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A survey of motif discovery methods in an integrated framework
Geir Kjetil Sandve, Finn Drabløs
Biol Direct. 2006; 1: 11. Published online 2006 April 6. doi: 10.1186/1745-6150-1-11
PMCID:
PMC1479319
Abstract Full Text PDF–431K

Is Cited by the Following 23 Articles in this Archive:

A novel candidate cis-regulatory motif pair in the promoters of germline and oogenesis genes in C. elegans
Chaim Linhart, Yonit Halperin, Amir Darom, Shahar Kidron, Limor Broday, Ron Shamir
Genome Res. 2012 January; 22(1): 76–83. doi: 10.1101/gr.115626.110
PMCID:
PMC3246208
Free in PMC on 2012/07/01
Large-scale motif discovery using DNA Gray code and equiprobable oligomers
Natsuhiro Ichinose, Tetsushi Yada, Osamu Gotoh
Bioinformatics. 2012 January 1; 28(1): 25–31. Published online 2011 November 3. doi: 10.1093/bioinformatics/btr606
PMCID:
PMC3244767
Abstract Full Text PDF–527K Supplementary Material
Tree-Based Position Weight Matrix Approach to Model Transcription Factor Binding Site Profiles
Yingtao Bi, Hyunsoo Kim, Ravi Gupta, Ramana V. Davuluri
PLoS One. 2011; 6(9): e24210. Published online 2011 September 2. doi: 10.1371/journal.pone.0024210
PMCID:
PMC3166302
Abstract Full Text PDF–1.6M Supplementary Material
MotifClick: prediction of cis-regulatory binding sites via merging cliques
Shaoqiang Zhang, Shan Li, Meng Niu, Phuc T Pham, Zhengchang Su
BMC Bioinformatics. 2011; 12: 238. Published online 2011 June 16. doi: 10.1186/1471-2105-12-238
PMCID:
PMC3225181
Abstract Full Text PDF–466K Supplementary Material
FITBAR: a web tool for the robust prediction of prokaryotic regulons
Jacques Oberto
BMC Bioinformatics. 2010; 11: 554. Published online 2010 November 11. doi: 10.1186/1471-2105-11-554
PMCID:
PMC3098098
Abstract Full Text PDF–899K
Identification of Context-Dependent Motifs by Contrasting ChIP Binding Data
Mike J. Mason, Kathrin Plath, Qing Zhou
Bioinformatics. 2010 November 15; 26(22): 2826–2832. Published online 2010 September 23. doi: 10.1093/bioinformatics/btq546
PMCID:
PMC2971577
Abstract Full Text PDF–532K Supplementary Material
PriorsEditor: a tool for the creation and use of positional priors in motif discovery
Kjetil Klepper, Finn Drabløs
Bioinformatics. 2010 September 1; 26(17): 2195–2197. Published online 2010 July 13. doi: 10.1093/bioinformatics/btq357
PMCID:
PMC2922893
Abstract Full Text PDF–429K
Mechanisms and Evolution of Control Logic in Prokaryotic Transcriptional Regulation
Sacha A. F. T. van Hijum, Marnix H. Medema, Oscar P. Kuipers
Microbiol Mol Biol Rev. 2009 September; 73(3): 481–509. doi: 10.1128/MMBR.00037-08
PMCID:
PMC2738135
Abstract Full Text PDF–4.4M
Regulatory element identification in subsets of transcripts: Comparison and integration of current computational methods
Danhua Fan, Peter B. Bitterman, Ola Larsson
RNA. 2009 August; 15(8): 1469–1482. doi: 10.1261/rna.1617009
PMCID:
PMC2714745
Abstract Full Text PDF–738K
seeMotif: exploring and visualizing sequence motifs in 3D structures
Darby Tien-Hao Chang, Ting-Ying Chien, Chien-Yu Chen
Nucleic Acids Res. 2009 July 1; 37(Web Server issue): W552–W558. Published online 2009 July 1. doi: 10.1093/nar/gkp439
PMCID:
PMC2703912
Abstract Full Text PDF–3.9M
Efficient exact motif discovery
Tobias Marschall, Sven Rahmann
Bioinformatics. 2009 June 15; 25(12): i356–i364. Published online 2009 May 27. doi: 10.1093/bioinformatics/btp188
PMCID:
PMC2687942
Abstract Full Text PDF–232K
Model selection and sensitivity analysis for sequence pattern models
Mayetri Gupta
Inst Math Stat Collect. Author manuscript; available in PMC 2010 June 17.
Published in final edited form as: Inst Math Stat Collect. 2009 January 1; 1: 390–407.
PMCID:
PMC2887058
Abstract Full Text PDF–2.2M
Compo: composite motif discovery using discrete models
Geir Kjetil Sandve, Osman Abul, Finn Drabløs
BMC Bioinformatics. 2008; 9: 527. Published online 2008 December 8. doi: 10.1186/1471-2105-9-527
PMCID:
PMC2614996
Abstract Full Text PDF–359K Supplementary Material
Limited functional conservation of a global regulator among related bacterial genera: Lrp in Escherichia, Proteus and Vibrio
Robert E Lintner, Pankaj K Mishra, Poonam Srivastava, Betsy M Martinez-Vaz, Arkady B Khodursky, Robert M Blumenthal
BMC Microbiol. 2008; 8: 60. Published online 2008 April 11. doi: 10.1186/1471-2180-8-60
PMCID:
PMC2374795
Abstract Full Text PDF–2.7M Supplementary Material
FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures
Gabriele Ausiello, Pier Federico Gherardini, Paolo Marcatili, Anna Tramontano, Allegra Via, Manuela Helmer-Citterich
BMC Bioinformatics. 2008; 9(Suppl 2): S2. Published online 2008 March 26. doi: 10.1186/1471-2105-9-S2-S2
PMCID:
PMC2323665
Abstract Full Text PDF–555K
Assessment of composite motif discovery methods
Kjetil Klepper, Geir K Sandve, Osman Abul, Jostein Johansen, Finn Drablos
BMC Bioinformatics. 2008; 9: 123. Published online 2008 February 26. doi: 10.1186/1471-2105-9-123
PMCID:
PMC2311304
Abstract Full Text PDF–310K Supplementary Material
Evaluating deterministic motif significance measures in protein databases
Pedro Gabriel Ferreira, Paulo J Azevedo
Algorithms Mol Biol. 2007; 2: 16. Published online 2007 December 24. doi: 10.1186/1748-7188-2-16
PMCID:
PMC2254621
Abstract Full Text PDF–899K Supplementary Material
Bioinformatic identification of novel putative photoreceptor specific cis-elements
Charles G Danko, Vera A McIlvain, Maochun Qin, Barry E Knox, Arkady M Pertsov
BMC Bioinformatics. 2007; 8: 407. Published online 2007 October 22. doi: 10.1186/1471-2105-8-407
PMCID:
PMC2225425
Abstract Full Text PDF–2.8M Supplementary Material
Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules
Valentina Boeva, Julien Clément, Mireille Régnier, Mikhail A Roytberg, Vsevolod J Makeev
Algorithms Mol Biol. 2007; 2: 13. Published online 2007 October 10. doi: 10.1186/1748-7188-2-13
PMCID:
PMC2174486
Abstract Full Text PDF–540K Supplementary Material
SCOPE: a web server for practical de novo motif discovery
Jonathan M. Carlson, Arijit Chakravarty, Charles E. DeZiel, Robert H. Gross
Nucleic Acids Res. 2007 July; 35(Web Server issue): W259–W264. Published online 2007 July. doi: 10.1093/nar/gkm310
PMCID:
PMC1933170
Abstract Full Text PDF–10M
The Gibbs Centroid Sampler
William A. Thompson, Lee A. Newberg, Sean Conlan, Lee Ann McCue, Charles E. Lawrence
Nucleic Acids Res. 2007 July; 35(Web Server issue): W232–W237. Published online 2007 July. doi: 10.1093/nar/gkm265
PMCID:
PMC1933196
Abstract Full Text PDF–209K
Improved benchmarks for computational motif discovery
Geir Kjetil Sandve, Osman Abul, Vegard Walseng, Finn Drabløs
BMC Bioinformatics. 2007; 8: 193. Published online 2007 June 8. doi: 10.1186/1471-2105-8-193
PMCID:
PMC1903367
Abstract Full Text PDF–909K Supplementary Material
Recent Computational Approaches to Understand Gene Regulation: Mining Gene Regulation In Silico
I Abnizova, T Subhankulova, WR Gilks
Curr Genomics. 2007 April; 8(2): 79–91.
PMCID:
PMC2435357
Abstract Full Text PDF–231K
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