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Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs.
Ivan A, Halfon MS, Sinha S. Ivan A, et al. Among authors: halfon ms. Genome Biol. 2008 Jan 28;9(1):R22. doi: 10.1186/gb-2008-9-1-r22. Genome Biol. 2008. PMID: 18226245 Free PMC article.
The Toll pathway is required in the epidermis for muscle development in the Drosophila embryo.
Halfon MS, Keshishian H. Halfon MS, et al. Dev Biol. 1998 Jul 1;199(1):164-74. doi: 10.1006/dbio.1998.8915. Dev Biol. 1998. PMID: 9676200
Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model.
Halfon MS, Grad Y, Church GM, Michelson AM. Halfon MS, et al. Genome Res. 2002 Jul;12(7):1019-28. doi: 10.1101/gr.228902. Genome Res. 2002. PMID: 12097338 Free PMC article.
Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura.
Grad YH, Roth FP, Halfon MS, Church GM. Grad YH, et al. Among authors: halfon ms. Bioinformatics. 2004 Nov 1;20(16):2738-50. doi: 10.1093/bioinformatics/bth320. Epub 2004 May 14. Bioinformatics. 2004. PMID: 15145800
REDfly: a Regulatory Element Database for Drosophila.
Gallo SM, Li L, Hu Z, Halfon MS. Gallo SM, et al. Among authors: halfon ms. Bioinformatics. 2006 Feb 1;22(3):381-3. doi: 10.1093/bioinformatics/bti794. Epub 2005 Nov 22. Bioinformatics. 2006. PMID: 16303794
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. Li L, et al. Among authors: halfon ms. Genome Biol. 2007;8(6):R101. doi: 10.1186/gb-2007-8-6-r101. Genome Biol. 2007. PMID: 17550599 Free PMC article.
REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila.
Halfon MS, Gallo SM, Bergman CM. Halfon MS, et al. Nucleic Acids Res. 2008 Jan;36(Database issue):D594-8. doi: 10.1093/nar/gkm876. Epub 2007 Nov 26. Nucleic Acids Res. 2008. PMID: 18039705 Free PMC article.
Complex organizational structure of the genome revealed by genome-wide analysis of single and alternative promoters in Drosophila melanogaster.
Zhu Q, Halfon MS. Zhu Q, et al. Among authors: halfon ms. BMC Genomics. 2009 Jan 7;10:9. doi: 10.1186/1471-2164-10-9. BMC Genomics. 2009. PMID: 19128496 Free PMC article.
Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse.
Kantorovitz MR, Kazemian M, Kinston S, Miranda-Saavedra D, Zhu Q, Robinson GE, Gƶttgens B, Halfon MS, Sinha S. Kantorovitz MR, et al. Among authors: halfon ms. Dev Cell. 2009 Oct;17(4):568-79. doi: 10.1016/j.devcel.2009.09.002. Dev Cell. 2009. PMID: 19853570 Free PMC article.
REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila.
Gallo SM, Gerrard DT, Miner D, Simich M, Des Soye B, Bergman CM, Halfon MS. Gallo SM, et al. Among authors: halfon ms. Nucleic Acids Res. 2011 Jan;39(Database issue):D118-23. doi: 10.1093/nar/gkq999. Epub 2010 Oct 21. Nucleic Acids Res. 2011. PMID: 20965965 Free PMC article.
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