149 related articles for article (PubMed ID: 18333759)
1. Computation-based discovery of cis-regulatory modules by hidden Markov model.
Wu J; Xie J
J Comput Biol; 2008 Apr; 15(3):279-90. PubMed ID: 18333759
[TBL] [Abstract][Full Text] [Related]
2. Hidden Markov model and its applications in motif findings.
Wu J; Xie J
Methods Mol Biol; 2010; 620():405-16. PubMed ID: 20652513
[TBL] [Abstract][Full Text] [Related]
3. MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes.
Marinescu VD; Kohane IS; Riva A
BMC Bioinformatics; 2005 Mar; 6():79. PubMed ID: 15799782
[TBL] [Abstract][Full Text] [Related]
4. De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets.
Niu M; Tabari ES; Su Z
BMC Genomics; 2014 Dec; 15():1047. PubMed ID: 25442502
[TBL] [Abstract][Full Text] [Related]
5. A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences.
Li W; Meyer CA; Liu XS
Bioinformatics; 2005 Jun; 21 Suppl 1():i274-82. PubMed ID: 15961467
[TBL] [Abstract][Full Text] [Related]
6. The MAPPER database: a multi-genome catalog of putative transcription factor binding sites.
Marinescu VD; Kohane IS; Riva A
Nucleic Acids Res; 2005 Jan; 33(Database issue):D91-7. PubMed ID: 15608292
[TBL] [Abstract][Full Text] [Related]
7. Genome-wide prediction of transcriptional regulatory elements of human promoters using gene expression and promoter analysis data.
Kim SY; Kim Y
BMC Bioinformatics; 2006 Jul; 7():330. PubMed ID: 16817975
[TBL] [Abstract][Full Text] [Related]
8. CisView: a browser and database of cis-regulatory modules predicted in the mouse genome.
Sharov AA; Dudekula DB; Ko MS
DNA Res; 2006 Jun; 13(3):123-34. PubMed ID: 16980320
[TBL] [Abstract][Full Text] [Related]
9. A discriminative model for identifying spatial cis-regulatory modules.
Segal E; Sharan R
J Comput Biol; 2005; 12(6):822-34. PubMed ID: 16108719
[TBL] [Abstract][Full Text] [Related]
10. 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; 99(2):757-62. PubMed ID: 11805330
[TBL] [Abstract][Full Text] [Related]
11. Modeling promoter grammars with evolving hidden Markov models.
Won KJ; Sandelin A; Marstrand TT; Krogh A
Bioinformatics; 2008 Aug; 24(15):1669-75. PubMed ID: 18535083
[TBL] [Abstract][Full Text] [Related]
12. Genome-wide identification of cis-regulatory motifs and modules underlying gene coregulation using statistics and phylogeny.
Rouault H; Mazouni K; Couturier L; Hakim V; Schweisguth F
Proc Natl Acad Sci U S A; 2010 Aug; 107(33):14615-20. PubMed ID: 20671200
[TBL] [Abstract][Full Text] [Related]
13. MORPH: probabilistic alignment combined with hidden Markov models of cis-regulatory modules.
Sinha S; He X
PLoS Comput Biol; 2007 Nov; 3(11):e216. PubMed ID: 17997594
[TBL] [Abstract][Full Text] [Related]
14. A concept for ab initio prediction of cis-regulatory modules.
Ecker K; Welch L
In Silico Biol; 2009; 9(5-6):285-306. PubMed ID: 22430433
[TBL] [Abstract][Full Text] [Related]
15. Computational methods for the detection of cis-regulatory modules.
Van Loo P; Marynen P
Brief Bioinform; 2009 Sep; 10(5):509-24. PubMed ID: 19498042
[TBL] [Abstract][Full Text] [Related]
16. 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; 32(13):3826-35. PubMed ID: 15266008
[TBL] [Abstract][Full Text] [Related]
17. Statistical extraction of Drosophila cis-regulatory modules using exhaustive assessment of local word frequency.
Nazina AG; Papatsenko DA
BMC Bioinformatics; 2003 Dec; 4():65. PubMed ID: 14690551
[TBL] [Abstract][Full Text] [Related]
18. Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers.
Gotea V; Visel A; Westlund JM; Nobrega MA; Pennacchio LA; Ovcharenko I
Genome Res; 2010 May; 20(5):565-77. PubMed ID: 20363979
[TBL] [Abstract][Full Text] [Related]
19. Expression-guided in silico evaluation of candidate cis regulatory codes for Drosophila muscle founder cells.
Philippakis AA; Busser BW; Gisselbrecht SS; He FS; Estrada B; Michelson AM; Bulyk ML
PLoS Comput Biol; 2006 May; 2(5):e53. PubMed ID: 16733548
[TBL] [Abstract][Full Text] [Related]
20. Identifying Cis-Regulatory Elements and Modules Using Conditional Random Fields.
Gan Y; Guan J; Zhou S; Zhang W
IEEE/ACM Trans Comput Biol Bioinform; 2014; 11(1):73-82. PubMed ID: 26355509
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]