Genome Biology | Volume 8 Issue 8

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	Volume 8 Issue 8
	Comment
	Comment My worries are no longer behind me Gregory A Petsko Genome Biology 2007, 8:109 (3 September 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The tragedy of colorectal cancer is that it is one of the most preventable of fatal diseases: regular screening has been shown to reduce colon cancer deaths.
	Review
	Minireview The Opossum genome reveals further evidence for regulatory evolution in mammalian diversification Bernardo Lemos Genome Biology 2007, 8:223 (9 August 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The first marsupial genome to be sequenced emphasizes the importance of noncoding sequences in mammalian evolution.
	Minireview Antagonizing Methuselah to extend life span Nazif Alic, Linda Partridge Genome Biology 2007, 8:222 (31 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A peptide ligand for the receptor Methuselah has been identified that extends fly life span.
	Report
	Meeting report Intranuclear changes in cancer cells David M Gilbert, Daniele Zink Genome Biology 2007, 8:312 (31 August 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the FASEB meeting 'Nuclear Structure and Cancer', Saxtons River, USA, 16-21 June 2007.
	Meeting report The rhythms of life Jürgen A Ripperger Genome Biology 2007, 8:313 (31 August 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the symposium 'Clocks and Rhythms', Cold Spring Harbor, USA, 30 May-4 June 2007.
	Research
	Research Violating the splicing rules: TG dinucleotides function as alternative 3' splice sites in U2-dependent introns Karol Szafranski, Stefanie Schindler, Stefan Taudien, Michael Hiller, Klaus Huse, Niels Jahn, Stefan Schreiber, Rolf Backofen, Matthias Platzer Genome Biology 2007, 8:R154 (1 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary TG dinucleotides functioning as alternative 3' splice sites were identified and experimentally verified in 36 human genes.
	Research Complexity, connectivity, and duplicability as barriers to lateral gene transfer Alon Wellner, Mor N Lurie, Uri Gophna Genome Biology 2007, 8:R156 (2 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Laterally transferred genes are shown to be less involved in protein-protein interactions, and essential genes that exhibit low duplicability and high connectivity do exhibit mostly vertical descent.
	Research An immune response gene expression module identifies a good prognosis subtype in estrogen receptor negative breast cancer Andrew E Teschendorff, Ahmad Miremadi, Sarah E Pinder, Ian O Ellis, Carlos Caldas Genome Biology 2007, 8:R157 (2 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A feature selection method was used in an analysis of three major microarray expression datasets to identify molecular subclasses and prognostic markers in estrogen receptor-negative breast cancer, showing that it is a heterogeneous disease with at least four main subtypes.
	Research Quantifying the major mechanisms of recent gene duplications in the human and mouse genomes: a novel strategy to estimate gene duplication rates Deng Pan, Liqing Zhang Genome Biology 2007, 8:R158 (2 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary By studying two mechanisms of gene duplication, unequal crossover and retrotranspostion, and looking at both small gene families and the entire genome, a new estimate for the rate of gene duplication is made which is more accurate for both small and large gene families.
	Research Exon expression profiling reveals stimulus-mediated exon use in neural cells Adrienne E McKee, Nicola Neretti, Luis E Carvalho, Clifford A Meyer, Edward A Fox, Alexander S Brodsky, Pamela A Silver Genome Biology 2007, 8:R159 (2 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Exon centric microarrays were used to resolve the calcium-modulated gene expression response into transcript-level an exon-level regulation.
	Research The global role of ppGpp synthesis in morphological differentiation and antibiotic production in Streptomyces coelicolor A3(2) Andrew Hesketh, Wenqiong Chen, Jamie Ryding, Sherman Chang, Mervyn Bibb Genome Biology 2007, 8:R161 (3 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The induction of ppGpp synthesis in Streptomyces coelicolor influenced the expression of several genomic elements characteristic of streptomycete biology, including antibiotic gene clusters, conservons, and morphogenetic proteins.
	Research Comparative transcriptome analysis of embryonic and adult stem cells with extended and limited differentiation capacity Fernando Ulloa-Montoya, Benjamin L Kidder, Karen A Pauwelyn, Lucas G Chase, Aernout Luttun, Annelies Crabbe, Martine Geraerts, Alexei A Sharov, Yulan Piao, Minoru SH Ko, Wei-Shou Hu, Catherine M Verfaillie Genome Biology 2007, 8:R163 (6 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary Comparison of the transcriptomes of pluripotent embryonic stem cells, multipotent adult progenitor cells and lineage restricted mesenchymal stem cells identified a unique gene expression profile of multipotent adult progenitor cells.
	Research Reduced selection leads to accelerated gene loss in Shigella Ruth Hershberg, Hua Tang, Dmitri A Petrov Genome Biology 2007, 8:R164 (8 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The rate of gene loss was studied in the facultative pathogens, E. coli and Shigella, and was found to be greater in the more niche-limited Shigella. This is demonstrated to be due to a genome-wide reduction in the effectiveness of selection.
	Research A physical map of the bovine genome Warren M Snelling, Readman Chiu, Jacqueline E Schein, Matthew Hobbs, Colette A Abbey, David L Adelson, Jan Aerts, Gary L Bennett, Ian E Bosdet, Mekki Boussaha, Rudiger Brauning, Alexandre R Caetano, Marcos M Costa, Allan M Crawford, Brian P Dalrymple, André Eggen, Annelie Everts-van der Wind, Sandrine Floriot, Mathieu Gautier, Clare A Gill, Ronnie D Green, Robert Holt, Oliver Jann, Steven JM Jones, Steven M Kappes, John W Keele, Pieter J de Jong, Denis M Larkin, Harris A Lewin, John C McEwan et al. Genome Biology 2007, 8:R165 (14 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new physical map of the bovine genome has been constructed by integrating data from genetic and radiation hybrid maps, and a new bovine BAC map, with the bovine genome draft assembly.
	Research The roles of binding site arrangement and combinatorial targeting in microRNA repression of gene expression Lawrence S Hon, Zemin Zhang Genome Biology 2007, 8:R166 (14 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome wide analysis of factors affecting repression of mRNAs by microRNAs reveals roles for 3'UTR length, the number of target sites on the mRNA and the distance between pairs of binding sites.
	Research Genomic mapping of Suppressor of Hairy-wing binding sites in Drosophila Boris Adryan, Gertrud Woerfel, Ian Birch-Machin, Shan Gao, Marie Quick, Lisa Meadows, Steven Russell, Robert White Genome Biology 2007, 8:R167 (16 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of Drosophila Su(Hw) binding allowed the identification of new, isolated, binding sites, and the construction of a new binding site consensus. Together with gene expression data, this supports a role for Su(Hw) in maintaining a constant genomic architecture.
	Research Lessons learned from the initial sequencing of the pig genome: comparative analysis of an 8 Mb region of pig chromosome 17 Elizabeth A Hart, Mario Caccamo, Jennifer L Harrow, Sean J Humphray, James GR Gilbert, Steve Trevanion, Tim Hubbard, Jane Rogers, Max F Rothschild Genome Biology 2007, 8:R168 (17 August 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The sequencing, annotation and comparative analysis of an 8Mb region of pig chromosome 17 allows the coverage and quality of the pig genome sequencing project to be assessed
	Research The impact of chromatin modifiers on the timing of locus replication in mouse embryonic stem cells Helle F Jørgensen, Véronique Azuara, Shannon Amoils, Mikhail Spivakov, Anna Terry, Tatyana Nesterova, Bradley S Cobb, Bernard Ramsahoye, Matthias Merkenschlager, Amanda G Fisher Genome Biology 2007, 8:R169 (17 August 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A panel of mutant embryonic stem (ES) cell lines lacking important chromatin modifiers was used to dissect the relationship between chromatin structure and replication timing, revealing the importance of several chromatin modifiers for maintaining correct replication of satellite sequences in pluripotent ES cells.
	Research Species-specific shifts in centromere sequence composition are coincident with breakpoint reuse in karyotypically divergent lineages Kira V Bulazel, Gianni C Ferreri, Mark DB Eldridge, Rachel J O'Neill Genome Biology 2007, 8:R170 (20 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The evolution of three classes of centromere sequences across nine species of macropodine marsupials were compared with that of other genes, showing that each species has experienced differential expansion and contraction of individual classes.
	Research Quantitative genomics of locomotor behavior in Drosophila melanogaster Katherine W Jordan, Mary Carbone, Akihiko Yamamoto, Theodore J Morgan, Trudy FC Mackay Genome Biology 2007, 8:R172 (21 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The locomotor behavior of Drosophila melanogaster was quantified in a large population of inbred lines derived from a single natural population, showing that many pleiotropic genes show correlated transcriptional responses to multiple behaviors.
	Research MicroRNAs show a wide diversity of expression profiles in the developing and mature central nervous system Marika Kapsimali, Wigard P Kloosterman, Ewart de Bruijn, Frederic Rosa, Ronald HA Plasterk, Stephen W Wilson Genome Biology 2007, 8:R173 (21 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A comprehensive analysis of the neuroanatomical expression profiles of 38 abundant conserved miRNAs in developing and adult zebrafish brain was performed.
	Research The temporal program of peripheral blood gene expression in the response of nonhuman primates to Ebola hemorrhagic fever Kathleen H Rubins, Lisa E Hensley, Victoria Wahl-Jensen, Kathleen M Daddario DiCaprio, Howard A Young, Douglas S Reed, Peter B Jahrling, Patrick O Brown, David A Relman, Thomas W Geisbert Genome Biology 2007, 8:R174 (28 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Primate blood cells were analysed for changes in global gene expression patterns at several time points following infection with Ebola virus, providing insights into potential mechanisms of viral pathogenesis and host defense.
	Research Disruption and pseudoautosomal localization of the major histocompatibility complex in monotremes Juliane C Dohm, Enkhjargal Tsend-Ayush, Richard Reinhardt, Frank Grützner, Heinz Himmelbauer Genome Biology 2007, 8:R175 (29 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The characterization and chromosomal mapping of major histocompatibility complex (MHC)-containing BAC clones from platypus and the short-beaked echidna reveals new insights into the evolution of both the mammalian MHC and monotreme sex chromosomes.
	Research Distribution patterns of small-molecule ligands in the protein universe and implications for origin of life and drug discovery Hong-Fang Ji, De-Xin Kong, Liang Shen, Ling-Ling Chen, Bin-Guang Ma, Hong-Yu Zhang Genome Biology 2007, 8:R176 (29 August 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Ligand-protein mapping was found to follow a power law and the preferential attachment principle, leading to the identification of the molecules, mostly nucleotide-containing compounds, that are likely to have evolved earliest.
	Research Comparative genomic analysis of the Tribolium immune system Zhen Zou, Jay D Evans, Zhiqiang Lu, Picheng Zhao, Michael Williams, Niranji Sumathipala, Charles Hetru, Dan Hultmark, Haobo Jiang Genome Biology 2007, 8:R177 (29 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The annotation, and comparison with homologous genes in other species, of immunity-related genes in the Tribolium castaneum genome allowed the identification of around 300 candidate defense proteins, and revealed a framework of information on Tribolium immunity.
	Method Network motif analysis of a multi-mode genetic-interaction network R James Taylor, Andrew F Siegel, Timothy Galitski Genome Biology 2007, 8:R160 (2 August 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Statistical and computational methods for the extraction of biological information from dense multi-mode genetic-interaction networks were developed and implemented in open-source software.
	Method Microarray-based gene expression profiles in multiple tissues of the domesticated silkworm, Bombyx mori Qingyou Xia, Daojun Cheng, Jun Duan, Genhong Wang, Tingcai Cheng, Xingfu Zha, Chun Liu, Ping Zhao, Fangyin Dai, Ze Zhang, Ningjia He, Liang Zhang, Zhonghuai Xiang Genome Biology 2007, 8:R162 (4 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using a genome-wide oligonucleotide microarray, gene expression was surveyed in multiple silkworm tissues on day 3 of the fifth instar, providing a new resource for annotating the silkworm genome.
	Method Model-based analysis of two-color arrays (MA2C) Jun S Song, W Evan Johnson, Xiaopeng Zhu, Xinmin Zhang, Wei Li, Arjun K Manrai, Jun S Liu, Runsheng Chen, X Shirley Liu Genome Biology 2007, 8:R178 (29 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A normalization method based on probe GC content for two-color tiling arrays and an algorithm for detecting peak regions are presented. They are available in a stand-alone Java program.
	Software RASTA-Bacteria: a web-based tool for identifying toxin-antitoxin loci in prokaryotes Emeric W Sevin, Frédérique Barloy-Hubler Genome Biology 2007, 8:R155 (1 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary RASTA-Bacteria is an automated method that allows quick and reliable identification of toxin/antitoxin loci in sequenced prokaryotic genomes, whether they are annotated Open Reading Frames or not.
	Software PyCogent: a toolkit for making sense from sequence Rob Knight, Peter Maxwell, Amanda Birmingham, Jason Carnes, J Gregory Caporaso, Brett C Easton, Michael Eaton, Micah Hamady, Helen Lindsay, Zongzhi Liu, Catherine Lozupone, Daniel McDonald, Michael Robeson, Raymond Sammut, Sandra Smit, Matthew J Wakefield, Jeremy Widmann, Shandy Wikman, Stephanie Wilson, Hua Ying, Gavin A Huttley Genome Biology 2007, 8:R171 (21 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The COmparative GENomic Toolkit, a framework for probabilistic analyses of biological sequences, devising workflows and generating publication quality graphics, has been implemented in Python.
	Correspondence
	Correspondence Impacts of yeast metabolic network structure on enzyme evolution Chenqi Lu, Ze Zhang, Lindsey Leach, MJ Kearsey, ZW Luo Genome Biology 2007, 8:407 (9 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Vitkup et al. recently presented an analysis of the influence of yeast metabolic network structure on enzyme evolution; different conclusions are reached when modularity is properly accounted for.

	Volume 8 Issue 8
	Comment
	Comment My worries are no longer behind me Gregory A Petsko Genome Biology 2007, 8:109 (3 September 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The tragedy of colorectal cancer is that it is one of the most preventable of fatal diseases: regular screening has been shown to reduce colon cancer deaths.
	Review
	Minireview The Opossum genome reveals further evidence for regulatory evolution in mammalian diversification Bernardo Lemos Genome Biology 2007, 8:223 (9 August 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The first marsupial genome to be sequenced emphasizes the importance of noncoding sequences in mammalian evolution.
	Minireview Antagonizing Methuselah to extend life span Nazif Alic, Linda Partridge Genome Biology 2007, 8:222 (31 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A peptide ligand for the receptor Methuselah has been identified that extends fly life span.
	Report
	Meeting report Intranuclear changes in cancer cells David M Gilbert, Daniele Zink Genome Biology 2007, 8:312 (31 August 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the FASEB meeting 'Nuclear Structure and Cancer', Saxtons River, USA, 16-21 June 2007.
	Meeting report The rhythms of life Jürgen A Ripperger Genome Biology 2007, 8:313 (31 August 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the symposium 'Clocks and Rhythms', Cold Spring Harbor, USA, 30 May-4 June 2007.
	Research
	Research Violating the splicing rules: TG dinucleotides function as alternative 3' splice sites in U2-dependent introns Karol Szafranski, Stefanie Schindler, Stefan Taudien, Michael Hiller, Klaus Huse, Niels Jahn, Stefan Schreiber, Rolf Backofen, Matthias Platzer Genome Biology 2007, 8:R154 (1 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary TG dinucleotides functioning as alternative 3' splice sites were identified and experimentally verified in 36 human genes.
	Research Complexity, connectivity, and duplicability as barriers to lateral gene transfer Alon Wellner, Mor N Lurie, Uri Gophna Genome Biology 2007, 8:R156 (2 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Laterally transferred genes are shown to be less involved in protein-protein interactions, and essential genes that exhibit low duplicability and high connectivity do exhibit mostly vertical descent.
	Research An immune response gene expression module identifies a good prognosis subtype in estrogen receptor negative breast cancer Andrew E Teschendorff, Ahmad Miremadi, Sarah E Pinder, Ian O Ellis, Carlos Caldas Genome Biology 2007, 8:R157 (2 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A feature selection method was used in an analysis of three major microarray expression datasets to identify molecular subclasses and prognostic markers in estrogen receptor-negative breast cancer, showing that it is a heterogeneous disease with at least four main subtypes.
	Research Quantifying the major mechanisms of recent gene duplications in the human and mouse genomes: a novel strategy to estimate gene duplication rates Deng Pan, Liqing Zhang Genome Biology 2007, 8:R158 (2 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary By studying two mechanisms of gene duplication, unequal crossover and retrotranspostion, and looking at both small gene families and the entire genome, a new estimate for the rate of gene duplication is made which is more accurate for both small and large gene families.
	Research Exon expression profiling reveals stimulus-mediated exon use in neural cells Adrienne E McKee, Nicola Neretti, Luis E Carvalho, Clifford A Meyer, Edward A Fox, Alexander S Brodsky, Pamela A Silver Genome Biology 2007, 8:R159 (2 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Exon centric microarrays were used to resolve the calcium-modulated gene expression response into transcript-level an exon-level regulation.
	Research The global role of ppGpp synthesis in morphological differentiation and antibiotic production in Streptomyces coelicolor A3(2) Andrew Hesketh, Wenqiong Chen, Jamie Ryding, Sherman Chang, Mervyn Bibb Genome Biology 2007, 8:R161 (3 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The induction of ppGpp synthesis in Streptomyces coelicolor influenced the expression of several genomic elements characteristic of streptomycete biology, including antibiotic gene clusters, conservons, and morphogenetic proteins.
	Research Comparative transcriptome analysis of embryonic and adult stem cells with extended and limited differentiation capacity Fernando Ulloa-Montoya, Benjamin L Kidder, Karen A Pauwelyn, Lucas G Chase, Aernout Luttun, Annelies Crabbe, Martine Geraerts, Alexei A Sharov, Yulan Piao, Minoru SH Ko, Wei-Shou Hu, Catherine M Verfaillie Genome Biology 2007, 8:R163 (6 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary Comparison of the transcriptomes of pluripotent embryonic stem cells, multipotent adult progenitor cells and lineage restricted mesenchymal stem cells identified a unique gene expression profile of multipotent adult progenitor cells.
	Research Reduced selection leads to accelerated gene loss in Shigella Ruth Hershberg, Hua Tang, Dmitri A Petrov Genome Biology 2007, 8:R164 (8 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The rate of gene loss was studied in the facultative pathogens, E. coli and Shigella, and was found to be greater in the more niche-limited Shigella. This is demonstrated to be due to a genome-wide reduction in the effectiveness of selection.
	Research A physical map of the bovine genome Warren M Snelling, Readman Chiu, Jacqueline E Schein, Matthew Hobbs, Colette A Abbey, David L Adelson, Jan Aerts, Gary L Bennett, Ian E Bosdet, Mekki Boussaha, Rudiger Brauning, Alexandre R Caetano, Marcos M Costa, Allan M Crawford, Brian P Dalrymple, André Eggen, Annelie Everts-van der Wind, Sandrine Floriot, Mathieu Gautier, Clare A Gill, Ronnie D Green, Robert Holt, Oliver Jann, Steven JM Jones, Steven M Kappes, John W Keele, Pieter J de Jong, Denis M Larkin, Harris A Lewin, John C McEwan et al. Genome Biology 2007, 8:R165 (14 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new physical map of the bovine genome has been constructed by integrating data from genetic and radiation hybrid maps, and a new bovine BAC map, with the bovine genome draft assembly.
	Research The roles of binding site arrangement and combinatorial targeting in microRNA repression of gene expression Lawrence S Hon, Zemin Zhang Genome Biology 2007, 8:R166 (14 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome wide analysis of factors affecting repression of mRNAs by microRNAs reveals roles for 3'UTR length, the number of target sites on the mRNA and the distance between pairs of binding sites.
	Research Genomic mapping of Suppressor of Hairy-wing binding sites in Drosophila Boris Adryan, Gertrud Woerfel, Ian Birch-Machin, Shan Gao, Marie Quick, Lisa Meadows, Steven Russell, Robert White Genome Biology 2007, 8:R167 (16 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of Drosophila Su(Hw) binding allowed the identification of new, isolated, binding sites, and the construction of a new binding site consensus. Together with gene expression data, this supports a role for Su(Hw) in maintaining a constant genomic architecture.
	Research Lessons learned from the initial sequencing of the pig genome: comparative analysis of an 8 Mb region of pig chromosome 17 Elizabeth A Hart, Mario Caccamo, Jennifer L Harrow, Sean J Humphray, James GR Gilbert, Steve Trevanion, Tim Hubbard, Jane Rogers, Max F Rothschild Genome Biology 2007, 8:R168 (17 August 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The sequencing, annotation and comparative analysis of an 8Mb region of pig chromosome 17 allows the coverage and quality of the pig genome sequencing project to be assessed
	Research The impact of chromatin modifiers on the timing of locus replication in mouse embryonic stem cells Helle F Jørgensen, Véronique Azuara, Shannon Amoils, Mikhail Spivakov, Anna Terry, Tatyana Nesterova, Bradley S Cobb, Bernard Ramsahoye, Matthias Merkenschlager, Amanda G Fisher Genome Biology 2007, 8:R169 (17 August 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A panel of mutant embryonic stem (ES) cell lines lacking important chromatin modifiers was used to dissect the relationship between chromatin structure and replication timing, revealing the importance of several chromatin modifiers for maintaining correct replication of satellite sequences in pluripotent ES cells.
	Research Species-specific shifts in centromere sequence composition are coincident with breakpoint reuse in karyotypically divergent lineages Kira V Bulazel, Gianni C Ferreri, Mark DB Eldridge, Rachel J O'Neill Genome Biology 2007, 8:R170 (20 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The evolution of three classes of centromere sequences across nine species of macropodine marsupials were compared with that of other genes, showing that each species has experienced differential expansion and contraction of individual classes.
	Research Quantitative genomics of locomotor behavior in Drosophila melanogaster Katherine W Jordan, Mary Carbone, Akihiko Yamamoto, Theodore J Morgan, Trudy FC Mackay Genome Biology 2007, 8:R172 (21 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The locomotor behavior of Drosophila melanogaster was quantified in a large population of inbred lines derived from a single natural population, showing that many pleiotropic genes show correlated transcriptional responses to multiple behaviors.
	Research MicroRNAs show a wide diversity of expression profiles in the developing and mature central nervous system Marika Kapsimali, Wigard P Kloosterman, Ewart de Bruijn, Frederic Rosa, Ronald HA Plasterk, Stephen W Wilson Genome Biology 2007, 8:R173 (21 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A comprehensive analysis of the neuroanatomical expression profiles of 38 abundant conserved miRNAs in developing and adult zebrafish brain was performed.
	Research The temporal program of peripheral blood gene expression in the response of nonhuman primates to Ebola hemorrhagic fever Kathleen H Rubins, Lisa E Hensley, Victoria Wahl-Jensen, Kathleen M Daddario DiCaprio, Howard A Young, Douglas S Reed, Peter B Jahrling, Patrick O Brown, David A Relman, Thomas W Geisbert Genome Biology 2007, 8:R174 (28 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Primate blood cells were analysed for changes in global gene expression patterns at several time points following infection with Ebola virus, providing insights into potential mechanisms of viral pathogenesis and host defense.
	Research Disruption and pseudoautosomal localization of the major histocompatibility complex in monotremes Juliane C Dohm, Enkhjargal Tsend-Ayush, Richard Reinhardt, Frank Grützner, Heinz Himmelbauer Genome Biology 2007, 8:R175 (29 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The characterization and chromosomal mapping of major histocompatibility complex (MHC)-containing BAC clones from platypus and the short-beaked echidna reveals new insights into the evolution of both the mammalian MHC and monotreme sex chromosomes.
	Research Distribution patterns of small-molecule ligands in the protein universe and implications for origin of life and drug discovery Hong-Fang Ji, De-Xin Kong, Liang Shen, Ling-Ling Chen, Bin-Guang Ma, Hong-Yu Zhang Genome Biology 2007, 8:R176 (29 August 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Ligand-protein mapping was found to follow a power law and the preferential attachment principle, leading to the identification of the molecules, mostly nucleotide-containing compounds, that are likely to have evolved earliest.
	Research Comparative genomic analysis of the Tribolium immune system Zhen Zou, Jay D Evans, Zhiqiang Lu, Picheng Zhao, Michael Williams, Niranji Sumathipala, Charles Hetru, Dan Hultmark, Haobo Jiang Genome Biology 2007, 8:R177 (29 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The annotation, and comparison with homologous genes in other species, of immunity-related genes in the Tribolium castaneum genome allowed the identification of around 300 candidate defense proteins, and revealed a framework of information on Tribolium immunity.
	Method Network motif analysis of a multi-mode genetic-interaction network R James Taylor, Andrew F Siegel, Timothy Galitski Genome Biology 2007, 8:R160 (2 August 2007) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Statistical and computational methods for the extraction of biological information from dense multi-mode genetic-interaction networks were developed and implemented in open-source software.
	Method Microarray-based gene expression profiles in multiple tissues of the domesticated silkworm, Bombyx mori Qingyou Xia, Daojun Cheng, Jun Duan, Genhong Wang, Tingcai Cheng, Xingfu Zha, Chun Liu, Ping Zhao, Fangyin Dai, Ze Zhang, Ningjia He, Liang Zhang, Zhonghuai Xiang Genome Biology 2007, 8:R162 (4 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using a genome-wide oligonucleotide microarray, gene expression was surveyed in multiple silkworm tissues on day 3 of the fifth instar, providing a new resource for annotating the silkworm genome.
	Method Model-based analysis of two-color arrays (MA2C) Jun S Song, W Evan Johnson, Xiaopeng Zhu, Xinmin Zhang, Wei Li, Arjun K Manrai, Jun S Liu, Runsheng Chen, X Shirley Liu Genome Biology 2007, 8:R178 (29 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A normalization method based on probe GC content for two-color tiling arrays and an algorithm for detecting peak regions are presented. They are available in a stand-alone Java program.
	Software RASTA-Bacteria: a web-based tool for identifying toxin-antitoxin loci in prokaryotes Emeric W Sevin, Frédérique Barloy-Hubler Genome Biology 2007, 8:R155 (1 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary RASTA-Bacteria is an automated method that allows quick and reliable identification of toxin/antitoxin loci in sequenced prokaryotic genomes, whether they are annotated Open Reading Frames or not.
	Software PyCogent: a toolkit for making sense from sequence Rob Knight, Peter Maxwell, Amanda Birmingham, Jason Carnes, J Gregory Caporaso, Brett C Easton, Michael Eaton, Micah Hamady, Helen Lindsay, Zongzhi Liu, Catherine Lozupone, Daniel McDonald, Michael Robeson, Raymond Sammut, Sandra Smit, Matthew J Wakefield, Jeremy Widmann, Shandy Wikman, Stephanie Wilson, Hua Ying, Gavin A Huttley Genome Biology 2007, 8:R171 (21 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The COmparative GENomic Toolkit, a framework for probabilistic analyses of biological sequences, devising workflows and generating publication quality graphics, has been implemented in Python.
	Correspondence
	Correspondence Impacts of yeast metabolic network structure on enzyme evolution Chenqi Lu, Ze Zhang, Lindsey Leach, MJ Kearsey, ZW Luo Genome Biology 2007, 8:407 (9 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Vitkup et al. recently presented an analysis of the influence of yeast metabolic network structure on enzyme evolution; different conclusions are reached when modularity is properly accounted for.

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Volume 8 Issue 8

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