Ahmet Ay | Colgate University - Faculty Directory

Colgate Directory


Ahmet Ay

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


BS Bilkent University 2002; PhD Michigan State University 2009

Teaching Experience

Teaching Assistant, Michigan State University (2002-2009)


Systems Biology, Mathematical Biology, Biological Regulatory Networks, cis-Regulation in Transcription


Decoding cis-regulation in transcription and understanding design principles of biological regulatory networks.


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

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


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