Genome Biology | Volume 7 Issue 2

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	Volume 7 Issue 2
	Comment
	Comment Sweden has the right idea Gregory A Petsko Genome Biology 2006, 7:103 (1 March 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The conservative funding system, which tends to prefer giving money to things that seem likely to work rather than to things that are innovative and therefore risky, rewards those with a track record so long as they continue to do the things they have a track record in.
	Review
	Protein family review The aquaporins Elisabeth Kruse, Norbert Uehlein, Ralf Kaldenhoff Genome Biology 2006, 7:206 (28 February 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Aquaporins are intrinsic membrane proteins found in all organisms, from archaea to mammals. They selectively allow water or other small uncharged molecules to pass along the osmotic gradient.
	Minireview Shuffling bacterial metabolomes Brendan Thomason, Timothy D Read Genome Biology 2006, 7:204 (27 February 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Horizontal gene transfer (HGT) is more important than gene duplication in bacterial evolution, as has recently been illustrated by work demonstrating the role of HGT in the emergence of bacterial metabolic networks.
	Minireview Sex-specific gene expression in preimplantation mouse embryos Guy S Eakin, Anna-Katerina Hadjantonakis Genome Biology 2006, 7:205 (1 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The 3.5-day-old blastocyst-stage mouse embryo has now been observed to express nearly 600 genes in a sex-specific fashion, including at least one gene (Rhox/Pem) expressed only in females from their paternal X chromosome.
	Opinion Prospective health care: the second transformation of medicine Ralph Snyderman, Jason Langheier Genome Biology 2006, 7:104 (27 February 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Emerging scientific technologies provide rich sources of predictive biomarkers, which will enable the development of tools to quantify risk and anticipate disease, so health care can become rational, preventive and personalized.
	Report
	Meeting report Multi-genome biology Thomas A Down Genome Biology 2006, 7:305 (10 February 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Genome Informatics meeting held at Cold Spring Harbor Laboratory, Cold Spring Harbor, USA, 28 October-1 November 2005.
	Meeting report Rats go genomic Bart MG Smits, Edwin Cuppen Genome Biology 2006, 7:306 (17 February 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the meeting 'Rat Genomics and Models', Cold Spring Harbor, USA, 8-11 December 2005.
	Meeting report Discovery and hypothesis generation through bioinformatics Joaquín Dopazo, Patrick Aloy Genome Biology 2006, 7:307 (27 February 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 4th European Conference on Computational Biology and the 6th Spanish Annual Meeting on Bioinformatics, Madrid, Spain, 28 September-1 October 2005.
	Research
	Research Release of extraction-resistant mRNA in stationary phase Saccharomyces cerevisiae produces a massive increase in transcript abundance in response to stress Anthony D Aragon, Gabriel A Quiñones, Edward V Thomas, Sushmita Roy, Margaret Werner-Washburne Genome Biology 2006, 7:R9 (8 February 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A rapid transcript increase due to the release of extraction-resistant mRNAs from yeast cells in response to stress is described.
	Research Alternate transcription of the Toll-like receptor signaling cascade Christine A Wells, Alistair M Chalk, Alistair Forrest, Darrin Taylor, Nic Waddell, Kate Schroder, S Roy Himes, Geoffrey Faulkner, Sandra Lo, Takeya Kasukawa, Hideya Kawaji, Chikatoshi Kai, Jun Kawai, Shintaro Katayama, Piero Carninci, Yoshihide Hayashizaki, David A Hume, Sean M Grimmond Genome Biology 2006, 7:R10 (17 February 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A systematic analysis of the FANTOM3 mouse cDNA dataset provides transcriptional evidence of widespread alternate splicing in the Toll-like receptor signaling pathway.
	Research Identification of signaling components required for the prediction of cytokine release in RAW 264.7 macrophages Sylvain Pradervand, Mano R Maurya, Shankar Subramaniam Genome Biology 2006, 7:R11 (20 February 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An integrative approach is used to identifying the pathways responsible for the release of seven cytokines in response to selected ligands.
	Research Lineage-specific expansion of proteins exported to erythrocytes in malaria parasites Tobias J Sargeant, Matthias Marti, Elisabet Caler, Jane M Carlton, Ken Simpson, Terence P Speed, Alan F Cowman Genome Biology 2006, 7:R12 (20 February 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A new software was used to predict exported proteins that are conserved between malaria parasites infecting rodents and those infecting humans, revealing a lineage-specific expansion of exported proteins.
	Research Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana Tineke Casneuf, Stefanie De Bodt, Jeroen Raes, Steven Maere, Yves Van de Peer Genome Biology 2006, 7:R13 (20 February 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of expression data of duplicated genes in Arabidopsis thaliana shows that the mode of duplication, the time since duplication and the function of the duplicated genes play a role in the divergence of their expression.
	Research Comparison of dot chromosome sequences from D. melanogaster and D. virilis reveals an enrichment of DNA transposon sequences in heterochromatic domains Elizabeth E Slawson, Christopher D Shaffer, Colin D Malone, Wilson Leung, Elmer Kellmann, Rachel B Shevchek, Carolyn A Craig, Seth M Bloom, James Bogenpohl, James Dee, Emiko TA Morimoto, Jenny Myoung, Andrew S Nett, Fatih Ozsolak, Mindy E Tittiger, Andrea Zeug, Mary-Lou Pardue, Jeremy Buhler, Elaine R Mardis, Sarah CR Elgin Genome Biology 2006, 7:R15 (20 February 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Sequencing and analysis of fosmid hybridization to the dot chromosomes of Drosophila virilis and D. melanogaster suggest that repetitive elements and density are important in determining higher-order chromatin packaging.
	Research Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes Mark J Lawson, Liqing Zhang Genome Biology 2006, 7:R14 (21 February 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comparative study of the distribution of single sequence repeats in rice and Arabidopsis reveals that the repeat patterns vary a lot in different genomic regions.
	Research The role of transposable element clusters in genome evolution and loss of synteny in the rice blast fungus Magnaporthe oryzae Michael R Thon, Huaqin Pan, Stephen Diener, John Papalas, Audrey Taro, Thomas K Mitchell, Ralph A Dean Genome Biology 2006, 7:R16 (28 February 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of the Magnaporthe oryzae chromosome 7 and comparison with syntenic regions in other fungal genomes suggests that transposable elements create localized segments with increased rates of chromosomal rearrangements, gene duplications and gene evolution.
	Method Predicting genes for orphan metabolic activities using phylogenetic profiles Lifeng Chen, Dennis Vitkup Genome Biology 2006, 7:R17 (15 February 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method that combines local structure of a metabolic network with phylogenetic profiles is described and used to assign genes to orphan metabolic activities in yeast and Escherichia coli.

	Volume 7 Issue 2
	Comment
	Comment Sweden has the right idea Gregory A Petsko Genome Biology 2006, 7:103 (1 March 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The conservative funding system, which tends to prefer giving money to things that seem likely to work rather than to things that are innovative and therefore risky, rewards those with a track record so long as they continue to do the things they have a track record in.
	Review
	Protein family review The aquaporins Elisabeth Kruse, Norbert Uehlein, Ralf Kaldenhoff Genome Biology 2006, 7:206 (28 February 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Aquaporins are intrinsic membrane proteins found in all organisms, from archaea to mammals. They selectively allow water or other small uncharged molecules to pass along the osmotic gradient.
	Minireview Shuffling bacterial metabolomes Brendan Thomason, Timothy D Read Genome Biology 2006, 7:204 (27 February 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Horizontal gene transfer (HGT) is more important than gene duplication in bacterial evolution, as has recently been illustrated by work demonstrating the role of HGT in the emergence of bacterial metabolic networks.
	Minireview Sex-specific gene expression in preimplantation mouse embryos Guy S Eakin, Anna-Katerina Hadjantonakis Genome Biology 2006, 7:205 (1 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The 3.5-day-old blastocyst-stage mouse embryo has now been observed to express nearly 600 genes in a sex-specific fashion, including at least one gene (Rhox/Pem) expressed only in females from their paternal X chromosome.
	Opinion Prospective health care: the second transformation of medicine Ralph Snyderman, Jason Langheier Genome Biology 2006, 7:104 (27 February 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Emerging scientific technologies provide rich sources of predictive biomarkers, which will enable the development of tools to quantify risk and anticipate disease, so health care can become rational, preventive and personalized.
	Report
	Meeting report Multi-genome biology Thomas A Down Genome Biology 2006, 7:305 (10 February 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Genome Informatics meeting held at Cold Spring Harbor Laboratory, Cold Spring Harbor, USA, 28 October-1 November 2005.
	Meeting report Rats go genomic Bart MG Smits, Edwin Cuppen Genome Biology 2006, 7:306 (17 February 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the meeting 'Rat Genomics and Models', Cold Spring Harbor, USA, 8-11 December 2005.
	Meeting report Discovery and hypothesis generation through bioinformatics Joaquín Dopazo, Patrick Aloy Genome Biology 2006, 7:307 (27 February 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 4th European Conference on Computational Biology and the 6th Spanish Annual Meeting on Bioinformatics, Madrid, Spain, 28 September-1 October 2005.
	Research
	Research Release of extraction-resistant mRNA in stationary phase Saccharomyces cerevisiae produces a massive increase in transcript abundance in response to stress Anthony D Aragon, Gabriel A Quiñones, Edward V Thomas, Sushmita Roy, Margaret Werner-Washburne Genome Biology 2006, 7:R9 (8 February 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A rapid transcript increase due to the release of extraction-resistant mRNAs from yeast cells in response to stress is described.
	Research Alternate transcription of the Toll-like receptor signaling cascade Christine A Wells, Alistair M Chalk, Alistair Forrest, Darrin Taylor, Nic Waddell, Kate Schroder, S Roy Himes, Geoffrey Faulkner, Sandra Lo, Takeya Kasukawa, Hideya Kawaji, Chikatoshi Kai, Jun Kawai, Shintaro Katayama, Piero Carninci, Yoshihide Hayashizaki, David A Hume, Sean M Grimmond Genome Biology 2006, 7:R10 (17 February 2006) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A systematic analysis of the FANTOM3 mouse cDNA dataset provides transcriptional evidence of widespread alternate splicing in the Toll-like receptor signaling pathway.
	Research Identification of signaling components required for the prediction of cytokine release in RAW 264.7 macrophages Sylvain Pradervand, Mano R Maurya, Shankar Subramaniam Genome Biology 2006, 7:R11 (20 February 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An integrative approach is used to identifying the pathways responsible for the release of seven cytokines in response to selected ligands.
	Research Lineage-specific expansion of proteins exported to erythrocytes in malaria parasites Tobias J Sargeant, Matthias Marti, Elisabet Caler, Jane M Carlton, Ken Simpson, Terence P Speed, Alan F Cowman Genome Biology 2006, 7:R12 (20 February 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A new software was used to predict exported proteins that are conserved between malaria parasites infecting rodents and those infecting humans, revealing a lineage-specific expansion of exported proteins.
	Research Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana Tineke Casneuf, Stefanie De Bodt, Jeroen Raes, Steven Maere, Yves Van de Peer Genome Biology 2006, 7:R13 (20 February 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of expression data of duplicated genes in Arabidopsis thaliana shows that the mode of duplication, the time since duplication and the function of the duplicated genes play a role in the divergence of their expression.
	Research Comparison of dot chromosome sequences from D. melanogaster and D. virilis reveals an enrichment of DNA transposon sequences in heterochromatic domains Elizabeth E Slawson, Christopher D Shaffer, Colin D Malone, Wilson Leung, Elmer Kellmann, Rachel B Shevchek, Carolyn A Craig, Seth M Bloom, James Bogenpohl, James Dee, Emiko TA Morimoto, Jenny Myoung, Andrew S Nett, Fatih Ozsolak, Mindy E Tittiger, Andrea Zeug, Mary-Lou Pardue, Jeremy Buhler, Elaine R Mardis, Sarah CR Elgin Genome Biology 2006, 7:R15 (20 February 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Sequencing and analysis of fosmid hybridization to the dot chromosomes of Drosophila virilis and D. melanogaster suggest that repetitive elements and density are important in determining higher-order chromatin packaging.
	Research Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes Mark J Lawson, Liqing Zhang Genome Biology 2006, 7:R14 (21 February 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comparative study of the distribution of single sequence repeats in rice and Arabidopsis reveals that the repeat patterns vary a lot in different genomic regions.
	Research The role of transposable element clusters in genome evolution and loss of synteny in the rice blast fungus Magnaporthe oryzae Michael R Thon, Huaqin Pan, Stephen Diener, John Papalas, Audrey Taro, Thomas K Mitchell, Ralph A Dean Genome Biology 2006, 7:R16 (28 February 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of the Magnaporthe oryzae chromosome 7 and comparison with syntenic regions in other fungal genomes suggests that transposable elements create localized segments with increased rates of chromosomal rearrangements, gene duplications and gene evolution.
	Method Predicting genes for orphan metabolic activities using phylogenetic profiles Lifeng Chen, Dennis Vitkup Genome Biology 2006, 7:R17 (15 February 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method that combines local structure of a metabolic network with phylogenetic profiles is described and used to assign genes to orphan metabolic activities in yeast and Escherichia coli.

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Volume 7 Issue 2

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