Genome Biology | Volume 6 Issue 11

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	Volume 6 Issue 11
	Comment
	Comment H5N1 Gregory A Petsko Genome Biology 2005, 6:121 (1 November 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An influenza pandemic is very much something to worry about.
	Review
	Review Large-scale approaches for glycobiology Christopher T Campbell, Kevin J Yarema Genome Biology 2005, 6:236 (3 November 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Glycosylation, the attachment of carbohydrates to proteins and lipids, influences many biological processes. This article reviews large-scale techniques for accelerating progress in glycobiology.
	Minireview Close encounters between active genes in the nucleus Chien-Hui Chuang, Andrew S Belmont Genome Biology 2005, 6:237 (19 October 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A recent paper demonstrates that coregulated genes on different chromosomes show surprisingly high frequencies of colocalization within the nucleus.
	Minireview Virus-host interactions: new insights from the small RNA world Edward P Browne, Junjie Li, Mark Chong, Dan R Littman Genome Biology 2005, 6:238 (31 October 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent findings show that the Tat protein of human immunodeficiency virus (HIV) can suppress the host's RNA-silencing pathway and may thus counteract host antiviral RNAs.
	Report
	Paper report Articles selected by Faculty of 1000 Biology: from an RNA to a DNA world; sex chromosome evolution; vertebrate whole-genome duplication; U5 snRNA variants in Drosophila; human influenza A virus variation Genome Biology 2005, 6:356 (24 October 2005) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 Biology covering the transition from an RNA to a DNA world; sex chromosome evolution; vertebrate whole-genome duplication; U5 snRNA variants in Drosophila; human influenza A virus variation.
	Paper report Articles selected by Faculty of 1000 Biology: bacterial chromosome segregation; a protein structure initiative; subcellular plant protein localization; transcriptional reprogramming of atrophic muscle; sex-determined recombination levels. Genome Biology 2005, 6:357 (1 November 2005) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 Biology covering bacterial chromosome segregation; a protein structure initiative; subcellular plant protein localization; transcriptional reprogramming of atrophic muscle; sex-determined recombination levels
	Meeting report Metabolomics shows the way to new discoveries Royston Goodacre Genome Biology 2005, 6:354 (31 October 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the First Annual Meeting of the Metabolomics Society, Tsuruoka, Japan, 20-23 June 2005.
	Meeting report Chromatin dynamics rule the genome Samantha G Pattenden, Mark JK Chandy, José L Gutiérrez, Jerry L Workman Genome Biology 2005, 6:355 (31 October 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the FASEB Summer Research Conference 'Chromatin and Transcription', Snowmass, USA, 9-14 July 2005.
	Meeting report Caenorhabditis elegans and friends in Los Angeles Ezequiel A Alvarez-Saavedra, Eric A Miska Genome Biology 2005, 6:358 (1 November 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 15th Biennial International C. elegans Conference, Los Angeles, USA, 25-29 June 2005.
	Deposited research article Conservation versus variation of dinucleotide frequencies across genomes: Evolutionary implications Shang-Hong Zhang, Jian-Hua Yang Genome Biology 2005, 6:P12 (11 October 2005) Abstract \| Full text \| PDF \| Editor’s summary The frequency profiles of dinucleotides of the whole-genome sequence from 130 prokaryotic species (including archaea and bacteria) were analyzed. This study identified conserved frequencies of several dinucleotides (AC, AG, CA, CT, GA, GT, TC, and TG) and suggests that these frequencies may be evolutionary relics of the primordial genome.
	Deposited research article Conservation and divergence of microRNA families in plants Tobias Dezulian, Javier F Palatnik, Daniel Huson, Detlef Weigel Genome Biology 2005, 6:P13 (11 October 2005) Abstract \| Full text \| PDF \| Editor’s summary Based on the bioinformatic identification of more than 200 additional members of known miRNA families in different species, an improved view of phylogenetic distribution, positional nucleotide preference, structural features and conservation of miRNA genes is presented. Furthermore, a classification of plant miRNA families is proposed and evidence for a common origin of the miR159 and miR319 families is presented.
	Research
	Research Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis Robert K Tran, Daniel Zilberman, Cecilia de Bustos, Renata F Ditt, Jorja G Henikoff, Anders M Lindroth, Jeffrey Delrow, Tom Boyle, Samson Kwong, Terri D Bryson, Steven E Jacobsen, Steven Henikoff Genome Biology 2005, 6:R90 (19 October 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Microarray-based profiling of the involvement of two DNA methyltransferases (CMT3 and DRM), a histone H3 lysine-9 methyltransferase (KYP) and an Argonaute-related siRNA silencing component (AGO4) in methylating target loci in Arabidopsis reveals that transposable elements are the targets of both DNA methylation and histone H3K9 methylation pathways, irrespective of element type and position.
	Research Do universal codon-usage patterns minimize the effects of mutation and translation error? Roberto Marquez, Sandra Smit, Rob Knight Genome Biology 2005, 6:R91 (19 October 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The analysis of codon usage in nearly 900 species of the three domains of life suggests that codon usage patterns in mRNA messages do not minimize the effects of translation error.
	Research The interferon-inducible p47 (IRG) GTPases in vertebrates: loss of the cell autonomous resistance mechanism in the human lineage Cemalettin Bekpen, Julia P Hunn, Christoph Rohde, Iana Parvanova, Libby Guethlein, Diane M Dunn, Eva Glowalla, Maria Leptin, Jonathan C Howard Genome Biology 2005, 6:R92 (31 October 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A survey of p47 GTPases in several vertebrate organisms shows that humans lack a p47 GTPase-based resistance system, suggesting that mice and humans deploy their immune resources against vacuolar pathogens in radically different ways.
	Research Transcriptome analysis of antigenic variation in Plasmodium falciparum - var silencing is not dependent on antisense RNA Stuart A Ralph, Emmanuel Bischoff, Denise Mattei, Odile Sismeiro, Marie-Agnès Dillies, Ghislaine Guigon, Jean-Yves Coppee, Peter H David, Artur Scherf Genome Biology 2005, 6:R93 (31 October 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A microarray analysis of Plasmodium falciparum selected to express different var genes suggests that antisense transcripts are not responsible for the transcriptional silencing of non-expressed var genes.
	Research Genome-wide gene expression in response to parasitoid attack in Drosophila Bregje Wertheim, Alex R Kraaijeveld, Eugene Schuster, Eric Blanc, Meirion Hopkins, Scott D Pletcher, Michael R Strand, Linda Partridge, H Charles J Godfray Genome Biology 2005, 6:R94 (31 October 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Expression profiling of the transcriptional response at 9 time points of Drosophila larvae attacked by insect parasites revealed 159 genes that were differentially expressed between parasitized and control larvae. Most genes with altered expression following parasitoid attack had not previously been associated with immune defense.
	Method A computational investigation of kinetoplastid trans-splicing Shuba Gopal, Saria Awadalla, Terry Gaasterland, George AM Cross Genome Biology 2005, 6:R95 (17 October 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel computational approach is presented and applied to predicting trans-splicing sites in 2 chromosomes of Leishmania major.
	Method Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization Francis D Gibbons, Markus Proft, Kevin Struhl, Frederick P Roth Genome Biology 2005, 6:R96 (1 November 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new method, implemented in software as 'Chipper', is described that allows genome-wide determination of protein-DNA binding sites from chromatin immunoprecipitation microarrays.
	Software ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data Michael J Buck, Andrew B Nobel, Jason D Lieb Genome Biology 2005, 6:R97 (19 October 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary ChIPOTle is a new software tool designed specifically for the analysis of ChIP-chip data.

	Volume 6 Issue 11
	Comment
	Comment H5N1 Gregory A Petsko Genome Biology 2005, 6:121 (1 November 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An influenza pandemic is very much something to worry about.
	Review
	Review Large-scale approaches for glycobiology Christopher T Campbell, Kevin J Yarema Genome Biology 2005, 6:236 (3 November 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Glycosylation, the attachment of carbohydrates to proteins and lipids, influences many biological processes. This article reviews large-scale techniques for accelerating progress in glycobiology.
	Minireview Close encounters between active genes in the nucleus Chien-Hui Chuang, Andrew S Belmont Genome Biology 2005, 6:237 (19 October 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A recent paper demonstrates that coregulated genes on different chromosomes show surprisingly high frequencies of colocalization within the nucleus.
	Minireview Virus-host interactions: new insights from the small RNA world Edward P Browne, Junjie Li, Mark Chong, Dan R Littman Genome Biology 2005, 6:238 (31 October 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent findings show that the Tat protein of human immunodeficiency virus (HIV) can suppress the host's RNA-silencing pathway and may thus counteract host antiviral RNAs.
	Report
	Paper report Articles selected by Faculty of 1000 Biology: from an RNA to a DNA world; sex chromosome evolution; vertebrate whole-genome duplication; U5 snRNA variants in Drosophila; human influenza A virus variation Genome Biology 2005, 6:356 (24 October 2005) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 Biology covering the transition from an RNA to a DNA world; sex chromosome evolution; vertebrate whole-genome duplication; U5 snRNA variants in Drosophila; human influenza A virus variation.
	Paper report Articles selected by Faculty of 1000 Biology: bacterial chromosome segregation; a protein structure initiative; subcellular plant protein localization; transcriptional reprogramming of atrophic muscle; sex-determined recombination levels. Genome Biology 2005, 6:357 (1 November 2005) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 Biology covering bacterial chromosome segregation; a protein structure initiative; subcellular plant protein localization; transcriptional reprogramming of atrophic muscle; sex-determined recombination levels
	Meeting report Metabolomics shows the way to new discoveries Royston Goodacre Genome Biology 2005, 6:354 (31 October 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the First Annual Meeting of the Metabolomics Society, Tsuruoka, Japan, 20-23 June 2005.
	Meeting report Chromatin dynamics rule the genome Samantha G Pattenden, Mark JK Chandy, José L Gutiérrez, Jerry L Workman Genome Biology 2005, 6:355 (31 October 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the FASEB Summer Research Conference 'Chromatin and Transcription', Snowmass, USA, 9-14 July 2005.
	Meeting report Caenorhabditis elegans and friends in Los Angeles Ezequiel A Alvarez-Saavedra, Eric A Miska Genome Biology 2005, 6:358 (1 November 2005) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 15th Biennial International C. elegans Conference, Los Angeles, USA, 25-29 June 2005.
	Deposited research article Conservation versus variation of dinucleotide frequencies across genomes: Evolutionary implications Shang-Hong Zhang, Jian-Hua Yang Genome Biology 2005, 6:P12 (11 October 2005) Abstract \| Full text \| PDF \| Editor’s summary The frequency profiles of dinucleotides of the whole-genome sequence from 130 prokaryotic species (including archaea and bacteria) were analyzed. This study identified conserved frequencies of several dinucleotides (AC, AG, CA, CT, GA, GT, TC, and TG) and suggests that these frequencies may be evolutionary relics of the primordial genome.
	Deposited research article Conservation and divergence of microRNA families in plants Tobias Dezulian, Javier F Palatnik, Daniel Huson, Detlef Weigel Genome Biology 2005, 6:P13 (11 October 2005) Abstract \| Full text \| PDF \| Editor’s summary Based on the bioinformatic identification of more than 200 additional members of known miRNA families in different species, an improved view of phylogenetic distribution, positional nucleotide preference, structural features and conservation of miRNA genes is presented. Furthermore, a classification of plant miRNA families is proposed and evidence for a common origin of the miR159 and miR319 families is presented.
	Research
	Research Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis Robert K Tran, Daniel Zilberman, Cecilia de Bustos, Renata F Ditt, Jorja G Henikoff, Anders M Lindroth, Jeffrey Delrow, Tom Boyle, Samson Kwong, Terri D Bryson, Steven E Jacobsen, Steven Henikoff Genome Biology 2005, 6:R90 (19 October 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Microarray-based profiling of the involvement of two DNA methyltransferases (CMT3 and DRM), a histone H3 lysine-9 methyltransferase (KYP) and an Argonaute-related siRNA silencing component (AGO4) in methylating target loci in Arabidopsis reveals that transposable elements are the targets of both DNA methylation and histone H3K9 methylation pathways, irrespective of element type and position.
	Research Do universal codon-usage patterns minimize the effects of mutation and translation error? Roberto Marquez, Sandra Smit, Rob Knight Genome Biology 2005, 6:R91 (19 October 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The analysis of codon usage in nearly 900 species of the three domains of life suggests that codon usage patterns in mRNA messages do not minimize the effects of translation error.
	Research The interferon-inducible p47 (IRG) GTPases in vertebrates: loss of the cell autonomous resistance mechanism in the human lineage Cemalettin Bekpen, Julia P Hunn, Christoph Rohde, Iana Parvanova, Libby Guethlein, Diane M Dunn, Eva Glowalla, Maria Leptin, Jonathan C Howard Genome Biology 2005, 6:R92 (31 October 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A survey of p47 GTPases in several vertebrate organisms shows that humans lack a p47 GTPase-based resistance system, suggesting that mice and humans deploy their immune resources against vacuolar pathogens in radically different ways.
	Research Transcriptome analysis of antigenic variation in Plasmodium falciparum - var silencing is not dependent on antisense RNA Stuart A Ralph, Emmanuel Bischoff, Denise Mattei, Odile Sismeiro, Marie-Agnès Dillies, Ghislaine Guigon, Jean-Yves Coppee, Peter H David, Artur Scherf Genome Biology 2005, 6:R93 (31 October 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A microarray analysis of Plasmodium falciparum selected to express different var genes suggests that antisense transcripts are not responsible for the transcriptional silencing of non-expressed var genes.
	Research Genome-wide gene expression in response to parasitoid attack in Drosophila Bregje Wertheim, Alex R Kraaijeveld, Eugene Schuster, Eric Blanc, Meirion Hopkins, Scott D Pletcher, Michael R Strand, Linda Partridge, H Charles J Godfray Genome Biology 2005, 6:R94 (31 October 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Expression profiling of the transcriptional response at 9 time points of Drosophila larvae attacked by insect parasites revealed 159 genes that were differentially expressed between parasitized and control larvae. Most genes with altered expression following parasitoid attack had not previously been associated with immune defense.
	Method A computational investigation of kinetoplastid trans-splicing Shuba Gopal, Saria Awadalla, Terry Gaasterland, George AM Cross Genome Biology 2005, 6:R95 (17 October 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel computational approach is presented and applied to predicting trans-splicing sites in 2 chromosomes of Leishmania major.
	Method Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization Francis D Gibbons, Markus Proft, Kevin Struhl, Frederick P Roth Genome Biology 2005, 6:R96 (1 November 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new method, implemented in software as 'Chipper', is described that allows genome-wide determination of protein-DNA binding sites from chromatin immunoprecipitation microarrays.
	Software ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data Michael J Buck, Andrew B Nobel, Jason D Lieb Genome Biology 2005, 6:R97 (19 October 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary ChIPOTle is a new software tool designed specifically for the analysis of ChIP-chip data.

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Volume 6 Issue 11

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