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Undergraduate student authors are underlined


Supporting the democratization of science during a pandemic: genomics Course-based Undergraduate Research Experiences (CUREs) as an effective remote learning strategy.                                                                                                                D. Lopatto, S. C. Silver Key, M. Van Stry, J. Siders, W. Leung, K. M. Sandlin, C. P. Rele, Genomics Education Partnership (incl. R. A. Drewell) 2023. Journal of Microbiology & Biology Education 24: e00039-23

Investigating the sequence landscape in the Drosophila initiator core promoter element using an enhanced MARZ algorithm.                                                                 J. M. Dresch, R. D. Conrad, D. Klonaros and R. A. Drewell. 2023. PeerJ 11: e15597

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

Transcriptome profile in Drosophila Kc and S2 embryonic cell lines.
D. Klonaros, J. M. Dresch, R. A. Drewell. 2023. G3: Genes, Genomes, Genetics 13: jkad054


Fitting thermodynamic-based models:  Incorporating parameter sensitivity improves the performance of an evolutionary algorithm.
M. J. Gaiewski, R. A. Drewell and J. M. Dresch. 2021. Mathematical Biosciences 342: 108716


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

Rapid and efficient purification of Drosophila homeodomain transcription factors for biophysical characterization.
R. Orlomoski, A. Bogle, J. Loss, R. Simons, J. M. Dresch, R. A. Drewell and D. E. Spratt. 2019. Protein Expression and Purification 158: 9-14.


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

The GEP: Crowd-sourcing big data with undergraduates.                                              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.


Spatial distribution of predicted transcription factor binding sites in Drosophila ChIP peaks.
K. P. Pettie, J. M. Dresch and R. A. Drewell. 2016. Mechanisms of Development 141: 51-61.

Nucleotide interdependency in transcription factor binding sites in the Drosophila genome.
J. M. DreschR. G. ZellersD. K. Bork and R. A. Drewell. 2016. Gene Regulation and Systems Biology 10: 21-33.

Parent-of-origin effects on genome-wide DNA methylation in the Cape honey bee (Apis mellifera capensis) may be confounded by allele-specific methylation.
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.


Global sensitivity analysis of a dynamic model for gene expression in Drosophila embryos.
G. D. McCarthy, R. A. Drewell and J. M. Dresch. 2015. PeerJ 3: e1022.

MARZ: an algorithm to combinatorially analyze gapped n-mer models of transcription factor binding.
R. G. Zellers, R. A. Drewell and J. M. Dresch.  2015.  BMC Bioinformatics 16: 30.


The dynamic DNA methylation cycle from egg to sperm in the honey bee Apis mellifera.
R. A. Drewell, E. C. Bush, E. J. Remnant, G. T. Wong, S. M. Beeler, J. L. Stringham, J. Lim and B. P. Oldroyd.  2014.  Development 141: 2702-2711.

Deciphering the combinatorial architecture of a Drosophila homeotic gene enhancer.
R. A. Drewell, M. J. Nevarez, J. S. Kurata, L. N. Winkler, L. Li and J. M. Dresch.  2014.  Mechanisms of Development 131: 68-77.

Whole genome DNA methylation profile of the jewel wasp (Nasonia vitripennis).
S. M. Beeler, G. T. Wong, J. M. Zheng, E. C. Bush, E. J. Remnant, B. P. Oldroyd and R. A. Drewell.  2014.  G3: Genes, Genomes, Genetics 4: 383-388.


A parent-of-origin effect on honeybee worker ovary size.
B. 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.

Flanking sequence context-dependent transcription factor binding in early Drosophila development.
J. L. Stringham, A. S. Brown, R. A. Drewell and J. M. Dresch.  2013.  BMC Bioinformatics 14: 298.


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

Kin conflict in insect societies: a new epigenetic perspective.
R. A. Drewell, N. Lo, P. R. Oxley and B. P. Oldroyd. 2012.Trends in Ecology and Evolution 27: 367-373.


Transcription factor binding site redundancy in embryonic enhancers of the Drosophila bithorax complex
R. A. Drewell. 2011. G3: Genes, Genomes, Genetics 1: 603-606.

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

Transcriptional repression by the proximal exonic region at the human TERT gene.
T. C. Wong, E. S. Sokol, A. N. Schep, M. Punjiya, D. A. Tran, D. Allen and R. A. Drewell. 2011. Gene 486: 65-73.

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


Characterization of an ultra-conserved putative cis-regulatory module at the mammalian telomerase reverse transcriptase gene.
D. A. Tran, T. C. Wong, A. N. Schep and R. A. Drewell. 2010. DNA and Cell Biology 29: 499-508.

Dissecting the regulatory switches of development: Lessons from enhancer evolution in Drosophila.
M. J. Borok, D. A. Tran, M. C. W. Ho and R. A. Drewell. 2010. Development 137: 5-13.


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

Non-genic transcription at the Drosophila bithorax complex – functional activity of the dark matter of the genome.
M. C. W. Ho, B. J. Schiller, S. E. Goetz and R. A. Drewell. 2009. International Journal of Developmental Biology 53: 459-468.


A concise Drosophila laboratory module to introduce the central concepts of genetics.
M. C. W. Ho, D. R. Venema and R. A. Drewell. 2008. Drosophila Information Service 91: 164-168.

Between transcription and translation: re-defining RNA and regulation.
M. C. W. Ho, B. J. Schiller, S. E. Goetz, J. M. Allen and R. A. Drewell. 2008. Fly 2: 152-155.

A novel promoter tethering element regulates enhancer-driven gene expression at the bithorax complex in the Drosophila embryo.
O. S. Akbari, E. Bae, H. Johnsen, A. Villaluz, D. Wong and R. A. Drewell. 2008. Development 135: 123-131.


The Abdominal-B promoter tethering element mediates promoter-enhancer specificity at the Drosophila bithorax complex.
O. S. Akbari, B. J. Schiller, S. E. Goetz, M. C. W. Ho, E. Bae and R. A. Drewell. 2007. Fly 1: 337-339

Chromatin looping mediates boundary element promoter interactions.
S. Celniker and R. A. Drewell. 2007. Bioessays 29: 7-10.


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

Unraveling cis-regulatory mechanisms at the abdominal-A and Abdominal-B genes in the Drosophila bithorax complex.
O. S. Akbari, A. Bousum, E. Bae and R. A. Drewell. 2006. Developmental Biology 293: 294-304.

The 3′ portion of the mouse H19 Imprinting-Control Region is required for proper tissue-specific expression of the Igf2 gene.
H. Hagge, R. Nasser, M. Weber, L. Milligan, N. Aptel, C. Jacquet, R.A. Drewell, L. Dandolo, M.A. Surani, G. Cathala, T. Fornè. 2006. Cytogenetic & Genome Research 113: 230-237.


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

Characterization of the intergenic RNA profile at abdominal-A and Abdominal-B in the Drosophila bithorax complex.
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.

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

Methylation-dependent silencing at the H19 imprinting control region by MeCP2.
R. A. Drewell, C. J. Goddard, J. O. Thomas and M. A. Surani. 2002. Nucleic Acids Research 30: 1139-1144


A conserved imprinting control region at the HYMAI/ZAC domain is implicated in transient neonatal diabetes mellitus.
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

Epigenetic reprogramming of the genome – from the germ line to the embryo and back again.
K. L. Arney, S. Erhardt, R. A. Drewell and M. A. Surani. 2001. International Journal of Developmental Biology 45: 533-540


Deletion of a silencer element disrupts H19 imprinting independently of a DNA methylation epigenetic switch.
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.

A novel imprinted gene, HYMAI is located within an imprinted domain on human chromosome 6 containing ZAC.
T. Arima, R. A. Drewell, M. Oshimura, N. Wake and M. A. Surani. 2000. Genomics 67: 248-255.


A silencer element identified in Drosophila is required for imprinting of H19 reporter transgenes in mice.
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.