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Conserved developmental transcriptomes in evolutionary 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)

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
Adam Ameur, Anna Wetterbom, Lars Feuk, Ulf Gyllensten
Genome Biology 2010, 11: R34    
(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]

Genome-wide DNA demethylation in mammals
Lionel A Sanz, Satya K Kota, Robert Feil
Genome Biology 2010, 11(3):110   
(16 March 2010)

New roles for the cytidine deaminase AID and elongator-complex proteins in DNA demethylation.

[Abstract] [Full text] [PDF]

Is canalization more than just a beautiful idea?
Kaoru Sato, Haruhiko Siomi
Genome Biology 2010, 11(3):109   
(16 March 2010)

The heat-shock protein Hsp90 has been shown to be involved in the repression of de novo transposon-mediated mutagenesis.

[Abstract] [Full text] [PDF]

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)

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] [PubMed] [Related articles]

Characterizing regulatory path motifs in integrated networks using perturbational data
Anagha Joshi, Thomas Van Parys, Yves Van de Peer, Tom Michoel
Genome Biology 2010, 11: R32    
(15 March 2010)

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

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

The amazing world of bacterial structured RNAs
Eric Westhof
Genome Biology 2010, 11(3):108   
(15 March 2010)

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.

[Abstract] [Full text] [PDF]

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)

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

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

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)

The of the relationship between co-fitness and co-inhibition of genes in chemicogenomic yeast screens provides insights into drug target prediction

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

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)

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.

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

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)

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]

XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments
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
Genome Biology 2010, 11: R27    
(9 March 2010)

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

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

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)

Novel human pseudogenes are identified that had previous functionality and their age is estimated. The rate of loss-of-function occurred uniformly.

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

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)

A novel and empirical method for normalization of RNA-seq data is presented

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

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)

A high resolution strand-specific transcriptional atlas of the budding yeast mitotic cell cycle, including both mRNA and non-coding RNA profiles.

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

Histone tales: echoes from the past, prospects for the future
Chris Murgatroyd, Dietmar Spengler
Genome Biology 2010, 11(2):105   
(26 February 2010)

Recent studies of the nematode dauer state provide new insights into epigenetic processes that underlie cellular memory.

[Abstract] [Full text] [PDF] [PubMed] [Related articles]

Lost in translation
Gregory A Petsko
Genome Biology 2010, 11(2):107   
(26 February 2010)

Objections to dividing biomedical research into 'translational' and 'basic' are not just a matter of semantics.

[Abstract] [Full text] [PDF] [PubMed] [Related articles]

PRDM9 points the zinc finger at meiotic recombination hotspots
Matthew J Neale
Genome Biology 2010, 11(2):104   
(26 February 2010)

Recent work shows that the histone methyltransferase PRDM9 determines the nonrandom genomic distribution of meiotic recombination hotspots.

[Abstract] [Full text] [PDF] [PubMed] [Related articles]

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)

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

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

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)

ChIA-PET Tool can be used to process long-range chromatin interaction data. Results are visualized on a user-friendly genome browser.

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

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