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Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs
Andra Ivan, Marc S Halfon, Saurabh Sinha
Genome Biol. 2008; 9(1): R22. Published online 2008 January 28. doi: 10.1186/gb-2008-9-1-r22
PMCID:
PMC2395258
Abstract Full Text PDF–1.0M Supplementary Material
 Is Cited by the Following 11 Articles in this Archive:
Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison
Majid Kazemian, Qiyun Zhu, Marc S. Halfon, Saurabh Sinha
Nucleic Acids Res. 2011 December; 39(22): 9463–9472. Published online 2011 August 5. doi: 10.1093/nar/gkr621
PMCID:
PMC3239187
Abstract Full Text PDF–6.8M
Computational Identification of Transcriptional Regulators in Human Endotoxemia
Tung T. Nguyen, Panagiota T. Foteinou, Steven E. Calvano, Stephen F. Lowry, Ioannis P. Androulakis
PLoS One. 2011; 6(5): e18889. Published online 2011 May 27. doi: 10.1371/journal.pone.0018889
PMCID:
PMC3103499
Abstract Full Text PDF–1.1M Supplementary Material
Genome surveyor 2.0: cis-regulatory analysis in Drosophila
Majid Kazemian, Michael H. Brodsky, Saurabh Sinha
Nucleic Acids Res. 2011 July 1; 39(Web Server issue): W79–W85. Published online 2011 May 18. doi: 10.1093/nar/gkr291
PMCID:
PMC3125742
Abstract Full Text PDF–7.7M
Alignment-Free Sequence Comparison (II): Theoretical Power of Comparison Statistics
Lin Wan, Gesine Reinert, Fengzhu Sun, Michael S. Waterman
J Comput Biol. 2010 November; 17(11): 1467–1490. doi: 10.1089/cmb.2010.0056
PMCID:
PMC3123933
Abstract Full Text PDF–931K Supplementary Material
An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes
Manonmani Arunachalam, Karthik Jayasurya, Pavel Tomancak, Uwe Ohler
Bioinformatics. 2010 September 1; 26(17): 2109–2115. Published online 2010 July 11. doi: 10.1093/bioinformatics/btq358
PMCID:
PMC2922894
Abstract Full Text PDF–304K Supplementary Material
Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate Paramecium
Francesco Catania, Michael Lynch
BMC Evol Biol. 2010; 10: 129. Published online 2010 May 4. doi: 10.1186/1471-2148-10-129
PMCID:
PMC2874801
Abstract Full Text PDF–652K Supplementary Material
Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse
Miriam R. Kantorovitz, Majid Kazemian, Sarah Kinston, Diego Miranda-Saavedra, Qiyun Zhu, Gene E. Robinson, Berthold Göttgens, Marc S. Halfon, Saurabh Sinha
Dev Cell. Author manuscript; available in PMC 2010 October 1.
Published in final edited form as: Dev Cell. 2009 October; 17(4): 568–579. doi: 10.1016/j.devcel.2009.09.002
PMCID:
PMC2768654
Abstract Full Text PDF–1.6M Supplementary Material
A systems biology approach to the identification and analysis of transcriptional regulatory networks in osteocytes
Angela K Dean, Stephen E Harris, Ivo Kalajzic, Jianhua Ruan
BMC Bioinformatics. 2009; 10(Suppl 9): S5. Published online 2009 September 17. doi: 10.1186/1471-2105-10-S9-S5
PMCID:
PMC2745692
Abstract Full Text PDF–382K
Identifying Cis-Regulatory Sequences by Word Profile Similarity
Garmay Leung, Michael B. Eisen
PLoS One. 2009; 4(9): e6901. Published online 2009 September 4. doi: 10.1371/journal.pone.0006901
PMCID:
PMC2731932
Abstract Full Text PDF–546K Supplementary Material
Identifying regulatory elements in eukaryotic genomes
Leelavati Narlikar, Ivan Ovcharenko
Brief Funct Genomic Proteomic. 2009 July; 8(4): 215–230. Published online 2009 June 4. doi: 10.1093/bfgp/elp014
PMCID:
PMC2764519
Abstract Full Text PDF–177K
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
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