Genome Biology | Volume 8 Issue 12

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	Volume 8 Issue 12
	Comment
	Comment Medicine man Gregory A Petsko Genome Biology 2007, 8:114 (28 December 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary It becomes imperative that our doctors bring to the practice of medicine a true scientific perspective; it may be just as important that those of us doing biomedical research try to learn more of what doctors know.
	Review
	Review Building on basic metagenomics with complementary technologies Falk Warnecke, Philip Hugenholtz Genome Biology 2007, 8:231 (28 December 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Supplementing metagenomic approaches to studying natural microbial communities with metatranscriptomics and metaproteomics should reap big dividends
	Protein family review The reticulons: a family of proteins with diverse functions Yvonne S Yang, Stephen M Strittmatter Genome Biology 2007, 8:234 (28 December 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The reticulon family is a diverse group of proteins that mostly localize to the endoplasmic reticulum and may be important in neurodegenerative diseases.
	Minireview Gene prediction: compare and CONTRAST Paul Flicek Genome Biology 2007, 8:233 (20 December 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The new gene-prediction program CONTRAST offers significant advances in accuracy over previous methods.
	Minireview Genomic clues to an ancient asexual scandal William R Rice, Urban Friberg Genome Biology 2007, 8:232 (28 December 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The bdelloid rotifers are a successful and diverse group of organisms, despite being entirely asexual. How do they do it?
	Report
	Meeting report The ins and outs of translation Jennifer L Clancy, Marco Nousch, Marina Rodnina, Thomas Preiss Genome Biology 2007, 8:321 (7 December 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 2nd EMBO Conference on Protein Synthesis and Translational Control, Heidelberg, Germany, 12-16 September 2007.
	Research
	Research Diversity and evolution of phycobilisomes in marine Synechococcus spp.: a comparative genomics study Christophe Six, Jean-Claude Thomas, Laurence Garczarek, Martin Ostrowski, Alexis Dufresne, Nicolas Blot, David J Scanlan, Frédéric Partensky Genome Biology 2007, 8:R259 (5 December 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary By comparing Synechococcus genomes, candidate genes required for the production of phycobiliproteins, which are part of the light-harvesting antenna complexes called phycobilisomes, were identified. Phylogenetic analyses suggest that the phycobilisome core evolved together with the core genome, whereas rods evolved independently.
	Research Contribution of telomerase RNA retrotranscription to DNA double-strand break repair during mammalian genome evolution Solomon G Nergadze, Marco Santagostino, Alberto Salzano, Chiara Mondello, Elena Giulotto Genome Biology 2007, 8:R260 (7 December 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A comparative analysis of two primate and two rodent genomes suggests that telomerase was utilized, in some instances, for the repair of DNA double-strand breaks during mammalian evolution.
	Research Transcriptional profiling of MnSOD-mediated lifespan extension in Drosophila reveals a species-general network of aging and metabolic genes Christina Curtis, Gary N Landis, Donna Folk, Nancy B Wehr, Nicholas Hoe, Morris Waskar, Diana Abdueva, Dmitriy Skvortsov, Daniel Ford, Allan Luu, Ananth Badrinath, Rodney L Levine, Timothy J Bradley, Simon Tavaré, John Tower Genome Biology 2007, 8:R262 (9 December 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcriptional profiling of MnSOD-mediated life-span extension in Drosophila identifies a set of candidate biomarkers of aging, consisting primarily of carbohydrate metabolism and electron transport genes.
	Research Gene-expression patterns reveal underlying biological processes in Kawasaki disease Stephen J Popper, Chisato Shimizu, Hiroko Shike, John T Kanegaye, Jane W Newburger, Robert P Sundel, Patrick O Brown, Jane C Burns, David A Relman Genome Biology 2007, 8:R261 (11 December 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of patterns of gene expression in peripheral blood from children with Kawasaki disease revealed dynamic and variable gene expression programs involving neutrophil activation and apoptosis.
	Research Evolution of allostery in the cyclic nucleotide binding module Natarajan Kannan, Jian Wu, Ganesh S Anand, Shibu Yooseph, Andrew F Neuwald, J Craig Venter, Susan S Taylor Genome Biology 2007, 8:R264 (12 December 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Analysis of cyclic nucleotide binding (CNB) domains shows that they have evolved to sense a wide variety of second messenger signals; a mechanism for allosteric regulation by CNB domains is proposed.
	Research Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray Hanni Willenbrock, Peter F Hallin, Trudy M Wassenaar, David W Ussery Genome Biology 2007, 8:R267 (18 December 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A high-density microarray has been designed that covers the genomes of 24 Escherichia coli and 8 Shigella strains. As a proof-of-principle the genomes of four probiotic E. coli strains were analyzed and their phylogenetic relationship to other E.coli strains investigated.
	Research Application of the comprehensive set of heterozygous yeast deletion mutants to elucidate the molecular basis of cellular chromium toxicity Sara Holland, Emma Lodwig, Theodora Sideri, Tom Reader, Ian Clarke, Konstantinos Gkargkas, David C Hoyle, Daniela Delneri, Stephen G Oliver, Simon V Avery Genome Biology 2007, 8:R268 (18 December 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Competitive growth between over 6,000 heterozygous yeast mutants in the presence of chromium together with microarray-based screens showed that proteasomal activity is crucial for cellular chromium resistance.
	Method A new computational approach to analyze human protein complexes and predict novel protein interactions Sara Zanivan, Ilaria Cascone, Chiara Peyron, Ivan Molineris, Serena Marchio, Michele Caselle, Federico Bussolino Genome Biology 2007, 8:R256 (4 December 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new approach to identifying interacting proteins based on gene-expression data uses hypergeometric distribution and Monte-Carlo simulations.
	Method Prediction of synergistic transcription factors by function conservation Zihua Hu, Boyu Hu, James F Collins Genome Biology 2007, 8:R257 (5 December 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new strategy is proposed for identifying synergistic transcription factors by function conservation, leading to the identification of 51 homotypic transcription-factor combinations.
	Method Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes Kriston L McGary, Insuk Lee, Edward M Marcotte Genome Biology 2007, 8:R258 (5 December 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Loss-of-function phenotypes of yeast genes can be predicted from the loss-of-function phenotypes of their neighbours in functional gene networks. This could potentially be applied to the prediction of human disease genes.
	Method Determining promoter location based on DNA structure first-principles calculations J Ramon Goñi, Alberto Pérez, David Torrents, Modesto Orozco Genome Biology 2007, 8:R263 (11 December 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new method is presented which predicts promoter regions based on atomistic molecular dynamics simulations of small oligonucleotides, without requiring information on sequence conservation or features.
	Method Quantification of global transcription patterns in prokaryotes using spotted microarrays Ben Sidders, Mike Withers, Sharon L Kendall, Joanna Bacon, Simon J Waddell, Jason Hinds, Paul Golby, Farahnaz Movahedzadeh, Robert A Cox, Rosangela Frita, Annemieke MC ten Bokum, Lorenz Wernisch, Neil G Stoker Genome Biology 2007, 8:R265 (13 December 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis is described, applicable to any spotted microarray dataset that is produced using genomic DNA as a reference for quantifying prokaryotic levels of mRNA on a genome-wide scale.
	Method Direct selection and phage display of a Gram-positive secretome Dragana Jankovic, Michael A Collett, Mark W Lubbers, Jasna Rakonjac Genome Biology 2007, 8:R266 (13 December 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A phage display system for direct selection, identification, expression and purification of bacterial secretome proteins has been developed.
	Method CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction Samuel S Gross, Chuong B Do, Marina Sirota, Serafim Batzoglou Genome Biology 2007, 8:R269 (20 December 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary CONTRAST is a gene predictor that directly incorporates information from multiple alignments and uses discriminative machine learning techniques to give large improvements in prediction over previous methods.
	Method Post-translational modifications of histones H3 and H4 associated with the histone methyltransferases Suv39h1 and G9a Philippe Robin, Lauriane Fritsch, Ophélie Philipot, Fedor Svinarchuk, Slimane Ait-Si-Ali Genome Biology 2007, 8:R270 (20 December 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Mass spectrometry analysis of the post-transcriptional modifications of histones H3 and H4 that were co-purified with histone methyltransferases Suv39h1 and G9a shows that, in HeLa cells, histone methyltransferases can be physically associated with acetylated histones, which normally mark transcriptionally active chromatin.
	Method Consistent dissection of the protein interaction network by combining global and local metrics Chunlin Wang, Chris Ding, Qiaofeng Yang, Stephen R Holbrook Genome Biology 2007, 8:R271 (21 December 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new network decomposition method is proposed that uses both a global metric and a local metric to identify protein interaction modules in the protein interaction network.

	Volume 8 Issue 12
	Comment
	Comment Medicine man Gregory A Petsko Genome Biology 2007, 8:114 (28 December 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary It becomes imperative that our doctors bring to the practice of medicine a true scientific perspective; it may be just as important that those of us doing biomedical research try to learn more of what doctors know.
	Review
	Review Building on basic metagenomics with complementary technologies Falk Warnecke, Philip Hugenholtz Genome Biology 2007, 8:231 (28 December 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Supplementing metagenomic approaches to studying natural microbial communities with metatranscriptomics and metaproteomics should reap big dividends
	Protein family review The reticulons: a family of proteins with diverse functions Yvonne S Yang, Stephen M Strittmatter Genome Biology 2007, 8:234 (28 December 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The reticulon family is a diverse group of proteins that mostly localize to the endoplasmic reticulum and may be important in neurodegenerative diseases.
	Minireview Gene prediction: compare and CONTRAST Paul Flicek Genome Biology 2007, 8:233 (20 December 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The new gene-prediction program CONTRAST offers significant advances in accuracy over previous methods.
	Minireview Genomic clues to an ancient asexual scandal William R Rice, Urban Friberg Genome Biology 2007, 8:232 (28 December 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The bdelloid rotifers are a successful and diverse group of organisms, despite being entirely asexual. How do they do it?
	Report
	Meeting report The ins and outs of translation Jennifer L Clancy, Marco Nousch, Marina Rodnina, Thomas Preiss Genome Biology 2007, 8:321 (7 December 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 2nd EMBO Conference on Protein Synthesis and Translational Control, Heidelberg, Germany, 12-16 September 2007.
	Research
	Research Diversity and evolution of phycobilisomes in marine Synechococcus spp.: a comparative genomics study Christophe Six, Jean-Claude Thomas, Laurence Garczarek, Martin Ostrowski, Alexis Dufresne, Nicolas Blot, David J Scanlan, Frédéric Partensky Genome Biology 2007, 8:R259 (5 December 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary By comparing Synechococcus genomes, candidate genes required for the production of phycobiliproteins, which are part of the light-harvesting antenna complexes called phycobilisomes, were identified. Phylogenetic analyses suggest that the phycobilisome core evolved together with the core genome, whereas rods evolved independently.
	Research Contribution of telomerase RNA retrotranscription to DNA double-strand break repair during mammalian genome evolution Solomon G Nergadze, Marco Santagostino, Alberto Salzano, Chiara Mondello, Elena Giulotto Genome Biology 2007, 8:R260 (7 December 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A comparative analysis of two primate and two rodent genomes suggests that telomerase was utilized, in some instances, for the repair of DNA double-strand breaks during mammalian evolution.
	Research Transcriptional profiling of MnSOD-mediated lifespan extension in Drosophila reveals a species-general network of aging and metabolic genes Christina Curtis, Gary N Landis, Donna Folk, Nancy B Wehr, Nicholas Hoe, Morris Waskar, Diana Abdueva, Dmitriy Skvortsov, Daniel Ford, Allan Luu, Ananth Badrinath, Rodney L Levine, Timothy J Bradley, Simon Tavaré, John Tower Genome Biology 2007, 8:R262 (9 December 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcriptional profiling of MnSOD-mediated life-span extension in Drosophila identifies a set of candidate biomarkers of aging, consisting primarily of carbohydrate metabolism and electron transport genes.
	Research Gene-expression patterns reveal underlying biological processes in Kawasaki disease Stephen J Popper, Chisato Shimizu, Hiroko Shike, John T Kanegaye, Jane W Newburger, Robert P Sundel, Patrick O Brown, Jane C Burns, David A Relman Genome Biology 2007, 8:R261 (11 December 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of patterns of gene expression in peripheral blood from children with Kawasaki disease revealed dynamic and variable gene expression programs involving neutrophil activation and apoptosis.
	Research Evolution of allostery in the cyclic nucleotide binding module Natarajan Kannan, Jian Wu, Ganesh S Anand, Shibu Yooseph, Andrew F Neuwald, J Craig Venter, Susan S Taylor Genome Biology 2007, 8:R264 (12 December 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Analysis of cyclic nucleotide binding (CNB) domains shows that they have evolved to sense a wide variety of second messenger signals; a mechanism for allosteric regulation by CNB domains is proposed.
	Research Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray Hanni Willenbrock, Peter F Hallin, Trudy M Wassenaar, David W Ussery Genome Biology 2007, 8:R267 (18 December 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A high-density microarray has been designed that covers the genomes of 24 Escherichia coli and 8 Shigella strains. As a proof-of-principle the genomes of four probiotic E. coli strains were analyzed and their phylogenetic relationship to other E.coli strains investigated.
	Research Application of the comprehensive set of heterozygous yeast deletion mutants to elucidate the molecular basis of cellular chromium toxicity Sara Holland, Emma Lodwig, Theodora Sideri, Tom Reader, Ian Clarke, Konstantinos Gkargkas, David C Hoyle, Daniela Delneri, Stephen G Oliver, Simon V Avery Genome Biology 2007, 8:R268 (18 December 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Competitive growth between over 6,000 heterozygous yeast mutants in the presence of chromium together with microarray-based screens showed that proteasomal activity is crucial for cellular chromium resistance.
	Method A new computational approach to analyze human protein complexes and predict novel protein interactions Sara Zanivan, Ilaria Cascone, Chiara Peyron, Ivan Molineris, Serena Marchio, Michele Caselle, Federico Bussolino Genome Biology 2007, 8:R256 (4 December 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new approach to identifying interacting proteins based on gene-expression data uses hypergeometric distribution and Monte-Carlo simulations.
	Method Prediction of synergistic transcription factors by function conservation Zihua Hu, Boyu Hu, James F Collins Genome Biology 2007, 8:R257 (5 December 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new strategy is proposed for identifying synergistic transcription factors by function conservation, leading to the identification of 51 homotypic transcription-factor combinations.
	Method Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes Kriston L McGary, Insuk Lee, Edward M Marcotte Genome Biology 2007, 8:R258 (5 December 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Loss-of-function phenotypes of yeast genes can be predicted from the loss-of-function phenotypes of their neighbours in functional gene networks. This could potentially be applied to the prediction of human disease genes.
	Method Determining promoter location based on DNA structure first-principles calculations J Ramon Goñi, Alberto Pérez, David Torrents, Modesto Orozco Genome Biology 2007, 8:R263 (11 December 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new method is presented which predicts promoter regions based on atomistic molecular dynamics simulations of small oligonucleotides, without requiring information on sequence conservation or features.
	Method Quantification of global transcription patterns in prokaryotes using spotted microarrays Ben Sidders, Mike Withers, Sharon L Kendall, Joanna Bacon, Simon J Waddell, Jason Hinds, Paul Golby, Farahnaz Movahedzadeh, Robert A Cox, Rosangela Frita, Annemieke MC ten Bokum, Lorenz Wernisch, Neil G Stoker Genome Biology 2007, 8:R265 (13 December 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis is described, applicable to any spotted microarray dataset that is produced using genomic DNA as a reference for quantifying prokaryotic levels of mRNA on a genome-wide scale.
	Method Direct selection and phage display of a Gram-positive secretome Dragana Jankovic, Michael A Collett, Mark W Lubbers, Jasna Rakonjac Genome Biology 2007, 8:R266 (13 December 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A phage display system for direct selection, identification, expression and purification of bacterial secretome proteins has been developed.
	Method CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction Samuel S Gross, Chuong B Do, Marina Sirota, Serafim Batzoglou Genome Biology 2007, 8:R269 (20 December 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary CONTRAST is a gene predictor that directly incorporates information from multiple alignments and uses discriminative machine learning techniques to give large improvements in prediction over previous methods.
	Method Post-translational modifications of histones H3 and H4 associated with the histone methyltransferases Suv39h1 and G9a Philippe Robin, Lauriane Fritsch, Ophélie Philipot, Fedor Svinarchuk, Slimane Ait-Si-Ali Genome Biology 2007, 8:R270 (20 December 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Mass spectrometry analysis of the post-transcriptional modifications of histones H3 and H4 that were co-purified with histone methyltransferases Suv39h1 and G9a shows that, in HeLa cells, histone methyltransferases can be physically associated with acetylated histones, which normally mark transcriptionally active chromatin.
	Method Consistent dissection of the protein interaction network by combining global and local metrics Chunlin Wang, Chris Ding, Qiaofeng Yang, Stephen R Holbrook Genome Biology 2007, 8:R271 (21 December 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new network decomposition method is proposed that uses both a global metric and a local metric to identify protein interaction modules in the protein interaction network.

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Volume 8 Issue 12

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