Ahmet Ay | Colgate University - Faculty Directory

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Ahmet Ay

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

Degree

BS Bilkent University 2002; PhD Michigan State University 2009

Specialties

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

Teaching Experience

Teaching Assistant, Michigan State University (2002-2009)

Interests

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.

Publications

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

  • Ay A*, Gong D*, Kahveci T (In press). Network-based Prediction of Cancer Under Genetic Storm. Cancer Inform ( * 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



Dissertation

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

Professional Experience

Assistant Professor, 2010-Present, 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

Distinctions

  • 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