Recent Publications

Mouawad R, Prasad J, Thorley D, Himadewi P, Kadiyala D, Wilson N, Kapranov P, Arnosti DN. “Diversification of retinoblastoma protein function associated with cis and trans adaptations.” Mol Biol Evol. (2019) Aug 16. doi: 10.1093/molbev/msz187

Sonnenschein A, Dworkin I, Arnosti D. “The Sheep and the Goats: Distinguishing transcriptional enhancers in a complex chromatin landscape.” G3. (2018) bioRxiv

Wei Y, Gokhale RH, Sonnenschein A, Montgomery KM, Ingersoll A, Arnosti DN. “Complex cis-regulatory landscape of the insulin receptor gene underlies the broad expression of a central signaling regulator.” Development (2016) Oct;143:3591-3603. doi::10.1242/dev.138073

Sayal R, Dresch JM, Pushel I, Taylor BR, Arnosti DN. “Quantitative perturbation-based analysis of gene expression predicts enhancer activity in early Drosophila embryo.” Elife. (2016) May 6;. doi:10.7554/eLife.08445

Dresch JM, Arnosti DN. “The Wisdom of Crowds: Can Mathematical Models Crack the cis Regulatory Code?” Cell Syst. (2015) Dec 23;1(6):379-80. doi:10.1016/j.cels.2015.12.006

Payankaulam S, Yeung K, McNeill H, Henry RW, Arnosti DN. “Regulation of cell polarity determinants by the Retinoblastoma tumor suppressor protein.” Sci Rep. (2016) Mar 14;6:22879. doi:10.1038/srep22879

Arnosti DN, Fay JC, Zeitlinger J. “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.” Bioessays. (2015) Oct;37(10):1042-4. doi:10.1002/bies.201500106

Kok K, Ay A, Li LM, Arnosti DN. “Genome-wide errant targeting by Hairy.” Elife. (2015) Aug 25. doi:10.7554/eLife.06394

Wei Y, Mondal SS, Mouawad R, Wilczynski B, Henry RW, Arnosti DN. “Genome-Wide Analysis of Drosophila RBf2 Protein Highlights the Diversity of RB Family Targets and Possible Role in Regulation of Ribosome Biosynthesis.” G3 (Bethesda). (2015) May 20;5(7):1503-15. doi:10.1534/g3.115.019166

Sengupta S, Lingnurkar R, Carey TS, Pomaville M, Kar P, Feig M, Wilson CA, Knott JG, Arnosti DN, Henry RW. “The Evolutionarily Conserved C-terminal Domains in the Mammalian Retinoblastoma Tumor Suppressor Family Serve as Dual Regulators of Protein Stability and Transcriptional Potency.” J Biol Chem. (2015) Jun 5;290(23):14462-75. doi:10.1074/jbc.M114.599993

Kok K, Arnosti DN. “Dynamic reprogramming of chromatin: paradigmatic palimpsests and HES factors.” Front Genet. (2015);6:29. doi:10.3389/fgene.2015.00029

Wei Y, Arnosti DN. “Enhancer trafficking: free throws and three-pointers.” Dev Cell. (2015) Jan 26;32(2):135-7. doi:10.1016/j.devcel.2015.01.006

Elenbaas JS, Mouawad R, Henry RW, Arnosti DN, Payankaulam S. “Role of Drosophila retinoblastoma protein instability element in cell growth and proliferation.” Cell Cycle. (2015);14(4):589-97. doi:10.4161/15384101.2014.991182

Zhang L, Wei Y, Pushel I, Heinze K, Elenbaas J, Henry RW, Arnosti DN. “Integrated stability and activity control of the Drosophila Rbf1 retinoblastoma protein.” J Biol Chem. (2014) Sep 5;289(36):24863-73. doi:10.1074/jbc.M114.586818

Suleimenov Y, Ay A, Samee MA, Dresch JM, Sinha S, Arnosti DN. “Global parameter estimation for thermodynamic models of transcriptional regulation.” Methods..  (2013);62(1): 99-108.

Dresch JM, Thompson MA, Arnosti DN, Chiu C. “TWO-LAYER MATHEMATICAL MODELING OF GENE EXPRESSION: INCORPORATING DNA-LEVEL INFORMATION AND SYSTEM DYNAMICS.” SIAM J Appl Math. (2013) Mar 1;73(2):804-826. doi:10.1137/120887588

Acharya P, Negre N, Johnston J, Wei Y, White KP, Henry RW, Arnosti DN. “Evidence for autoregulation and cell signaling pathway regulation from genome-wide binding of the Drosophila retinoblastoma protein.” G3 (Bethesda). (2012) Nov;2(11):1459-72. doi:10.1534/g3.112.004424

Raj N, Zhang L, Wei Y, Arnosti DN, Henry RW. “Ubiquitination of retinoblastoma family protein 1 potentiates gene-specific repression function.” J Biol Chem. (2012) Dec 7;287(50):41835-43. doi:10.1074/jbc.M112.422428

Arnosti DN, Ay A. “Boolean modeling of gene regulatory networks: Driesch redux.” Proc Natl Acad Sci U S A. (2012) Nov 6;109(45):18239-40. doi:10.1073/pnas.1215732109

Raj N, Zhang L, Wei Y, Arnosti DN, Henry RW. “Rbf1 degron dysfunction enhances cellular DNA replication.” Cell Cycle. (2012) Oct 15;11(20):3731-8. doi:10.4161/cc.21665

Arnosti DN. “Transcriptional repressors: shutting off gene expression at the source affects developmental dynamics.” Curr Biol. (2011) Oct 25;21(20):R859-60. doi:10.1016/j.cub.2011.09.022