Genome Biology | Volume 7 Issue 5

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Articles

	Volume 7 Issue 5
	Comment
	Comment The next epidemic Gregory A Petsko Genome Biology 2006, 7:108 (31 May 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary We are witnessing an explosion of people well past their reproductive years. Older, non-reproducing organisms consume resources that might better serve their younger. And chief among these resources is medical care.
	Review
	Review An overview of the serpin superfamily Ruby HP Law, Qingwei Zhang, Sheena McGowan, Ashley M Buckle, Gary A Silverman, Wilson Wong, Carlos J Rosado, Chris G Langendorf, Rob N Pike, Philip I Bird, James C Whisstock Genome Biology 2006, 7:216 (30 May 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Serpins are protease inhibitors that use a conformational change to inhibit target enzymes and are important in many proteolytic cascades, including the mammalian coagulation and inflammatory-response pathways.
	Minireview Histone H4 lysine 16 acetylation breaks the genome's silence Wei-Jong Shia, Samantha G Pattenden, Jerry L Workman Genome Biology 2006, 7:217 (10 May 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The acetylation of histone H4 on lysine 16 is a crucial event in switching chromatin from a repressive to a transcriptionally active state.
	Minireview RNA at the steering wheel Sabine Schmitt, Renato Paro Genome Biology 2006, 7:218 (26 May 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Noncoding RNAs transcribed from control elements in DNA provide an anti-silencing mechanism by targeting chromatin-modifying enzymes to these genes.
	Minireview RNA interference pinpoints regulators of cell size and the cell cycle Megan J Cully, Sally J Leevers Genome Biology 2006, 7:219 (30 May 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A genome-wide RNA interference screen in Drosophila cells has identified genes involved in regulating cell-cycle progression, cell size and apoptosis.
	Minireview RNA interference has a role in regulating Drosophila telomeres Elena Casacuberta, Mary-Lou Pardue Genome Biology 2006, 7:220 (31 May 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary RNA interference is implicated in the maintenance of Drosophila telomeres by retrotransposons.
	Report
	Meeting report Stem cells in the genomic age Sally Lowell Genome Biology 2006, 7:315 (22 May 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the 2006 Joint Spring Meeting of the British Society for Developmental Biology and the British Society for Cell Biology, York, UK, 20-23 March 2006.
	Meeting report Systems biology of gene regulation fulfills its promise Adrienne E McKee, Pamela A Silver Genome Biology 2006, 7:316 (22 May 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the meeting 'Systems Biology: Global Regulation of Gene Expression' at Cold Spring Harbor, New York, USA, 23-26 March 2006.
	Meeting report Splicing bioinformatics to biology Douglas L Black, Brenton R Graveley Genome Biology 2006, 7:317 (26 May 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 2nd Symposium on Alternative Transcript Diversity, Heidelberg, Germany, 21-23 March 2006.
	Research
	Research RNA interference is not involved in natural antisense mediated regulation of gene expression in mammals Mohammad Faghihi, Claes Wahlestedt Genome Biology 2006, 7:R38 (9 May 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The study of two examples of endogenous genes with coding or non-coding natural antisense transcript partners provides evidence against the involvement of RNAi in the natural antisense-mediated regulation of mammalian gene expression.
	Research Influence of metabolic network structure and function on enzyme evolution Dennis Vitkup, Peter Kharchenko, Andreas Wagner Genome Biology 2006, 7:R39 (9 May 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of evolutionary constraints, gene duplication and essentiability in the yeast metabolic network demonstrates that the structure and function of a metabolic network shapes the evolution of its enzymes.
	Research Large-scale and high-confidence proteomic analysis of human seminal plasma Bartosz Pilch, Matthias Mann Genome Biology 2006, 7:R40 (18 May 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The high-confidence identification of 923 proteins in seminal fluid provides an inventory of proteins with potential roles in fertilization.
	Research Intron gain and loss in segmentally duplicated genes in rice Haining Lin, Wei Zhu, Joana C Silva, Xun Gu, C Robin Buell Genome Biology 2006, 7:R41 (23 May 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of over 3,000 co-linear paired genes in rice shows more intron loss than intron gain following segmental duplication.
	Research The gain and loss of genes during 600 million years of vertebrate evolution Tine Blomme, Klaas Vandepoele, Stefanie De Bodt, Cedric Simillion, Steven Maere, Yves Van de Peer Genome Biology 2006, 7:R43 (24 May 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Phylogenetic analysis of gene gain and loss during vertebrate evolution provides evidence for the importance of early gene or genome duplication events in evolution of complex vertebrates.
	Research PI3K signaling and miRNA expression during the response of quiescent human fibroblasts to distinct proliferative stimuli Jian Gu, Vishwanath R Iyer Genome Biology 2006, 7:R42 (31 May 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Global transcriptional profiling of human fibroblasts from two different tissue sources reveals distinct as well as conserved responses to different growth stimuli.
	Research Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli Bob Mau, Jeremy D Glasner, Aaron E Darling, Nicole T Perna Genome Biology 2006, 7:R44 (31 May 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Multiple alignment of E. coli and Shigella genomes reveals that intraspecific recombination is more common than previously thought.
	Method Inferring transcriptional modules from ChIP-chip, motif and microarray data Karen Lemmens, Thomas Dhollander, Tijl De Bie, Pieter Monsieurs, Kristof Engelen, Bart Smets, Joris Winderickx, Bart De Moor, Kathleen Marchal Genome Biology 2006, 7:R37 (5 May 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary ReMoDiscovery, a module discovery algorithm and software that uses ChIP-chip data, motif information and gene-expression profiles, is presented.
	Method The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo Richard Bonneau, David J Reiss, Paul Shannon, Marc Facciotti, Leroy Hood, Nitin S Baliga, Vesteinn Thorsson Genome Biology 2006, 7:R36 (10 May 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Inferelator, a method for deriving genome-wide transcriptional regulatory interactions, successfully predicted global expression in Halobacterium under novel perturbations.
	Correspondence
	Correspondence The success (or not) of HUGO nomenclature Javier Tamames, Alfonso Valencia Genome Biology 2006, 7:402 (15 May 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A literature search shows that biologists do not follow the official nomenclature guidelines for a substantial fraction of gene names.

	Volume 7 Issue 5
	Comment
	Comment The next epidemic Gregory A Petsko Genome Biology 2006, 7:108 (31 May 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary We are witnessing an explosion of people well past their reproductive years. Older, non-reproducing organisms consume resources that might better serve their younger. And chief among these resources is medical care.
	Review
	Review An overview of the serpin superfamily Ruby HP Law, Qingwei Zhang, Sheena McGowan, Ashley M Buckle, Gary A Silverman, Wilson Wong, Carlos J Rosado, Chris G Langendorf, Rob N Pike, Philip I Bird, James C Whisstock Genome Biology 2006, 7:216 (30 May 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Serpins are protease inhibitors that use a conformational change to inhibit target enzymes and are important in many proteolytic cascades, including the mammalian coagulation and inflammatory-response pathways.
	Minireview Histone H4 lysine 16 acetylation breaks the genome's silence Wei-Jong Shia, Samantha G Pattenden, Jerry L Workman Genome Biology 2006, 7:217 (10 May 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The acetylation of histone H4 on lysine 16 is a crucial event in switching chromatin from a repressive to a transcriptionally active state.
	Minireview RNA at the steering wheel Sabine Schmitt, Renato Paro Genome Biology 2006, 7:218 (26 May 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Noncoding RNAs transcribed from control elements in DNA provide an anti-silencing mechanism by targeting chromatin-modifying enzymes to these genes.
	Minireview RNA interference pinpoints regulators of cell size and the cell cycle Megan J Cully, Sally J Leevers Genome Biology 2006, 7:219 (30 May 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A genome-wide RNA interference screen in Drosophila cells has identified genes involved in regulating cell-cycle progression, cell size and apoptosis.
	Minireview RNA interference has a role in regulating Drosophila telomeres Elena Casacuberta, Mary-Lou Pardue Genome Biology 2006, 7:220 (31 May 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary RNA interference is implicated in the maintenance of Drosophila telomeres by retrotransposons.
	Report
	Meeting report Stem cells in the genomic age Sally Lowell Genome Biology 2006, 7:315 (22 May 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report on the 2006 Joint Spring Meeting of the British Society for Developmental Biology and the British Society for Cell Biology, York, UK, 20-23 March 2006.
	Meeting report Systems biology of gene regulation fulfills its promise Adrienne E McKee, Pamela A Silver Genome Biology 2006, 7:316 (22 May 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the meeting 'Systems Biology: Global Regulation of Gene Expression' at Cold Spring Harbor, New York, USA, 23-26 March 2006.
	Meeting report Splicing bioinformatics to biology Douglas L Black, Brenton R Graveley Genome Biology 2006, 7:317 (26 May 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 2nd Symposium on Alternative Transcript Diversity, Heidelberg, Germany, 21-23 March 2006.
	Research
	Research RNA interference is not involved in natural antisense mediated regulation of gene expression in mammals Mohammad Faghihi, Claes Wahlestedt Genome Biology 2006, 7:R38 (9 May 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The study of two examples of endogenous genes with coding or non-coding natural antisense transcript partners provides evidence against the involvement of RNAi in the natural antisense-mediated regulation of mammalian gene expression.
	Research Influence of metabolic network structure and function on enzyme evolution Dennis Vitkup, Peter Kharchenko, Andreas Wagner Genome Biology 2006, 7:R39 (9 May 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of evolutionary constraints, gene duplication and essentiability in the yeast metabolic network demonstrates that the structure and function of a metabolic network shapes the evolution of its enzymes.
	Research Large-scale and high-confidence proteomic analysis of human seminal plasma Bartosz Pilch, Matthias Mann Genome Biology 2006, 7:R40 (18 May 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The high-confidence identification of 923 proteins in seminal fluid provides an inventory of proteins with potential roles in fertilization.
	Research Intron gain and loss in segmentally duplicated genes in rice Haining Lin, Wei Zhu, Joana C Silva, Xun Gu, C Robin Buell Genome Biology 2006, 7:R41 (23 May 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of over 3,000 co-linear paired genes in rice shows more intron loss than intron gain following segmental duplication.
	Research The gain and loss of genes during 600 million years of vertebrate evolution Tine Blomme, Klaas Vandepoele, Stefanie De Bodt, Cedric Simillion, Steven Maere, Yves Van de Peer Genome Biology 2006, 7:R43 (24 May 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Phylogenetic analysis of gene gain and loss during vertebrate evolution provides evidence for the importance of early gene or genome duplication events in evolution of complex vertebrates.
	Research PI3K signaling and miRNA expression during the response of quiescent human fibroblasts to distinct proliferative stimuli Jian Gu, Vishwanath R Iyer Genome Biology 2006, 7:R42 (31 May 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Global transcriptional profiling of human fibroblasts from two different tissue sources reveals distinct as well as conserved responses to different growth stimuli.
	Research Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli Bob Mau, Jeremy D Glasner, Aaron E Darling, Nicole T Perna Genome Biology 2006, 7:R44 (31 May 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Multiple alignment of E. coli and Shigella genomes reveals that intraspecific recombination is more common than previously thought.
	Method Inferring transcriptional modules from ChIP-chip, motif and microarray data Karen Lemmens, Thomas Dhollander, Tijl De Bie, Pieter Monsieurs, Kristof Engelen, Bart Smets, Joris Winderickx, Bart De Moor, Kathleen Marchal Genome Biology 2006, 7:R37 (5 May 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary ReMoDiscovery, a module discovery algorithm and software that uses ChIP-chip data, motif information and gene-expression profiles, is presented.
	Method The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo Richard Bonneau, David J Reiss, Paul Shannon, Marc Facciotti, Leroy Hood, Nitin S Baliga, Vesteinn Thorsson Genome Biology 2006, 7:R36 (10 May 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Inferelator, a method for deriving genome-wide transcriptional regulatory interactions, successfully predicted global expression in Halobacterium under novel perturbations.
	Correspondence
	Correspondence The success (or not) of HUGO nomenclature Javier Tamames, Alfonso Valencia Genome Biology 2006, 7:402 (15 May 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A literature search shows that biologists do not follow the official nomenclature guidelines for a substantial fraction of gene names.

Explore Genome Biology

Articles

Volume 7 Issue 5

Comment

Review

Report

Research

Correspondence