Ahmet Ay | Colgate University - Faculty Directory

Colgate Directory

Ahmet Ay Professor of Biology and Mathematics

Ahmet Ay

Associate Professor of Biology and Mathematics
Biology, 206 Olin Hall
p 315-228-6176


BS Bilkent University 2002; PhD Michigan State University 2009


Systems Biology, Mathematical Biology, Bioinformatics, Biological Regulatory Networks, Zebrafish Segmentation and cis-Regulation in Transcription.

Teaching Experience

Teaching Assistant, Michigan State University (2002-2009)


My main scientific interests lie in applying mathematical modeling to understand biological regulatory networks. Specifically, understanding the design principles of biological gene regulatory networks, mechanisms that control zebrafish segmentation during development and cis-regulation in transcription. My teaching interests include Systems Biology, Bioinformatics, Modeling of Biological Systems, Numerical Analysis, Differential Equations, Linear Algebra, Calculus and Statistics.


Undergraduate Student Authors = Natalie Wilner, Adriana Sperlea, Jack Holland, Sebastian Sangervasi, Megan Richards, Yerzhan Suleimenov, Xiaozhou Liu and Evan Dayringer

Alim MA*, Ay A*, Hasan MM, Thai M, Kahveci T. Multiple Reference Networks Improve Accuracy of Signaling Network Construction. (Accepted to the IEEE/ACM Transactions on Computational Biology and Bioinformatics, * Equal Contribution)
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. 
J Circadian Rhythms 13: Art-4
Ay A, Wilner N, Yildirim N (2015). Dynamics matter: Differences and similarities between alternatively designed regulatory mechanisms. Mol BioSyst (DOI: 10.1039/C5MB00269A)
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, 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 Biochem 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  (* Corresponding Authors)
Ay A*, Arnosti DN* (2010) Nucleosome Positioning: An Essential Component of the Enhancer Regulatory Code? Cur Biol 20: R404-406 (* Corresponding Authors)
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. 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 (* Equal Contribution)
Ay A, Gürses M, Zheltukhin K (2003) Hamiltonian equations in R3. J Math Phys 44: 5688-5705


Deciphering cis-Regulatory Transcriptional Grammar in Drosophila melanogaster by Mathematical Models

Professional Experience

Associate Professor, 2016-Present, Departments of Biology and Mathematics, Colgate University
Assistant Professor, 2010-2016, Departments of Biology and Mathematics, Colgate University
Research Associate, 2009-2010, Department of Biochemistry & Molecular Biology, Michigan State University
Teaching Assistant, 2002-2009, Department of Mathematics, Michigan State University


  • Carter Wallace Fellowship, 2013, Colgate University, NY
  • Faculty Development Council Grant, 2010, Colgate University, NY
  • Sigma Xi (the scientific research society) Graduate Student Award, 2009, MI
  • Senior Teaching Assistant Award for Excellence in Teaching (Honorable Mention), 2009, Michigan State University, MI
  • Gene Expression in Development and Disease (GEDD) Outstanding Research Award, 2009, Michigan State University, MI
  • GEDD Graduate Student Fellowship, 2008-2009, Michigan State University, MI
  • Quantitative Biology Graduate Student Fellowship, 2007-2008, 2006-2007 Michigan State University, MI