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Results: 1 to 20 of 86

1.

The CRIT framework for identifying cross patterns in systems biology and application to chemogenomics.

Gianoulis TA, Agarwal A, Snyder M, Gerstein MB.

Genome Biol. 2011;12(3):R32. doi: 10.1186/gb-2011-12-3-r32. Epub 2011 Mar 31.

PMID:
21453526
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

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. doi: 10.1186/1471-2105-10-S4-S1.

PMID:
19426448
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Combining sequence and time series expression data to learn transcriptional modules.

Kundaje A, Middendorf M, Gao F, Wiggins C, Leslie C.

IEEE/ACM Trans Comput Biol Bioinform. 2005 Jul-Sep;2(3):194-202.

PMID:
17044183
[PubMed - indexed for MEDLINE]
4.

Biological data warehousing system for identifying transcriptional regulatory sites from gene expressions of microarray data.

Tsou AP, Sun YM, Liu CL, Huang HD, Horng JT, Tsai MF, Liu BJ.

IEEE Trans Inf Technol Biomed. 2006 Jul;10(3):550-8.

PMID:
16871724
[PubMed - indexed for MEDLINE]
5.

CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments.

Sharan R, Ovcharenko I, Ben-Hur A, Karp RM.

Bioinformatics. 2003;19 Suppl 1:i283-91.

PMID:
12855471
[PubMed - indexed for MEDLINE]
Free Article
6.

A chemogenomics view on protein-ligand spaces.

Strömbergsson H, Kleywegt GJ.

BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S13. doi: 10.1186/1471-2105-10-S6-S13.

PMID:
19534738
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Finding composite regulatory patterns in DNA sequences.

Eskin E, Pevzner PA.

Bioinformatics. 2002;18 Suppl 1:S354-63.

PMID:
12169566
[PubMed - indexed for MEDLINE]
Free Article
8.

Fast and practical algorithms for planted (l, d) motif search.

Davila J, Balla S, Rajasekaran S.

IEEE/ACM Trans Comput Biol Bioinform. 2007 Oct-Dec;4(4):544-52.

PMID:
17975266
[PubMed - indexed for MEDLINE]
9.

Identification of promoter regions and regulatory sites.

Solovyev VV, Shahmuradov IA, Salamov AA.

Methods Mol Biol. 2010;674:57-83. doi: 10.1007/978-1-60761-854-6_5.

PMID:
20827586
[PubMed - indexed for MEDLINE]
10.

High-resolution network biology: connecting sequence with function.

Ryan CJ, Cimermančič P, Szpiech ZA, Sali A, Hernandez RD, Krogan NJ.

Nat Rev Genet. 2013 Dec;14(12):865-79. doi: 10.1038/nrg3574. Epub 2013 Nov 7. Review.

PMID:
24197012
[PubMed - indexed for MEDLINE]
11.

Dissecting the transcription networks of a cell using computational genomics.

Li H, Wang W.

Curr Opin Genet Dev. 2003 Dec;13(6):611-6. Review.

PMID:
14638323
[PubMed - indexed for MEDLINE]
12.

A specialized learner for inferring structured cis-regulatory modules.

Noto K, Craven M.

BMC Bioinformatics. 2006 Dec 5;7:528.

PMID:
17147812
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Constraint-based knowledge discovery from SAGE data.

Klémal J, Blachon S, Soulet A, Crémilleux B, Gandrillon O.

In Silico Biol. 2008;8(2):157-75.

PMID:
18928203
[PubMed - indexed for MEDLINE]
14.

A systems biology approach to transcription factor binding site prediction.

Zhou X, Sumazin P, Rajbhandari P, Califano A.

PLoS One. 2010 Mar 26;5(3):e9878. doi: 10.1371/journal.pone.0009878.

PMID:
20360861
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

A mathematical and computational framework for quantitative comparison and integration of large-scale gene expression data.

Hart CE, Sharenbroich L, Bornstein BJ, Trout D, King B, Mjolsness E, Wold BJ.

Nucleic Acids Res. 2005 May 10;33(8):2580-94. Print 2005.

PMID:
15886390
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Knowledge-guided multi-scale independent component analysis for biomarker identification.

Chen L, Xuan J, Wang C, Shih IeM, Wang Y, Zhang Z, Hoffman E, Clarke R.

BMC Bioinformatics. 2008 Oct 6;9:416. doi: 10.1186/1471-2105-9-416.

PMID:
18837990
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Efficient composite pattern finding from monad patterns.

Zhou J, Sander J, Lin G.

Int J Bioinform Res Appl. 2007;3(1):86-99.

PMID:
18048174
[PubMed - indexed for MEDLINE]
18.

Connectivity in the yeast cell cycle transcription network: inferences from neural networks.

Hart CE, Mjolsness E, Wold BJ.

PLoS Comput Biol. 2006 Dec 22;2(12):e169. Epub 2006 Oct 30.

PMID:
17194216
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Discovering transcription factor regulatory targets using gene expression and binding data.

Maienschein-Cline M, Zhou J, White KP, Sciammas R, Dinner AR.

Bioinformatics. 2012 Jan 15;28(2):206-13. doi: 10.1093/bioinformatics/btr628. Epub 2011 Nov 13.

PMID:
22084256
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Discovery of sequence motifs related to coexpression of genes using evolutionary computation.

Fogel GB, Weekes DG, Varga G, Dow ER, Harlow HB, Onyia JE, Su C.

Nucleic Acids Res. 2004 Jul 20;32(13):3826-35. Print 2004.

PMID:
15266008
[PubMed - indexed for MEDLINE]
Free PMC Article

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