Genome Biology | Volume 5 Issue 12

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	Volume 5 Issue 12
	Comment
	Comment Color blind Gregory A Petsko Genome Biology 2004, 5:119 (26 November 2004) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary Does identifying genetic differences between groups itself constitute an act of racism?
	Review
	Review Silencing of transposons in plant genomes: kick them when they're down Daniel Zilberman, Steven Henikoff Genome Biology 2004, 5:249 (16 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Recent progress in understanding the silencing of transposable elements in the model plant Arabidopsis has revealed an interplay between DNA methylation, histone methylation and small interfering RNAs.
	Protein family review The Janus kinases (Jaks) Kunihiro Yamaoka, Pipsa Saharinen, Marko Pesu, Vance ET Holt, Olli Silvennoinen, John J O'Shea Genome Biology 2004, 5:253 (30 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Janus kinase (Jak) family, including Jak1, Jak2, Jak3 and Tyrosine kinase 2 (Tyk2), bind cytokine receptors through amino-terminal FERM domains and link them to other molecules, especially members of the signal transducer and activator of transcription (Stat) family.
	Minireview Tetraodon genome confirms Takifugu findings: most fish are ancient polyploids Yves Van de Peer Genome Biology 2004, 5:250 (25 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome of Tetraodon nigroviridis confirms that ray-finned fish underwent an acient whole-genome duplication.
	Minireview The origin of recent introns: transposons? Scott W Roy Genome Biology 2004, 5:251 (29 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A recent study makes considerable progress towards answering the question of how genes acquire introns by identifying numerous recently gained introns in nematodes.
	Minireview Chromatin architecture and gene expression in Escherichia coli Hanni Willenbrock, David W Ussery Genome Biology 2004, 5:252 (1 December 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Two recent genome-scale analyses underscore the importance of DNA topology and chromatin structure in regulating transcription in Escherichia coli.
	Report
	Paper report Articles selected by Faculty of 1000: chromosome pairing in Arabidopsis; hybrid inviability in birds and mammals; endogenous siRNAs in Arabidopsis; evolution of sex-biased genes in Drosophila; human patterns of genetic variation Genome Biology 2004, 5:360 (5 November 2004) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering chromosome pairing in Arabidopsis; hybrid inviability in birds and mammals; endogenous siRNAs in Arabidopsis; evolution of sex-biased genes in Drosophila; human patterns of genetic variation.
	Paper report Articles selected by Faculty of 1000: phage receptor-binding proteins; genetic diversity in Toxoplasma; ribosome biogenesis and cell size; gene regulation by retrotransposons; manipulation of the cancer epigenome Genome Biology 2004, 5:361 (18 November 2004) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering phage receptor-binding proteins; genetic diversity in Toxoplasma; ribosome biogenesis and cell size; gene regulation by retrotransposons; manipulation of the cancer epigenome.
	Meeting report Why genomics is more than genomes Jeffrey G Lawrence Genome Biology 2004, 5:357 (16 November 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 2004 meeting on Molecular Genetics of Bacteria and Bacteriophages, Cold Spring Harbor, USA, 25-29 August 2004.
	Meeting report Mice get their annual check-up Virginia E Papaioannou Genome Biology 2004, 5:358 (16 November 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 2004 meeting on Mouse Molecular Genetics, Cold Spring Harbor, USA, 1-5 September 2004.
	Meeting report Translational regulation of gene expression Stephanie Kervestin, Nadia Amrani Genome Biology 2004, 5:359 (25 November 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Cold Spring Harbor Laboratory meeting 'Translational Control', Cold Spring Harbor, USA, 7-12 September 2004.
	Research news How meiotic arrest happens Cathy Holding Genome Biology 2004, 5:spotlight-20041210-01 (10 December 2004) Abstract \| Full text \| Editor’s summary Mouse needs G-protein-coupled receptor to keep its eggs fresh, according to study
	Research news A link for unrelated viruses Charles Choi Genome Biology 2004, 5:spotlight-20041210-03 (10 December 2004) Abstract \| Full text \| Editor’s summary Viruses which infect all three domains of life could be descended from bacteriophage
	Research news 'Respiratory burst' enzyme found Clementine Wallace Genome Biology 2004, 5:spotlight-20041210-02 (10 December 2004) Abstract \| Full text \| Editor’s summary Researchers report elucidation of key step in sea urchin fertilization
	Research news Tandem repeats take, make shape Melissa Phillips Genome Biology 2004, 5:spotlight-20041215-01 (15 December 2004) Abstract \| Full text \| Editor’s summary Presence in developmental genes may underlie evolution of morphological diversity
	Research news Phosphorylation without ATP Charles Q Choi Genome Biology 2004, 5:spotlight-20041220-01 (20 December 2004) Abstract \| Full text \| Editor’s summary IP7 offers a nonenzymatic alternative for adding phosphate to proteins
	Research news Polymerase may be key to flu's virulence Cathy Holding Genome Biology 2004, 5:spotlight-20051206-01 (6 December 2005) Abstract \| Full text \| Editor’s summary Model points to importance of polymerase activity in species jump
	Research news Man's best genome? Aileen Constans Genome Biology 2004, 5:spotlight-20051209-01 (9 December 2005) Abstract \| Full text \| Editor’s summary Scientists generate the highest-resolution draft sequence of the domestic dog
	Research news Gene implicated in human pigment variation Ishani Ganguli Genome Biology 2004, 5:spotlight-20051223-01 (23 December 2005) Abstract \| Full text \| Editor’s summary Single nucleotide distinguishes African and European skin colors
	Research
	Research A Drosophila protein-interaction map centered on cell-cycle regulators Clement A Stanyon, Guozhen Liu, Bernardo A Mangiola, Nishi Patel, Loic Giot, Bing Kuang, Huamei Zhang, Jinhui Zhong, Russell L Finley Genome Biology 2004, 5:R96 (26 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A Drosophila protein-protein interaction map was constructed using the LexA system, complementing a previous map using the GAL4 system and adding many new interactions.
	Research Integrating phenotypic and expression profiles to map arsenic-response networks Astrid C Haugen, Ryan Kelley, Jennifer B Collins, Charles J Tucker, Changchun Deng, Cynthia A Afshari, J Martin Brown, Trey Ideker, Bennett Van Houten Genome Biology 2004, 5:R95 (29 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary By integrating phenotypic and transcriptional profiling and mapping the data onto metabolic and regulatory networks, it was shown that arsenic probably channels sulfur into glutathione for detoxification, leads to indirect oxidative stress by depleting glutathione pools, and alters protein turnover via arsenation of sulfhydryl groups on proteins.
	Research Hidden localization motifs: naturally occurring peroxisomal targeting signals in non-peroxisomal proteins Georg Neuberger, Markus Kunze, Frank Eisenhaber, Johannes Berger, Andreas Hartig, Cecile Brocard Genome Biology 2004, 5:R97 (30 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Functional but silent peroxisomal targeting signals have been found in non- peroxisomal proteins. This discovery has important implications for sequence-based signal prediction and for evolution.
	Method Model-independent fluxome profiling from ²H and ¹³C experiments for metabolic variant discrimination Nicola Zamboni, Uwe Sauer Genome Biology 2004, 5:R99 (16 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel method for intracellular fluxome profiling that does not require a priori knowledge of the metabolic system allowed the identification of characteristic flux fingerprints in 10 Bacillus mutants from 132 ²H and ¹³C tracers experiments.
	Method MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model Alan M Moses, Derek Y Chiang, Daniel A Pollard, Venky N Iyer, Michael B Eisen Genome Biology 2004, 5:R98 (30 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary MONKEY is a new method for identifying conserved transcription-factor binding sites from multiple-sequence alignments.
	Method Estimating genomic coexpression networks using first-order conditional independence Paul M Magwene, Junhyong Kim Genome Biology 2004, 5:R100 (30 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A computationally efficient statistical framework for estimating networks of coexpressed genes is presented that exploits first-order conditional independence relationships among gene expression measurements.
	Software GOToolBox: functional analysis of gene datasets based on Gene Ontology David Martin, Christine Brun, Elisabeth Remy, Pierre Mouren, Denis Thieffry, Bernard Jacq Genome Biology 2004, 5:R101 (26 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Tools are presented to identify Gene Ontology terms that are over- or under-represented in a dataset, to cluster genes by function and to find genes with similar annotations.
	Software The ASRG database: identification and survey of Arabidopsis thaliana genes involved in pre-mRNA splicing Bing-Bing Wang, Volker Brendel Genome Biology 2004, 5:R102 (29 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The database of Arabidopsis splicing related genes includes classification of genes encoding snRNAs and other splicing related proteins, together with information on gene structure, alternative splicing, gene duplications and phylogenetic relationships.

	Volume 5 Issue 12
	Comment
	Comment Color blind Gregory A Petsko Genome Biology 2004, 5:119 (26 November 2004) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary Does identifying genetic differences between groups itself constitute an act of racism?
	Review
	Review Silencing of transposons in plant genomes: kick them when they're down Daniel Zilberman, Steven Henikoff Genome Biology 2004, 5:249 (16 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Recent progress in understanding the silencing of transposable elements in the model plant Arabidopsis has revealed an interplay between DNA methylation, histone methylation and small interfering RNAs.
	Protein family review The Janus kinases (Jaks) Kunihiro Yamaoka, Pipsa Saharinen, Marko Pesu, Vance ET Holt, Olli Silvennoinen, John J O'Shea Genome Biology 2004, 5:253 (30 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Janus kinase (Jak) family, including Jak1, Jak2, Jak3 and Tyrosine kinase 2 (Tyk2), bind cytokine receptors through amino-terminal FERM domains and link them to other molecules, especially members of the signal transducer and activator of transcription (Stat) family.
	Minireview Tetraodon genome confirms Takifugu findings: most fish are ancient polyploids Yves Van de Peer Genome Biology 2004, 5:250 (25 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome of Tetraodon nigroviridis confirms that ray-finned fish underwent an acient whole-genome duplication.
	Minireview The origin of recent introns: transposons? Scott W Roy Genome Biology 2004, 5:251 (29 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A recent study makes considerable progress towards answering the question of how genes acquire introns by identifying numerous recently gained introns in nematodes.
	Minireview Chromatin architecture and gene expression in Escherichia coli Hanni Willenbrock, David W Ussery Genome Biology 2004, 5:252 (1 December 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Two recent genome-scale analyses underscore the importance of DNA topology and chromatin structure in regulating transcription in Escherichia coli.
	Report
	Paper report Articles selected by Faculty of 1000: chromosome pairing in Arabidopsis; hybrid inviability in birds and mammals; endogenous siRNAs in Arabidopsis; evolution of sex-biased genes in Drosophila; human patterns of genetic variation Genome Biology 2004, 5:360 (5 November 2004) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering chromosome pairing in Arabidopsis; hybrid inviability in birds and mammals; endogenous siRNAs in Arabidopsis; evolution of sex-biased genes in Drosophila; human patterns of genetic variation.
	Paper report Articles selected by Faculty of 1000: phage receptor-binding proteins; genetic diversity in Toxoplasma; ribosome biogenesis and cell size; gene regulation by retrotransposons; manipulation of the cancer epigenome Genome Biology 2004, 5:361 (18 November 2004) Abstract \| Full text \| Editor’s summary A selection of evaluations from Faculty of 1000 covering phage receptor-binding proteins; genetic diversity in Toxoplasma; ribosome biogenesis and cell size; gene regulation by retrotransposons; manipulation of the cancer epigenome.
	Meeting report Why genomics is more than genomes Jeffrey G Lawrence Genome Biology 2004, 5:357 (16 November 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 2004 meeting on Molecular Genetics of Bacteria and Bacteriophages, Cold Spring Harbor, USA, 25-29 August 2004.
	Meeting report Mice get their annual check-up Virginia E Papaioannou Genome Biology 2004, 5:358 (16 November 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 2004 meeting on Mouse Molecular Genetics, Cold Spring Harbor, USA, 1-5 September 2004.
	Meeting report Translational regulation of gene expression Stephanie Kervestin, Nadia Amrani Genome Biology 2004, 5:359 (25 November 2004) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Cold Spring Harbor Laboratory meeting 'Translational Control', Cold Spring Harbor, USA, 7-12 September 2004.
	Research news How meiotic arrest happens Cathy Holding Genome Biology 2004, 5:spotlight-20041210-01 (10 December 2004) Abstract \| Full text \| Editor’s summary Mouse needs G-protein-coupled receptor to keep its eggs fresh, according to study
	Research news A link for unrelated viruses Charles Choi Genome Biology 2004, 5:spotlight-20041210-03 (10 December 2004) Abstract \| Full text \| Editor’s summary Viruses which infect all three domains of life could be descended from bacteriophage
	Research news 'Respiratory burst' enzyme found Clementine Wallace Genome Biology 2004, 5:spotlight-20041210-02 (10 December 2004) Abstract \| Full text \| Editor’s summary Researchers report elucidation of key step in sea urchin fertilization
	Research news Tandem repeats take, make shape Melissa Phillips Genome Biology 2004, 5:spotlight-20041215-01 (15 December 2004) Abstract \| Full text \| Editor’s summary Presence in developmental genes may underlie evolution of morphological diversity
	Research news Phosphorylation without ATP Charles Q Choi Genome Biology 2004, 5:spotlight-20041220-01 (20 December 2004) Abstract \| Full text \| Editor’s summary IP7 offers a nonenzymatic alternative for adding phosphate to proteins
	Research news Polymerase may be key to flu's virulence Cathy Holding Genome Biology 2004, 5:spotlight-20051206-01 (6 December 2005) Abstract \| Full text \| Editor’s summary Model points to importance of polymerase activity in species jump
	Research news Man's best genome? Aileen Constans Genome Biology 2004, 5:spotlight-20051209-01 (9 December 2005) Abstract \| Full text \| Editor’s summary Scientists generate the highest-resolution draft sequence of the domestic dog
	Research news Gene implicated in human pigment variation Ishani Ganguli Genome Biology 2004, 5:spotlight-20051223-01 (23 December 2005) Abstract \| Full text \| Editor’s summary Single nucleotide distinguishes African and European skin colors
	Research
	Research A Drosophila protein-interaction map centered on cell-cycle regulators Clement A Stanyon, Guozhen Liu, Bernardo A Mangiola, Nishi Patel, Loic Giot, Bing Kuang, Huamei Zhang, Jinhui Zhong, Russell L Finley Genome Biology 2004, 5:R96 (26 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A Drosophila protein-protein interaction map was constructed using the LexA system, complementing a previous map using the GAL4 system and adding many new interactions.
	Research Integrating phenotypic and expression profiles to map arsenic-response networks Astrid C Haugen, Ryan Kelley, Jennifer B Collins, Charles J Tucker, Changchun Deng, Cynthia A Afshari, J Martin Brown, Trey Ideker, Bennett Van Houten Genome Biology 2004, 5:R95 (29 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary By integrating phenotypic and transcriptional profiling and mapping the data onto metabolic and regulatory networks, it was shown that arsenic probably channels sulfur into glutathione for detoxification, leads to indirect oxidative stress by depleting glutathione pools, and alters protein turnover via arsenation of sulfhydryl groups on proteins.
	Research Hidden localization motifs: naturally occurring peroxisomal targeting signals in non-peroxisomal proteins Georg Neuberger, Markus Kunze, Frank Eisenhaber, Johannes Berger, Andreas Hartig, Cecile Brocard Genome Biology 2004, 5:R97 (30 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Functional but silent peroxisomal targeting signals have been found in non- peroxisomal proteins. This discovery has important implications for sequence-based signal prediction and for evolution.
	Method Model-independent fluxome profiling from ²H and ¹³C experiments for metabolic variant discrimination Nicola Zamboni, Uwe Sauer Genome Biology 2004, 5:R99 (16 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel method for intracellular fluxome profiling that does not require a priori knowledge of the metabolic system allowed the identification of characteristic flux fingerprints in 10 Bacillus mutants from 132 ²H and ¹³C tracers experiments.
	Method MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model Alan M Moses, Derek Y Chiang, Daniel A Pollard, Venky N Iyer, Michael B Eisen Genome Biology 2004, 5:R98 (30 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary MONKEY is a new method for identifying conserved transcription-factor binding sites from multiple-sequence alignments.
	Method Estimating genomic coexpression networks using first-order conditional independence Paul M Magwene, Junhyong Kim Genome Biology 2004, 5:R100 (30 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A computationally efficient statistical framework for estimating networks of coexpressed genes is presented that exploits first-order conditional independence relationships among gene expression measurements.
	Software GOToolBox: functional analysis of gene datasets based on Gene Ontology David Martin, Christine Brun, Elisabeth Remy, Pierre Mouren, Denis Thieffry, Bernard Jacq Genome Biology 2004, 5:R101 (26 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Tools are presented to identify Gene Ontology terms that are over- or under-represented in a dataset, to cluster genes by function and to find genes with similar annotations.
	Software The ASRG database: identification and survey of Arabidopsis thaliana genes involved in pre-mRNA splicing Bing-Bing Wang, Volker Brendel Genome Biology 2004, 5:R102 (29 November 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The database of Arabidopsis splicing related genes includes classification of genes encoding snRNAs and other splicing related proteins, together with information on gene structure, alternative splicing, gene duplications and phylogenetic relationships.

Explore Genome Biology

Articles

Volume 5 Issue 12

Comment

Review

Report

Research