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Ahmet Ay
Ahmet Ay
Colgate University: Departments of Biology and Mathematics
Verified email at colgate.edu - Homepage
Title
Cited by
Cited by
Year
Mathematical modeling of gene expression: a guide for the perplexed biologist
A Ay, DN Arnosti
Critical reviews in biochemistry and molecular biology 46 (2), 137-151, 2011
1512011
Deciphering a transcriptional regulatory code: modeling short‐range repression in the Drosophila embryo
WD Fakhouri, A Ay, R Sayal, J Dresch, E Dayringer, DN Arnosti
Molecular systems biology 6 (1), 341, 2010
1402010
Thermodynamic modeling of transcription: sensitivity analysis differentiates biological mechanism from mathematical model-induced effects
JM Dresch, X Liu, DN Arnosti, A Ay
BMC systems biology 4 (1), 1-11, 2010
642010
Hamiltonian equations in
A Ay, M Gürses, K Zheltukhin
Journal of mathematical physics 44 (12), 5688-5705, 2003
472003
Circadian clock model supports molecular link between PER3 and human anxiety
AR Liberman, SB Kwon, HT Vu, A Filipowicz, A Ay, KK Ingram
Scientific reports 7 (1), 1-10, 2017
412017
Short-lived Her proteins drive robust synchronized oscillations in the zebrafish segmentation clock
A Ay, S Knierer, A Sperlea, J Holland, EM Özbudak
Development 140 (15), 3244-3253, 2013
412013
Molecular insights into chronotype and time-of-day effects on decision-making
KK Ingram, A Ay, SB Kwon, K Woods, S Escobar, M Gordon, IH Smith, ...
Scientific Reports 6 (1), 1-9, 2016
362016
Shifts in bird migration timing in North American long-distance and short-distance migrants are associated with climate change
J Zaifman, D Shan, A Ay, AG Jimenez
International Journal of Zoology 2017, 2017
342017
Modeling strengthens molecular link between circadian polymorphisms and major mood disorders
AR Liberman, L Halitjaha, A Ay, KK Ingram
Journal of Biological Rhythms 33 (3), 318-336, 2018
322018
Noise in the vertebrate segmentation clock is boosted by time delays but tamed by notch signaling
S Keskin, GS Devakanmalai, SB Kwon, HT Vu, Q Hong, YY Lee, M Soltani, ...
Cell reports 23 (7), 2175-2185. e4, 2018
312018
Diurnal preference predicts phase differences in expression of human peripheral circadian clock genes
A Ferrante, D Gellerman, A Ay, KP Woods, AM Filipowicz, K Jain, ...
Journal of circadian rhythms 13, 2015
292015
Spatial gradients of protein-level time delays set the pace of the traveling segmentation clock waves
A Ay, J Holland, A Sperlea, GS Devakanmalai, S Knierer, S Sangervasi, ...
Development 141 (21), 4158-4167, 2014
252014
Boolean modeling of gene regulatory networks: Driesch redux
DN Arnosti, A Ay
Proceedings of the National Academy of Sciences 109 (45), 18239-18240, 2012
142012
Global parameter estimation for thermodynamic models of transcriptional regulation
Y Suleimenov, A Ay, MAH Samee, JM Dresch, S Sinha, DN Arnosti
Methods 62 (1), 99-108, 2013
132013
Image Processing and Analysis for Quantifying Gene Expression from Early Drosophila Embryos
A Ay, WD Fakhouri, C Chiu, DN Arnosti
Tissue engineering Part A 14 (9), 1517-1526, 2008
132008
Pairing of segmentation clock genes drives robust pattern formation
OQH Zinani, K Keseroğlu, A Ay, EM Özbudak
Nature 589 (7842), 431-436, 2021
102021
Genome-wide errant targeting by Hairy
K Kok, A Ay, LM Li, DN Arnosti
Elife 4, e06394, 2015
102015
A primer on thermodynamic-based models for deciphering transcriptional regulatory logic
JM Dresch, M Richards, A Ay
Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1829 (9), 946-953, 2013
92013
Finding conserved patterns in multilayer networks
Y Ren, A Sarkar, A Ay, A Dobra, T Kahveci
Proceedings of the 10th ACM International Conference on Bioinformatics …, 2019
82019
Network-based prediction of cancer under genetic storm
A Ay, D Gong, T Kahveci
Cancer informatics 13, CIN. S14025, 2014
82014
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Articles 1–20