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Items: 1 to 20 of 23


LMethyR-SVM: Predict Human Enhancers Using Low Methylated Regions based on Weighted Support Vector Machines.

Xu J, Hu H, Dai Y.

PLoS One. 2016 Sep 23;11(9):e0163491. doi: 10.1371/journal.pone.0163491. Erratum in: PLoS One. 2016 Oct 20;11(10 ):e0165551.


Cis-regulatory architecture of a brain signaling center predates the origin of chordates.

Yao Y, Minor PJ, Zhao YT, Jeong Y, Pani AM, King AN, Symmons O, Gan L, Cardoso WV, Spitz F, Lowe CJ, Epstein DJ.

Nat Genet. 2016 May;48(5):575-80. doi: 10.1038/ng.3542.


Two Forkhead transcription factors regulate cardiac progenitor specification by controlling the expression of receptors of the fibroblast growth factor and Wnt signaling pathways.

Ahmad SM, Bhattacharyya P, Jeffries N, Gisselbrecht SS, Michelson AM.

Development. 2016 Jan 15;143(2):306-17. doi: 10.1242/dev.122952.


An Orthologous Epigenetic Gene Expression Signature Derived from Differentiating Embryonic Stem Cells Identifies Regulators of Cardiogenesis.

Busser BW, Lin Y, Yang Y, Zhu J, Chen G, Michelson AM.

PLoS One. 2015 Oct 20;10(10):e0141066. doi: 10.1371/journal.pone.0141066.


Quantitative multivariate analysis of dynamic multicellular morphogenic trajectories.

White DE, Sylvester JB, Levario TJ, Lu H, Streelman JT, McDevitt TC, Kemp ML.

Integr Biol (Camb). 2015 Jul;7(7):825-33. doi: 10.1039/c5ib00072f.


High resolution mapping of enhancer-promoter interactions.

Reeder C, Closser M, Poh HM, Sandhu K, Wichterle H, Gifford D.

PLoS One. 2015 May 13;10(5):e0122420. doi: 10.1371/journal.pone.0122420.


The myogenic repressor gene Holes in muscles is a direct transcriptional target of Twist and Tinman in the Drosophila embryonic mesoderm.

Elwell JA, Lovato TL, Adams MM, Baca EM, Lee T, Cripps RM.

Dev Biol. 2015 Apr 15;400(2):266-76. doi: 10.1016/j.ydbio.2015.02.005.


High-resolution genome-wide DNA methylation maps of mouse primary female dermal fibroblasts and keratinocytes.

Chatterjee R, He X, Huang D, FitzGerald P, Smith A, Vinson C.

Epigenetics Chromatin. 2014 Dec 2;7:35. doi: 10.1186/1756-8935-7-35.


Muscle cell fate choice requires the T-box transcription factor midline in Drosophila.

Kumar RP, Dobi KC, Baylies MK, Abmayr SM.

Genetics. 2015 Mar;199(3):777-91. doi: 10.1534/genetics.115.174300.


Enhancer modeling uncovers transcriptional signatures of individual cardiac cell states in Drosophila.

Busser BW, Haimovich J, Huang D, Ovcharenko I, Michelson AM.

Nucleic Acids Res. 2015 Feb 18;43(3):1726-39. doi: 10.1093/nar/gkv011.


Integrating diverse datasets improves developmental enhancer prediction.

Erwin GD, Oksenberg N, Truty RM, Kostka D, Murphy KK, Ahituv N, Pollard KS, Capra JA.

PLoS Comput Biol. 2014 Jun 26;10(6):e1003677. doi: 10.1371/journal.pcbi.1003677.


Imogene: identification of motifs and cis-regulatory modules underlying gene co-regulation.

Rouault H, Santolini M, Schweisguth F, Hakim V.

Nucleic Acids Res. 2014 Jun;42(10):6128-45. doi: 10.1093/nar/gku209.


Genome-wide analysis of functional and evolutionary features of tele-enhancers.

Huang D, Ovcharenko I.

G3 (Bethesda). 2014 Apr 16;4(4):579-93. doi: 10.1534/g3.114.010447.


Machine learning classification of cell-specific cardiac enhancers uncovers developmental subnetworks regulating progenitor cell division and cell fate specification.

Ahmad SM, Busser BW, Huang D, Cozart EJ, Michaud S, Zhu X, Jeffries N, Aboukhalil A, Bulyk ML, Ovcharenko I, Michelson AM.

Development. 2014 Feb;141(4):878-88. doi: 10.1242/dev.101709.


Contribution of distinct homeodomain DNA binding specificities to Drosophila embryonic mesodermal cell-specific gene expression programs.

Busser BW, Gisselbrecht SS, Shokri L, Tansey TR, Gamble CE, Bulyk ML, Michelson AM.

PLoS One. 2013 Jul 26;8(7):e69385. doi: 10.1371/journal.pone.0069385.


Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos.

Gisselbrecht SS, Barrera LA, Porsch M, Aboukhalil A, Estep PW 3rd, Vedenko A, Palagi A, Kim Y, Zhu X, Busser BW, Gamble CE, Iagovitina A, Singhania A, Michelson AM, Bulyk ML.

Nat Methods. 2013 Aug;10(8):774-80. doi: 10.1038/nmeth.2558.


RFECS: a random-forest based algorithm for enhancer identification from chromatin state.

Rajagopal N, Xie W, Li Y, Wagner U, Wang W, Stamatoyannopoulos J, Ernst J, Kellis M, Ren B.

PLoS Comput Biol. 2013;9(3):e1002968. doi: 10.1371/journal.pcbi.1002968.


Genome-wide screens for in vivo Tinman binding sites identify cardiac enhancers with diverse functional architectures.

Jin H, Stojnic R, Adryan B, Ozdemir A, Stathopoulos A, Frasch M.

PLoS Genet. 2013;9(1):e1003195. doi: 10.1371/journal.pgen.1003195.

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