Log on / register
Feedback | Support | My details
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
[Full text] [PubMed] [Related articles] [Cited on BioMed Central]


printer friendly 
to  [Help]

BioMed Central articles that cite the above article:

1.


Research article    
OHMM: a Hidden Markov Model accurately predicting the occupancy of a transcription factor with a self-overlapping binding motif
Drawid A, Gupta N, Nagaraj VH, Gélinas C, Sengupta AM
BMC Bioinformatics 2009, 10:208 (7 July 2009)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles]
2.


Research article    
Finding evolutionarily conserved cis-regulatory modules with a universal set of motifs
Wilczynski B, Dojer N, Patelak M, Tiuryn J
BMC Bioinformatics 2009, 10:82 (10 March 2009)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles]
3.

Review   
Integrating sequence, evolution and functional genomics in regulatory genomics
Vingron M, Brazma A, Coulson R, van Helden J, Manke T, Palin K, Sand O, Ukkonen E
Genome Biology 2009, 10:202 (30 January 2009)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles]
4.


Methodology article    
Better estimation of protein-DNA interaction parameters improve prediction of functional sites
Nagaraj VH, O'Flanagan RA, Sengupta AM
BMC Biotechnology 2008, 8:94 (23 December 2008)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles]
5.


Method    
ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues?
Van Loo P, Aerts S, Thienpont B, De Moor B, Moreau Y, Marynen P
Genome Biology 2008, 9:R66 (7 April 2008)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
6.


Method    
Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs
Ivan A, Halfon MS, Sinha S
Genome Biology 2008, 9:R22 (28 January 2008)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
7.


Research article    
Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors
Yu X, Lin J, Zack DJ, Qian J
BMC Bioinformatics 2007, 8:437 (9 November 2007)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
8.


Review    
Finding regulatory elements and regulatory motifs: a general probabilistic framework
van Nimwegen E
BMC Bioinformatics 2007, 8(Suppl 6):S4 (27 September 2007)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
9.


Methodology article    
A novel ensemble learning method for de novo computational identification of DNA binding sites
Chakravarty A, Carlson JM, Khetani RS, Gross RH
BMC Bioinformatics 2007, 8:249 (12 July 2007)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
10.




Research    
Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses
Li L, Zhu Q, He X, Sinha S, Halfon MS
Genome Biology 2007, 8:R101 (5 June 2007)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [F1000 Biology] [Cited on BioMed Central]
11.


Research article    
Multiple non-collinear TF-map alignments of promoter regions
Blanco E, Guigó R, Messeguer X
BMC Bioinformatics 2007, 8:138 (24 April 2007)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
12.


Methodology article    
Statistical significance of cis-regulatory modules
Schones DE, Smith AD, Zhang MQ
BMC Bioinformatics 2007, 8:19 (22 January 2007)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
13.


Methodology article    
A specialized learner for inferring structured cis-regulatory modules
Noto K, Craven M
BMC Bioinformatics 2006, 7:528 (5 December 2006)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles]
14.


Methodology article    
Using hexamers to predict cis-regulatory motifs in Drosophila
Chan BY, Kibler D
BMC Bioinformatics 2005, 6:262 (27 October 2005)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
15.


Methodology article    
Some statistical properties of regulatory DNA sequences, and their use in predicting regulatory regions in the Drosophila genome: the fluffy-tail test
Abnizova I, te Boekhorst R, Walter K, Gilks WR
BMC Bioinformatics 2005, 6:109 (27 April 2005)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
16.


Software    
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, 6:79 (30 March 2005)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
17.




Research article    
Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila
Sinha S, Schroeder MD, Unnerstall U, Gaul U, Siggia ED
BMC Bioinformatics 2004, 5:129 (9 September 2004)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [F1000 Biology] [Cited on BioMed Central]
18.


Research    
Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura
Berman BP, Pfeiffer BD, Laverty TR, Salzberg SL, Rubin GM, Eisen MB, Celniker SE
Genome Biology 2004, 5:R61 (20 August 2004)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
19.


Research article    
Assessment of clusters of transcription factor binding sites in relationship to human promoter, CpG islands and gene expression
Murakami K, Kojima T, Sakaki Y
BMC Genomics 2004, 5:16 (23 February 2004)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles]
20.


Review    
Computational prediction of transcription-factor binding site locations
Bulyk ML
Genome Biology 2003, 5:201 (23 December 2003)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
21.


Research article    
Statistical extraction of Drosophila cis-regulatory modules using exhaustive assessment of local word frequency
Nazina AG, Papatsenko DA
BMC Bioinformatics 2003, 4:65 (22 December 2003)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
22.


Research article    
Genomic characterization of a repetitive motif strongly associated with developmental genes in Drosophila
Costas J, Vieira CP, Casares F, Vieira J
BMC Genomics 2003, 4:52 (16 December 2003)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles]
23.




Research article    
Conservation of regulatory elements between two species of Drosophila
Emberly E, Rajewsky N, Siggia ED
BMC Bioinformatics 2003, 4:57 (20 November 2003)
 [Abstract] [Full text] [PDF] [PubMed] [Related articles] [F1000 Biology] [Cited on BioMed Central]

This article is also cited by a further 33 articles in PubMed Central


You can also check ISI Web of Science for additional citations (subscription required)
  
printer friendly 
to  [Help]
Terms and Conditions Privacy statement Information for advertisers Jobs at BMC Contact us
© 1999-2009 BioMed Central Ltd unless otherwise stated. Part of Springer Science+Business Media.