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Two forkhead transcription factors regulate the division of cardiac progenitor cells by a Polo-dependent pathway.

Ahmad SM, Tansey TR, Busser BW, Nolte MT, Jeffries N, Gisselbrecht SS, Rusan NM, Michelson AM.

Dev Cell. 2012 Jul 17;23(1):97-111. doi: 10.1016/j.devcel.2012.05.011.


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.


Differential regulation of mesodermal gene expression by Drosophila cell type-specific Forkhead transcription factors.

Zhu X, Ahmad SM, Aboukhalil A, Busser BW, Kim Y, Tansey TR, Haimovich A, Jeffries N, Bulyk ML, Michelson AM.

Development. 2012 Apr;139(8):1457-66. doi: 10.1242/dev.069005. Epub 2012 Feb 29.


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.


Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development.

Bonn S, Zinzen RP, Girardot C, Gustafson EH, Perez-Gonzalez A, Delhomme N, Ghavi-Helm Y, Wilczyński B, Riddell A, Furlong EE.

Nat Genet. 2012 Jan 8;44(2):148-56. doi: 10.1038/ng.1064.


A cis-regulatory map of the Drosophila genome.

Nègre N, Brown CD, Ma L, Bristow CA, Miller SW, Wagner U, Kheradpour P, Eaton ML, Loriaux P, Sealfon R, Li Z, Ishii H, Spokony RF, Chen J, Hwang L, Cheng C, Auburn RP, Davis MB, Domanus M, Shah PK, Morrison CA, Zieba J, Suchy S, Senderowicz L, Victorsen A, Bild NA, Grundstad AJ, Hanley D, MacAlpine DM, Mannervik M, Venken K, Bellen H, White R, Gerstein M, Russell S, Grossman RL, Ren B, Posakony JW, Kellis M, White KP.

Nature. 2011 Mar 24;471(7339):527-31. doi: 10.1038/nature09990.


Charting histone modifications and the functional organization of mammalian genomes.

Zhou VW, Goren A, Bernstein BE.

Nat Rev Genet. 2011 Jan;12(1):7-18. doi: 10.1038/nrg2905. Epub 2010 Nov 30. Review.


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.


Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same.

Weirauch MT, Hughes TR.

Trends Genet. 2010 Feb;26(2):66-74. doi: 10.1016/j.tig.2009.12.002. Epub 2010 Jan 18. Review.


Genome-wide discovery of human heart enhancers.

Narlikar L, Sakabe NJ, Blanski AA, Arimura FE, Westlund JM, Nobrega MA, Ovcharenko I.

Genome Res. 2010 Mar;20(3):381-92. doi: 10.1101/gr.098657.109. Epub 2010 Jan 14.


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.


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.


Genomic location analysis by ChIP-Seq.

Barski A, Zhao K.

J Cell Biochem. 2009 May 1;107(1):11-8. doi: 10.1002/jcb.22077. 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.


Myoblast fusion in fly and vertebrates: new genes, new processes and new perspectives.

Richardson BE, Nowak SJ, Baylies MK.

Traffic. 2008 Jul;9(7):1050-9. doi: 10.1111/j.1600-0854.2008.00756.x. Epub 2008 Apr 24. Review.


Functional analysis of the zinc finger and activation domains of Glis3 and mutant Glis3(NDH1).

Beak JY, Kang HS, Kim YS, Jetten AM.

Nucleic Acids Res. 2008 Mar;36(5):1690-702. doi: 10.1093/nar/gkn009. Epub 2008 Feb 7.


High-resolution profiling of histone methylations in the human genome.

Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K.

Cell. 2007 May 18;129(4):823-37.

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