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Results: 1 to 20 of 109

1.

Enriching for direct regulatory targets in perturbed gene-expression profiles.

Tringe SG, Wagner A, Ruby SW.

Genome Biol. 2004;5(4):R29. Epub 2004 Mar 30.

PMID:
15059262
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data.

Gao F, Foat BC, Bussemaker HJ.

BMC Bioinformatics. 2004 Mar 18;5:31.

PMID:
15113405
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Computational discovery of gene modules and regulatory networks.

Bar-Joseph Z, Gerber GK, Lee TI, Rinaldi NJ, Yoo JY, Robert F, Gordon DB, Fraenkel E, Jaakkola TS, Young RA, Gifford DK.

Nat Biotechnol. 2003 Nov;21(11):1337-42. Epub 2003 Oct 12.

PMID:
14555958
[PubMed - indexed for MEDLINE]
Free Article
4.

Quantitative inference of dynamic regulatory pathways via microarray data.

Chang WC, Li CW, Chen BS.

BMC Bioinformatics. 2005 Mar 7;6:44.

PMID:
15748298
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach.

Zoppoli P, Morganella S, Ceccarelli M.

BMC Bioinformatics. 2010 Mar 25;11:154. doi: 10.1186/1471-2105-11-154.

PMID:
20338053
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

A fuzzy logic approach to analyzing gene expression data.

Woolf PJ, Wang Y.

Physiol Genomics. 2000 Jun 29;3(1):9-15.

PMID:
11015595
[PubMed - indexed for MEDLINE]
7.

A hybrid Bayesian network learning method for constructing gene networks.

Wang M, Chen Z, Cloutier S.

Comput Biol Chem. 2007 Oct;31(5-6):361-72. Epub 2007 Aug 19.

PMID:
17889617
[PubMed - indexed for MEDLINE]
8.

Modelling gene functional linkages using yeast microarray data.

Wang T, Xue G, Touchman JW.

Int J Bioinform Res Appl. 2007;3(2):170-86.

PMID:
18048187
[PubMed - indexed for MEDLINE]
9.

Combined analysis of expression data and transcription factor binding sites in the yeast genome.

Nagaraj VH, O'Flanagan RA, Bruning AR, Mathias JR, Vershon AK, Sengupta AM.

BMC Genomics. 2004 Aug 26;5(1):59.

PMID:
15331021
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Network inference algorithms elucidate Nrf2 regulation of mouse lung oxidative stress.

Taylor RC, Acquaah-Mensah G, Singhal M, Malhotra D, Biswal S.

PLoS Comput Biol. 2008 Aug 29;4(8):e1000166. doi: 10.1371/journal.pcbi.1000166.

PMID:
18769717
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Correlation and prediction of gene expression level from amino acid and dipeptide composition of its protein.

Raghava GP, Han JH.

BMC Bioinformatics. 2005 Mar 17;6:59.

PMID:
15773999
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Sample scale-free gene regulatory network using gene ontology.

Chen G, Larsen P, Almasri E, Dai Y.

Conf Proc IEEE Eng Med Biol Soc. 2006;1:5523-6.

PMID:
17946312
[PubMed - indexed for MEDLINE]
13.

Genome-wide expression profiling, in vivo DNA binding analysis, and probabilistic motif prediction reveal novel Abf1 target genes during fermentation, respiration, and sporulation in yeast.

Schlecht U, Erb I, Demougin P, Robine N, Borde V, van Nimwegen E, Nicolas A, Primig M.

Mol Biol Cell. 2008 May;19(5):2193-207. doi: 10.1091/mbc.E07-12-1242. Epub 2008 Feb 27.

PMID:
18305101
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Interpreting patterns of gene expression: signatures of coregulation, the data processing inequality, and triplet motifs.

Ku WL, Duggal G, Li Y, Girvan M, Ott E.

PLoS One. 2012;7(2):e31969. doi: 10.1371/journal.pone.0031969. Epub 2012 Feb 29.

PMID:
22393375
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Reconstructing genetic networks in yeast.

Zhang Z, Gerstein M.

Nat Biotechnol. 2003 Nov;21(11):1295-7. No abstract available.

PMID:
14595359
[PubMed - indexed for MEDLINE]
16.

Using directed information to build biologically relevant influence networks.

Rao A, Hero AO 3rd, States DJ, Engel JD.

Comput Syst Bioinformatics Conf. 2007;6:145-56.

PMID:
17951820
[PubMed - indexed for MEDLINE]
Free Article
17.

Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data.

Wu WS, Li WH, Chen BS.

BMC Bioinformatics. 2007 Jun 8;8:188.

PMID:
17559637
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Global and threshold-free Transcriptional Regulatory Networks reconstruction through integrating ChIP-Chip and expression data.

Liu Q, Yang Y, Li Y, Zhang Z.

Curr Protein Pept Sci. 2011 Nov;12(7):631-42.

PMID:
21827425
[PubMed - indexed for MEDLINE]
19.

Transcriptional networks: reverse-engineering gene regulation on a global scale.

Chua G, Robinson MD, Morris Q, Hughes TR.

Curr Opin Microbiol. 2004 Dec;7(6):638-46. Review.

PMID:
15556037
[PubMed - indexed for MEDLINE]
20.

Construction of gene networks with hybrid approach from expression profile and gene ontology.

Jing L, Ng MK, Liu Y.

IEEE Trans Inf Technol Biomed. 2010 Jan;14(1):107-18. doi: 10.1109/TITB.2009.2033056. Epub 2009 Sep 29.

PMID:
19789116
[PubMed - indexed for MEDLINE]

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