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Items: 17

1.

Detection of functional DNA motifs via statistical over-representation.

Frith MC, Fu Y, Yu L, Chen JF, Hansen U, Weng Z.

Nucleic Acids Res. 2004 Feb 26;32(4):1372-81. Print 2004.

2.

Finding functional sequence elements by multiple local alignment.

Frith MC, Hansen U, Spouge JL, Weng Z.

Nucleic Acids Res. 2004 Jan 2;32(1):189-200. Print 2004.

3.
4.

JASPAR: an open-access database for eukaryotic transcription factor binding profiles.

Sandelin A, Alkema W, Engström P, Wasserman WW, Lenhard B.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D91-4.

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
6.

PromoSer: A large-scale mammalian promoter and transcription start site identification service.

Halees AS, Leyfer D, Weng Z.

Nucleic Acids Res. 2003 Jul 1;31(13):3554-9.

7.

Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells.

Elkon R, Linhart C, Sharan R, Shamir R, Shiloh Y.

Genome Res. 2003 May;13(5):773-80.

8.

An approach to identify over-represented cis-elements in related sequences.

Zheng J, Wu J, Sun Z.

Nucleic Acids Res. 2003 Apr 1;31(7):1995-2005. Erratum in: Nucleic Acids Res. 2004;32(8):2675.

9.

Computationally identifying novel NF-kappa B-regulated immune genes in the human genome.

Liu R, McEachin RC, States DJ.

Genome Res. 2003 Apr;13(4):654-61. Epub 2003 Mar 12.

10.

Toucan: deciphering the cis-regulatory logic of coregulated genes.

Aerts S, Thijs G, Coessens B, Staes M, Moreau Y, De Moor B.

Nucleic Acids Res. 2003 Mar 15;31(6):1753-64.

11.
12.

DNA binding sites: representation and discovery.

Stormo GD.

Bioinformatics. 2000 Jan;16(1):16-23. Review.

PMID:
10812473
13.
14.

TRANSFAC, TRRD and COMPEL: towards a federated database system on transcriptional regulation.

Wingender E, Kel AE, Kel OV, Karas H, Heinemeyer T, Dietze P, Knüppel R, Romaschenko AG, Kolchanov NA.

Nucleic Acids Res. 1997 Jan 1;25(1):265-8.

15.

Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment.

Lawrence CE, Altschul SF, Boguski MS, Liu JS, Neuwald AF, Wootton JC.

Science. 1993 Oct 8;262(5131):208-14.

PMID:
8211139
16.

Fitting a mixture model by expectation maximization to discover motifs in biopolymers.

Bailey TL, Elkan C.

Proc Int Conf Intell Syst Mol Biol. 1994;2:28-36.

PMID:
7584402
17.

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