{"id":16,"date":"2015-05-26T14:36:35","date_gmt":"2015-05-26T14:36:35","guid":{"rendered":"https:\/\/wordpress.clarku.edu\/jdresch\/?page_id=16"},"modified":"2025-08-24T14:53:45","modified_gmt":"2025-08-24T14:53:45","slug":"publications","status":"publish","type":"page","link":"https:\/\/wordpress.clarku.edu\/jdresch\/?page_id=16","title":{"rendered":"Publications"},"content":{"rendered":"

Undergraduate student authors are underlined<\/span>.<\/p>\n

2025<\/strong><\/span><\/p>\n

Drewell RA, Dresch JM (2025) Identification of novel components of the retinal determination gene network in Drosophila<\/em> cell lines<\/a>. Open Biology.<\/em> 15:250012<\/p>\n

Gelashvili Z<\/span>, Larochelle DA, Dresch JM, Hincher M<\/span>, Tabima JF, Drewell RA (2025) Dissecting the function of the DNMT2-homolog (DNMA) in Dictyostelium discoideum<\/em><\/a>. G3: Genes, Genomes, Genetics<\/em>. 15: jkaf152<\/p>\n

Mekkaoui F, Drewell RA, <\/strong>Dresch JM, Spratt DE (2025) Experimental approaches to investigate biophysical interactions between homeodomain transcription factors and DNA.<\/a><\/strong>  <\/strong>BBA – Gene Regulatory Mechanisms.<\/em> 1868: 195074<\/p>\n

Dresch JM, Nurie LL<\/span>, Conrad RD<\/span>, Carlson LT<\/span>, Tchantouridze EI<\/span>, Tesafye B<\/span>, Verhagen E<\/span>, Gupta M, Borges-Rivera D, Drewell RA (2025) Two coacting shadow enhancers regulate twin of eyeless <\/em>expression during early Drosophila <\/em>development. <\/a><\/strong>Genetics.<\/em> 229: 1-43<\/p>\n

2024<\/strong><\/span><\/p>\n

Drewell RA, Klonaros D, Dresch JM (2024) Transcription factor expression landscape in Drosophila<\/em> embryonic cell lines<\/a>. BMC Genomics.<\/em> 25: 307<\/p>\n

2023<\/strong><\/span><\/p>\n

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Dresch JM, Conrad RD<\/span>, Klonaros D, Drewell RA (2023) Investigating the sequence landscape in the Drosophila<\/em> Initiator core promoter element using an enhanced MARZ algorithm<\/span><\/a>. PeerJ. <\/em>11:e15597 DOI 10.7717\/peerj.15597<\/p>\n

Drewell RA, Cormier TA, Steenwyk JL, St. Denis J<\/span>, Tabima JF, Dresch JM, Larochelle DA (2023) The Dictyostelium discoideum<\/em> genome lacks significant DNA methylation and uncovers palindromic sequences as a source of false positives in bisulfite sequencing<\/a>. NAR Genomics and Bioinformatics.<\/em> 5(2):lqad035.<\/p>\n<\/div>\n<\/div>\n<\/div>\n

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Klonaros D, Dresch JM, Drewell RA (2023) Transcriptome profile in Drosophila<\/em> Kc and S2 embryonic cell lines<\/a>. G3: Genes|Genomes|Genetics.<\/em> doi: 10.1093\/g3journal\/jkad054<\/p>\n<\/div>\n<\/div>\n<\/div>\n

2021<\/strong><\/span><\/p>\n

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Gaiewski MJ<\/span>, Drewell RA, Dresch JM (2021) Fitting thermodynamic-based models: Incorporating parameter sensitivity improves the performance of an evolutionary algorithm<\/a>. Mathematical Biosciences.<\/em> 342: 108716.<\/p>\n<\/div>\n<\/div>\n<\/div>\n

2019<\/strong><\/span><\/p>\n

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McCarthy GD<\/span>, Drewell RA, Dresch JM (2019) Analyzing the stability of gene expression using a simple reaction-diffusion model in an early Drosophila<\/em> embryo<\/a>. Mathematical Biosciences<\/em> 316: 108239.<\/p>\n<\/div>\n<\/div>\n<\/div>\n

Orlomoski R, Bogle A, Loss J, Simons R<\/span>, Dresch JM, Drewell RA, Spratt DE (2019) Rapid and efficient purification of Drosophila<\/em> homeodomain transcription factors for biophysical characterization.<\/a> Protein Expression and Purification<\/em>. 158:9-14.<\/p>\n

2017<\/strong><\/span><\/p>\n

Steenwyk JL, St. Denis J<\/span>, Dresch JM, Larochelle DA, Drewell RA (2017) Whole genome bisulfite sequencing reveals a sparse, but robust pattern of DNA methylation in the Dictyostelium discoideum<\/em> genome.<\/a> BIORXIV\/2017\/166033.<\/p>\n

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

2016<\/strong><\/span><\/p>\n

Pettie KP<\/span>, Dresch JM, Drewell RA (2016) Spatial distribution of predicted transcription factor binding sites in Drosophila<\/em> ChIP peaks.<\/a> Mechanisms of Development. 141:51-61.<\/em><\/p>\n

Dresch JM, <\/strong>Zellers RG<\/span>, Bork DK<\/span> and Drewell RA (2016) Nucleotide interdependency in transcription factor binding sites in the Drosophila<\/em> genome.<\/a> Gene Regulation and Systems Biology<\/em>. 10:21-33.<\/p>\n

*Sayal R, *Dresch JM, Pushel I<\/span>, Taylor BR<\/span>, Arnosti DN (2016) Quantitative perturbation-based analysis of gene expression predicts enhancer activity in early Drosophila<\/em> embryo.<\/a> eLife <\/em>5:e08445 (* – equal contribution)<\/p>\n

2015<\/strong><\/span><\/p>\n

Dresch, JM, Arnosti DN (2015) The Wisdom of Crowds: Can Mathematical Models Crack the cis<\/em> Regulatory Code?<\/a> Cell Systems<\/span><\/em> 1(6):<\/span>379\u2013380.<\/span><\/p>\n

McCarthy GD<\/span>, Drewell RA, Dresch JM (2015) Global sensitivity analysis of a dynamic model for gene expression in Drosophila <\/i>embryos.<\/a> PeerJ<\/em> 3:e1022 <\/p>\n

Zellers RG<\/span>, Drewell RA, Dresch JM (2015) MARZ: An algorithm to combinatorially analyze gapped n<\/em>-mer models of transcription factor binding.<\/a> BMC Bioinformatics. <\/em>16: 30.<\/p>\n

2014<\/strong><\/span><\/p>\n

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

2013<\/strong><\/span><\/p>\n

*Stringham JL<\/span>, *Brown AS<\/span>, Drewell RA, Dresch JM (2013) Flanking sequence context-dependent transcription factor binding in early Drosophila<\/em> development.<\/a> BMC Bioinformatics<\/em>. 14:298 (* – equal contribution)<\/p>\n

Suleimenov Y<\/span>, Ay A, Samee MA, Dresch JM, Sinha S, Arnosti DN (2013) Global parameter estimation for thermodynamic models of transcriptional regulation.<\/a> Methods<\/em>. 62(1):99-108.<\/p>\n

Dresch JM, Richards M<\/span>, Ay A (2013) A Primer on Thermodynamic-based Models for Deciphering Transcriptional Regulatory Logic.<\/a> <\/strong>BBA \u2013 Gene Regulatory Mechanisms.<\/em> 1829(9):946-53.<\/p>\n

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

2012<\/strong><\/span><\/p>\n

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

Chiu C, Fakhouri W, Liu N, Dayringer E<\/span>, Dresch J, Arnosti D (2012) A two-scale mathematical model for DNA transcription.<\/a> Mathematical Biosciences.<\/em> <\/em>236(2):132-140.<\/p>\n

2010<\/strong><\/span><\/p>\n

Dresch JM, Liu X<\/span>, Arnosti DN, Ay A (2010) Thermodynamic modeling of transcription: Sensitivity analysis differentiates biological mechanism from mathematical model-induced effects.<\/a> BMC Systems Biology. <\/em>4:142.<\/p>\n

*Fakhouri WD, *Ay A, Sayal R, Dresch J, Dayringer E<\/span>, Arnosti DN (2010) Deciphering a transcriptional regulatory code: modeling short-range repression in the Drosophila<\/em> embryo.<\/a> Molecular Systems Biology. <\/em>6:341. (* – equal contribution)<\/p>\n

2007<\/strong><\/span><\/p>\n

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

Dresch JM<\/span>, Hansen NC<\/span>, Hartvigsen G, Leary CC, Macula AJ (2007) Component Averages of subgraphs in Circulant-like Graphs. Bulletin of the Institute for Combinatorics and its Application<\/em> 51: 55-68.<\/p>\n","protected":false},"excerpt":{"rendered":"

Undergraduate student authors are underlined. 2025 Drewell RA, Dresch JM (2025) Identification of novel components of the retinal determination gene network in Drosophila cell lines. Open Biology. 15:250012 Gelashvili Z, Larochelle DA, Dresch JM, Hincher M, Tabima JF, Drewell RA (2025) … Continue reading →<\/span><\/a><\/p>\n","protected":false},"author":571,"featured_media":0,"parent":0,"menu_order":4,"comment_status":"closed","ping_status":"closed","template":"","meta":{"ngg_post_thumbnail":0,"footnotes":""},"class_list":["post-16","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/wordpress.clarku.edu\/jdresch\/index.php?rest_route=\/wp\/v2\/pages\/16","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/wordpress.clarku.edu\/jdresch\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/wordpress.clarku.edu\/jdresch\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/wordpress.clarku.edu\/jdresch\/index.php?rest_route=\/wp\/v2\/users\/571"}],"replies":[{"embeddable":true,"href":"https:\/\/wordpress.clarku.edu\/jdresch\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=16"}],"version-history":[{"count":0,"href":"https:\/\/wordpress.clarku.edu\/jdresch\/index.php?rest_route=\/wp\/v2\/pages\/16\/revisions"}],"wp:attachment":[{"href":"https:\/\/wordpress.clarku.edu\/jdresch\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=16"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}