Genome Biology | Volume 9 Issue 8

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	Volume 9 Issue 8
	Comment
	Comment Biodefense versus bioterrorism Gregory A Petsko Genome Biology 2008, 9:108 (1 September 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genomics was essential for identifying the source of the deadly anthrax strain released after the September 11 terrorist attacks in the US. The same research that is needed to combat low-probability bioterror attacks is needed to combat high-probability natural infectious agents.
	Review
	Review The phytochrome red/far-red photoreceptor superfamily Robert A Sharrock Genome Biology 2008, 9:230 (28 August 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The phytochrome protein superfamily reveals a diversity of mechanisms of action.
	Minireview Reduced-representation methylation mapping Jeffrey A Jeddeloh, John M Greally, Oliver J Rando Genome Biology 2008, 9:231 (1 September 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Massively parallel sequencing has been harnessed to map DNA methylation patterns in the mouse genome.
	Opinion Isolated populations and complex disease gene identification Kati Kristiansson, Jussi Naukkarinen, Leena Peltonen Genome Biology 2008, 9:109 (26 August 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Isolated populations can be useful for the identification of genes underlying common complex diseases.
	Report
	Meeting report DNA replication can still spring surprises Heather L Hendrickson Genome Biology 2008, 9:317 (7 August 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the first EMBO conference in a biennial series 'Replication and Segregation of Chromosomes', Geilo, Norway, 16-20 June 2008.
	Meeting report Human genetics branches out in Barcelona Raquel Rabionet, Yolanda Espinosa-Parrilla, Xavier Estivill Genome Biology 2008, 9:318 (13 August 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the European Human Genetics Conference, Barcelona, Spain, 31 May-3 June 2008.
	Research
	Research Diarrhea as a cause of mortality in a mouse model of infectious colitis Diana Borenshtein, Rebecca C Fry, Elizabeth B Groff, Prashant R Nambiar, Vincent J Carey, James G Fox, David B Schauer Genome Biology 2008, 9:R122 (4 August 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| f1000 \| Editor’s summary Analysis of gene expression in the colons of Citrobacter rodentium-infected susceptible and resistant mice suggests that mortality is associated with impaired intestinal ion transport.
	Research Novel genes dramatically alter regulatory network topology in amphioxus Qing Zhang, Christian M Zmasek, Larry J Dishaw, M Gail Mueller, Yuzhen Ye, Gary W Litman, Adam Godzik Genome Biology 2008, 9:R123 (4 August 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| f1000 \| Editor’s summary Domain rearrangements in the innate immune network of amphioxus suggests that domain shuffling has shaped the evolution of immune systems.
	Research Metabolic changes in schizophrenia and human brain evolution Philipp Khaitovich, Helen E Lockstone, Matthew T Wayland, Tsz M Tsang, Samantha D Jayatilaka, Arfu J Guo, Jie Zhou, Mehmet Somel, Laura W Harris, Elaine Holmes, Svante Pääbo, Sabine Bahn Genome Biology 2008, 9:R124 (5 August 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Human cognitive evolution involved genes implicated in energy metabolism and energy-expensive brain functions that are also altered in schizophrenia, suggesting that human brains may have reached their metabolic limit, with schizophrenia as a costly by-product.
	Research Genomic analysis of the relationship between gene expression variation and DNA polymorphism in Drosophila simulans Mara KN Lawniczak, Alisha K Holloway, David J Begun, Corbin D Jones Genome Biology 2008, 9:R125 (12 August 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Analysis of six Drosophila simulans genotypes revealed that genes with greater variation in gene expression between genotypes also have higher levels of sequence polymorphism in many gene features.
	Research Analysis of the mouse embryonic stem cell regulatory networks obtained by ChIP-chip and ChIP-PET Divya Mathur, Timothy W Danford, Laurie A Boyer, Richard A Young, David K Gifford, Rudolf Jaenisch Genome Biology 2008, 9:R126 (13 August 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary OCT4 and NANOG genomic targets were identified in mouse embryonic stem cells by ChIP-chip and were compared with previously reported ChIP-PET results.
	Research The miR-17-5p microRNA is a key regulator of the G1/S phase cell cycle transition Nicole Cloonan, Mellissa K Brown, Anita L Steptoe, Shivangi Wani, Wei Chan, Alistair RR Forrest, Gabriel Kolle, Brian Gabrielli, Sean M Grimmond Genome Biology 2008, 9:R127 (14 August 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Novel targets of the oncogenic miR-17-92 cluster have been identified and the mechanism of regulation of proliferation at the G1/S phase cell cycle transition via the miR-17-5p microRNA has been elucidated.
	Research Integrative analyses of genetic variation in enzyme activities of primary carbohydrate metabolism reveal distinct modes of regulation in Arabidopsis thaliana Joost JB Keurentjes, Ronan Sulpice, Yves Gibon, Marie-Caroline Steinhauser, Jingyuan Fu, Maarten Koornneef, Mark Stitt, Dick Vreugdenhil Genome Biology 2008, 9:R129 (18 August 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Multiparallel QTL analysis of 15 Arabidopsis primary carbohydrate metabolism enzymes reveals that traits affecting primary metabolism are often correlated.
	Research Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development Michael F Covington, Julin N Maloof, Marty Straume, Steve A Kay, Stacey L Harmer Genome Biology 2008, 9:R130 (18 August 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcript abundance of roughly a third of expressed Arabidopsis thaliana genes is circadian-regulated.
	Research Molecular evolution of neuropeptides in the genus Drosophila Christian Wegener, Anton Gorbashov Genome Biology 2008, 9:R131 (21 August 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The first genomic and chemical characterization of fruit fly neuropeptides outside Drosophila melanogaster provides insights into the evolution of the neuropeptidome in this genus.
	Research Preferential regulation of duplicated genes by microRNAs in mammals Jingjing Li, Gabriel Musso, Zhaolei Zhang Genome Biology 2008, 9:R132 (26 August 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of duplicate genes and predicted microRNA targets in human and mouse shows that microRNAs are important in how the regulatory patterns of mammalian paralogs have evolved.
	Research Gene expression regulation in the context of mouse interspecific mosaic genomes David L'Hôte, Catherine Serres, Reiner A Veitia, Xavier Montagutelli, Ahmad Oulmouden, Daniel Vaiman Genome Biology 2008, 9:R133 (27 August 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The testis transcriptome of mouse strains containing homozygous segments of Mus spretus origin in a Mus musculus background was analyzed.
	Software Proteopedia - a scientific 'wiki' bridging the rift between three-dimensional structure and function of biomacromolecules Eran Hodis, Jaime Prilusky, Eric Martz, Israel Silman, John Moult, Joel L Sussman Genome Biology 2008, 9:R121 (3 August 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| f1000 \| Editor’s summary Proteopedia is an interactive wiki-style web resource that presents 3D structural and functional information in a user-friendly manner and allows real-time community annotation.
	Software MotifCluster: an interactive online tool for clustering and visualizing sequences using shared motifs Micah Hamady, Jeremy Widmann, Shelley D Copley, Rob Knight Genome Biology 2008, 9:R128 (15 August 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary MotifCluster finds related motifs in a set of sequences and clusters the sequences into families using the motifs they contain.
	Correspondence
	Correction Correction: Statistical modeling for selecting housekeeper genes Aniko Szabo, Charles M Perou, Mehmet Karaca, Laurent Perreard, Robert Palais, John F Quackenbush, Philip S Bernard Genome Biology 2008, 9:405 (5 August 2008) Abstract \| Full text \| PDF \| PubMed

	Volume 9 Issue 8
	Comment
	Comment Biodefense versus bioterrorism Gregory A Petsko Genome Biology 2008, 9:108 (1 September 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genomics was essential for identifying the source of the deadly anthrax strain released after the September 11 terrorist attacks in the US. The same research that is needed to combat low-probability bioterror attacks is needed to combat high-probability natural infectious agents.
	Review
	Review The phytochrome red/far-red photoreceptor superfamily Robert A Sharrock Genome Biology 2008, 9:230 (28 August 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The phytochrome protein superfamily reveals a diversity of mechanisms of action.
	Minireview Reduced-representation methylation mapping Jeffrey A Jeddeloh, John M Greally, Oliver J Rando Genome Biology 2008, 9:231 (1 September 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Massively parallel sequencing has been harnessed to map DNA methylation patterns in the mouse genome.
	Opinion Isolated populations and complex disease gene identification Kati Kristiansson, Jussi Naukkarinen, Leena Peltonen Genome Biology 2008, 9:109 (26 August 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Isolated populations can be useful for the identification of genes underlying common complex diseases.
	Report
	Meeting report DNA replication can still spring surprises Heather L Hendrickson Genome Biology 2008, 9:317 (7 August 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the first EMBO conference in a biennial series 'Replication and Segregation of Chromosomes', Geilo, Norway, 16-20 June 2008.
	Meeting report Human genetics branches out in Barcelona Raquel Rabionet, Yolanda Espinosa-Parrilla, Xavier Estivill Genome Biology 2008, 9:318 (13 August 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the European Human Genetics Conference, Barcelona, Spain, 31 May-3 June 2008.
	Research
	Research Diarrhea as a cause of mortality in a mouse model of infectious colitis Diana Borenshtein, Rebecca C Fry, Elizabeth B Groff, Prashant R Nambiar, Vincent J Carey, James G Fox, David B Schauer Genome Biology 2008, 9:R122 (4 August 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| f1000 \| Editor’s summary Analysis of gene expression in the colons of Citrobacter rodentium-infected susceptible and resistant mice suggests that mortality is associated with impaired intestinal ion transport.
	Research Novel genes dramatically alter regulatory network topology in amphioxus Qing Zhang, Christian M Zmasek, Larry J Dishaw, M Gail Mueller, Yuzhen Ye, Gary W Litman, Adam Godzik Genome Biology 2008, 9:R123 (4 August 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| f1000 \| Editor’s summary Domain rearrangements in the innate immune network of amphioxus suggests that domain shuffling has shaped the evolution of immune systems.
	Research Metabolic changes in schizophrenia and human brain evolution Philipp Khaitovich, Helen E Lockstone, Matthew T Wayland, Tsz M Tsang, Samantha D Jayatilaka, Arfu J Guo, Jie Zhou, Mehmet Somel, Laura W Harris, Elaine Holmes, Svante Pääbo, Sabine Bahn Genome Biology 2008, 9:R124 (5 August 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Human cognitive evolution involved genes implicated in energy metabolism and energy-expensive brain functions that are also altered in schizophrenia, suggesting that human brains may have reached their metabolic limit, with schizophrenia as a costly by-product.
	Research Genomic analysis of the relationship between gene expression variation and DNA polymorphism in Drosophila simulans Mara KN Lawniczak, Alisha K Holloway, David J Begun, Corbin D Jones Genome Biology 2008, 9:R125 (12 August 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Analysis of six Drosophila simulans genotypes revealed that genes with greater variation in gene expression between genotypes also have higher levels of sequence polymorphism in many gene features.
	Research Analysis of the mouse embryonic stem cell regulatory networks obtained by ChIP-chip and ChIP-PET Divya Mathur, Timothy W Danford, Laurie A Boyer, Richard A Young, David K Gifford, Rudolf Jaenisch Genome Biology 2008, 9:R126 (13 August 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary OCT4 and NANOG genomic targets were identified in mouse embryonic stem cells by ChIP-chip and were compared with previously reported ChIP-PET results.
	Research The miR-17-5p microRNA is a key regulator of the G1/S phase cell cycle transition Nicole Cloonan, Mellissa K Brown, Anita L Steptoe, Shivangi Wani, Wei Chan, Alistair RR Forrest, Gabriel Kolle, Brian Gabrielli, Sean M Grimmond Genome Biology 2008, 9:R127 (14 August 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Novel targets of the oncogenic miR-17-92 cluster have been identified and the mechanism of regulation of proliferation at the G1/S phase cell cycle transition via the miR-17-5p microRNA has been elucidated.
	Research Integrative analyses of genetic variation in enzyme activities of primary carbohydrate metabolism reveal distinct modes of regulation in Arabidopsis thaliana Joost JB Keurentjes, Ronan Sulpice, Yves Gibon, Marie-Caroline Steinhauser, Jingyuan Fu, Maarten Koornneef, Mark Stitt, Dick Vreugdenhil Genome Biology 2008, 9:R129 (18 August 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Multiparallel QTL analysis of 15 Arabidopsis primary carbohydrate metabolism enzymes reveals that traits affecting primary metabolism are often correlated.
	Research Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development Michael F Covington, Julin N Maloof, Marty Straume, Steve A Kay, Stacey L Harmer Genome Biology 2008, 9:R130 (18 August 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcript abundance of roughly a third of expressed Arabidopsis thaliana genes is circadian-regulated.
	Research Molecular evolution of neuropeptides in the genus Drosophila Christian Wegener, Anton Gorbashov Genome Biology 2008, 9:R131 (21 August 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The first genomic and chemical characterization of fruit fly neuropeptides outside Drosophila melanogaster provides insights into the evolution of the neuropeptidome in this genus.
	Research Preferential regulation of duplicated genes by microRNAs in mammals Jingjing Li, Gabriel Musso, Zhaolei Zhang Genome Biology 2008, 9:R132 (26 August 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of duplicate genes and predicted microRNA targets in human and mouse shows that microRNAs are important in how the regulatory patterns of mammalian paralogs have evolved.
	Research Gene expression regulation in the context of mouse interspecific mosaic genomes David L'Hôte, Catherine Serres, Reiner A Veitia, Xavier Montagutelli, Ahmad Oulmouden, Daniel Vaiman Genome Biology 2008, 9:R133 (27 August 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The testis transcriptome of mouse strains containing homozygous segments of Mus spretus origin in a Mus musculus background was analyzed.
	Software Proteopedia - a scientific 'wiki' bridging the rift between three-dimensional structure and function of biomacromolecules Eran Hodis, Jaime Prilusky, Eric Martz, Israel Silman, John Moult, Joel L Sussman Genome Biology 2008, 9:R121 (3 August 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| f1000 \| Editor’s summary Proteopedia is an interactive wiki-style web resource that presents 3D structural and functional information in a user-friendly manner and allows real-time community annotation.
	Software MotifCluster: an interactive online tool for clustering and visualizing sequences using shared motifs Micah Hamady, Jeremy Widmann, Shelley D Copley, Rob Knight Genome Biology 2008, 9:R128 (15 August 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary MotifCluster finds related motifs in a set of sequences and clusters the sequences into families using the motifs they contain.
	Correspondence
	Correction Correction: Statistical modeling for selecting housekeeper genes Aniko Szabo, Charles M Perou, Mehmet Karaca, Laurent Perreard, Robert Palais, John F Quackenbush, Philip S Bernard Genome Biology 2008, 9:405 (5 August 2008) Abstract \| Full text \| PDF \| PubMed

Explore Genome Biology

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Volume 9 Issue 8

Comment

Review

Report

Research

Correspondence