{"id":24,"date":"2014-12-15T20:19:03","date_gmt":"2014-12-15T20:19:03","guid":{"rendered":"https:\/\/wordpress.clarku.edu\/drewelllab\/?page_id=24"},"modified":"2025-07-16T11:01:45","modified_gmt":"2025-07-16T11:01:45","slug":"publications","status":"publish","type":"page","link":"https:\/\/wordpress.clarku.edu\/drewelllab\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"

Google Scholar<\/a><\/h3>\n

Pubmed<\/a><\/h3>\n

Undergraduate student authors are in bold<\/strong><\/h3>\n

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

Identification of novel components of the retinal determination gene network in Drosophila<\/em> cell lines.<\/a>                                                                                                           <\/strong>R. A. Drewell and J. M. Dresch. 2025. Open Biology 15: 250012<\/p>\n

Dissecting the function of the DNMT2-homolog (DNMA) in Dictyostelium discoideum<\/em>.<\/a>                                                                                                                        Z. Gelashvili<\/strong>, D. A. Larochelle, J. M. Dresch, M. Hincher<\/strong>, J. F. Tabima and R. A. Drewell. 2025. G3: Genes, Genomes, Genetics 15: jkaf152<\/p>\n

Experimental approaches to investigate biophysical interactions between homeodomain transcription factors and DNA.<\/a>                                                                 <\/strong>F. Mekkaoui, R. A. Drewell, <\/strong>J. M. Dresch and D. E. Spratt. 2025. BBA – Gene Regulatory Mechanisms 1868: 195074<\/p>\n

Two coacting shadow enhancers regulate twin of eyeless <\/em>expression during early Drosophila <\/em>development.<\/a>                                                                                           <\/strong>J. M. Dresch, L. L. Nurie<\/strong>, R. D. Conrad<\/strong>, L. T. Carlson<\/strong>, E. I. Tchantouridze<\/strong>, B. Tesafye<\/strong>, E. Verhagen<\/strong>, M. Gupta, D. Borges-Rivera and R. A. Drewell. 2025. Genetics 229: iyae176<\/p>\n

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

Transcription factor expression landscape in Drosophila<\/em> embryonic cell lines.<\/a><\/strong>
\n<\/strong>R. A. Drewell, D. Klonaros and J. M. Dresch. 2024. BMC Genomics 25: 307<\/span><\/p>\n

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

Supporting the democratization of science during a pandemic: genomics Course-based Undergraduate Research Experiences (CUREs) as an effective remote learning strategy.<\/a>                                                                                                                <\/strong>D. Lopatto, S. C. Silver Key, M. Van Stry, J. Siders, W. Leung, K. M. Sandlin, C. P. <\/span>Rele, Genomics Education Partnership (incl. R. A. Drewell) 2023. Journal of Microbiology & Biology Education 24: e<\/span>00039-23<\/span><\/p>\n

Investigating the sequence landscape in the Drosophila<\/em> initiator core promoter element using an enhanced MARZ algorithm.<\/a>                                                                 <\/strong>J. M. Dresch, R. D. Conrad<\/strong>, D. Klonaros and R. A. Drewell. 2023. PeerJ 11: e15597<\/p>\n

The Dictyostelium discoideum<\/em> genome lacks significant DNA methylation and uncovers palindromic sequences as a source of false positives in bisulfite sequencing.<\/a>
\n<\/strong><\/strong>R. A. Drewell, T. C. Cormier<\/strong>, J. L. Steenwyk<\/strong>, J. St. Denis<\/strong>, J. F. Tabima, J. M. Dresch and D. A. Larochelle. 2023. NAR Genomics and Bioinformatics 5: lqad035 <\/span><\/p>\n

Transcriptome profile in Drosophila<\/em> Kc and S2 embryonic cell lines.<\/a><\/strong>
\n<\/strong>D. Klonaros, J. M. Dresch, R. A. Drewell. 2023. G3: Genes, Genomes, Genetics 13: jkad054<\/span><\/p>\n

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

Fitting thermodynamic-based models:  Incorporating parameter sensitivity improves the performance of an evolutionary algorithm.<\/a><\/strong>
\n<\/strong>M. J. Gaiewski<\/span><\/strong>, <\/span>R. A. Drewell and J. M. Dresch. 2021. Mathematical Biosciences 342: 108716<\/span><\/p>\n

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

Analyzing the stability of gene expression using a simple reaction-diffusion model in an early Drosophila<\/em> embryo.<\/a><\/strong>
\n<\/strong>G. D. McCarthy<\/span><\/strong>, <\/span>R. A. Drewell and J. M. Dresch. 2019. Mathematical Biosciences 316: 108239<\/span><\/p>\n

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

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

Whole genome bisulfite sequencing reveals a sparse, but robust pattern of DNA methylation in the Dictyostelium discoideum <\/em>genome.<\/a>
\nJ. L. Steenwyk<\/strong>, J. St. Denis<\/strong>, J. M. Dresch, D. A. Larochelle and R. A. Drewell. 2017. BIORXIV\/2017\/166033<\/p>\n

The GEP: Crowd-sourcing big data with undergraduates<\/span>.<\/span><\/a><\/strong>                                              C. R. Elgin, C. Hauser, T. M. Holzen, C. Jones, A. Kleinschmit, J. Leatherman, Genomics Education Partnership (incl. R. A. Drewell). 2017. Trends in Genetics 33: 81-85.<\/p>\n

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

Spatial distribution of predicted transcription factor binding sites in Drosophila<\/em> ChIP peaks.<\/span><\/a>
\nK. P. Pettie<\/span><\/strong>, J. M. Dresch and R. A. Drewell. 2016. Mechanisms of Development 141: 51-61.<\/p>\n

Nucleotide interdependency in transcription factor binding sites in the Drosophila<\/em> genome.<\/span><\/a>
\n<\/strong>J. M. Dresch, R. G. Zellers<\/span><\/strong>, D. K. Bork<\/span><\/strong> and R. A. Drewell. 2016. Gene Regulation and Systems Biology 10: 21-33.<\/p>\n

Parent-of-origin effects on genome-wide DNA methylation in the <\/span>Cape honey bee (Apis <\/em>mellifera<\/i> capensis<\/em>) may be confounded by allele-specific methylation.<\/span><\/a>
\n<\/strong>E. J. Remnant, A. Ashe, P. Young, G. Buchmann, M. Beekman, M. H. Allsopp, C. M. Suter, R. A. Drewell and B. P. Oldroyd.  2016.  BMC Genomics 17: 226.<\/p>\n

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

Global sensitivity analysis of a dynamic model for gene expression in Drosophila<\/em> embryos.<\/strong><\/a>
\n<\/strong>G. D. McCarthy<\/strong>,<\/span> R. A. Drewell and J. M. Dresch. 2015. PeerJ 3: e1022.
\n<\/span>
\n<\/strong><\/a>MARZ: an algorithm to combinatorially analyze ga<\/strong>pped n<\/em>-mer models of transcription factor binding<\/strong><\/span>.<\/span><\/span><\/a>
\nR. G. Zellers<\/strong>,<\/span> R. A. Drewell and J. M. Dresch.  2015.  BMC Bioinformatics 16: 30.<\/p>\n

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

The dynamic DNA methylation cycle from egg to sperm in the honey bee Apis mellifera<\/em>.<\/a><\/strong>
\nR. A. Drewell, E. C. Bush, E. J. Remnant, G. T. Wong<\/strong>, S. M. Beeler<\/strong>, J. L. Stringham<\/strong><\/span>, J. Lim and B. P. Oldroyd.  2014.  Development 141: 2702-2711.<\/p>\n

Deciphering the combinatorial architecture of a Drosophila<\/em> homeotic gene enhancer.<\/a><\/strong>
\nR. A. Drewell, M. J. Nevarez<\/strong>, J. S. Kurata<\/strong>, L. N. Winkler<\/strong><\/span>, L. Li and J. M. Dresch.  2014.  Mechanisms of Development 131: 68-77.<\/p>\n

Whole genome DNA methylation profile of the jewel wasp (Na<\/em><\/span>sonia<\/span><\/em> vitripennis<\/em>)<\/span>.<\/span><\/a><\/strong><\/b>
\nS. M. Beeler<\/strong>, G. T. Wong<\/strong>, J. M. Zheng<\/strong><\/span>, E. C. Bush, E. J. Remnant, B. P. Oldroyd and R. A. Drewell.  2014.  G3: Genes, Genomes, Genetics 4: 383-388.<\/span><\/p>\n

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

A parent-of-origin effect on honeybee worker ovary size.<\/a><\/strong>
\nB. P. Oldroyd, M. H. Allsopp, K. M. Roth, E. J. Remnant, R. A. Drewell and M. Beekman.  2013.  Proceedings of the Royal Society B 281: 20132388.<\/p>\n

Flanking sequence context-dependent transcription factor binding in early Drosophila<\/em> development.<\/a><\/strong>
\nJ. L. Stringham<\/strong>, A. S. Brown<\/strong><\/span>, R. A. Drewell and J. M. Dresch.  2013.  BMC Bioinformatics 14: 298.<\/p>\n

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

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

Kin conflict in insect societies: a new epigenetic perspective<\/a><\/strong>.
\nR. A. Drewell, N. Lo, P. R. Oxley and B. P. Oldroyd. 2012.Trends in Ecology and Evolution 27: 367-373.<\/p>\n

2011<\/strong><\/p>\n

Transcription factor binding site redundancy in embryonic enhancers of the Drosophila<\/em> bithorax complex<\/strong>
\n<\/a> R. A. Drewell. 2011. G3: Genes, Genomes, Genetics 1: 603-606.<\/p>\n

Molecular dissection of cis<\/em>-regulatory modules at the Drosophila <\/em>bithorax complex reveals critical transcription factor signature motifs.<\/strong>
\n<\/a>M. O. Starr<\/strong>, M. C. W. Ho<\/strong>, E. J. M. Gunther<\/strong>, Y. K. Tu<\/strong>, A. S. Shur<\/strong>, S. E. Goetz<\/strong>, M. J. Borok<\/strong><\/span>, V. Kang and R. A. Drewell. 2011. Developmental Biology 359: 290-302.<\/p>\n

Transcriptional repression by the proximal exonic region at the human TERT<\/em> gene.<\/strong>
\n<\/a>T. C. Wong<\/strong>, E. S. Sokol<\/strong>, A. N. Schep<\/strong>, M. Punjiya<\/strong>, D. A. Tran<\/strong>, D. Allen<\/strong><\/span> and R. A. Drewell. 2011. Gene 486: 65-73.<\/p>\n

Disruption of the Abdominal-B<\/em> promoter tethering element results in a loss of long-range enhancer-directed Hox gene expression in Drosophila<\/em>.<\/strong>
\n<\/a>M. C. W. Ho<\/strong>, B. J. Schiller<\/strong><\/span>, O. S. Akbari, E. Bae and R. A. Drewell. 2011. PLoS One 6: e16283.<\/p>\n

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

Characterization of an ultra-conserved putative cis<\/em>-regulatory module at the mammalian telomerase reverse transcriptase gene.<\/strong>
\n<\/a> D. A. Tran<\/strong>, T. C. Wong<\/strong>, A. N. Schep<\/strong><\/span> and R. A. Drewell. 2010. DNA and Cell Biology 29: 499-508.<\/p>\n

Dissecting the regulatory switches of development: Lessons from enhancer evolution in Drosophila<\/em>.<\/strong>
\n<\/a>M. J. Borok<\/strong>, D. A. Tran<\/strong>, M. C. W. Ho<\/strong><\/span> and R. A. Drewell. 2010. Development 137: 5-13.<\/p>\n

2009<\/strong><\/p>\n

Functional evolution of cis<\/em>-regulatory modules at a homeotic gene in Drosophila<\/em>.<\/strong>
\n<\/a> M. C. W. Ho<\/strong>, H. Johnsen<\/strong>, S. E. Goetz<\/strong>, B. J. Schiller<\/strong><\/span>, E. Bae, D. A. Tran<\/strong>, A. S. Shur<\/strong>, J. M. Allen<\/strong>, C. Rau<\/strong><\/span>, W. Bender, W. W. Fisher, S. E. Celniker and R. A. Drewell. 2009. PLoS Genetics 5: e1000709.<\/p>\n

Non-genic transcription at the Drosophila<\/em> bithorax complex \u2013 functional activity of the dark matter of the genome<\/strong>.
\n<\/a>M. C. W. Ho<\/strong>, B. J. Schiller<\/strong>, S. E. Goetz<\/strong><\/span> and R. A. Drewell. 2009. International Journal of Developmental Biology 53: 459-468.<\/p>\n

2008<\/strong><\/p>\n

A concise Drosophila<\/em> laboratory module to introduce the central concepts of genetics<\/strong>.<\/span>
\n<\/a> M. C. W. Ho<\/span><\/strong>, D. R. Venema and R. A. Drewell. 2008. Drosophila Information Service 91: 164-168.<\/p>\n

Between transcription and translation: re-defining RNA and regulation.<\/strong>
\n<\/a>M. C. W. Ho<\/strong>, B. J. Schiller<\/strong>, S. E. Goetz<\/strong>, J. M. Allen<\/strong><\/span> and R. A. Drewell. 2008. Fly 2: 152-155.<\/p>\n

A novel promoter tethering element regulates enhancer-driven gene expression at the bithorax complex in the Drosophila<\/em> embryo.<\/strong>
\n<\/a>O. S. Akbari, E. Bae, H. Johnsen<\/strong>, A. Villaluz<\/strong>, D. Wong<\/strong><\/span> and R. A. Drewell. 2008. Development 135: 123-131.<\/p>\n

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

The Abdominal-B<\/em> promoter tethering element mediates promoter-enhancer specificity at the Drosophila<\/em> bithorax complex.<\/strong>
\n<\/a> O. S. Akbari, B. J. Schiller<\/strong>, S. E. Goetz<\/strong>, M. C. W. Ho<\/strong><\/span>, E. Bae and R. A. Drewell. 2007. Fly 1: 337-339<\/p>\n

Chromatin looping mediates boundary element promoter interactions.<\/strong>
\n<\/a>S. Celniker and R. A. Drewell. 2007. Bioessays 29: 7-10.<\/p>\n

2006<\/strong><\/p>\n

The human and mouse H19<\/em> imprinting control regions harbor an evolutionarily conserved silencer element that functions on transgenes in Drosophila<\/em>.<\/strong>
\n<\/a> K. L. Arney, E. Bae, C. E. Olsen<\/span><\/strong> and R. A. Drewell. 2006. Development, Genes and Evolution 216: 811-819.<\/p>\n

Unraveling cis<\/em>-regulatory mechanisms at the abdominal-A<\/em> and Abdominal-B<\/em> genes in the Drosophila<\/em> bithorax complex.<\/strong>
\n<\/a>O. S. Akbari, A. Bousum, E. Bae and R. A. Drewell. 2006. Developmental Biology 293: 294-304.<\/p>\n

The 3\u2032 portion of the mouse H19<\/em> Imprinting-Control Region is required for proper tissue-specific expression of the Igf2<\/em> gene.<\/strong>
\n<\/a>H. Hagge, R. Nasser, M. Weber, L. Milligan, N. Aptel, C. Jacquet, R.A. Drewell, L. Dandolo, M.A. Surani, G. Cathala, T. Forn\u00e8. 2006. Cytogenetic & Genome Research 113: 230-237.<\/p>\n

2002<\/strong><\/p>\n

Transcription defines the embryonic domains of cis<\/em>-regulatory activity at the Drosophila<\/em> bithorax complex.<\/strong>
\n<\/a> R. A. Drewell, E. Bae, J. Burr and E. B. Lewis. 2002. Proceedings of the National Academy of Sciences USA 99: 16853-16858.<\/p>\n

Characterization of the intergenic RNA profile at abdominal-A<\/em> and Abdominal-B<\/em> in the Drosophila<\/em> bithorax complex.<\/strong>
\n<\/a>E. Bae, V. C. Calhoun, M. Levine, E. B. Lewis and R. A. Drewell. 2002. Proceedings of the National Academy of Sciences USA 99: 16847-16852.<\/p>\n

Novel conserved elements upstream of the H19<\/em> gene are transcribed and act as mesoderm enhancers<\/strong>.
\n<\/a>R. A. Drewell, K. L. Arney, T. Arima, S. C. Barton, J. D. Brenton and M. A. Surani. 2002. Development 129: 1205-1213<\/p>\n

Methylation-dependent silencing at the H19<\/em> imprinting control region by MeCP2.<\/strong>
\n<\/a>R. A. Drewell, C. J. Goddard, J. O. Thomas and M. A. Surani. 2002. Nucleic Acids Research 30: 1139-1144<\/p>\n

2001<\/strong><\/p>\n

A conserved imprinting control region at the HYMAI\/ZAC<\/em> domain is implicated in transient neonatal diabetes mellitus.<\/strong>
\n<\/a> T. Arima, R. A. Drewell, K. L. Arney, J. Inoue, Y. Makita, A. Hata, M. Oshimura, N. Wake, and M. A. Surani. 2001. Human Molecular Genetics 10: 1475-1483<\/p>\n

Epigenetic reprogramming of the genome \u2013 from the germ line to the embryo and back again.<\/strong>
\n<\/a>K. L. Arney, S. Erhardt, R. A. Drewell and M. A. Surani. 2001. International Journal of Developmental Biology 45: 533-540<\/p>\n

2000<\/strong><\/p>\n

Deletion of a silencer element disrupts H19<\/em> imprinting independently of a DNA methylation epigenetic switch.<\/strong>
\n<\/a> R. A. Drewell, J. D. Brenton, J. F-X Ainscough, S. C. Barton, K. J. Hilton, K. L. Arney, L. Dandolo and M. A. Surani. 2000. Development 127: 3419-3428.<\/p>\n

A novel imprinted gene, HYMAI<\/em> is located within an imprinted domain on human chromosome 6 containing ZAC<\/em>.<\/strong>
\n<\/a>T. Arima, R. A. Drewell, M. Oshimura, N. Wake and M. A. Surani. 2000. Genomics 67: 248-255.<\/p>\n

1999<\/strong><\/p>\n

A silencer element identified in Drosophila<\/em> is required for imprinting of H19<\/em> reporter transgenes in mice.<\/strong>
\n<\/a>J. D. Brenton, R. A. Drewell, S. Viville, K. J. Hilton, S. C. Barton, J. F.-X. Ainscough, and M. A. Surani. 1999. Proceedings of the National Academy of Sciences USA 96: 9242-9247.<\/p>\n","protected":false},"excerpt":{"rendered":"

Google Scholar Pubmed Undergraduate student authors are in bold 2025 Identification of novel components of the retinal determination gene network in Drosophila cell lines.                                 … Continue reading →<\/span><\/a><\/p>\n","protected":false},"author":498,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"ngg_post_thumbnail":0,"footnotes":""},"class_list":["post-24","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/wordpress.clarku.edu\/drewelllab\/wp-json\/wp\/v2\/pages\/24","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/wordpress.clarku.edu\/drewelllab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/wordpress.clarku.edu\/drewelllab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/wordpress.clarku.edu\/drewelllab\/wp-json\/wp\/v2\/users\/498"}],"replies":[{"embeddable":true,"href":"https:\/\/wordpress.clarku.edu\/drewelllab\/wp-json\/wp\/v2\/comments?post=24"}],"version-history":[{"count":0,"href":"https:\/\/wordpress.clarku.edu\/drewelllab\/wp-json\/wp\/v2\/pages\/24\/revisions"}],"wp:attachment":[{"href":"https:\/\/wordpress.clarku.edu\/drewelllab\/wp-json\/wp\/v2\/media?parent=24"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}