundance changes were analyzed in evolved and ancestor strains of Escherichia coli in three different evolutionary conditions
	Research Erect wing regulates synaptic growth in Drosophila by integration of multiple signaling pathways Irmgard U Haussmann, Kalpana White, Matthias Soller Genome Biology 2008, 9:R73 (17 April 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The neuronally expressed transcription factor gene ewg is shown to be a major target of the RNA-binding protein ELAV. EWG restricts synaptic growth at neuromuscular junctionsby integrating multiple signal pathways.
	Research The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants Lisa C Crossman, Virginia C Gould, J Maxwell Dow, Georgios S Vernikos, Aki Okazaki, Mohammed Sebaihia, David Saunders, Claire Arrowsmith, Tim Carver, Nicholas Peters, Ellen Adlem, Arnaud Kerhornou, Angela Lord, Lee Murphy, Katharine Seeger, Robert Squares, Simon Rutter, Michael A Quail, Mari-Adele Rajandream, David Harris, Carol Churcher, Stephen D Bentley, Julian Parkhill, Nicholas R Thomson, Matthew B Avison Genome Biology 2008, 9:R74 (17 April 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The complete Stenotrophomonas maltophilia genome sequence suggests that it can act as a reservoir of antibiotic resistance determinants.
	Research Widespread duplications in the genomes of laboratory stocks of Dictyostelium discoideum Gareth Bloomfield, Yoshimasa Tanaka, Jason Skelton, Alasdair Ivens, Robert R Kay Genome Biology 2008, 9:R75 (22 April 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative genome hybridization in 38 widely used laboratory strains of the social amoeba Dictyostelium discoideum detects previously unreported duplications and deletions in the Dictyostelium genome and highlights genetic variability between strains.
	Research Human-macaque comparisons illuminate variation in neutral substitution rates Svitlana Tyekucheva, Kateryna D Makova, John E Karro, Ross C Hardison, Webb Miller, Francesca Chiaromonte Genome Biology 2008, 9:R76 (30 April 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The evolutionary distance between human and macaque is particularly attractive for investigating neutral substitution rates, which were calculated as a function of a number of genomic parameters.
	Method Validation and extension of an empirical Bayes method for SNP calling on Affymetrix microarrays Shin Lin, Benilton Carvalho, David J Cutler, Dan E Arking, Aravinda Chakravarti, Rafael A Irizarry Genome Biology 2008, 9:R63 (3 April 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary Extended and validated CRLMM is shown to be more accurate than the Affymetrix default programs, and datasets and methods for validation are presented that can serve as standard benchmarks by which future SNP chip calling algorithms can be measured.
	Method A pathway sensor for genome-wide screens of intracellular proteolytic cleavage Robin Ketteler, Zairen Sun, Karl F Kovacs, Wei-Wu He, Brian Seed Genome Biology 2008, 9:R64 (3 April 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new system based on non-conventional secretion of the luciferase from Gaussia princeps (GLUC) can be used to detect intracellular proteolysis in vivo.
	Method ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues? Peter Van Loo, Stein Aerts, Bernard Thienpont, Bart De Moor, Yves Moreau, Peter Marynen Genome Biology 2008, 9:R66 (7 April 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary ModuleMiner detects cis-regulatory modules in a set of co-expressed genes in tissue-specific microarray clusters and in embryonic development datasets.
	Method Evolutionary potentials: structure specific knowledge-based potentials exploiting the evolutionary record of sequence homologs Alejandro Panjkovich, Francisco Melo, Marc A Marti-Renom Genome Biology 2008, 9:R68 (8 April 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary So-called ‘Evolutionary potentials’ for protein structure prediction are derived using a single experimental protein structure and all three-dimensional models of its homologous sequences.

	Volume 9 Issue 4
	Comment
	Comment Not debatable Gregory A Petsko Genome Biology 2008, 9:104 (30 April 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Science is essential to the economic future and national security. The next US President needs to understand the importance of science, communicate that to the public, and use scientific information properly.
	Review
	Review Genetic determinants of phenotypic diversity in humans Nazli G Rahim, Olivier Harismendy, Eric J Topol, Kelly A Frazer Genome Biology 2008, 9:215 (24 April 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary New techniques are enabling the identification of genetic variants underlying complex diseases and phenotypic traits.
	Review The AAA+ superfamily of functionally diverse proteins Jamie Snider, Guillaume Thibault, Walid A Houry Genome Biology 2008, 9:216 (30 April 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The AAA+ superfamily is a large superfamily of ATPases that are characterized by a conserved catalytic module, the AAA+ module. Members are involved in an astonishing range of different cellular processes.
	Minireview Lifting the veil on the transcriptome Kevin P Callahan, J Butler Genome Biology 2008, 9:218 (24 April 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Inhibition of the cellular RNA surveillance system in Arabidopsis reveals a normally hidden transcriptome of small noncoding RNAs.
	Minireview New tricks for old NODs Eric M Pietras, Genhong Cheng Genome Biology 2008, 9:217 (25 April 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The mammalian NOD-like receptor NLRX1 appears to have a role as a regulator of antiviral response pathways.
	Minireview The topless plant developmental phenotype explained! Karen S Osmont, Christian S Hardtke Genome Biology 2008, 9:219 (30 April 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary TOPLESS acts as a corepressor of auxin-mediated gene expresssion in plant development.
	Report
	Meeting report Maize genome in motion Virginia Walbot Genome Biology 2008, 9:303 (7 April 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the Maize Genetics Conference held in Washington DC, USA, 27 February-1 March, 2008.
	Meeting report Plant immunity from A to Z Silke Robatzek, Yusuke Saijo Genome Biology 2008, 9:304 (9 April 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of The Keystone Symposium on Plant Innate Immunity, Keystone, USA, 10-15 February 2008.
	Meeting report Chromatin organization and expression Elaine Sanij, Ross D Hannan Genome Biology 2008, 9:305 (14 April 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 29th Lorne Genome Conference on the Organization and Expression of the Genome, Lorne, Australia, 17-21 February 2008.
	Research
	Research Histone deacetylase inhibition accelerates the early events of stem cell differentiation: transcriptomic and epigenetic analysis Efthimia Karantzali, Herbert Schulz, Oliver Hummel, Norbert Hubner, AK Hatzopoulos, Androniki Kretsovali Genome Biology 2008, 9:R65 (4 April 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A gene profiling study of mouse embryonic stem cells treated with the histone deacetylase inhibitor trichostatin A shows that inhibition of histone deacetylases accelerates the early events of differentiation, by regulating the expression of pluripotency- and differentiation-associated in an opposite manner.
	Research Membrane transporters and protein traffic networks differentially affecting metal tolerance: a genomic phenotyping study in yeast Roberta Ruotolo, Gessica Marchini, Simone Ottonello Genome Biology 2008, 9:R67 (7 April 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genomic phenotyping was used to assess the role of all non-essential S. cerevisiae proteins in modulating cell viability after exposure to cadmium, nickel and other metals.
	Research Natural selection of protein structural and functional properties: a single nucleotide polymorphism perspective Jinfeng Liu, Yan Zhang, Xingye Lei, Zemin Zhang Genome Biology 2008, 9:R69 (8 April 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A large-scale survey using single nucleotide polymorphism data from dbSNP provides insights into the evolutionary selection constraints on human proteins of different structural and functional categories.
	Research Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes Sandip Paul, Sumit K Bag, Sabyasachi Das, Eric T Harvill, Chitra Dutta Genome Biology 2008, 9:R70 (9 April 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comparative genomic and proteomic study of halophilic and non-halophilic prokaryotes identifies specific genomic and proteomic features typical of halophilic species that are independent from genomic GC-content and taxonomic position.
	Research Genomic context analysis in Archaea suggests previously unrecognized links between DNA replication and translation Jonathan Berthon, Diego Cortez, Patrick Forterre Genome Biology 2008, 9:R71 (9 April 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Specific functional interactions of proteins involved in DNA replication and/or DNA repair or transcription might occur in Archaea, suggesting a previously unrecognized regulatory network coupling DNA replication and translation, which might also exist in Eukarya.
	Research Perceiving molecular evolution processes in Escherichia coli by comprehensive metabolite and gene expression profiling Chandran Vijayendran, Aiko Barsch, Karl Friehs, Karsten Niehaus, Anke Becker, Erwin Flaschel Genome Biology 2008, 9:R72 (10 April 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcript and metabolite abundance changes were analyzed in evolved and ancestor strains of Escherichia coli in three different evolutionary conditions
	Research Erect wing regulates synaptic growth in Drosophila by integration of multiple signaling pathways Irmgard U Haussmann, Kalpana White, Matthias Soller Genome Biology 2008, 9:R73 (17 April 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The neuronally expressed transcription factor gene ewg is shown to be a major target of the RNA-binding protein ELAV. EWG restricts synaptic growth at neuromuscular junctionsby integrating multiple signal pathways.
	Research The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants Lisa C Crossman, Virginia C Gould, J Maxwell Dow, Georgios S Vernikos, Aki Okazaki, Mohammed Sebaihia, David Saunders, Claire Arrowsmith, Tim Carver, Nicholas Peters, Ellen Adlem, Arnaud Kerhornou, Angela Lord, Lee Murphy, Katharine Seeger, Robert Squares, Simon Rutter, Michael A Quail, Mari-Adele Rajandream, David Harris, Carol Churcher, Stephen D Bentley, Julian Parkhill, Nicholas R Thomson, Matthew B Avison Genome Biology 2008, 9:R74 (17 April 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The complete Stenotrophomonas maltophilia genome sequence suggests that it can act as a reservoir of antibiotic resistance determinants.
	Research Widespread duplications in the genomes of laboratory stocks of Dictyostelium discoideum Gareth Bloomfield, Yoshimasa Tanaka, Jason Skelton, Alasdair Ivens, Robert R Kay Genome Biology 2008, 9:R75 (22 April 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparative genome hybridization in 38 widely used laboratory strains of the social amoeba Dictyostelium discoideum detects previously unreported duplications and deletions in the Dictyostelium genome and highlights genetic variability between strains.
	Research Human-macaque comparisons illuminate variation in neutral substitution rates Svitlana Tyekucheva, Kateryna D Makova, John E Karro, Ross C Hardison, Webb Miller, Francesca Chiaromonte Genome Biology 2008, 9:R76 (30 April 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The evolutionary distance between human and macaque is particularly attractive for investigating neutral substitution rates, which were calculated as a function of a number of genomic parameters.
	Method Validation and extension of an empirical Bayes method for SNP calling on Affymetrix microarrays Shin Lin, Benilton Carvalho, David J Cutler, Dan E Arking, Aravinda Chakravarti, Rafael A Irizarry Genome Biology 2008, 9:R63 (3 April 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary Extended and validated CRLMM is shown to be more accurate than the Affymetrix default programs, and datasets and methods for validation are presented that can serve as standard benchmarks by which future SNP chip calling algorithms can be measured.
	Method A pathway sensor for genome-wide screens of intracellular proteolytic cleavage Robin Ketteler, Zairen Sun, Karl F Kovacs, Wei-Wu He, Brian Seed Genome Biology 2008, 9:R64 (3 April 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new system based on non-conventional secretion of the luciferase from Gaussia princeps (GLUC) can be used to detect intracellular proteolysis in vivo.
	Method ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues? Peter Van Loo, Stein Aerts, Bernard Thienpont, Bart De Moor, Yves Moreau, Peter Marynen Genome Biology 2008, 9:R66 (7 April 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary ModuleMiner detects cis-regulatory modules in a set of co-expressed genes in tissue-specific microarray clusters and in embryonic development datasets.
	Method Evolutionary potentials: structure specific knowledge-based potentials exploiting the evolutionary record of sequence homologs Alejandro Panjkovich, Francisco Melo, Marc A Marti-Renom Genome Biology 2008, 9:R68 (8 April 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary So-called ‘Evolutionary potentials’ for protein structure prediction are derived using a single experimental protein structure and all three-dimensional models of its homologous sequences.

Explore Genome Biology

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Volume 9 Issue 4

Comment

Review

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