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 and statistical learning to understand biological regulatory networks.

Publications:
Undergraduate student authors mentored by me = Amanda Liberman, Son Bin Kwon, Ha T. Vu, George Armstrong, Nate Larson, Jonathan Kahn, Natalie Wilner, Adriana Sperlea, Jack Holland, Sebastian Sangervasi, Megan Richards, Yerzhan Suleimenov, Xiaozhou Liu and Evan Dayringer

  • Liberman AR, Kwon S, Vu HT, Filipowicz A, Ay A, and Krista K. Ingram (2017) Circadian clock model supports molecular link between PER3 and human anxiety. Scientific Reports 7: 9893
  • Armstrong G, Mahmood A, Nugent A, Dexter S, Hutto E, McCay T, Ay A (2017) WORMSPREAD: An individual-based model of invasive earthworm population dynamics. Computational Ecology and Software 7: 109
  • Alim MA*, Ay A*, Hasan MM, Thai MT, Kahveci T (2017) Construction of signaling pathways with RNAi data and multiple reference networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics 99 (* Equal Contribution)
  • Yildirim N, Aktas ME, Ozcan SN, Akbas E, Ay A (2017) Differential transcriptional regulation by alternatively designed molecular mechanisms: A mathematical modeling approach. In Silico Biology 12: 95-127
  • Wang A, Ren Y, Hasan MM, Ay A, Kahveci T (2016) Signaling network construction with incomplete RNAi data. BMC Systems Biology 10(2): 231
  • Ingram KK, Ay A, Kwon S, Woods K, Escobar S, Gordon M, Smith I, Bearden I, Filipowicz A, Jain K (2016) Molecular basis for chronotype and time-of-day effects on decision-making. Nature Scientific Reports 6: 29392
  • Belanger KD, Larson N, Kahn J, Tkachev D, Ay A (2016) Mutant Screen Report: Microarray Analysis of Gene Expression in S. cerevisiae kap108 Mutants Upon Addition of Oxidative Stress. G3: Genes | Genomes | Genetics pp. g3-116.
  • Wang Q, Ren Y, Hasan MM, Ay A, Kahveci T (2015) Construction of signaling networks with incomplete RNAi data. Bioinformatics and Biomedicine (BIBM) - 2015 IEEE International Conference, pp. 157-162
  • Alim MA*, Ay A*, Hasan MM, Thai MT, Kahveci T (2015) Multiple reference networks improve accuracy of signaling network construction. Proceedings of the 6th ACM Conference on Bioinformatics - Computational Biology and Health Informatics, pp. 176-185 (* Equal Contribution)
  • Kok K, Ay A, Li LM, Arnosti DN (2015) Genome-wide errant targeting by Hairy. eLife 4: e06394
  • Ferrante A, Gellerman D, Ay A, Woods K, Filipowicz A, Jain K, Bearden N, Ingram K (2015) Diurnal preference predicts phase differences in expression of human peripheral circadian clock genes. Journal of Circadian Rhythms 13: Art-4
  • Ay A, Wilner N, Yildirim N (2015) Mathematical modeling deciphers the benefits of alternatively-designed conserved activatory and inhibitory gene circuits. Molecular BioSystems 11(7): 2017-2030
  • Ay A*, Gong D*, Kahveci T (2015) Hierarchical Decomposition of Dynamically Evolving Regulatory Networks. BMC Bioinformatics 16(1): 161 (* 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 Informatics S(14025):15-31 (* Equal Contribution)
  • Ay A, Yildirim N (2014) Dynamics matter: Differences and similarities between alternatively designed regulatory mechanisms. Molecular BioSystems 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. Biochimica et Biophysica Acta 1829: 946-953
  • Arnosti DN, Ay A (2012) Boolean modeling of gene regulatory networks : Driesch redux. Proceedings of the National Academy of Sciences USA 109(45): 18239-18240
  • Ay A, Arnosti DN (2011) Mathematical modeling of gene expression: A guide for the perplexed biologist. Critical Reviews in Biochemistry and Molecular Biology 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 Systems Biology 4: 142 
  • Ay A, Arnosti DN (2010) Nucleosome Positioning: An Essential Component of the Enhancer Regulatory Code? Current Biology 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 Molecular Systems Biology 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 Engineering Part A 14: 1517-1526
  • Ay A, Gürses M, Zheltukhin K (2003) Hamiltonian equations in R3. Journal of Mathematical Physics 44: 5688-5705