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Results: 1 to 20 of 98

1.

Computational discovery of regulatory elements in a continuous expression space.

Lajoie M, Gascuel O, Lefort V, Bréhélin L.

Genome Biol. 2012 Nov 27;13(11):R109. doi: 10.1186/gb-2012-13-11-r109.

PMID:
23186104
[PubMed - in process]
Free PMC Article
2.

CompMoby: comparative MobyDick for detection of cis-regulatory motifs.

Chaivorapol C, Melton C, Wei G, Yeh RF, Ramalho-Santos M, Blelloch R, Li H.

BMC Bioinformatics. 2008 Oct 27;9:455. doi: 10.1186/1471-2105-9-455.

PMID:
18950538
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Promzea: a pipeline for discovery of co-regulatory motifs in maize and other plant species and its application to the anthocyanin and phlobaphene biosynthetic pathways and the Maize Development Atlas.

Liseron-Monfils C, Lewis T, Ashlock D, McNicholas PD, Fauteux F, Strömvik M, Raizada MN.

BMC Plant Biol. 2013 Mar 15;13:42. doi: 10.1186/1471-2229-13-42.

PMID:
23497159
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

A cluster refinement algorithm for motif discovery.

Li G, Chan TM, Leung KS, Lee KH.

IEEE/ACM Trans Comput Biol Bioinform. 2010 Oct-Dec;7(4):654-68. doi: 10.1109/TCBB.2009.25.

PMID:
21030733
[PubMed - indexed for MEDLINE]
5.

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.

PMID:
23368633
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

In silico discovery of transcription regulatory elements in Plasmodium falciparum.

Young JA, Johnson JR, Benner C, Yan SF, Chen K, Le Roch KG, Zhou Y, Winzeler EA.

BMC Genomics. 2008 Feb 7;9:70. doi: 10.1186/1471-2164-9-70.

PMID:
18257930
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Clustering and re-clustering for pattern discovery in gene expression data.

Ma PC, Chan KC, Chiu DK.

J Bioinform Comput Biol. 2005 Apr;3(2):281-301.

PMID:
15852506
[PubMed - indexed for MEDLINE]
8.

Motif-guided sparse decomposition of gene expression data for regulatory module identification.

Gong T, Xuan J, Chen L, Riggins RB, Li H, Hoffman EP, Clarke R, Wang Y.

BMC Bioinformatics. 2011 Mar 22;12:82. doi: 10.1186/1471-2105-12-82.

PMID:
21426557
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

NIFTI: an evolutionary approach for finding number of clusters in microarray data.

Jonnalagadda S, Srinivasan R.

BMC Bioinformatics. 2009 Jan 30;10:40. doi: 10.1186/1471-2105-10-40.

PMID:
19178750
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Using SCOPE to identify potential regulatory motifs in coregulated genes.

Martyanov V, Gross RH.

J Vis Exp. 2011 May 31;(51). pii: 2703. doi: 10.3791/2703.

PMID:
21673638
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

A mutation degree model for the identification of transcriptional regulatory elements.

Zhang C, Wang J, Hua X, Fang J, Zhu H, Gao X.

BMC Bioinformatics. 2011 Jun 27;12:262. doi: 10.1186/1471-2105-12-262.

PMID:
21708002
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Learning "graph-mer" motifs that predict gene expression trajectories in development.

Li X, Panea C, Wiggins CH, Reinke V, Leslie C.

PLoS Comput Biol. 2010 Apr 29;6(4):e1000761. doi: 10.1371/journal.pcbi.1000761.

PMID:
20454681
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks.

Reiss DJ, Baliga NS, Bonneau R.

BMC Bioinformatics. 2006 Jun 2;7:280.

PMID:
16749936
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data.

Huber BR, Bulyk ML.

BMC Bioinformatics. 2006 Apr 27;7:229.

PMID:
16643658
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

M are better than one: an ensemble-based motif finder and its application to regulatory element prediction.

Yanover C, Singh M, Zaslavsky E.

Bioinformatics. 2009 Apr 1;25(7):868-74. doi: 10.1093/bioinformatics/btp090. Epub 2009 Feb 17.

PMID:
19223448
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Paradigm of tunable clustering using Binarization of Consensus Partition Matrices (Bi-CoPaM) for gene discovery.

Abu-Jamous B, Fa R, Roberts DJ, Nandi AK.

PLoS One. 2013;8(2):e56432. doi: 10.1371/journal.pone.0056432. Epub 2013 Feb 11.

PMID:
23409186
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

A survey of DNA motif finding algorithms.

Das MK, Dai HK.

BMC Bioinformatics. 2007 Nov 1;8 Suppl 7:S21. Review.

PMID:
18047721
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

More robust detection of motifs in coexpressed genes by using phylogenetic information.

Monsieurs P, Thijs G, Fadda AA, De Keersmaecker SC, Vanderleyden J, De Moor B, Marchal K.

BMC Bioinformatics. 2006 Mar 20;7:160.

PMID:
16549017
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

A multistep bioinformatic approach detects putative regulatory elements in gene promoters.

Bortoluzzi S, Coppe A, Bisognin A, Pizzi C, Danieli GA.

BMC Bioinformatics. 2005 May 18;6:121.

PMID:
15904489
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Regulatory motif discovery using a population clustering evolutionary algorithm.

Lones MA, Tyrrell AM.

IEEE/ACM Trans Comput Biol Bioinform. 2007 Jul-Sep;4(3):403-14.

PMID:
17666760
[PubMed - indexed for MEDLINE]

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