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A census of human transcription factors: function, expression and evolution.
Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM. Vaquerizas JM, et al. Nat Rev Genet. 2009 Apr;10(4):252-63. doi: 10.1038/nrg2538. Nat Rev Genet. 2009. PMID: 19274049 Review.
Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities.
Jolma A, Kivioja T, Toivonen J, Cheng L, Wei G, Enge M, Taipale M, Vaquerizas JM, Yan J, Sillanpää MJ, Bonke M, Palin K, Talukder S, Hughes TR, Luscombe NM, Ukkonen E, Taipale J. Jolma A, et al. Genome Res. 2010 Jun;20(6):861-73. doi: 10.1101/gr.100552.109. Epub 2010 Apr 8. Genome Res. 2010. PMID: 20378718 Free PMC article.
Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets.
Reimand J, Vaquerizas JM, Todd AE, Vilo J, Luscombe NM. Reimand J, et al. Nucleic Acids Res. 2010 Aug;38(14):4768-77. doi: 10.1093/nar/gkq232. Epub 2010 Apr 12. Nucleic Acids Res. 2010. PMID: 20385592 Free PMC article.
Structure and evolution of transcriptional regulatory networks.
Babu MM, Luscombe NM, Aravind L, Gerstein M, Teichmann SA. Babu MM, et al. Curr Opin Struct Biol. 2004 Jun;14(3):283-91. doi: 10.1016/j.sbi.2004.05.004. Curr Opin Struct Biol. 2004. PMID: 15193307 Review.
Genomic analysis of regulatory network dynamics reveals large topological changes.
Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, Gerstein M. Luscombe NM, et al. Nature. 2004 Sep 16;431(7006):308-12. doi: 10.1038/nature02782. Nature. 2004. PMID: 15372033
Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C.
Mifsud B, Tavares-Cadete F, Young AN, Sugar R, Schoenfelder S, Ferreira L, Wingett SW, Andrews S, Grey W, Ewels PA, Herman B, Happe S, Higgs A, LeProust E, Follows GA, Fraser P, Luscombe NM, Osborne CS. Mifsud B, et al. Nat Genet. 2015 Jun;47(6):598-606. doi: 10.1038/ng.3286. Epub 2015 May 4. Nat Genet. 2015. PMID: 25938943
hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1.
Sugimoto Y, Vigilante A, Darbo E, Zirra A, Militti C, D'Ambrogio A, Luscombe NM, Ule J. Sugimoto Y, et al. Nature. 2015 Mar 26;519(7544):491-4. doi: 10.1038/nature14280. Epub 2015 Mar 18. Nature. 2015. PMID: 25799984 Free PMC article.
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