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Volume 11 Issue 3
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Comment |
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No stone unturned
Gregory A Petsko Genome Biology 2010, 11:112 (29 March 2010)
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Editor’s summary
Gregory Petsko proposes a new motto for the National Institutes of Health.
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The amazing world of bacterial structured RNAs
Eric Westhof Genome Biology 2010, 11:108 (15 March 2010)
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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. |
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Is canalization more than just a beautiful idea?
Kaoru Sato, Haruhiko Siomi Genome Biology 2010, 11:109 (16 March 2010)
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Editor’s summary
The heat-shock protein Hsp90 has been shown to be involved in the repression of de novo transposon-mediated mutagenesis. |
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Genome-wide DNA demethylation in mammals
Lionel A Sanz, Satya K Kota, Robert Feil Genome Biology 2010, 11:110 (16 March 2010)
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Editor’s summary
New roles for the cytidine deaminase AID and elongator-complex proteins in DNA demethylation. |
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Tracing the evolution of tissue identity with microRNAs
Katrien De Mulder, Eugene Berezikov Genome Biology 2010, 11:111 (30 March 2010)
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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.
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Review |
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The yin and yang of chromatin spatial organization
Nathan F Cope, Peter Fraser, Christopher H Eskiw Genome Biology 2010, 11:204 (29 March 2010)
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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. |
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Research |
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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)
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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. |
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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)
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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. |
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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)
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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. |
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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)
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Editor’s summary
Novel motifs identified in a comparative genomic analysis of bacterial, archaeal and metagenomic data reveals over 100 candidate structured RNAs. |
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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)
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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. |
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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)
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Editor’s summary
Transcriptional profiling of Dictyostelium development reveals significant conservation of transcriptional profiles between evolutionarily divergent species. |
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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)
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Editor’s summary
A novel and empirical method for normalization of RNA-seq data is presented |
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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)
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Editor’s summary
A method for determining false segmental duplications in vertebrate genomes, thus correcting mis-assemblies and providing more accurate estimates of duplications. |
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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)
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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. |
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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)
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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. |
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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)
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Editor’s summary
XGAP, a software platform for the integration and analysis of genotype and phenotype data. |
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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)
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Editor’s summary
Pathicular – a Cytoscape plugin for analysing cellular responses to transcription factor perturbations is presented |
