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.refereed research


Genome Biology aims to provide the best possible service to authors and readers of primary research articles. The refereed research section publishes peer-reviewed research in all areas of molecular, cellular, organismal and population biology that are informed by genomics. All research articles are made available free to individuals through the web, and there are no restrictions on article length or on the types of information that can be included. The publication schedule is very fast, using electronic systems for article delivery, proofing and peer-review. For more details about how refereed research is published in Genome Biology and for instructions for authors, see 'about refereed research'.

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Refereed research

Conserved developmental transcriptomes in evolutionary divergent species

Research    
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
(17 March 2010)

Transcriptional profiling of Dictyostelium development reveals significant conservation of transcriptional profiles between evolutionarily divergent species.

[Abstract] [Provisional PDF]

Global and unbiased detection of splice junctions from RNA-seq data

Method    
Adam Ameur, Anna Wetterbom, Lars Feuk, Ulf Gyllensten
(17 March 2010)

SplitSeek can be used to detect novel splicing events in SOLiD RNA-seq data without the need for a pre-defined library.

[Abstract] [Provisional PDF]

Basal core promoters control the equilibrium between negative cofactor 2 and preinitiation complexes in human cells

Research    
Thomas K Albert, Krobinian Grote, Stefan Boeing, Michael Meisterernst
(15 March 2010)

Genome-wide mapping of the human TFIIB and NC2 transcription factor binding sites reveals insights into the formation of the pre-initiation complex.

[Abstract] [Provisional PDF]

Characterizing regulatory path motifs in integrated networks using perturbational data

Software    
Anagha Joshi, Thomas Van Parys, Yves Van de Peer, Tom Michoel
(15 March 2010)

Pathicular a Cytoscape plugin for analysing cellular responses to transcription factor perturbations is presented

[Abstract] [Provisional PDF]

Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea and their metagenomes

Research    
Zasha Weinberg, Joy X Wang, Jarrod Bogue, Jingying Yang, Keith Corbino, Ryan H Moy, Ronald R Breaker
(15 March 2010)

Novel motifs identified in a comparative genomic analysis of bacterial, archaeal and metagenomic data reveals over 100 candidate structured RNAs.

[Abstract] [Provisional PDF]

Detection and correction of false segmental duplications caused by genome mis-assembly

Method    
David R Kelley, Steven L Salzberg
(10 March 2010)

A method for determining false segmental duplications in vertebrate genomes, thus correcting mis-assemblies and providing more accurate estimates of duplications.

[Abstract] [Provisional PDF] [PubMed] [Related articles]

Genome-wide functional analysis of human 5'untranslated region introns

Research    
Can Cenik, Adnan Derti, Joseph C Mellor, Gabriel F Berriz, Frederick P Roth
(11 March 2010)

Genes with short 5UTR introns have higher expression than genes with no or long 5UTR introns. Complex evolutionary forces act on these introns.

[Abstract] [Provisional PDF] [PubMed] [Related articles]

XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments

Software    
Morris A Swertz, K Joeri van der 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 Parkinson, Coordination of Mouse Informatics Resources Consortium (CASIMIR), Genotype-To-Phenotype Project (GEN2PHEN), Ritsert C Jansen
(9 March 2010)

XGAP, a software platform for the integration and analysis of genotype and phenotype data.

[Abstract] [Provisional PDF] [PubMed] [Related articles]



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