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Items: 1 to 50 of 68

1.

Diversification of retinoblastoma protein function associated with cis and trans adaptations.

Mouawad R, Prasad J, Thorley D, Himadewi P, Kadiyala D, Wilson N, Kapranov P, Arnosti DN.

Mol Biol Evol. 2019 Aug 16. pii: msz187. doi: 10.1093/molbev/msz187. [Epub ahead of print]

PMID:
31418797
2.

Complex cis-regulatory landscape of the insulin receptor gene underlies the broad expression of a central signaling regulator.

Wei Y, Gokhale RH, Sonnenschein A, Montgomery KM, Ingersoll A, Arnosti DN.

Development. 2016 Oct 1;143(19):3591-3603.

3.

Melatonin decreases estrogen receptor binding to estrogen response elements sites on the OCT4 gene in human breast cancer stem cells.

Lopes J, Arnosti D, Trosko JE, Tai MH, Zuccari D.

Genes Cancer. 2016 May;7(5-6):209-17. doi: 10.18632/genesandcancer.107.

4.

Quantitative perturbation-based analysis of gene expression predicts enhancer activity in early Drosophila embryo.

Sayal R, Dresch JM, Pushel I, Taylor BR, Arnosti DN.

Elife. 2016 May 6;5. pii: e08445. doi: 10.7554/eLife.08445.

5.

The Wisdom of Crowds: Can Mathematical Models Crack the cis Regulatory Code?

Dresch JM, Arnosti DN.

Cell Syst. 2015 Dec 23;1(6):379-80. doi: 10.1016/j.cels.2015.12.006. Epub 2015 Dec 23.

6.

Regulation of cell polarity determinants by the Retinoblastoma tumor suppressor protein.

Payankaulam S, Yeung K, McNeill H, Henry RW, Arnosti DN.

Sci Rep. 2016 Mar 14;6:22879. doi: 10.1038/srep22879.

7.

Cori meets Dobzhansky: Evolution and Gene Expression in St. Louis: A report on the "Evolution and Core Processes in Gene Regulation" meeting in St. Louis, June 25-28, 2015.

Arnosti DN, Fay JC, Zeitlinger J.

Bioessays. 2015 Oct;37(10):1042-4. doi: 10.1002/bies.201500106. Epub 2015 Sep 10.

PMID:
26354485
8.

Genome-wide errant targeting by Hairy.

Kok K, Ay A, Li LM, Arnosti DN.

Elife. 2015 Aug 25;4. doi: 10.7554/eLife.06394.

9.

Genome-Wide Analysis of Drosophila RBf2 Protein Highlights the Diversity of RB Family Targets and Possible Role in Regulation of Ribosome Biosynthesis.

Wei Y, Mondal SS, Mouawad R, WilczyƄski B, Henry RW, Arnosti DN.

G3 (Bethesda). 2015 May 20;5(7):1503-15. doi: 10.1534/g3.115.019166.

10.

The Evolutionarily Conserved C-terminal Domains in the Mammalian Retinoblastoma Tumor Suppressor Family Serve as Dual Regulators of Protein Stability and Transcriptional Potency.

Sengupta S, Lingnurkar R, Carey TS, Pomaville M, Kar P, Feig M, Wilson CA, Knott JG, Arnosti DN, Henry RW.

J Biol Chem. 2015 Jun 5;290(23):14462-75. doi: 10.1074/jbc.M114.599993. Epub 2015 Apr 22.

11.

Dynamic reprogramming of chromatin: paradigmatic palimpsests and HES factors.

Kok K, Arnosti DN.

Front Genet. 2015 Feb 10;6:29. doi: 10.3389/fgene.2015.00029. eCollection 2015.

12.

Enhancer trafficking: free throws and three-pointers.

Wei Y, Arnosti DN.

Dev Cell. 2015 Jan 26;32(2):135-7. doi: 10.1016/j.devcel.2015.01.006.

13.

Role of Drosophila retinoblastoma protein instability element in cell growth and proliferation.

Elenbaas JS, Mouawad R, Henry RW, Arnosti DN, Payankaulam S.

Cell Cycle. 2015;14(4):589-97. doi: 10.4161/15384101.2014.991182.

14.

Integrated stability and activity control of the Drosophila Rbf1 retinoblastoma protein.

Zhang L, Wei Y, Pushel I, Heinze K, Elenbaas J, Henry RW, Arnosti DN.

J Biol Chem. 2014 Sep 5;289(36):24863-73. doi: 10.1074/jbc.M114.586818. Epub 2014 Jul 21.

15.

Global parameter estimation for thermodynamic models of transcriptional regulation.

Suleimenov Y, Ay A, Samee MA, Dresch JM, Sinha S, Arnosti DN.

Methods. 2013 Jul 15;62(1):99-108. doi: 10.1016/j.ymeth.2013.05.012. Epub 2013 May 30.

PMID:
23726942
16.

TWO-LAYER MATHEMATICAL MODELING OF GENE EXPRESSION: INCORPORATING DNA-LEVEL INFORMATION AND SYSTEM DYNAMICS.

Dresch JM, Thompson MA, Arnosti DN, Chiu C.

SIAM J Appl Math. 2013 Mar 1;73(2):804-826.

17.

Evidence for autoregulation and cell signaling pathway regulation from genome-wide binding of the Drosophila retinoblastoma protein.

Acharya P, Negre N, Johnston J, Wei Y, White KP, Henry RW, Arnosti DN.

G3 (Bethesda). 2012 Nov;2(11):1459-72. doi: 10.1534/g3.112.004424. Epub 2012 Nov 1.

18.

Ubiquitination of retinoblastoma family protein 1 potentiates gene-specific repression function.

Raj N, Zhang L, Wei Y, Arnosti DN, Henry RW.

J Biol Chem. 2012 Dec 7;287(50):41835-43. doi: 10.1074/jbc.M112.422428. Epub 2012 Oct 18.

19.

Boolean modeling of gene regulatory networks: Driesch redux.

Arnosti DN, Ay A.

Proc Natl Acad Sci U S A. 2012 Nov 6;109(45):18239-40. doi: 10.1073/pnas.1215732109. Epub 2012 Oct 1. No abstract available.

20.

Rbf1 degron dysfunction enhances cellular DNA replication.

Raj N, Zhang L, Wei Y, Arnosti DN, Henry RW.

Cell Cycle. 2012 Oct 15;11(20):3731-8. doi: 10.4161/cc.21665. Epub 2012 Aug 16.

21.

A two-scale mathematical model for DNA transcription.

Chiu C, Fakhouri W, Liu N, Dayringer E, Dresch J, Arnosti D.

Math Biosci. 2012 Apr;236(2):132-40. doi: 10.1016/j.mbs.2011.12.006. Epub 2012 Feb 16.

PMID:
22343054
22.

Transcriptional repressors: shutting off gene expression at the source affects developmental dynamics.

Arnosti DN.

Curr Biol. 2011 Oct 25;21(20):R859-60. doi: 10.1016/j.cub.2011.09.022.

23.

Mathematical modeling of gene expression: a guide for the perplexed biologist.

Ay A, Arnosti DN.

Crit Rev Biochem Mol Biol. 2011 Apr;46(2):137-51. doi: 10.3109/10409238.2011.556597. Review.

24.

Long- and short-range transcriptional repressors induce distinct chromatin states on repressed genes.

Li LM, Arnosti DN.

Curr Biol. 2011 Mar 8;21(5):406-12. doi: 10.1016/j.cub.2011.01.054. Epub 2011 Feb 25.

25.
26.
27.

Thermodynamic modeling of transcription: sensitivity analysis differentiates biological mechanism from mathematical model-induced effects.

Dresch JM, Liu X, Arnosti DN, Ay A.

BMC Syst Biol. 2010 Oct 24;4:142. doi: 10.1186/1752-0509-4-142.

28.

Paradoxical instability-activity relationship defines a novel regulatory pathway for retinoblastoma proteins.

Acharya P, Raj N, Buckley MS, Zhang L, Duperon S, Williams G, Henry RW, Arnosti DN.

Mol Biol Cell. 2010 Nov 15;21(22):3890-901. doi: 10.1091/mbc.E10-06-0520. Epub 2010 Sep 22.

29.

Transcriptional repression: conserved and evolved features.

Payankaulam S, Li LM, Arnosti DN.

Curr Biol. 2010 Sep 14;20(17):R764-71. doi: 10.1016/j.cub.2010.06.037. Review.

30.

Fine mapping of chromatin structure in Drosophila melanogaster embryos using micrococcal nuclease.

Li LM, Arnosti DN.

Fly (Austin). 2010 Jul-Sep;4(3):213-5. doi: 10.4161/fly.4.3.12200. Epub 2010 Jul 1.

31.

Nucleosome positioning: an essential component of the enhancer regulatory code?

Ay A, Arnosti DN.

Curr Biol. 2010 May 11;20(9):R404-6. doi: 10.1016/j.cub.2010.03.051.

32.

Deciphering a transcriptional regulatory code: modeling short-range repression in the Drosophila embryo.

Fakhouri WD, Ay A, Sayal R, Dresch J, Dayringer E, Arnosti DN.

Mol Syst Biol. 2010;6:341. doi: 10.1038/msb.2009.97. Epub 2010 Jan 19.

33.

Groucho corepressor functions as a cofactor for the Knirps short-range transcriptional repressor.

Payankaulam S, Arnosti DN.

Proc Natl Acad Sci U S A. 2009 Oct 13;106(41):17314-9. doi: 10.1073/pnas.0904507106. Epub 2009 Sep 28.

34.

Transcriptional perspectives from San Diego.

Arnosti DN.

Fly (Austin). 2008 May-Jun;2(3):138-40. Epub 2008 May 30. No abstract available.

PMID:
18820429
35.

Image processing and analysis for quantifying gene expression from early Drosophila embryos.

Ay A, Fakhouri WD, Chiu C, Arnosti DN.

Tissue Eng Part A. 2008 Sep;14(9):1517-26. doi: 10.1089/ten.tea.2008.0202.

36.

Gene regulation: boundaries within limits.

Payankaulam S, Arnosti DN.

Curr Biol. 2008 Aug 5;18(15):R653-R655. doi: 10.1016/j.cub.2008.06.040.

37.

Spreading of a corepressor linked to action of long-range repressor hairy.

Martinez CA, Arnosti DN.

Mol Cell Biol. 2008 Apr;28(8):2792-802. doi: 10.1128/MCB.01203-07. Epub 2008 Feb 19.

38.

Role of NAD binding and catalytic residues in the C-terminal binding protein corepressor.

Mani-Telang P, Sutrias-Grau M, Williams G, Arnosti DN.

FEBS Lett. 2007 Nov 13;581(27):5241-6. Epub 2007 Oct 12.

39.

New tools, resources for gene regulatory analysis in Drosophila.

Halfon MS, Arnosti DN.

Fly (Austin). 2007 Mar-Apr;1(2):123-4. No abstract available.

PMID:
19378457
40.

Retinoblastoma protein regulation by the COP9 signalosome.

Ullah Z, Buckley MS, Arnosti DN, Henry RW.

Mol Biol Cell. 2007 Apr;18(4):1179-86. Epub 2007 Jan 24.

41.
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44.

Transcriptional enhancers: Intelligent enhanceosomes or flexible billboards?

Arnosti DN, Kulkarni MM.

J Cell Biochem. 2005 Apr 1;94(5):890-8. Review.

PMID:
15696541
45.

Distinct developmental expression of Drosophila retinoblastoma factors.

Keller SA, Ullah Z, Buckley MS, Henry RW, Arnosti DN.

Gene Expr Patterns. 2005 Feb;5(3):411-21.

PMID:
15661648
46.
47.

Quantitative contributions of CtBP-dependent and -independent repression activities of Knirps.

Struffi P, Corado M, Kulkarni M, Arnosti DN.

Development. 2004 May;131(10):2419-29.

48.

Information display by transcriptional enhancers.

Kulkarni MM, Arnosti DN.

Development. 2003 Dec;130(26):6569-75.

49.
50.

Analysis and function of transcriptional regulatory elements: insights from Drosophila.

Arnosti DN.

Annu Rev Entomol. 2003;48:579-602. Epub 2001 Sep 28. Review.

PMID:
12359740

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