Undergraduate student authors are underlined.
2024
Drewell RA, Klonaros D, Dresch JM (2024) Transcription factor expression landscape in Drosophila embryonic cell lines. BMC Genomics. 25: 307
2023
Dresch JM, Conrad RD, Klonaros D, Drewell RA (2023) Investigating the sequence landscape in the Drosophila Initiator core promoter element using an enhanced MARZ algorithm. PeerJ. 11:e15597 DOI 10.7717/peerj.15597
Drewell RA, Cormier TA, Steenwyk JL, St. Denis J, Tabima JF, Dresch JM, Larochelle DA (2023) The Dictyostelium discoideum genome lacks significant DNA methylation and uncovers palindromic sequences as a source of false positives in bisulfite sequencing. NAR Genomics and Bioinformatics. 5(2):lqad035.
Klonaros D, Dresch JM, Drewell RA (2023) Transcriptome profile in Drosophila Kc and S2 embryonic cell lines. G3: Genes|Genomes|Genetics. doi: 10.1093/g3journal/jkad054
2021
Gaiewski MJ, Drewell RA, Dresch JM (2021) Fitting thermodynamic-based models: Incorporating parameter sensitivity improves the performance of an evolutionary algorithm. Mathematical Biosciences. 342: 108716.
2019
McCarthy GD, Drewell RA, Dresch JM (2019) Analyzing the stability of gene expression using a simple reaction-diffusion model in an early Drosophila embryo. Mathematical Biosciences 316: 108239.
Orlomoski R, Bogle A, Loss J, Simons R, Dresch JM, Drewell RA, Spratt DE (2019) Rapid and efficient purification of Drosophila homeodomain transcription factors for biophysical characterization. Protein Expression and Purification. 158:9-14.
2017
Steenwyk JL, St. Denis J, Dresch JM, Larochelle DA, Drewell RA (2017) Whole genome bisulfite sequencing reveals a sparse, but robust pattern of DNA methylation in the Dictyostelium discoideum genome. BIORXIV/2017/166033.
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 RG, Bork 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 predicts enhancer activity 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
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.