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Silencers, Enhancers, and the Multifunctional Regulatory Genome.
Halfon MS. Halfon MS. Trends Genet. 2020 Mar;36(3):149-151. doi: 10.1016/j.tig.2019.12.005. Epub 2020 Jan 7. Trends Genet. 2020. PMID: 31918861 Free PMC article.
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.
Identification of receptor-tyrosine-kinase-signaling target genes reveals receptor-specific activities and pathway branchpoints during Drosophila development.
Leatherbarrow JR, Halfon MS. Leatherbarrow JR, et al. Among authors: halfon ms. Genetics. 2009 Apr;181(4):1335-45. doi: 10.1534/genetics.108.098475. Epub 2009 Feb 2. Genetics. 2009. PMID: 19189950 Free PMC article.
Genome-wide search identifies Ccnd2 as a direct transcriptional target of Elf5 in mouse mammary gland.
Escamilla-Hernandez R, Chakrabarti R, Romano RA, Smalley K, Zhu Q, Lai W, Halfon MS, Buck MJ, Sinha S. Escamilla-Hernandez R, et al. Among authors: halfon ms. BMC Mol Biol. 2010 Sep 10;11:68. doi: 10.1186/1471-2199-11-68. BMC Mol Biol. 2010. PMID: 20831799 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.
Erroneous attribution of relevant transcription factor binding sites despite successful prediction of cis-regulatory modules.
Halfon MS, Zhu Q, Brennan ER, Zhou Y. Halfon MS, et al. BMC Genomics. 2011 Nov 25;12:578. doi: 10.1186/1471-2164-12-578. BMC Genomics. 2011. PMID: 22115527 Free PMC article.
Regulation of gene expression in the genomic context.
Atkinson TJ, Halfon MS. Atkinson TJ, et al. Among authors: halfon ms. Comput Struct Biotechnol J. 2014 Jan 29;9:e201401001. doi: 10.5936/csbj.201401001. eCollection 2014. Comput Struct Biotechnol J. 2014. PMID: 24688749 Free PMC article. Review.
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