David N. Arnosti
Recent Publications
Arnosti DN and Ay A. Boolean modeling of gene regulatory networks - Driesch redux" Proc Natl. Acad. Sci. USA, in press.
Acharya P, Negre N, Johnston J, Wei Y, White KP, Henry RW, and Arnosti DN. Evidence for autoregulation and cell signaling pathway regulation from genome-wide binding of the Drosophila retinoblastoma protein. G3:Genes, Genomes, Genetics, in press.
Raj N, Zhang L, Wei Y, Arnosti DN, and Henry RW. 2012. Ubiquitination of retinoblastoma family protein 1potentiates gene-specific repression function. J. Biol Chem., 287(50):41835-43. Link to article
Suleimenov Y, Ay A, Samee MAH, Dresch JM, Sinha S and Arnosti DN. Global parameter estimation for thermodynamic models of transcriptional regulation. Under review.
Dresch JM, Thompson MA, Arnosti DN, and Chiu C. Two-layer mathematical modeling of gene expression: Incorporating DNA-level information and systems dynamics. Under review.
N Raj, L Zhang, Y Wei, DN Arnosti, RW Henry. 2012. Rbf1 degron dysfunction enhances cellular DNA replication. Cell Cycle. 2012 Oct 15;11(20). Link to abstract
DN. Arnosti (2011) Transcriptional Repressors: Shutting off gene expression at the source affects developmental dynamics. Current Biology, 21:R859-860. Link to article
Li M. Li and David N. Arnosti (2011) Long- and short-range transcriptional repressors induce distinct chromatin states on repressed genes. Current Biology, 21:406-12. Link to article
A Ay and DN Arnosti (2011) Mathematical modeling of gene expression: a guide for the perplexed biologist. CRC Critical Reviews in Biochemistry and Molecular Biology, 46(2): 137–151. Link to article
R Sayal, S-M Ryu, and DN Arnosti (2011) Optimization of reporter gene architecture for quantitative measurements of gene expression in the Drosophila embryo. FLY, 5(1):47-52. Link to article.
YW Zhang and DN Arnosti (2010) Conserved catalytic and C-terminal regulatory domains of the CtBP corepressor fine tune transcriptional response in development. Mol. Cell. Biol., 31(2)375-384. Link to article
JM Dresch, X Liu, DN Arnosti and A Ay (2010) Thermodynamic modeling of transcription: Sensitivity analysis differentiates biological mechanism from mathematical model-induced effects. BMC Systems Biology, 4:142.Link to article Supplemental info
P Acharya, N Raj, MS Buckley, L Zhang, S Duperon, G Williams, RW Henry, and DN Arnosti (2010) Paradoxical instability-activity relationship defines a novel regulatory pathway for retinoblastoma proteins MBoC. 21 3890-3901. See pdf
S Payankaulam, LM Li, and DN Arnosti (2010) Transcriptional repression: conserved and evolved features. Current Biology, 20(17):R764-71. See pdf
LM Li, DN Arnosti. Fine mapping of chromatin structure in Drosophila melanogaster embryos using micrococcal nuclease. Fly (Austin). 2010 Jul 29;4(3). [Epub ahead of print] See pdf
WD Fakhouri*, A Ay*, R Sayal, J Dresch, E Dayringer, C Chiu, DN Arnosti. (2010) Deciphering a transcriptional regulatory code: modeling short-range repression in the Drosophila embryo. Molecular Systems Biology. 6:341. (* - equal contribution) See pdf
A Ay, DN Arnosti. (2010) Nucleosome Positioning: An Essential Component of the Enhancer Regulatory Code? Current Biology. 20 R404-R406. See pdf
S Payankaulam and DN Arnosti. (2009) Groucho corepressor functions as a cofactor for the Knirps short-range transcriptional repressor. Proc Natl Acad Sci USA (PNAS). 13;106(41):17314-9. See pdf
Ay A, Fakhouri WD, Chiu C, Arnosti DN. (2008) Image Processing and Analysis for Quantifying Gene Expression from Early Drosophila Embryos. Tissue Eng Part A. 14(9):1517-26. See abstract
Payankaulam S, Arnosti DN. (2008) Gene Regulation: Boundaries within Limits. Curr Biol. 18(15):R653-5. See pdf
Martinez, C. A. and D. N. Arnosti. (2008) Spreading of corepressor linked to action of long-range repressor Hairy. Mol Cell Biol. 28(8):2792-802. See pdf
Mani-Telang P, Sutrias-Grau M, Williams G, Arnosti DN. (2007) Role of NAD binding and catalytic residues in the C-terminal binding protein corepressor. FEBS Lett. 581:5241-6. See abstract
Halfon, M.S., Arnosti, D.N. 2007. New Tools, Resources for Gene Regulatory Analysis in Drosophila. [Epub ahead of print] e1 Fly 2007; Vol. 1 Issue 2. See abstract
Z Ullah, M Buckley, DN Arnosti, and RW Henry. (2007) Retinoblastoma Protein Regulation by the COP9 Signalosome. Mol Biol Cell(4):1179-86. See abstract
Mani-Telang P, Arnosti DN. (2006) Developmental expression and phylogenetic conservation of alternatively spliced forms of the C-terminal binding protein corepressor. Dev Genes Evol. 217(2):127-35. See abstract
Struffi P, Arnosti DN. (2005) Functional interaction between the Drosophila knirps short-range transcriptional repressor and Rpd3 histone deacetylase. J. Biol. Chem. Dec 9;280(49):40757-65.See pdf.DN Arnosti and MM Kulkarni.(2005) Transcriptional Enhancers: Intelligent Enhanceosomes or Flexible Billboards? J. Cell. Biochem. 94: 890-898. See pdf
SA Keller, Z Ullah, MS Buckley, RW Henry and DN Arnosti. (2005) Distinct developmental expression of Drosophila retinoblastoma factors. Mechanisms of Development, Gene Expression Patterns 5: 411-421. See pdf
MM Kulkarni and DN Arnosti. 2005. Cis-regulatory logic of short-range transcriptional repression in Drosophila. Mol. Cell Biol 9: 3411-20. See pdf
M. Sutrias-Grau and D. N. Arnosti. (2004) CtBP contributes quantitatively to Knirps repression activity in an NAD binding dependent manner. Molecular and Cellular Biology 245953-245966. See pdf.
