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Items: 1 to 20 of 101

1.

Identification of cis-regulatory elements in gene co-expression networks using A-GLAM.

Mariño-Ramírez L, Tharakaraman K, Bodenreider O, Spouge J, Landsman D.

Methods Mol Biol. 2009;541:1-22. doi: 10.1007/978-1-59745-243-4_1. Review.

2.

Promoter analysis: gene regulatory motif identification with A-GLAM.

Mariño-Ramírez L, Tharakaraman K, Spouge JL, Landsman D.

Methods Mol Biol. 2009;537:263-76. doi: 10.1007/978-1-59745-251-9_13.

3.

Alignments anchored on genomic landmarks can aid in the identification of regulatory elements.

Tharakaraman K, Mariño-Ramírez L, Sheetlin S, Landsman D, Spouge JL.

Bioinformatics. 2005 Jun;21 Suppl 1:i440-8.

4.

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
5.

Expression-based network biology identifies immune-related functional modules involved in plant defense.

Tully JP, Hill AE, Ahmed HM, Whitley R, Skjellum A, Mukhtar MS.

BMC Genomics. 2014 Jun 3;15:421. doi: 10.1186/1471-2164-15-421.

6.

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
7.

A genome-wide cis-regulatory element discovery method based on promoter sequences and gene co-expression networks.

Gao Z, Zhao R, Ruan J.

BMC Genomics. 2013;14 Suppl 1:S4. doi: 10.1186/1471-2164-14-S1-S4. Epub 2013 Jan 21.

8.

A universal framework for regulatory element discovery across all genomes and data types.

Elemento O, Slonim N, Tavazoie S.

Mol Cell. 2007 Oct 26;28(2):337-50.

9.

Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis.

Cliften PF, Hillier LW, Fulton L, Graves T, Miner T, Gish WR, Waterston RH, Johnston M.

Genome Res. 2001 Jul;11(7):1175-86.

10.

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.

12.
13.

Characterization of complex regulatory networks and identification of promoter regulatory elements in yeast: "in silico" and "wet-lab" approaches.

Mira NP, Teixeira MC, Sá-Correia I.

Methods Mol Biol. 2012;809:27-48. doi: 10.1007/978-1-61779-376-9_2.

PMID:
22113266
14.
15.

Scanning sequences after Gibbs sampling to find multiple occurrences of functional elements.

Tharakaraman K, Mariño-Ramírez L, Sheetlin SL, Landsman D, Spouge JL.

BMC Bioinformatics. 2006 Sep 8;7:408.

16.

Using network component analysis to dissect regulatory networks mediated by transcription factors in yeast.

Ye C, Galbraith SJ, Liao JC, Eskin E.

PLoS Comput Biol. 2009 Mar;5(3):e1000311. doi: 10.1371/journal.pcbi.1000311. Epub 2009 Mar 20.

17.

GPMiner: an integrated system for mining combinatorial cis-regulatory elements in mammalian gene group.

Lee TY, Chang WC, Hsu JB, Chang TH, Shien DM.

BMC Genomics. 2012;13 Suppl 1:S3. doi: 10.1186/1471-2164-13-S1-S3. Epub 2012 Jan 17.

18.

Using local gene expression similarities to discover regulatory binding site modules.

Wilczyński B, Hvidsten TR, Kryshtafovych A, Tiuryn J, Komorowski J, Fidelis K.

BMC Bioinformatics. 2006 Nov 17;7:505.

19.

Predicting rules on organization of cis-regulatory elements, taking the order of elements into account.

Terai G, Takagi T.

Bioinformatics. 2004 May 1;20(7):1119-28. Epub 2004 Feb 5.

PMID:
14764548
20.

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