Genome Biology | Volume 11 Issue 4

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	Volume 11 Issue 4
	Comment
	Comment The devil's in the details Gregory A Petsko Genome Biology 2010, 11:117 (30 April 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Cures Acceleration Network brought in by the US Health Care Reform Bill looks good but could take funding from other research.
	Research highlight Complex-trait analysis in plants Thomas Mitchell-Olds Genome Biology 2010, 11:113 (20 April 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Identifying quantitative trait loci in Arabidopsis by population and pedigree studies.
	Research highlight Two different genomes that produce the same result Richard H Kessin Genome Biology 2010, 11:114 (27 April 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Despite differences in genomic sequence, the developmental program of two distantly related Dictyostelium species is remarkably similar.
	Research highlight Phenotypic connections in surprising places Bolan Linghu, Charles DeLisi Genome Biology 2010, 11:116 (28 April 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Connections have been revealed between very different human diseases using phenotype associations in other species
	Research highlight Mapping the complexity of transcription control in higher eukaryotes Pavel Tomancak, Uwe Ohler Genome Biology 2010, 11:115 (30 April 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent large analyses suggest the importance of combinatorial regulation by broadly expressed transcription factors rather than expression domains characterized by highly specific factors.
	Review
	Review Are homologies in vertebrate sex determination due to shared ancestry or to limited options? Jennifer A Marshall Graves, Catherine L Peichel Genome Biology 2010, 11:205 (30 April 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The bewildering array of different sex-determination systems in vertebrates is built on a common set of genes and chromosomes.
	Report
	Meeting report Advances in understanding genome maintenance Kyle M Miller Genome Biology 2010, 11:301 (20 April 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report from the Abcam genome stability conference 'Maintenance of Genome Stability', Jolly Beach Resort, Antigua, 8-11 March 2010.
	Research
	Research Phylogenetic assessment of alignments reveals neglected tree signal in gaps Christophe Dessimoz, Manuel Gil Genome Biology 2010, 11:R37 (6 April 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Tree-based tests of alignment methods enable the evaluation of the effect of gap placement on the inference of phylogenetic relationships.
	Research Phylogenetic detection of numerous gene duplications shared by animals, fungi and plants Xiaofan Zhou, Zhenguo Lin, Hong Ma Genome Biology 2010, 11:R38 (6 April 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A phylogentic analysis reveals that many gene duplications occurred prior to the split in animals, fungi and plants.
	Research The developmental expression dynamics of Drosophila melanogaster transcription factors Boris Adryan, Sarah A Teichmann Genome Biology 2010, 11:R40 (12 April 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary High levels of combinatorial complexity of transcription factors during embryogenesis in Drosophila melanogaster shed light on mechanisms of transcriptional control.
	Research Monovalent and unpoised status of most genes in undifferentiated cell-enriched Drosophila testis Qiang Gan, Dustin E Schones, Suk Ho Eun, Gang Wei, Kairong Cui, Keji Zhao, Xin Chen Genome Biology 2010, 11:R42 (15 April 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In undifferentiated Drosophila cells, differentiation-associated genes have monovalent, not bivalent histone modifications, in contrast to differentiation-associated genes in stem cells.
	Research Small variable segments constitute a major type of diversity of bacterial genomes at the species level Fabrice Touzain, Erick Denamur, Claudine Médigue, Valérie Barbe, Meriem El Karoui, Marie-Agnès Petit Genome Biology 2010, 11:R45 (30 April 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of all available genomes of three bacterial species suggests that a large part of genome diversity is contributed by short regions.
	Research DNA transposons and the role of recombination in mutation accumulation in Daphnia pulex Sarah Schaack, Eunjin Choi, Michael Lynch, Ellen J Pritham Genome Biology 2010, 11:R46 (30 April 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary Transposable elements in Daphnia pulex are identified and the impact of sex on their evolution is experimentally assessed
	Method Optimized design and data analysis of tag-based cytosine methylation assays Masako Suzuki, Qiang Jing, Daniel Lia, Marién Pascual, Andrew McLellan, John M Greally Genome Biology 2010, 11:R36 (1 April 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Genome-wide, tag-based cytosine methylation analysis is optimized.
	Method miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data David Hendrix, Michael Levine, Weiyang Shi Genome Biology 2010, 11:R39 (6 April 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel method for prediction of miRs from deep sequencing data. Its utility is demonstrated when applied to Ciona data.
	Method Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps Isheng J Tsai, Thomas D Otto, Matthew Berriman Genome Biology 2010, 11:R41 (13 April 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary IMAGE generates local assemblies, closing gaps in genomes assembled from paired-end next generation sequencing data, often without the need for new data
	Method Flux balance analysis accounting for metabolite dilution Tomer Benyamini, Ori Folger, Eytan Ruppin, Tomer Shlomi Genome Biology 2010, 11:R43 (16 April 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A flux balance analysis method for gene essentiality prediction, which takes into account variation in biomass composition under different growth conditions.
	Method Restriction Site Tiling Analysis: accurate discovery and quantitative genotyping of genome-wide polymorphisms using nucleotide arrays Melissa H Pespeni, Thomas A Oliver, Mollie K Manier, Stephen R Palumbi Genome Biology 2010, 11:R44 (19 April 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method for the simultaneous identification of polymorphic loci and the quantitative genotyping of thousands of loci in individuals is presented.

	Volume 11 Issue 4
	Comment
	Comment The devil's in the details Gregory A Petsko Genome Biology 2010, 11:117 (30 April 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Cures Acceleration Network brought in by the US Health Care Reform Bill looks good but could take funding from other research.
	Research highlight Complex-trait analysis in plants Thomas Mitchell-Olds Genome Biology 2010, 11:113 (20 April 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Identifying quantitative trait loci in Arabidopsis by population and pedigree studies.
	Research highlight Two different genomes that produce the same result Richard H Kessin Genome Biology 2010, 11:114 (27 April 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Despite differences in genomic sequence, the developmental program of two distantly related Dictyostelium species is remarkably similar.
	Research highlight Phenotypic connections in surprising places Bolan Linghu, Charles DeLisi Genome Biology 2010, 11:116 (28 April 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Connections have been revealed between very different human diseases using phenotype associations in other species
	Research highlight Mapping the complexity of transcription control in higher eukaryotes Pavel Tomancak, Uwe Ohler Genome Biology 2010, 11:115 (30 April 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent large analyses suggest the importance of combinatorial regulation by broadly expressed transcription factors rather than expression domains characterized by highly specific factors.
	Review
	Review Are homologies in vertebrate sex determination due to shared ancestry or to limited options? Jennifer A Marshall Graves, Catherine L Peichel Genome Biology 2010, 11:205 (30 April 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The bewildering array of different sex-determination systems in vertebrates is built on a common set of genes and chromosomes.
	Report
	Meeting report Advances in understanding genome maintenance Kyle M Miller Genome Biology 2010, 11:301 (20 April 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report from the Abcam genome stability conference 'Maintenance of Genome Stability', Jolly Beach Resort, Antigua, 8-11 March 2010.
	Research
	Research Phylogenetic assessment of alignments reveals neglected tree signal in gaps Christophe Dessimoz, Manuel Gil Genome Biology 2010, 11:R37 (6 April 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Tree-based tests of alignment methods enable the evaluation of the effect of gap placement on the inference of phylogenetic relationships.
	Research Phylogenetic detection of numerous gene duplications shared by animals, fungi and plants Xiaofan Zhou, Zhenguo Lin, Hong Ma Genome Biology 2010, 11:R38 (6 April 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A phylogentic analysis reveals that many gene duplications occurred prior to the split in animals, fungi and plants.
	Research The developmental expression dynamics of Drosophila melanogaster transcription factors Boris Adryan, Sarah A Teichmann Genome Biology 2010, 11:R40 (12 April 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary High levels of combinatorial complexity of transcription factors during embryogenesis in Drosophila melanogaster shed light on mechanisms of transcriptional control.
	Research Monovalent and unpoised status of most genes in undifferentiated cell-enriched Drosophila testis Qiang Gan, Dustin E Schones, Suk Ho Eun, Gang Wei, Kairong Cui, Keji Zhao, Xin Chen Genome Biology 2010, 11:R42 (15 April 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In undifferentiated Drosophila cells, differentiation-associated genes have monovalent, not bivalent histone modifications, in contrast to differentiation-associated genes in stem cells.
	Research Small variable segments constitute a major type of diversity of bacterial genomes at the species level Fabrice Touzain, Erick Denamur, Claudine Médigue, Valérie Barbe, Meriem El Karoui, Marie-Agnès Petit Genome Biology 2010, 11:R45 (30 April 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of all available genomes of three bacterial species suggests that a large part of genome diversity is contributed by short regions.
	Research DNA transposons and the role of recombination in mutation accumulation in Daphnia pulex Sarah Schaack, Eunjin Choi, Michael Lynch, Ellen J Pritham Genome Biology 2010, 11:R46 (30 April 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary Transposable elements in Daphnia pulex are identified and the impact of sex on their evolution is experimentally assessed
	Method Optimized design and data analysis of tag-based cytosine methylation assays Masako Suzuki, Qiang Jing, Daniel Lia, Marién Pascual, Andrew McLellan, John M Greally Genome Biology 2010, 11:R36 (1 April 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Genome-wide, tag-based cytosine methylation analysis is optimized.
	Method miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data David Hendrix, Michael Levine, Weiyang Shi Genome Biology 2010, 11:R39 (6 April 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel method for prediction of miRs from deep sequencing data. Its utility is demonstrated when applied to Ciona data.
	Method Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps Isheng J Tsai, Thomas D Otto, Matthew Berriman Genome Biology 2010, 11:R41 (13 April 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary IMAGE generates local assemblies, closing gaps in genomes assembled from paired-end next generation sequencing data, often without the need for new data
	Method Flux balance analysis accounting for metabolite dilution Tomer Benyamini, Ori Folger, Eytan Ruppin, Tomer Shlomi Genome Biology 2010, 11:R43 (16 April 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A flux balance analysis method for gene essentiality prediction, which takes into account variation in biomass composition under different growth conditions.
	Method Restriction Site Tiling Analysis: accurate discovery and quantitative genotyping of genome-wide polymorphisms using nucleotide arrays Melissa H Pespeni, Thomas A Oliver, Mollie K Manier, Stephen R Palumbi Genome Biology 2010, 11:R44 (19 April 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method for the simultaneous identification of polymorphic loci and the quantitative genotyping of thousands of loci in individuals is presented.

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Volume 11 Issue 4

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