Ahmet Ay

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Ahmet Ay

Associate Professor of Biology and Mathematics

Department/Office Information

Biology, Mathematics


PhD Michigan State University (2009)

  • 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

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

My teaching interests include Systems Biology, Bioinformatics, Modeling of Biological Systems, Biostatistics, Numerical Analysis, Differential Equations, Linear Algebra and Calculus.

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.

Undergraduate Student Authors = Soo Bin Kwon, Nate Larson, Jonathan Kahn, Natalie Wilner, Adriana Sperlea, Jack Holland, Sebastian Sangervasi, Megan Richards, Yerzhan Suleimenov, Xiaozhou Liu and Evan Dayringer

Yildirim N, Aktas ME, Ozcan SN, Akbas E, Ay A (2016) Differential DNA level regulation by alternatively designed molecular mechanisms: A mathematical modeling approach. In Silico Biology Preprint: 1-33.

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 M, Kahveci T. 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). Dynamics matter: Differences and similarities between alternatively designed regulatory mechanisms. Mol BioSystems (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 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 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  (* Corresponding Authors)

Ay A*, Arnosti DN* (2010) Nucleosome Positioning: An Essential Component of the Enhancer Regulatory Code? Current Biology 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. 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 (* Equal Contribution)

Ay A, Gürses M, Zheltukhin K (2003) Hamiltonian equations in R3. Journal of Mathematical Physics 44: 5688-5705

  • Picker Interdisciplinary Science Institute, $153000, 2016-2018, Co-PI on collaborative grant entitled, "An Interdisciplinary Approach to Understanding Ongoing Biological Invasions by Crazy Worms (Amynthas) in North America", Colgate University, NY
  • Picker Interdisciplinary Science Institute, $107000, 2016-2018, Co-PI on collaborative grant entitled, "Interdisciplinary Investigation of the Vertebral Segmentation Clock", Colgate University, NY  
  • Gaurth Hansen Alumnus Award, 2016, Department of Biochemistry and Molecular Biology, Michigan State University, MI
  • Faculty Research Council Grants, 2010-2016, Colgate University, NY
  • 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