Publications

Undergraduate student authors are underlined.

2017

Elmas A, Wang X, Dresch JM (2017) The folded k-spectrum kernel: A machine learning approach to detecting transcription factor binding sites with gapped nucleotide dependencies. PLoS ONE 12(10): e0185570.

2016

Pettie KP, Dresch JM, Drewell RA (2016) Spatial distribution of predicted transcription factor binding sites in Drosophila ChIP peaks. Mechanisms of Development. 141:51-61.

Dresch JM, Zellers RGBork DK and Drewell RA (2016) Nucleotide interdependency in transcription factor binding sites in the Drosophila genome. Gene Regulation and Systems Biology. 10:21-33.

*Sayal R, *Dresch JM, Pushel I, Taylor BR, Arnosti DN (2016) Quantitative perturbation-based analysis of gene expression in early Drosophila embryo. eLife 5:e08445 (* – equal contribution)

2015

Dresch, JM, Arnosti DN (2015) The Wisdom of Crowds: Can Mathematical Models Crack the cis Regulatory Code? Cell Systems 1(6):379–380.

McCarthy GD, Drewell RA, Dresch JM (2015) Global sensitivity analysis of a dynamic model for gene expression in Drosophila embryos. PeerJ 3:e1022 https://dx.doi.org/10.7717/peerj.1022

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.

2014

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.

2013

*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 Y, Ay A, Samee MA, Dresch JM, Sinha S, Arnosti DN (2013) Global parameter estimation for thermodynamic models of transcriptional regulation. Methods. 62(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.

2012

Dresch JM and Drewell RA (2012) Decoding the cis-regulatory grammar behind enhancer architecture. Genomics III: Methods, Techniques and Applications (iConcepts Press, book chapter) ISBN: 978-1-922227-096.

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.

2010

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)

2007

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.