Submitted by Jacqueline M. Dresch on Monday, 3/23/2015, at 6:28 PM

Zellers RG, Drewell RA, Dresch JM (2015) MARZ: An algorithm to combinatorially analyze gapped n-mer models of transcription factor binding. BMC Bioinformatics. 16: 30.


Drewell RA, Nevarez MJ, Kurata JS, Winkler LN, Li L, Dresch JM (2014) Deciphering the combinatorial architecture of a Drosophila homeotic gene enhancer. Mechanisms of Development. 131:68-77.


 *Stringham JL, *Brown AS, Drewell RA, Dresch JM (2013) Flanking sequence context-dependent transcription factor binding in early Drosophila development. BMC Bioinformatics. 14:298 (* - equal contribution)


Suleimenov YAy ASamee MADresch JMSinha SArnosti DN (2013) Global parameter estimation for thermodynamic models of transcriptional regulation. Methods62(1):99-108.


Dresch JM, Richards M, Ay A (2013) A Primer on Thermodynamic-based Models for Deciphering Transcriptional Regulatory Logic. BBA – Gene Regulatory Mechanisms. 1829(9):946-53.


Dresch JM, Thompson MA, Arnosti DN, Chiu C (2013) Two-Layer Mathematical Modeling of Gene Expression: Incorporating DNA-level Information and System Dynamics. SIAM Journal of Applied Mathematics 73(2): 804-826.


Dresch JM and Drewell RA (2012) Decoding the cis-regulatory grammar behind enhancer architecture. In iConcept Press, Introduction to Sequence and Genome Analysis. ISBN: 978014802541-4-5.


Chiu C, Fakhouri W, Liu N, Dayringer E, Dresch J, Arnosti D (2012) A two-scale mathematical model for DNA transcription. Mathematical Biosciences. 236(2):132-140.


Dresch JM, Liu X, Arnosti DN, Ay A (2010) Thermodynamic modeling of transcription: Sensitivity analysis differentiates biological mechanism from mathematical model-induced effects. BMC Systems Biology 4:142.


*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. Molecular Systems Biology 6:341. (* - equal contribution)


Hartvigsen G, Dresch JM, Zielinski AL, Macula AJ, Leary CC (2007) Network structure and vaccination strategy and effort interact to affect the dynamics of influenza epidemics. Journal of Theoretical Biology 246(2): 205-213.


Dresch JM, Hansen NC, Hartvigsen G, Leary CC, Macula AJ (2007) Component Averages of subgraphs in Circulant-like Graphs. Bulletin of the Institute for Combinatorics and its Application 51: 55-68.