Research Interests:
The analysis of regulatory networks holds the key for understanding how central biological processes are regulated. Subtle changes, such as an increase or decrease of regulatory protein levels, can have profound effects in many biological processes including human diseases such as cancer, population differences, and the evolution of morphological novelties. My main scientific interests lie in applying mathematical modeling to understand biological regulatory networks.

Undergraduate student authors = Adriana Sperlea, Jack Holland, Sebastian Sangervasi, Yerzhan Suleimenov, Megan Richards, Xiaozhou Liu and Evan Dayringer

  • Ay A, Wilner N, Yildirim N. Mathematical modeling deciphers the benefits of alternatively-designed conserved activatory and inhibitory gene circuits. (Accepted to Mol BioSyst)
  • Ay A*, Gong D*, Kahveci T. Hierarchical Decomposition of Dynamically Evolving Regulatory Networks. (Accepted to BMC Bioinformatics) (* Equal Contribution)
  • Ay A*, Holland J, Sperlea A, Devakanmalai GS, Knierer S, Sangervasi S, Stevenson A, and Ozbudak EM* (2014). Spatial Gradients of Protein Time-Delays Set the Pace of the Traveling Segmentation Clock Waves. Development 141(21): 4158-4167 (* Corresponding Author)
  • Ay A*, Gong D*, Kahveci T (2014) Network-based Prediction of Cancer Under Genetic Storm. Cancer Inform S(14025):15-31 (* Equal Contribution)
  • Ay A, Yildirim N (2014) Dynamics matter: Differences and similarities between alternatively designed regulatory mechanisms. Mol BioSyst 10(7):1948-1957
  • Ay A*, Knierer S, Sperlea A, Holland J, Ozbudak EM* (2013) Short-lived Her Proteins Drive Robust Synchronized Oscillations in the Zebrafish Segmentation Clock. Development 140: 3244-3253 (* Corresponding Author)
  • Suleimenov Y*, Ay A*, Samee MA, Sinha S, Dresch JM, Arnosti DN (2013) Global Parameter Estimation for Thermodynamic Models of Transcriptional Regulation. Methods (Elsevier) 62(1):99-108 (* Equal Contribution)
  • Dresch J, Richards M, Ay A (2013) A Primer on Thermodynamic Models for Deciphering Transcriptional Regulatory Logic. Biochim Biophys Acta 1829: 946-953
  • Arnosti DN, Ay A (2012) Boolean modeling of gene regulatory networks : Driesch redux. Proc Natl Acad Sci USA 109(45): 18239-18240
  • Ay A, Arnosti DN (2011) Mathematical modeling of gene expression: A guide for the perplexed biologist. Crit Rev Mol Biol 46: 137-151
  • Dresch J, Liu X , Arnosti DN, Ay A (2010) Thermodynamic modeling of transcription: Sensitivity analysis differentiates biological mechanism from model-induced effects. BMC Syst Biol 4: 142 
  • Ay A, Arnosti DN (2010) Nucleosome Positioning: An Essential Component of the Enhancer Regulatory Code? Cur Biol 20: R404-406
  • Fakhouri WD*, Ay A*, Sayal R, Dresch J, Dayringer E, Arnosti DN (2010) Deciphering a transcriptional regulatory code: modeling short-range repression in the Drosophila embryo. Nature/EMBO Mol Syst Biol 6: 341 (* Equal Contribution)
  • 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: 1517-1526
  • Ay A, Gürses M, Zheltukhin K (2003) Hamiltonian equations in R3. J Math Phys 44: 5688-5705