Genome Biology | Volume 11 Issue 3

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	Volume 11 Issue 3
	Comment
	Comment No stone unturned Gregory A Petsko Genome Biology 2010, 11:112 (29 March 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Gregory Petsko proposes a new motto for the National Institutes of Health.
	Research highlight The amazing world of bacterial structured RNAs Eric Westhof Genome Biology 2010, 11:108 (15 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The discovery of several new structured non-coding RNAs in bacterial and archaeal genomes and metagenomes raises burning questions about their biological and biochemical functions.
	Research highlight Is canalization more than just a beautiful idea? Kaoru Sato, Haruhiko Siomi Genome Biology 2010, 11:109 (16 March 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The heat-shock protein Hsp90 has been shown to be involved in the repression of de novo transposon-mediated mutagenesis.
	Research highlight Genome-wide DNA demethylation in mammals Lionel A Sanz, Satya K Kota, Robert Feil Genome Biology 2010, 11:110 (16 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary New roles for the cytidine deaminase AID and elongator-complex proteins in DNA demethylation.
	Research highlight Tracing the evolution of tissue identity with microRNAs Katrien De Mulder, Eugene Berezikov Genome Biology 2010, 11:111 (30 March 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparison of microRNA expression identified tissues present in the last common ancestor of Bilaterians and put evolution of microRNAs in the context of tissue evolution.
	Review
	Review The yin and yang of chromatin spatial organization Nathan F Cope, Peter Fraser, Christopher H Eskiw Genome Biology 2010, 11:204 (29 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Chromatin interactions, both in cis and trans and between transcriptionally active and silent regions, mean that the spatial organization of the genome is non-random.
	Research
	Research High-resolution transcription atlas of the mitotic cell cycle in budding yeast Marina V Granovskaia, Lars J Jensen, Matthew E Ritchie, Joern Toedling, Ye Ning, Peer Bork, Wolfgang Huber, Lars M Steinmetz Genome Biology 2010, 11:R24 (1 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A high resolution strand-specific transcriptional atlas of the budding yeast mitotic cell cycle, including both mRNA and non-coding RNA profiles.
	Research Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates Zhengdong D Zhang, Adam Frankish, Toby Hunt, Jennifer Harrow, Mark Gerstein Genome Biology 2010, 11:R26 (8 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Novel human pseudogenes are identified that had previous functionality and their age is estimated. The rate of loss-of-function occurred uniformly.
	Research Genome-wide functional analysis of human 5' untranslated region introns Can Cenik, Adnan Derti, Joseph C Mellor, Gabriel F Berriz, Frederick P Roth Genome Biology 2010, 11:R29 (11 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genes with short 5'UTR introns have higher expression than genes with no or long 5'UTR introns. Complex evolutionary forces act on these introns.
	Research Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes Zasha Weinberg, Joy X Wang, Jarrod Bogue, Jingying Yang, Keith Corbino, Ryan H Moy, Ronald R Breaker Genome Biology 2010, 11:R31 (15 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Novel motifs identified in a comparative genomic analysis of bacterial, archaeal and metagenomic data reveals over 100 candidate structured RNAs.
	Research Basal core promoters control the equilibrium between negative cofactor 2 and preinitiation complexes in human cells Thomas K Albert, Korbinian Grote, Stefan Boeing, Michael Meisterernst Genome Biology 2010, 11:R33 (15 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genome-wide mapping of the human TFIIB and NC2 transcription factor binding sites reveals insights into the formation of the pre-initiation complex.
	Research Conserved developmental transcriptomes in evolutionarily divergent species Anup Parikh, Edward Roshan Miranda, Mariko Katoh-Kurasawa, Danny Fuller, Gregor Rot, Lan Zagar, Tomaz Curk, Richard Sucgang, Rui Chen, Blaz Zupan, William F Loomis, Adam Kuspa, Gad Shaulsky Genome Biology 2010, 11:R35 (17 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcriptional profiling of Dictyostelium development reveals significant conservation of transcriptional profiles between evolutionarily divergent species.
	Method A scaling normalization method for differential expression analysis of RNA-seq data Mark D Robinson, Alicia Oshlack Genome Biology 2010, 11:R25 (2 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel and empirical method for normalization of RNA-seq data is presented
	Method Detection and correction of false segmental duplications caused by genome mis-assembly David R Kelley, Steven L Salzberg Genome Biology 2010, 11:R28 (10 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for determining false segmental duplications in vertebrate genomes, thus correcting mis-assemblies and providing more accurate estimates of duplications.
	Method Systematic analysis of genome-wide fitness data in yeast reveals novel gene function and drug action Maureen E Hillenmeyer, Elke Ericson, Ronald W Davis, Corey Nislow, Daphne Koller, Guri Giaever Genome Biology 2010, 11:R30 (12 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The relationship between co-fitness and co-inhibition of genes in chemicogenomic yeast screens provides insights into gene function and drug target prediction.
	Method Global and unbiased detection of splice junctions from RNA-seq data Adam Ameur, Anna Wetterbom, Lars Feuk, Ulf Gyllensten Genome Biology 2010, 11:R34 (17 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary SplitSeek can be used to detect novel splicing events in SOLiD RNA-seq data without the need for a pre-defined library.
	Software XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments Morris A Swertz, K Joeri Velde, Bruno M Tesson, Richard A Scheltema, Danny Arends, Gonzalo Vera, Rudi Alberts, Martijn Dijkstra, Paul Schofield, Klaus Schughart, John M Hancock, Damian Smedley, Katy Wolstencroft, Carole Goble, Engbert O de Brock, Andrew R Jones, Helen E Parkinson, members of the Coordination of Mouse Informatics Resources (CASIMIR), Genotype-To-Phenotype (GEN2PHEN) Consortiums, Ritsert C Jansen Genome Biology 2010, 11:R27 (9 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary XGAP, a software platform for the integration and analysis of genotype and phenotype data.
	Software Characterizing regulatory path motifs in integrated networks using perturbational data Anagha Joshi, Thomas Van Parys, Yves Peer, Tom Michoel Genome Biology 2010, 11:R32 (11 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Pathicular – a Cytoscape plugin for analysing cellular responses to transcription factor perturbations is presented

	Volume 11 Issue 3
	Comment
	Comment No stone unturned Gregory A Petsko Genome Biology 2010, 11:112 (29 March 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Gregory Petsko proposes a new motto for the National Institutes of Health.
	Research highlight The amazing world of bacterial structured RNAs Eric Westhof Genome Biology 2010, 11:108 (15 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The discovery of several new structured non-coding RNAs in bacterial and archaeal genomes and metagenomes raises burning questions about their biological and biochemical functions.
	Research highlight Is canalization more than just a beautiful idea? Kaoru Sato, Haruhiko Siomi Genome Biology 2010, 11:109 (16 March 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The heat-shock protein Hsp90 has been shown to be involved in the repression of de novo transposon-mediated mutagenesis.
	Research highlight Genome-wide DNA demethylation in mammals Lionel A Sanz, Satya K Kota, Robert Feil Genome Biology 2010, 11:110 (16 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary New roles for the cytidine deaminase AID and elongator-complex proteins in DNA demethylation.
	Research highlight Tracing the evolution of tissue identity with microRNAs Katrien De Mulder, Eugene Berezikov Genome Biology 2010, 11:111 (30 March 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Comparison of microRNA expression identified tissues present in the last common ancestor of Bilaterians and put evolution of microRNAs in the context of tissue evolution.
	Review
	Review The yin and yang of chromatin spatial organization Nathan F Cope, Peter Fraser, Christopher H Eskiw Genome Biology 2010, 11:204 (29 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Chromatin interactions, both in cis and trans and between transcriptionally active and silent regions, mean that the spatial organization of the genome is non-random.
	Research
	Research High-resolution transcription atlas of the mitotic cell cycle in budding yeast Marina V Granovskaia, Lars J Jensen, Matthew E Ritchie, Joern Toedling, Ye Ning, Peer Bork, Wolfgang Huber, Lars M Steinmetz Genome Biology 2010, 11:R24 (1 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A high resolution strand-specific transcriptional atlas of the budding yeast mitotic cell cycle, including both mRNA and non-coding RNA profiles.
	Research Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates Zhengdong D Zhang, Adam Frankish, Toby Hunt, Jennifer Harrow, Mark Gerstein Genome Biology 2010, 11:R26 (8 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Novel human pseudogenes are identified that had previous functionality and their age is estimated. The rate of loss-of-function occurred uniformly.
	Research Genome-wide functional analysis of human 5' untranslated region introns Can Cenik, Adnan Derti, Joseph C Mellor, Gabriel F Berriz, Frederick P Roth Genome Biology 2010, 11:R29 (11 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genes with short 5'UTR introns have higher expression than genes with no or long 5'UTR introns. Complex evolutionary forces act on these introns.
	Research Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes Zasha Weinberg, Joy X Wang, Jarrod Bogue, Jingying Yang, Keith Corbino, Ryan H Moy, Ronald R Breaker Genome Biology 2010, 11:R31 (15 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Novel motifs identified in a comparative genomic analysis of bacterial, archaeal and metagenomic data reveals over 100 candidate structured RNAs.
	Research Basal core promoters control the equilibrium between negative cofactor 2 and preinitiation complexes in human cells Thomas K Albert, Korbinian Grote, Stefan Boeing, Michael Meisterernst Genome Biology 2010, 11:R33 (15 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genome-wide mapping of the human TFIIB and NC2 transcription factor binding sites reveals insights into the formation of the pre-initiation complex.
	Research Conserved developmental transcriptomes in evolutionarily divergent species Anup Parikh, Edward Roshan Miranda, Mariko Katoh-Kurasawa, Danny Fuller, Gregor Rot, Lan Zagar, Tomaz Curk, Richard Sucgang, Rui Chen, Blaz Zupan, William F Loomis, Adam Kuspa, Gad Shaulsky Genome Biology 2010, 11:R35 (17 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcriptional profiling of Dictyostelium development reveals significant conservation of transcriptional profiles between evolutionarily divergent species.
	Method A scaling normalization method for differential expression analysis of RNA-seq data Mark D Robinson, Alicia Oshlack Genome Biology 2010, 11:R25 (2 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel and empirical method for normalization of RNA-seq data is presented
	Method Detection and correction of false segmental duplications caused by genome mis-assembly David R Kelley, Steven L Salzberg Genome Biology 2010, 11:R28 (10 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for determining false segmental duplications in vertebrate genomes, thus correcting mis-assemblies and providing more accurate estimates of duplications.
	Method Systematic analysis of genome-wide fitness data in yeast reveals novel gene function and drug action Maureen E Hillenmeyer, Elke Ericson, Ronald W Davis, Corey Nislow, Daphne Koller, Guri Giaever Genome Biology 2010, 11:R30 (12 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The relationship between co-fitness and co-inhibition of genes in chemicogenomic yeast screens provides insights into gene function and drug target prediction.
	Method Global and unbiased detection of splice junctions from RNA-seq data Adam Ameur, Anna Wetterbom, Lars Feuk, Ulf Gyllensten Genome Biology 2010, 11:R34 (17 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary SplitSeek can be used to detect novel splicing events in SOLiD RNA-seq data without the need for a pre-defined library.
	Software XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments Morris A Swertz, K Joeri Velde, Bruno M Tesson, Richard A Scheltema, Danny Arends, Gonzalo Vera, Rudi Alberts, Martijn Dijkstra, Paul Schofield, Klaus Schughart, John M Hancock, Damian Smedley, Katy Wolstencroft, Carole Goble, Engbert O de Brock, Andrew R Jones, Helen E Parkinson, members of the Coordination of Mouse Informatics Resources (CASIMIR), Genotype-To-Phenotype (GEN2PHEN) Consortiums, Ritsert C Jansen Genome Biology 2010, 11:R27 (9 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary XGAP, a software platform for the integration and analysis of genotype and phenotype data.
	Software Characterizing regulatory path motifs in integrated networks using perturbational data Anagha Joshi, Thomas Van Parys, Yves Peer, Tom Michoel Genome Biology 2010, 11:R32 (11 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Pathicular – a Cytoscape plugin for analysing cellular responses to transcription factor perturbations is presented

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Volume 11 Issue 3

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