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Items: 1 to 20 of 31

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.

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.

4.

Cluster-Buster: Finding dense clusters of motifs in DNA sequences.

Frith MC, Li MC, Weng Z.

Nucleic Acids Res. 2003 Jul 1;31(13):3666-8.

5.

Regulatory sequence analysis tools.

van Helden J.

Nucleic Acids Res. 2003 Jul 1;31(13):3593-6.

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.

INCLUSive: A web portal and service registry for microarray and regulatory sequence analysis.

Coessens B, Thijs G, Aerts S, Marchal K, De Smet F, Engelen K, Glenisson P, Moreau Y, Mathys J, De Moor B.

Nucleic Acids Res. 2003 Jul 1;31(13):3468-70.

8.

Integrating biological databases.

Stein LD.

Nat Rev Genet. 2003 May;4(5):337-45. Review.

PMID:
12728276
9.

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.

10.

Genome-specific higher-order background models to improve motif detection.

Marchal K, Thijs G, De Keersmaecker S, Monsieurs P, De Moor B, Vanderleyden J.

Trends Microbiol. 2003 Feb;11(2):61-6.

PMID:
12598125
11.

SeqVISTA: a graphical tool for sequence feature visualization and comparison.

Hu Z, Frith M, Niu T, Weng Z.

BMC Bioinformatics. 2003 Jan 4;4:1. Epub 2003 Jan 4.

12.

Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo.

Rajewsky N, Vergassola M, Gaul U, Siggia ED.

BMC Bioinformatics. 2002 Oct 24;3:30. Epub 2002 Oct 24.

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15.

A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes.

Thijs G, Marchal K, Lescot M, Rombauts S, De Moor B, Rouzé P, Moreau Y.

J Comput Biol. 2002;9(2):447-64.

PMID:
12015892
16.

Creating a bioinformatics nation.

Stein L.

Nature. 2002 May 9;417(6885):119-20. No abstract available.

PMID:
12000935
17.

Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome.

Berman BP, Nibu Y, Pfeiffer BD, Tomancak P, Celniker SE, Levine M, Rubin GM, Eisen MB.

Proc Natl Acad Sci U S A. 2002 Jan 22;99(2):757-62.

18.

Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo.

Markstein M, Markstein P, Markstein V, Levine MS.

Proc Natl Acad Sci U S A. 2002 Jan 22;99(2):763-8. Epub 2001 Dec 18.

19.

A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling.

Thijs G, Lescot M, Marchal K, Rombauts S, De Moor B, Rouzé P, Moreau Y.

Bioinformatics. 2001 Dec;17(12):1113-22.

PMID:
11751219
20.

Detection of cis-element clusters in higher eukaryotic DNA.

Frith MC, Hansen U, Weng Z.

Bioinformatics. 2001 Oct;17(10):878-89.

PMID:
11673232

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