Genome Biology | Volume 10 Issue 1

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	Volume 10 Issue 1
	Comment
	Comment Life is a Ponzi scheme Gregory A Petsko Genome Biology 2009, 10:101 (27 January 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Before too long a smaller number of young people will be having to support a larger number of the very old, a typical and unsustainable Ponzi scheme.
	Review
	Review Identifying protein-coding genes in genomic sequences Jennifer Harrow, Alinda Nagy, Alexandre Reymond, Tyler Alioto, Laszlo Patthy, Stylianos E Antonarakis, Roderic Guigó Genome Biology 2009, 10:201 (30 January 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A review of the main computational pipelines used to generate the human reference protein-coding gene sets.
	Review Integrating sequence, evolution and functional genomics in regulatory genomics Martin Vingron, Alvis Brazma, Richard Coulson, Jacques van Helden, Thomas Manke, Kimmo Palin, Olivier Sand, Esko Ukkonen Genome Biology 2009, 10:202 (30 January 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Finding transcription factor binding sites in regulatory regions of the genome
	Minireview Cross-talk in the gut Jennifer E Dinalo, David A Relman Genome Biology 2009, 10:203 (23 January 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Modification of host signaling by the gut microbiota can influence weight gain and fat deposition.
	Minireview Regulating highly dynamic unstructured proteins and their coding mRNAs Buyong Ma, Ruth Nussinov Genome Biology 2009, 10:204 (28 January 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Orchestration of the lifetimes and conformations of intrinsically unstructured proteins and their mRNAs ensure precision and flexibility in biological control.
	Minireview The secret(ion) life of worms David McK Bird, Charles H Opperman Genome Biology 2009, 10:205 (28 January 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The secretomes of plant and human parasitic nematodes reveal molecular similarities that reflect the shared need to counter host defenses.
	Report
	Meeting report Copy number variation goes clinical Cédric Le Caignec, Richard Redon Genome Biology 2009, 10:301 (23 January 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the First Golden Helix Symposium 'Copy Number Variation (CNV) and Genomic Alterations in Health and Disease', Athens, Greece, 28-29 November 2008.
	Research
	Research Analysis of the platypus genome suggests a transposon origin for mammalian imprinting Andrew J Pask, Anthony T Papenfuss, Eleanor I Ager, Kaighin A McColl, Terence P Speed, Marilyn B Renfree Genome Biology 2009, 10:R1 (2 January 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparisons between the platypus and eutherian mammalian genomes provides new insights into how epigenetic imprinting may have evolved in mammalian genomes.
	Research Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes Suganthi Balasubramanian, Deyou Zheng, Yuen-Jong Liu, Gang Fang, Adam Frankish, Nicholas Carriero, Rebecca Robilotto, Philip Cayting, Mark Gerstein Genome Biology 2009, 10:R2 (5 January 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of ribosomal protein pseudogenes in the four mammalian genomes reveals no correlation between number of pseudogenes and mRNA abundance.
	Research Studying alternative splicing regulatory networks through partial correlation analysis Liang Chen, Sika Zheng Genome Biology 2009, 10:R3 (9 January 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The identification of links between exons and their regulators or targets and between co-spliced exons in human, mouse and rat provides novel insights into the alternative splicing regulatory network.
	Research Insight into the molecular requirements for pathogenicity of Fusarium oxysporum f. sp. lycopersici through large-scale insertional mutagenesis Caroline B Michielse, Ringo van Wijk, Linda Reijnen, Ben JC Cornelissen, Martijn Rep Genome Biology 2009, 10:R4 (9 January 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An insertional mutagenesis screen identifies pathogenicity-related genes in the plant fungal pathogen Fusarium oxysporum.
	Research Development and application of versatile high density microarrays for genome-wide analysis of Streptomyces coelicolor: characterization of the HspR regulon Giselda Bucca, Emma Laing, Vassilis Mersinias, Nicholas Allenby, Douglas Hurd, Jolyon Holdstock, Volker Brenner, Marcus Harrison, Colin P Smith Genome Biology 2009, 10:R5 (16 January 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Development of high-density microarrays for global analysis of gene expression and transcription factor binding in Streptomyces coelicolor suggests a novel role for HspR in stress adaptation.
	Research Characterization and comparative profiling of the small RNA transcriptomes in two phases of locust Yuanyuan Wei, Shuang Chen, Pengcheng Yang, Zongyuan Ma, Le Kang Genome Biology 2009, 10:R6 (16 January 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary High-throughput sequencing of the small RNA transcriptome of locust reveals differences in post-transcriptional regulation between solitary and swarming phases and provides insights into the evolution of insect small RNAs.
	Research A genome-wide genetic signature of Jewish ancestry perfectly separates individuals with and without full Jewish ancestry in a large random sample of European Americans Anna C Need, Dalia Kasperavičiūtė, Elizabeth T Cirulli, David B Goldstein Genome Biology 2009, 10:R7 (22 January 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| f1000 \| Editor’s summary A principal components analysis of genomic information showed that individuals with full Jewish ancestry formed a clearly distinct cluster from those individuals with no Jewish ancestry.
	Research Characterization of taxonomically restricted genes in a phylum-restricted cell type Sabine Milde, Georg Hemmrich, Friederike Anton-Erxleben, Konstantin Khalturin, Jörg Wittlieb, Thomas CG Bosch Genome Biology 2009, 10:R8 (22 January 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Computational and functional genomic analyses in Hydra magnipapillata suggest that taxonomically-restricted genes are involved in the evolution of morphological novelties such as the cnidarian nematocyte
	Research Profiling RE1/REST-mediated histone modifications in the human genome Deyou Zheng, Keji Zhao, Mark F Mehler Genome Biology 2009, 10:R9 (27 January 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An in silico analysis of REST binding in non-neuronal human cells reveals how it can induce chromatin remodeling and reposition nucleosomes.
	Research Coding region structural heterogeneity and turnover of transcription start sites contribute to divergence in expression between duplicate genes Chungoo Park, Kateryna D Makova Genome Biology 2009, 10:R10 (28 January 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Gene expression data for duplicated gene pairs in humans provides insights into the regulatory factors affecting the expression divergence of these genes and implications for their evolution.
	Research Global analysis of alternative splicing regulation by insulin and wingless signaling in Drosophila cells Britta Hartmann, Robert Castelo, Marco Blanchette, Stephanie Boue, Donald C Rio, Juan Valcárcel Genome Biology 2009, 10:R11 (29 January 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A genome-wide analysis of the response to insulin and wingless activation using splicing-sensitive microarrays shows distinct but overlapping programs of transcriptional and posttranscriptional regulation.
	Research Universal features in the genome-level evolution of protein domains Marco Cosentino Lagomarsino, Alessandro L Sellerio, Philip D Heijning, Bruno Bassetti Genome Biology 2009, 10:R12 (30 January 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Novel protein domain stochastic duplication/innovation models that are independent of genome-specific features are used to interpret global trends of genome evolution.

	Volume 10 Issue 1
	Comment
	Comment Life is a Ponzi scheme Gregory A Petsko Genome Biology 2009, 10:101 (27 January 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Before too long a smaller number of young people will be having to support a larger number of the very old, a typical and unsustainable Ponzi scheme.
	Review
	Review Identifying protein-coding genes in genomic sequences Jennifer Harrow, Alinda Nagy, Alexandre Reymond, Tyler Alioto, Laszlo Patthy, Stylianos E Antonarakis, Roderic Guigó Genome Biology 2009, 10:201 (30 January 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A review of the main computational pipelines used to generate the human reference protein-coding gene sets.
	Review Integrating sequence, evolution and functional genomics in regulatory genomics Martin Vingron, Alvis Brazma, Richard Coulson, Jacques van Helden, Thomas Manke, Kimmo Palin, Olivier Sand, Esko Ukkonen Genome Biology 2009, 10:202 (30 January 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Finding transcription factor binding sites in regulatory regions of the genome
	Minireview Cross-talk in the gut Jennifer E Dinalo, David A Relman Genome Biology 2009, 10:203 (23 January 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Modification of host signaling by the gut microbiota can influence weight gain and fat deposition.
	Minireview Regulating highly dynamic unstructured proteins and their coding mRNAs Buyong Ma, Ruth Nussinov Genome Biology 2009, 10:204 (28 January 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Orchestration of the lifetimes and conformations of intrinsically unstructured proteins and their mRNAs ensure precision and flexibility in biological control.
	Minireview The secret(ion) life of worms David McK Bird, Charles H Opperman Genome Biology 2009, 10:205 (28 January 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The secretomes of plant and human parasitic nematodes reveal molecular similarities that reflect the shared need to counter host defenses.
	Report
	Meeting report Copy number variation goes clinical Cédric Le Caignec, Richard Redon Genome Biology 2009, 10:301 (23 January 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the First Golden Helix Symposium 'Copy Number Variation (CNV) and Genomic Alterations in Health and Disease', Athens, Greece, 28-29 November 2008.
	Research
	Research Analysis of the platypus genome suggests a transposon origin for mammalian imprinting Andrew J Pask, Anthony T Papenfuss, Eleanor I Ager, Kaighin A McColl, Terence P Speed, Marilyn B Renfree Genome Biology 2009, 10:R1 (2 January 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparisons between the platypus and eutherian mammalian genomes provides new insights into how epigenetic imprinting may have evolved in mammalian genomes.
	Research Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes Suganthi Balasubramanian, Deyou Zheng, Yuen-Jong Liu, Gang Fang, Adam Frankish, Nicholas Carriero, Rebecca Robilotto, Philip Cayting, Mark Gerstein Genome Biology 2009, 10:R2 (5 January 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of ribosomal protein pseudogenes in the four mammalian genomes reveals no correlation between number of pseudogenes and mRNA abundance.
	Research Studying alternative splicing regulatory networks through partial correlation analysis Liang Chen, Sika Zheng Genome Biology 2009, 10:R3 (9 January 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The identification of links between exons and their regulators or targets and between co-spliced exons in human, mouse and rat provides novel insights into the alternative splicing regulatory network.
	Research Insight into the molecular requirements for pathogenicity of Fusarium oxysporum f. sp. lycopersici through large-scale insertional mutagenesis Caroline B Michielse, Ringo van Wijk, Linda Reijnen, Ben JC Cornelissen, Martijn Rep Genome Biology 2009, 10:R4 (9 January 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An insertional mutagenesis screen identifies pathogenicity-related genes in the plant fungal pathogen Fusarium oxysporum.
	Research Development and application of versatile high density microarrays for genome-wide analysis of Streptomyces coelicolor: characterization of the HspR regulon Giselda Bucca, Emma Laing, Vassilis Mersinias, Nicholas Allenby, Douglas Hurd, Jolyon Holdstock, Volker Brenner, Marcus Harrison, Colin P Smith Genome Biology 2009, 10:R5 (16 January 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Development of high-density microarrays for global analysis of gene expression and transcription factor binding in Streptomyces coelicolor suggests a novel role for HspR in stress adaptation.
	Research Characterization and comparative profiling of the small RNA transcriptomes in two phases of locust Yuanyuan Wei, Shuang Chen, Pengcheng Yang, Zongyuan Ma, Le Kang Genome Biology 2009, 10:R6 (16 January 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary High-throughput sequencing of the small RNA transcriptome of locust reveals differences in post-transcriptional regulation between solitary and swarming phases and provides insights into the evolution of insect small RNAs.
	Research A genome-wide genetic signature of Jewish ancestry perfectly separates individuals with and without full Jewish ancestry in a large random sample of European Americans Anna C Need, Dalia Kasperavičiūtė, Elizabeth T Cirulli, David B Goldstein Genome Biology 2009, 10:R7 (22 January 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| f1000 \| Editor’s summary A principal components analysis of genomic information showed that individuals with full Jewish ancestry formed a clearly distinct cluster from those individuals with no Jewish ancestry.
	Research Characterization of taxonomically restricted genes in a phylum-restricted cell type Sabine Milde, Georg Hemmrich, Friederike Anton-Erxleben, Konstantin Khalturin, Jörg Wittlieb, Thomas CG Bosch Genome Biology 2009, 10:R8 (22 January 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Computational and functional genomic analyses in Hydra magnipapillata suggest that taxonomically-restricted genes are involved in the evolution of morphological novelties such as the cnidarian nematocyte
	Research Profiling RE1/REST-mediated histone modifications in the human genome Deyou Zheng, Keji Zhao, Mark F Mehler Genome Biology 2009, 10:R9 (27 January 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An in silico analysis of REST binding in non-neuronal human cells reveals how it can induce chromatin remodeling and reposition nucleosomes.
	Research Coding region structural heterogeneity and turnover of transcription start sites contribute to divergence in expression between duplicate genes Chungoo Park, Kateryna D Makova Genome Biology 2009, 10:R10 (28 January 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Gene expression data for duplicated gene pairs in humans provides insights into the regulatory factors affecting the expression divergence of these genes and implications for their evolution.
	Research Global analysis of alternative splicing regulation by insulin and wingless signaling in Drosophila cells Britta Hartmann, Robert Castelo, Marco Blanchette, Stephanie Boue, Donald C Rio, Juan Valcárcel Genome Biology 2009, 10:R11 (29 January 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A genome-wide analysis of the response to insulin and wingless activation using splicing-sensitive microarrays shows distinct but overlapping programs of transcriptional and posttranscriptional regulation.
	Research Universal features in the genome-level evolution of protein domains Marco Cosentino Lagomarsino, Alessandro L Sellerio, Philip D Heijning, Bruno Bassetti Genome Biology 2009, 10:R12 (30 January 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Novel protein domain stochastic duplication/innovation models that are independent of genome-specific features are used to interpret global trends of genome evolution.

Explore Genome Biology

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Volume 10 Issue 1

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