Genome Biology | Volume 11 Issue 2

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	Volume 11 Issue 2
	Comment
	Comment Lost in translation Gregory A Petsko Genome Biology 2010, 11:107 (26 February 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Objections to dividing biomedical research into 'translational' and 'basic' are not just a matter of semantics.
	Research highlight Filling the gaps in the genomic landscape David Williams, J Peter Gogarten, Pascal Lapierre Genome Biology 2010, 11:103 (16 February 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Sequencing of genomes from many different bacterial and archaeal groups is broadening the picture of the prokaryotic pan-genome.
	Research highlight The pea aphid genome sequence brings theories of insect defense into question Christine G Elsik Genome Biology 2010, 11:106 (23 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome sequence of the pea aphid is the first for a basal hemimetabolous insect and provides insights into developmental plasticity, symbiosis and insect immunity.
	Research highlight PRDM9 points the zinc finger at meiotic recombination hotspots Matthew J Neale Genome Biology 2010, 11:104 (26 February 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent work shows that the histone methyltransferase PRDM9 determines the nonrandom genomic distribution of meiotic recombination hotspots.
	Research highlight Histone tales: echoes from the past, prospects for the future Chris Murgatroyd, Dietmar Spengler Genome Biology 2010, 11:105 (26 February 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent studies of the nematode dauer state provide new insights into epigenetic processes that underlie cellular memory.
	Research
	Research Candidate genes for alcohol preference identified by expression profiling in alcohol-preferring and -nonpreferring reciprocal congenic rats Tiebing Liang, Mark W Kimpel, Jeanette N McClintick, Ashley R Skillman, Kevin McCall, Howard J Edenberg, Lucinda G Carr Genome Biology 2010, 11:R11 (3 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcriptional profiling of specific regions of inbred rat brains reveals genes associated with alcohol preference in a known QTL locus on chromosome 4
	Research Genomic and small RNA sequencing of Miscanthus × giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses Kankshita Swaminathan, Magdy S Alabady, Kranthi Varala, Emanuele De Paoli, Isaac Ho, Dan S Rokhsar, Aru K Arumuganathan, Ray Ming, Pamela J Green, Blake C Meyers, Stephen P Moose, Matthew E Hudson Genome Biology 2010, 11:R12 (3 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genomic data together with sequencing of tissue specific small RNA libraries reveals insights into the genome content, small RNA repertoire and evolutionary origins of the grass Miscanthus × giganteus.
	Research Genome-wide analysis of the diatom cell cycle unveils a novel type of cyclins involved in environmental signaling Marie JJ Huysman, Cindy Martens, Klaas Vandepoele, Jeroen Gillard, Edda Rayko, Marc Heijde, Chris Bowler, Dirk Inzé, Yves Peer, Lieven De Veylder, Wim Vyverman Genome Biology 2010, 11:R17 (8 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genes controlling the cell cycle in two diatoms have been identified and functionally characterized, revealing environmental regulation of the cell cycle.
	Research 2× genomes - depth does matter Michel C Milinkovitch, Raphaël Helaers, Eric Depiereux, Athanasia C Tzika, Toni Gabaldón Genome Biology 2010, 11:R16 (9 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The use of low coverage genomes in comparative evolutionary analyses skews estimates of gene gains and losses.
	Research Genomic features defining exonic variants that modulate splicing Adam Woolfe, James C Mullikin, Laura Elnitski Genome Biology 2010, 11:R20 (16 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comparative analysis of SNPs and their exonic and intronic environments identifies the features predictive of splice affecting variants.
	Research Immunity and other defenses in pea aphids, Acyrthosiphon pisum Nicole M Gerardo, Boran Altincicek, Caroline Anselme, Hagop Atamian, Seth M Barribeau, Martin de Vos, Elizabeth J Duncan, Jay D Evans, Toni Gabaldón, Murad Ghanim, Adelaziz Heddi, Isgouhi Kaloshian, Amparo Latorre, Andres Moya, Atsushi Nakabachi, Benjamin J Parker, Vincente Pérez-Brocal, Miguel Pignatelli, Yvan Rahbé, John S Ramsey, Chelsea J Spragg, Javier Tamames, Daniel Tamarit, Cecilia Tamborindeguy, Caroline Vincent-Monegat, Andreas Vilcinskas Genome Biology 2010, 11:R21 (23 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome of the pea aphid Acyrthosiphon pisum lacks genes thought to be crucial in other insects for recognition, signaling and killing of microbes.
	Method Inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegans aging Kristen Fortney, Max Kotlyar, Igor Jurisica Genome Biology 2010, 11:R13 (3 February 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An algorithm for determining networks from gene expression data enables the identification of genes potentially linked to aging in worms.
	Method Gene ontology analysis for RNA-seq: accounting for selection bias Matthew D Young, Matthew J Wakefield, Gordon K Smyth, Alicia Oshlack Genome Biology 2010, 11:R14 (4 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary GOseq is a method for GO analysis of RNA-seq data that takes into account the length bias inherent in RNA-seq
	Method A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454 Niall J Lennon, Robert E Lintner, Scott Anderson, Pablo Alvarez, Andrew Barry, William Brockman, Riza Daza, Rachel L Erlich, Georgia Giannoukos, Lisa Green, Andrew Hollinger, Cindi A Hoover, David B Jaffe, Frank Juhn, Danielle McCarthy, Danielle Perrin, Karen Ponchner, Taryn L Powers, Kamran Rizzolo, Dana Robbins, Elizabeth Ryan, Carsten Russ, Todd Sparrow, John Stalker, Scott Steelman, Michael Weiand, Andrew Zimmer, Matthew R Henn, Chad Nusbaum, Robert Nicol et al. Genome Biology 2010, 11:R15 (5 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An automated method for constructing libraries for 454 sequencing significantly reduces the cost and time required.
	Method A fuzzy gene expression-based computational approach improves breast cancer prognostication Benjamin Haibe-Kains, Christine Desmedt, Françoise Rothé, Martine Piccart, Christos Sotiriou, Gianluca Bontempi Genome Biology 2010, 11:R18 (15 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A fuzzy computational approach that takes into account several molecular subtypes in order to provide more accurate breast cancer prognosis
	Method Evidence-ranked motif identification Stoyan Georgiev, Alan P Boyle, Karthik Jayasurya, Xuan Ding, Sayan Mukherjee, Uwe Ohler Genome Biology 2010, 11:R19 (15 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new computational method for the identification of regulatory motifs from large genomic datasets is presented here
	Method Identification of functional modules that correlate with phenotypic difference: the influence of network topology Jui-Hung Hung, Troy W Whitfield, Tun-Hsiang Yang, Zhenjun Hu, Zhiping Weng, Charles DeLisi Genome Biology 2010, 11:R23 (26 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A gene set enrichment analysis method for including network topology in the identification of genes involved in phenotypic alterations is described. Classifications: Genome studies, Methods
	Software ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing Guoliang Li, Melissa J Fullwood, Han Xu, Fabianus Hendriyan Mulawadi, Stoyan Velkov, Vinsensius Vega, Pramila Nuwantha Ariyaratne, Yusoff Bin Mohamed, Hong-Sain Ooi, Chandana Tennakoon, Chia-Lin Wei, Yijun Ruan, Wing-Kin Sung Genome Biology 2010, 11:R22 (25 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary ChIA-PET Tool can be used to process long-range chromatin interaction data. Results are visualized on a user-friendly genome browser.

	Volume 11 Issue 2
	Comment
	Comment Lost in translation Gregory A Petsko Genome Biology 2010, 11:107 (26 February 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Objections to dividing biomedical research into 'translational' and 'basic' are not just a matter of semantics.
	Research highlight Filling the gaps in the genomic landscape David Williams, J Peter Gogarten, Pascal Lapierre Genome Biology 2010, 11:103 (16 February 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Sequencing of genomes from many different bacterial and archaeal groups is broadening the picture of the prokaryotic pan-genome.
	Research highlight The pea aphid genome sequence brings theories of insect defense into question Christine G Elsik Genome Biology 2010, 11:106 (23 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome sequence of the pea aphid is the first for a basal hemimetabolous insect and provides insights into developmental plasticity, symbiosis and insect immunity.
	Research highlight PRDM9 points the zinc finger at meiotic recombination hotspots Matthew J Neale Genome Biology 2010, 11:104 (26 February 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent work shows that the histone methyltransferase PRDM9 determines the nonrandom genomic distribution of meiotic recombination hotspots.
	Research highlight Histone tales: echoes from the past, prospects for the future Chris Murgatroyd, Dietmar Spengler Genome Biology 2010, 11:105 (26 February 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Recent studies of the nematode dauer state provide new insights into epigenetic processes that underlie cellular memory.
	Research
	Research Candidate genes for alcohol preference identified by expression profiling in alcohol-preferring and -nonpreferring reciprocal congenic rats Tiebing Liang, Mark W Kimpel, Jeanette N McClintick, Ashley R Skillman, Kevin McCall, Howard J Edenberg, Lucinda G Carr Genome Biology 2010, 11:R11 (3 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcriptional profiling of specific regions of inbred rat brains reveals genes associated with alcohol preference in a known QTL locus on chromosome 4
	Research Genomic and small RNA sequencing of Miscanthus × giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses Kankshita Swaminathan, Magdy S Alabady, Kranthi Varala, Emanuele De Paoli, Isaac Ho, Dan S Rokhsar, Aru K Arumuganathan, Ray Ming, Pamela J Green, Blake C Meyers, Stephen P Moose, Matthew E Hudson Genome Biology 2010, 11:R12 (3 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genomic data together with sequencing of tissue specific small RNA libraries reveals insights into the genome content, small RNA repertoire and evolutionary origins of the grass Miscanthus × giganteus.
	Research Genome-wide analysis of the diatom cell cycle unveils a novel type of cyclins involved in environmental signaling Marie JJ Huysman, Cindy Martens, Klaas Vandepoele, Jeroen Gillard, Edda Rayko, Marc Heijde, Chris Bowler, Dirk Inzé, Yves Peer, Lieven De Veylder, Wim Vyverman Genome Biology 2010, 11:R17 (8 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genes controlling the cell cycle in two diatoms have been identified and functionally characterized, revealing environmental regulation of the cell cycle.
	Research 2× genomes - depth does matter Michel C Milinkovitch, Raphaël Helaers, Eric Depiereux, Athanasia C Tzika, Toni Gabaldón Genome Biology 2010, 11:R16 (9 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The use of low coverage genomes in comparative evolutionary analyses skews estimates of gene gains and losses.
	Research Genomic features defining exonic variants that modulate splicing Adam Woolfe, James C Mullikin, Laura Elnitski Genome Biology 2010, 11:R20 (16 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comparative analysis of SNPs and their exonic and intronic environments identifies the features predictive of splice affecting variants.
	Research Immunity and other defenses in pea aphids, Acyrthosiphon pisum Nicole M Gerardo, Boran Altincicek, Caroline Anselme, Hagop Atamian, Seth M Barribeau, Martin de Vos, Elizabeth J Duncan, Jay D Evans, Toni Gabaldón, Murad Ghanim, Adelaziz Heddi, Isgouhi Kaloshian, Amparo Latorre, Andres Moya, Atsushi Nakabachi, Benjamin J Parker, Vincente Pérez-Brocal, Miguel Pignatelli, Yvan Rahbé, John S Ramsey, Chelsea J Spragg, Javier Tamames, Daniel Tamarit, Cecilia Tamborindeguy, Caroline Vincent-Monegat, Andreas Vilcinskas Genome Biology 2010, 11:R21 (23 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome of the pea aphid Acyrthosiphon pisum lacks genes thought to be crucial in other insects for recognition, signaling and killing of microbes.
	Method Inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegans aging Kristen Fortney, Max Kotlyar, Igor Jurisica Genome Biology 2010, 11:R13 (3 February 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An algorithm for determining networks from gene expression data enables the identification of genes potentially linked to aging in worms.
	Method Gene ontology analysis for RNA-seq: accounting for selection bias Matthew D Young, Matthew J Wakefield, Gordon K Smyth, Alicia Oshlack Genome Biology 2010, 11:R14 (4 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary GOseq is a method for GO analysis of RNA-seq data that takes into account the length bias inherent in RNA-seq
	Method A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454 Niall J Lennon, Robert E Lintner, Scott Anderson, Pablo Alvarez, Andrew Barry, William Brockman, Riza Daza, Rachel L Erlich, Georgia Giannoukos, Lisa Green, Andrew Hollinger, Cindi A Hoover, David B Jaffe, Frank Juhn, Danielle McCarthy, Danielle Perrin, Karen Ponchner, Taryn L Powers, Kamran Rizzolo, Dana Robbins, Elizabeth Ryan, Carsten Russ, Todd Sparrow, John Stalker, Scott Steelman, Michael Weiand, Andrew Zimmer, Matthew R Henn, Chad Nusbaum, Robert Nicol et al. Genome Biology 2010, 11:R15 (5 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An automated method for constructing libraries for 454 sequencing significantly reduces the cost and time required.
	Method A fuzzy gene expression-based computational approach improves breast cancer prognostication Benjamin Haibe-Kains, Christine Desmedt, Françoise Rothé, Martine Piccart, Christos Sotiriou, Gianluca Bontempi Genome Biology 2010, 11:R18 (15 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A fuzzy computational approach that takes into account several molecular subtypes in order to provide more accurate breast cancer prognosis
	Method Evidence-ranked motif identification Stoyan Georgiev, Alan P Boyle, Karthik Jayasurya, Xuan Ding, Sayan Mukherjee, Uwe Ohler Genome Biology 2010, 11:R19 (15 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new computational method for the identification of regulatory motifs from large genomic datasets is presented here
	Method Identification of functional modules that correlate with phenotypic difference: the influence of network topology Jui-Hung Hung, Troy W Whitfield, Tun-Hsiang Yang, Zhenjun Hu, Zhiping Weng, Charles DeLisi Genome Biology 2010, 11:R23 (26 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A gene set enrichment analysis method for including network topology in the identification of genes involved in phenotypic alterations is described. Classifications: Genome studies, Methods
	Software ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing Guoliang Li, Melissa J Fullwood, Han Xu, Fabianus Hendriyan Mulawadi, Stoyan Velkov, Vinsensius Vega, Pramila Nuwantha Ariyaratne, Yusoff Bin Mohamed, Hong-Sain Ooi, Chandana Tennakoon, Chia-Lin Wei, Yijun Ruan, Wing-Kin Sung Genome Biology 2010, 11:R22 (25 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary ChIA-PET Tool can be used to process long-range chromatin interaction data. Results are visualized on a user-friendly genome browser.

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Volume 11 Issue 2

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