PubMed

Serial ChIP as a tool to investigate the co-localization or exclusion of proteins on plant genes.

Xie Z, Grotewold E.

Plant Methods. 2008 Oct 27;4:25.PMID: 18954450 [PubMed - in process]Related articlesFree article

Genome-wide profiling of histone H3 lysine 9 acetylation and dimethylation in Arabidopsis reveals correlation between multiple histone marks and gene expression.

Zhou J, Wang X, He K, Charron JB, Elling AA, Deng XW.

Plant Mol Biol. 2010 Jan 7. [Epub ahead of print]PMID: 20054610 [PubMed - as supplied by publisher]Related articles

A systems approach reveals regulatory circuitry for Arabidopsis trichome initiation by the GL3 and GL1 selectors.

Morohashi K, Grotewold E.

PLoS Genet. 2009 Feb;5(2):e1000396. Epub 2009 Feb 27.PMID: 19247443 [PubMed - indexed for MEDLINE]Related articlesFree article

Characterization of WRKY co-regulatory networks in rice and Arabidopsis.

Berri S, Abbruscato P, Faivre-Rampant O, Brasileiro AC, Fumasoni I, Satoh K, Kikuchi S, Mizzi L, Morandini P, Pè ME, Piffanelli P.

BMC Plant Biol. 2009 Sep 22;9:120.PMID: 19772648 [PubMed - indexed for MEDLINE]Related articlesFree article

The capacity for multistability in small gene regulatory networks.

Siegal-Gaskins D, Grotewold E, Smith GD.

BMC Syst Biol. 2009 Sep 21;3:96.PMID: 19772572 [PubMed - indexed for MEDLINE]Related articlesFree article

Identifying promoter features of co-regulated genes with similar network motifs.

Harari O, del Val C, Romero-Zaliz R, Shin D, Huang H, Groisman EA, Zwir I.

BMC Bioinformatics. 2009 Apr 29;10 Suppl 4:S1.PMID: 19426448 [PubMed - indexed for MEDLINE]Related articlesFree article

Seed storage protein gene promoters contain conserved DNA motifs in Brassicaceae, Fabaceae and Poaceae.

Fauteux F, Strömvik MV.

BMC Plant Biol. 2009 Oct 20;9:126.PMID: 19843335 [PubMed - indexed for MEDLINE]Related articlesFree article

An ensemble learning approach to reverse-engineering transcriptional regulatory networks from time-series gene expression data.

Ruan J, Deng Y, Perkins EJ, Zhang W.

BMC Genomics. 2009 Jul 7;10 Suppl 1:S8.PMID: 19594885 [PubMed - indexed for MEDLINE]Related articlesFree article

ContDist: a tool for the analysis of quantitative gene and promoter properties.

Hackenberg M, Lasso G, Matthiesen R.

BMC Bioinformatics. 2009 Jan 7;10:7.PMID: 19128472 [PubMed - indexed for MEDLINE]Related articlesFree article

FORCA, a promoter element that responds to crosstalk between defense and light signaling.

Evrard A, Ndatimana T, Eulgem T.

BMC Plant Biol. 2009 Jan 7;9:2.PMID: 19128484 [PubMed - indexed for MEDLINE]Related articlesFree article

Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells.

Mason MJ, Fan G, Plath K, Zhou Q, Horvath S.

BMC Genomics. 2009 Jul 20;10:327.PMID: 19619308 [PubMed - indexed for MEDLINE]Related articlesFree article

A combinatorial approach to determine the context-dependent role in transcriptional and posttranscriptional regulation in Arabidopsis thaliana.

Lu L, Li J.

BMC Syst Biol. 2009 Apr 28;3:43.PMID: 19400940 [PubMed - indexed for MEDLINE]Related articlesFree article

PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups.

Chang WC, Lee TY, Huang HD, Huang HY, Pan RL.

BMC Genomics. 2008 Nov 26;9:561.PMID: 19036138 [PubMed - indexed for MEDLINE]Related articlesFree article

Studying alternative splicing regulatory networks through partial correlation analysis.

Chen L, Zheng S.

Genome Biol. 2009;10(1):R3. Epub 2009 Jan 9.PMID: 19133160 [PubMed - indexed for MEDLINE]Related articlesFree article

Transcriptional regulation of BRD7 expression by Sp1 and c-Myc.

Liu H, Zhou M, Luo X, Zhang L, Niu Z, Peng C, Ma J, Peng S, Zhou H, Xiang B, Li X, Li S, He J, Li X, Li G.

BMC Mol Biol. 2008 Dec 27;9:111.PMID: 19111069 [PubMed - indexed for MEDLINE]Related articlesFree article

A new set of ESTs and cDNA clones from full-length and normalized libraries for gene discovery and functional characterization in citrus.

Marques MC, Alonso-Cantabrana H, Forment J, Arribas R, Alamar S, Conejero V, Perez-Amador MA.

BMC Genomics. 2009 Sep 11;10:428.PMID: 19747386 [PubMed - indexed for MEDLINE]Related articlesFree article

Identifying transcriptional regulatory regions using reporter genes and DNA-protein interactions by chromatin immunoprecipitation.

Ooi L, Wood IC.

Methods Mol Biol. 2008;491:3-17.PMID: 18998080 [PubMed - indexed for MEDLINE]Related articles

Using ChIP-chip and ChIP-seq to study the regulation of gene expression: genome-wide localization studies reveal widespread regulation of transcription elongation.

Gilchrist DA, Fargo DC, Adelman K.

Methods. 2009 Aug;48(4):398-408. Epub 2009 Mar 9. Review.PMID: 19275938 [PubMed - indexed for MEDLINE]Related articles

Jasmonic acid control of GLABRA3 links inducible defense and trichome patterning in Arabidopsis.

Yoshida Y, Sano R, Wada T, Takabayashi J, Okada K.

Development. 2009 Mar;136(6):1039-48.PMID: 19234066 [PubMed - indexed for MEDLINE]Related articlesFree article

ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes.

Margolin AA, Palomero T, Sumazin P, Califano A, Ferrando AA, Stolovitzky G.

Proc Natl Acad Sci U S A. 2009 Jan 6;106(1):244-9. Epub 2008 Dec 31.PMID: 19118200 [PubMed - indexed for MEDLINE]Related articlesFree article