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A machine learning approach for identifying novel cell type-specific transcriptional regulators of myogenesis.

Busser BW, Taher L, Kim Y, Tansey T, Bloom MJ, Ovcharenko I, Michelson AM.

PLoS Genet. 2012;8(3):e1002531. doi: 10.1371/journal.pgen.1002531. Epub 2012 Mar 8.


Molecular mechanism underlying the regulatory specificity of a Drosophila homeodomain protein that specifies myoblast identity.

Busser BW, Shokri L, Jaeger SA, Gisselbrecht SS, Singhania A, Berger MF, Zhou B, Bulyk ML, Michelson AM.

Development. 2012 Mar;139(6):1164-74. doi: 10.1242/dev.077362. Epub 2012 Feb 1.


The cis-regulatory logic of Hedgehog gradient responses: key roles for gli binding affinity, competition, and cooperativity.

Parker DS, White MA, Ramos AI, Cohen BA, Barolo S.

Sci Signal. 2011 Jun 7;4(176):ra38. doi: 10.1126/scisignal.2002077.


UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions.

Robasky K, Bulyk ML.

Nucleic Acids Res. 2011 Jan;39(Database issue):D124-8. doi: 10.1093/nar/gkq992. Epub 2010 Oct 30.


Diversification of muscle types: recent insights from Drosophila.

Tixier V, Bataillé L, Jagla K.

Exp Cell Res. 2010 Nov 1;316(18):3019-27. doi: 10.1016/j.yexcr.2010.07.013. Epub 2010 Jul 29. Review.


Combinatorial binding leads to diverse regulatory responses: Lmd is a tissue-specific modulator of Mef2 activity.

Cunha PM, Sandmann T, Gustafson EH, Ciglar L, Eichenlaub MP, Furlong EE.

PLoS Genet. 2010 Jul 1;6(7):e1001014. doi: 10.1371/journal.pgen.1001014.


Precise temporal control of the eye regulatory gene Pax6 via enhancer-binding site affinity.

Rowan S, Siggers T, Lachke SA, Yue Y, Bulyk ML, Maas RL.

Genes Dev. 2010 May 15;24(10):980-5. doi: 10.1101/gad.1890410. Epub 2010 Apr 22.


Combinatorial binding predicts spatio-temporal cis-regulatory activity.

Zinzen RP, Girardot C, Gagneur J, Braun M, Furlong EE.

Nature. 2009 Nov 5;462(7269):65-70. doi: 10.1038/nature08531.


Hox specificity unique roles for cofactors and collaborators.

Mann RS, Lelli KM, Joshi R.

Curr Top Dev Biol. 2009;88:63-101. doi: 10.1016/S0070-2153(09)88003-4. Review.


Diversity and complexity in DNA recognition by transcription factors.

Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, Jaeger SA, Chan ET, Metzler G, Vedenko A, Chen X, Kuznetsov H, Wang CF, Coburn D, Newburger DE, Morris Q, Hughes TR, Bulyk ML.

Science. 2009 Jun 26;324(5935):1720-3. doi: 10.1126/science.1162327. Epub 2009 May 14.


The winged-helix transcription factor JUMU is a haplo-suppressor/triplo-enhancer of PEV in various tissues but exhibits reverse PEV effects in the brain of Drosophila melanogaster.

Hofmann A, Br√ľnner M, Korge G.

Chromosome Res. 2009;17(3):347-58. doi: 10.1007/s10577-009-9026-1. Epub 2009 Mar 20.


cis-Regulatory networks during development: a view of Drosophila.

Bonn S, Furlong EE.

Curr Opin Genet Dev. 2008 Dec;18(6):513-20. doi: 10.1016/j.gde.2008.09.005. Epub 2008 Oct 16. Review.


Toward a systems-level understanding of developmental regulatory networks.

Busser BW, Bulyk ML, Michelson AM.

Curr Opin Genet Dev. 2008 Dec;18(6):521-9. doi: 10.1016/j.gde.2008.09.003. Epub 2008 Oct 9. Review.


E2F in vivo binding specificity: comparison of consensus versus nonconsensus binding sites.

Rabinovich A, Jin VX, Rabinovich R, Xu X, Farnham PJ.

Genome Res. 2008 Nov;18(11):1763-77. doi: 10.1101/gr.080622.108. Epub 2008 Oct 3.


Shaping segments: Hox gene function in the genomic age.

Hueber SD, Lohmann I.

Bioessays. 2008 Oct;30(10):965-79. doi: 10.1002/bies.20823. Review.


Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation.

Hare EE, Peterson BK, Iyer VN, Meier R, Eisen MB.

PLoS Genet. 2008 Jun 27;4(6):e1000106. doi: 10.1371/journal.pgen.1000106.


Systematic identification of mammalian regulatory motifs' target genes and functions.

Warner JB, Philippakis AA, Jaeger SA, He FS, Lin J, Bulyk ML.

Nat Methods. 2008 Apr;5(4):347-53. doi: 10.1038/nmeth.1188. Epub 2008 Mar 2.


Exploiting position effects and the gypsy retrovirus insulator to engineer precisely expressed transgenes.

Markstein M, Pitsouli C, Villalta C, Celniker SE, Perrimon N.

Nat Genet. 2008 Apr;40(4):476-83. doi: 10.1038/ng.101. Epub 2008 Mar 2.


Temporal ChIP-on-chip reveals Biniou as a universal regulator of the visceral muscle transcriptional network.

Jakobsen JS, Braun M, Astorga J, Gustafson EH, Sandmann T, Karzynski M, Carlsson P, Furlong EE.

Genes Dev. 2007 Oct 1;21(19):2448-60.


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