Dissecting the regulatory switches of development: lessons from enhancer evolution in Drosophila

A gene complex controlling segmentation in Drosophila

Lewis, E. B. (1978) · Nature · doi:10.1038/276565a0 · Cited by 3,813 · see citing works

Expression of a β-globin gene is enhanced by remote SV40 DNA sequences

Banerji, J., Rusconi, S., & Schaffner, W. (1981) · Cell · doi:10.1016/0092-8674(81)90413-x · Cited by 1,724 · see citing works

ChIP-seq accurately predicts tissue-specific activity of enhancers

Visel, A., Blow, M. J., Li, Z., Zhang, T., Akiyama, J. A., Holt, A., Plajzer-Frick, I., Shoukry, M., Wright, C., Chen, F., et al. (2009) · Nature · doi:10.1038/nature07730 · Cited by 1,639 · see citing works

A lymphocyte-specific cellular enhancer is located downstream of the joining region in immunoglobulin heavy chain genes

Banerji, J., Olson, L., & Schaffner, W. (1983) · Cell · doi:10.1016/0092-8674(83)90015-6 · Cited by 1,407 · see citing works

In vivo sequence requirements of the SV40 early promoter region

Benoist, C., & Chambon, P. (1981) · Nature · doi:10.1038/290304a0 · Cited by 1,074 · see citing works

A gradient of bicoid protein in Drosophila embryos

Driever, W., & Nüsslein‐Volhard, C. (1988) · Cell · doi:10.1016/0092-8674(88)90182-1 · Cited by 1,018 · see citing works

Virus induction of human IFNβ gene expression requires the assembly of an enhanceosome

Thanos, D., & Maniatis, T. (1995) · Cell · doi:10.1016/0092-8674(95)90136-1 · Cited by 1,014 · see citing works

Gene regulation by proteins acting nearby and at a distance

Ptashne, M. (1986) · Nature · doi:10.1038/322697a0 · Cited by 860 · see citing works

The role of localization of bicoid RNA in organizing the anterior pattern of the Drosophila embryo.

Berleth, T., Burri, M., Thoma, G., Bopp, D., Richstein, S., Frigerio, G., Noll, M., & Nüsslein‐Volhard, C. (1988) · The EMBO Journal · doi:10.1002/j.1460-2075.1988.tb03004.x · Cited by 734 · see citing works

Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila

Gompel, N., Prud'homme, B., Wittkopp, P. J., Kassner, V. A., & Carroll, S. B. (2005) · Nature · doi:10.1038/nature03235 · Cited by 646 · see citing works

The gradient morphogen bicoid is a concentration-dependent transcriptional activator

Struhl, G., Struhl, K., & Macdonald, P. M. (1989) · Cell · doi:10.1016/0092-8674(89)90062-7 · Cited by 633 · see citing works

An Atomic Model of the Interferon-β Enhanceosome

Panne, D., Maniatis, T., & Harrison, S. C. (2007) · Cell · doi:10.1016/j.cell.2007.05.019 · Cited by 625 · see citing works

Scanning Human Gene Deserts for Long-Range Enhancers

Nobrega, M. A., Ovcharenko, I., Afzal, V., & Rubin, E. M. (2003) · Science · doi:10.1126/science.1088328 · Cited by 608 · see citing works

Temporal Patterns of Fruit Fly (Drosophila) Evolution Revealed by Mutation Clocks

Tamura, K. (2003) · Molecular Biology and Evolution · doi:10.1093/molbev/msg236 · Cited by 574 · see citing works

Evidence for stabilizing selection in a eukaryotic enhancer element

Ludwig, M. Z., Bergman, C., Patel, N. H., & Kreitman, M. (2000) · Nature · doi:10.1038/35000615 · Cited by 563 · see citing works

Emerging principles of regulatory evolution

Prud’homme, B., Gompel, N., & Carroll, S. B. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0700488104 · Cited by 556 · see citing works

Regulation of even‐skipped stripe 2 in the Drosophila embryo.

Small, S., Blair, A., & Levine, M. (1992) · The EMBO Journal · doi:10.1002/j.1460-2075.1992.tb05498.x · Cited by 515 · see citing works

Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene

Prud'homme, B., Gompel, N., Rokas, A., Kassner, V. A., Williams, T. M., Yeh, S.-D., True, J. R., & Carroll, S. B. (2006) · Nature · doi:10.1038/nature04597 · Cited by 507 · see citing works

Transcriptional activators direct histone acetyltransferase complexes to nucleosomes

Utley, R. T., Ikeda, K., Grant, P. A., Côté, J., Steger, D. J., Eberharter, A., John, S., & Workman, J. L. (1998) · Nature · doi:10.1038/28886 · Cited by 499 · see citing works

Transcriptional repression of eukaryotic promoters

Levine, M., & Manley, J. L. (1989) · Cell · doi:10.1016/0092-8674(89)90024-x · Cited by 470 · see citing works

Regulation of RNA Polymerase II Transcription by Sequence-Specific DNA Binding Factors

Kadonaga, J. T. (2004) · Cell · doi:10.1016/s0092-8674(03)01078-x · Cited by 403 · see citing works

Control elements of the Drosophila segmentation gene fushi tarazu

Hiromi, Y., Kuroiwa, A., & Gehring, W. J. (1985) · Cell · doi:10.1016/0092-8674(85)90232-6 · Cited by 397 · see citing works

Isolation, structure, and expression of even-skipped: A second pair-rule gene of Drosophila containing a homeo box

Macdonald, P. M., Ingham, P., & Struhl, G. (1986) · Cell · doi:10.1016/0092-8674(86)90515-5 · Cited by 375 · see citing works

The dorsal morphogen gradient regulates the mesoderm determinant twist in early Drosophila embryos.

Jiang, J., Kosman, D., Ip, Y. T., & Levine, M. (1991) · Genes & Development · doi:10.1101/gad.5.10.1881 · Cited by 365 · see citing works

Hox protein mutation and macroevolution of the insect body plan

Ronshaugen, M., McGinnis, N., & McGinnis, W. J. (2002) · Nature · doi:10.1038/nature716 · Cited by 361 · see citing works

Transcriptional regulation of a pair-rule stripe in Drosophila.

Small, S., Kraut, R., Hoey, T., Warrior, R., & Levine, M. (1991) · Genes & Development · doi:10.1101/gad.5.5.827 · Cited by 349 · see citing works

The abdominal region of the bithorax complex

Karch, F. (1985) · Cell · doi:10.1016/0092-8674(85)90014-5 · Cited by 324 · see citing works

Coordination of PIC Assembly and Chromatin Remodeling During Differentiation-Induced Gene Activation

Soutoglou, E., & Talianidis, I. (2002) · Science · doi:10.1126/science.1068356 · Cited by 302 · see citing works

Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation

Hare, E. E., Peterson, B. K., Iyer, V. N., Meier, R., & Eisen, M. B. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000106 · Cited by 302 · see citing works

Whole-genome ChIP–chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the <i>Drosophila</i> embryo

Zeitlinger, J., Zinzen, R. P., Stark, A., Kellis, M., Zhang, H., Young, R. A., & Levine, M. (2007) · Genes &amp; Development · doi:10.1101/gad.1509607 · Cited by 286 · see citing works

Early and late periodic patterns of even skipped expression are controlled by distinct regulatory elements that respond to different spatial cues

Goto, T., Macdonald, P., & Maniatis, T. (1989) · Cell · doi:10.1016/0092-8674(89)90916-1 · Cited by 277 · see citing works

Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change

Ludwig, M. Z., Patel, N. H., & Kreitman, M. (1998) · Development · doi:10.1242/dev.125.5.949 · Cited by 270 · see citing works

Sequence-specific DNA-binding activities of the gap proteins encoded by hunchback and Krüppel in Drosophila

Štanojević, D., Hoey, T. C., & Levine, M. (1989) · Nature · doi:10.1038/341331a0 · Cited by 263 · see citing works

Autoregulatory and gap gene response elements of the even‐skipped promoter of Drosophila.

Harding, K. W., Hoey, T. C., Warrior, R., & Levine, M. (1989) · The EMBO Journal · doi:10.1002/j.1460-2075.1989.tb03493.x · Cited by 249 · see citing works

Regulation of Body Pigmentation by the Abdominal-B Hox Protein and Its Gain and Loss in Drosophila Evolution

Jeong, S., Rokas, A., & Carroll, S. B. (2006) · Cell · doi:10.1016/j.cell.2006.04.043 · Cited by 245 · see citing works

Regulation of Two Pair-Rule Stripes by a Single Enhancer in theDrosophilaEmbryo

Small, S., Blair, A., & Levine, M. (1996) · Developmental Biology · doi:10.1006/dbio.1996.0117 · Cited by 240 · see citing works

The dorsal morphogen is a sequence-specific DNA-binding protein that interacts with a long-range repression element in drosophila

Ip, Y. T., Kraut, R. S., Levine, M., & Rushlow, C. A. (1991) · Cell · doi:10.1016/0092-8674(91)90651-e · Cited by 227 · see citing works

Conservation and Evolution of Cis-Regulatory Systems in Ascomycete Fungi

Gasch, A. P., Moses, A. M., Chiang, D. Y., Fraser, H. B., Berardini, M. D., & Eisen, M. B. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020398 · Cited by 227 · see citing works

The eve stripe 2 enhancer employs multiple modes of transcriptional synergy

Arnosti, D. N., Barolo, S., Levine, M., & Small, S. (1996) · Development · doi:10.1242/dev.122.1.205 · Cited by 226 · see citing works

The molecular genetics of the bithorax complex of Drosophila: cis‐regulation in the Abdominal‐B domain.

Celniker, S., Sharma, S., Keelan, D. J., & Lewis, E. B. (1990) · The EMBO Journal · doi:10.1002/j.1460-2075.1990.tb07876.x · Cited by 210 · see citing works

A 3′ enhancer is required for temporal and tissue-specific transcriptional activation of the chicken adult β-globin gene

Choi, O.-R., & Engel, J. D. (1986) · Nature · doi:10.1038/323731a0 · Cited by 192 · see citing works

p38 MAPK signalling cascades: ancient roles and new functions

Martı́n-Blanco, E. (2000) · BioEssays · doi:10.1002/1521-1878(200007)22:7 · Cited by 189 · see citing works

Stimulation of in vitro transcription from the SV40 early promoter by the enhancer involves a specific trans‐acting factor.

Wildeman, A. G., Sassone‐Corsi, P., Grundström, T., Zenke, M., & Chambon, P. (1984) · The EMBO Journal · doi:10.1002/j.1460-2075.1984.tb02269.x · Cited by 183 · see citing works

The bx region enhancer, a distant cis‐control element of the Drosophila Ubx gene and its regulation by hunchback and other segmentation genes.

Qian, S., Capovilla, M., & Pirrotta, V. (1991) · The EMBO Journal · doi:10.1002/j.1460-2075.1991.tb07662.x · Cited by 166 · see citing works

Promoter-proximal tethering elements regulate enhancer-promoter specificity in the Drosophila Antennapedia complex

Calhoun, V. C., Stathopoulos, A., & Levine, M. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.142291299 · Cited by 163 · see citing works

Short-range repression permits multiple enhancers to function autonomously within a complex promoter.Preprint

Gray, S., Szymanski, P., & Levine, M. (1994) · Genes & Development · doi:10.1101/gad.8.15.1829 · Cited by 156 · see citing works

Threshold responses to the dorsal regulatory gradient and the subdivision of primary tissue territories in the Drosophila embryo

Rusch, J., & Levine, M. (1996) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(96)80062-1 · Cited by 150 · see citing works

The dorsal protein is distributed in a gradient in early drosophila embryos

Steward, R., Zusman, S. B., Huang, L. H., & Schedl, P. D. (1988) · Cell · doi:10.1016/0092-8674(88)90035-9 · Cited by 136 · see citing works

Genetic properties and chromatin structure of the yeast gal regulatory element: an enhancer-like sequence.

Struhl, K. (1984) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.81.24.7865 · Cited by 134 · see citing works

Evolutionary dynamics of the enhancer region of even-skipped in Drosophila.

Ludwig, M. Z., & Kreitman, M. (1995) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040277 · Cited by 131 · see citing works

Information display by transcriptional enhancers

Kulkarni, M. M., & Arnosti, D. N. (2003) · Development · doi:10.1242/dev.00890 · Cited by 118 · see citing works

Coordinate enhancers share common organizational features in the <i>Drosophila</i> genome

Erives, A., & Levine, M. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0400611101 · Cited by 117 · see citing works

Irreversible gene repression model for control of development: Lessening of developmental potential may result from progressive repression of previously active genes

Caplan, A. I., & Ordahl, C. P. (1978) · Science · doi:10.1126/science.351805 · Cited by 116 · see citing works

Modular cis-regulatory organization of developmentally expressed genes: two genes transcribed territorially in the sea urchin embryo, and additional examples.

Kirchhamer, C. V., Yuh, C., & Davidson, E. H. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.18.9322 · Cited by 105 · see citing works

Ten Years of Enhancer Detection: Lessons from the Fly

Bellen, H. J. (1999) · The Plant Cell · doi:10.1105/tpc.11.12.2271 · Cited by 96 · see citing works

Transcriptional control of Drosophila fushi tarazu zebra stripe expression.Preprint

Dearolf, C. R., Topol, J., & Parker, C. S. (1989) · Genes & Development · doi:10.1101/gad.3.3.384 · Cited by 91 · see citing works

The Immunoglobulin Heavy Chain Locus Control Region Increases Histone Acetylation along Linked c-myc Genes

Madisen, L., Krumm, A., Hebbes, T. R., & Groudine, M. T. (1998) · Molecular and Cellular Biology · doi:10.1128/mcb.18.11.6281 · Cited by 89 · see citing works

Evolution Acts on Enhancer Organization to Fine-Tune Gradient Threshold Readouts

Crocker, J., Tamori, Y., & Erives, A. J. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060263 · Cited by 89 · see citing works

A chromatin insulator mediates transgene homing and very long-range enhancer-promoter communication

Fujioka, M., Wu, X., & Jaynes, J. B. (2009) · Development · doi:10.1242/dev.036467 · Cited by 82 · see citing works

Anterior repression of aDrosophilastripe enhancer requires three position-specific mechanisms

Andrioli, L. P. M., Vasisht, V., Theodosopoulou, E., Oberstein, A., & Small, S. (2002) · Development · doi:10.1242/dev.129.21.4931 · Cited by 78 · see citing works

Direct interaction of the tau 1 transactivation domain of the human glucocorticoid receptor with the basal transcriptional machinery

McEwan, I. J., Wright, A. P. H., Dahlman-Wright, K., Carlstedt-Duke, J., & Gustafsson, J.-Å. (1993) · Molecular and Cellular Biology · doi:10.1128/mcb.13.1.399-407.1993 · Cited by 65 · see citing works

Direct interaction of the tau 1 transactivation domain of the human glucocorticoid receptor with the basal transcriptional machinery.

McEwan, I. J., Wright, A. P. H., Dahlman‐Wright, K., Carlstedt‐Duke, J., & Gustafsson, J.-Α. (1993) · Molecular and Cellular Biology · doi:10.1128/mcb.13.1.399 · Cited by 62 · see citing works

A novel promoter-tethering element regulates enhancer-driven gene expression at the bithorax complex in theDrosophilaembryo

Akbari, O. S., Bae, E., Johnsen, H., Villaluz, A., Wong, D., & Drewell, R. A. (2007) · Development · doi:10.1242/dev.010744 · Cited by 61 · see citing works

Enhancer-promoter communication at theDrosophila engrailedlocus

Kwon, D. Y., Mucci, D., Langlais, K. K., Americo, J. L., DeVido, S. K., Cheng, Y., & Kassis, J. A. (2009) · Development · doi:10.1242/dev.036426 · Cited by 58 · see citing works

Big Genomes Facilitate the Comparative Identification of Regulatory Elements

Peterson, B. K., Hare, E. E., Iyer, V. N., Storage, S. S., Conner, L. D. C., Papaj, D. R., Kurashima, R., Jang, E. B., & Eisen, M. B. (2009) · PLoS ONE · doi:10.1371/journal.pone.0004688 · Cited by 46 · see citing works

Functional Evolution of cis-Regulatory Modules at a Homeotic Gene in Drosophila

Ho, M. C. W., Johnsen, H., Goetz, S. E., Schiller, B. J., Bae, E., Tran, D. A., Shur, A., Allen, J. M., Rau, C., Bender, W. W., et al. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000709 · Cited by 46 · see citing works

Evolving enhancer-promoter interactions within the tinman complex of the flour beetle,Tribolium castaneum

Cande, J., Chopra, V. S., & Levine, M. (2009) · Development · doi:10.1242/dev.038034 · Cited by 43 · see citing works

A Human Globin Enhancer Causes both Discrete and Widespread Alterations in Chromatin Structure

Kim, A., & Dean, A. (2003) · Molecular and Cellular Biology · doi:10.1128/mcb.23.22.8099-8109.2003 · Cited by 42 · see citing works

Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motifPreprint

Cheng, Y., King, D. C., Doré, L. C., Zhang, X., Zhou, Y., Zhang, Y., Dorman, C. M., Abebe, D. F., Kumar, S. A., Chiaromonte, F., et al. (2008) · Genome Research · doi:10.1101/gr.083089.108 · Cited by 29 · see citing works

A Careful Look at Binding Site Reorganization in the even-skipped Enhancers of Drosophila and Sepsids

Hare, E. E., Peterson, B. K., & Eisen, M. B. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000268 · Cited by 28 · see citing works

A Closer Look at the eve Stripe 2 Enhancers of Drosophila and Themira

Crocker, J., & Erives, A. J. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000276 · Cited by 23 · see citing works

Developmental Control of Drosophila Yolk Protein 1 Gene by cis-acting DNA ElementsPreprint

Shepherd, B., Garabedian, M. J., Hung, M.-C., & Wensink, P. C. (1985) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.1985.050.01.064 · Cited by 23 · see citing works

Gene regulation in the Drosophila embryo

Sauer, F., Rivera-Pomar, R. V., Hoch, M., & Jäckle, H. (1996) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.1996.0057 · Cited by 20 · see citing works

The Dorsal Rel Homology Domain Plays an Active Role in Transcriptional Regulation

Jia, S., Flores-Saaib, R. D., & Courey, A. J. (2002) · Molecular and Cellular Biology · doi:10.1128/mcb.22.14.5089-5099.2002 · Cited by 18 · see citing works

The Abdominal-B Promoter Tethering Element Mediates Promoter-Enhancer Specificity at the Drosophila Bithorax Complex

Akbari, O. S., Schiller, B. J., Goetz, S. E., Ho, M. C. W., Bae, E., & Drewell, R. A. (2007) · Fly · doi:10.4161/fly.5607 · Cited by 13 · see citing works

Global view of enhancer–promoter interactome in human cells

He, B., Chen, C., Teng, L., & Tan, K. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1320308111 · Cited by 258 · see citing works

Invertebrate Models for Biomedical Research, Testing, and Education

Wilson-Sanders, S. E. (2011) · ILAR Journal · doi:10.1093/ilar.52.2.126 · Cited by 139 · see citing works

Cell-Type-Specific Control of Enhancer Activity by H3K9 Trimethylation

Zhu, Y., van Essen, D., & Saccani, S. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.05.011 · Cited by 117 · see citing works

Transcriptional enhancers and their communication with gene promoters

Ray-Jones, H., & Spivakov, M. (2021) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-021-03903-w · Cited by 81 · see citing works

Global transcriptome analysis and enhancer landscape of human primary T follicular helper and T effector lymphocytes

Weinstein, J. S., Lezon-Geyda, K., Maksimova, Y. D., Craft, S., Zhang, Y., Su, M. Y., Schulz, V., Craft, J. E., & Gallagher, P. G. (2014) · Blood · doi:10.1182/blood-2014-06-582700 · Cited by 67 · see citing works

The regulatory landscape of early maize inflorescence development

Parvathaneni, R. K., Bertolini, E., Shamimuzzaman, M., Vera, D. L., Lung, P.-Y., Rice, B. R., Zhang, J., Brown, P. J., Lipka, A. E., Bass, H. W., et al. (2020) · Genome biology · doi:10.1186/s13059-020-02070-8 · Cited by 66 · see citing works

Intronic Cis-Regulatory Modules Mediate Tissue-Specific and Microbial Control of angptl4/fiaf Transcription

Camp, J. G., Jazwa, A. L., Trent, C. M., & Rawls, J. F. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002585 · Cited by 58 · see citing works

Cellular resolution models for even skipped regulation in the entire Drosophila embryo

Ilsley, G. R., Fisher, J., Apweiler, R., DePace, A. H., & Luscombe, N. M. (2013) · eLife · doi:10.7554/elife.00522 · Cited by 51 · see citing works

Identification of Biologically Relevant Enhancers in Human Erythroid Cells

Su, M. Y., Steiner, L. A., Bogardus, H. H., Mishra, T., Schulz, V., Hardison, R. C., & Gallagher, P. G. (2013) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.413260 · Cited by 47 · see citing works

Functional anatomy of distant-acting mammalian enhancers

Dickel, D. E., Visel, A., & Pennacchio, L. A. (2013) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2012.0359 · Cited by 40 · see citing works

GATA3-Controlled Nucleosome Eviction Drives MYC Enhancer Activity in T-cell Development and Leukemia

Belver, L., Yang, A. Y., Alberó, R., Herranz, D., Brundu, F. G., Quinn, S. A., Pérez‐Durán, P., Álvarez, S., Gianni, F., Rashkovan, M., et al. (2019) · Cancer Discovery · doi:10.1158/2159-8290.cd-19-0471 · Cited by 35 · see citing works

Role of Architecture in the Function and Specificity of Two Notch-Regulated Transcriptional Enhancer Modules

Liu, F., & Posakony, J. W. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002796 · Cited by 33 · see citing works

Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogasterPreprint

Slattery, M., Ma, L., Spokony, R. F., Arthur, R. K., Kheradpour, P., Kundaje, A., Nègre, N., Crofts, A., Ptashkin, R., Zieba, J., et al. (2014) · Genome Research · doi:10.1101/gr.168807.113 · Cited by 33 · see citing works

The Relationship Between Long-Range Chromatin Occupancy and Polymerization of theDrosophilaETS Family Transcriptional Repressor Yan

Webber, J. L., Zhang, J., Cote, L. E., Vivekanand, P., Ni, X., Zhou, J. H. S., Negre, N. N., Carthew, R. W., White, K. P., & Rebay, I. (2012) · Genetics · doi:10.1534/genetics.112.146647 · Cited by 32 · see citing works

Cis -acting variation is common across regulatory layers but is often buffered during embryonic developmentPreprint

Floc’hlay, S., Wong, E. S. W., Zhao, B., Viales, R. R., Thomas‐Chollier, M., Thieffry, D., Garfield, D. A., & Furlong, E. E. M. (2020) · Genome Research · doi:10.1101/gr.266338.120 · Cited by 29 · see citing works

Molecular dissection of cis-regulatory modules at the Drosophila bithorax complex reveals critical transcription factor signature motifs

Starr, M. O., Ho, M. C. W., Gunther, E. J. M., Tu, Y.-K., Shur, A., Goetz, S. E., Borok, M. J., Kang, V., & Drewell, R. A. (2011) · Developmental Biology · doi:10.1016/j.ydbio.2011.07.028 · Cited by 24 · see citing works

Deciphering the combinatorial architecture of a Drosophila homeotic gene enhancer

Drewell, R. A., Nevarez, M. J., Kurata, J. S., Winkler, L. N., Li, L., & Dresch, J. M. (2013) · Mechanisms of Development · doi:10.1016/j.mod.2013.10.002 · Cited by 20 · see citing works

Dynamic patterning by morphogens illuminated by cis-regulatory studies

Irizarry, J., & Stathopoulos, A. (2021) · Development · doi:10.1242/dev.196113 · Cited by 19 · see citing works

Flanking sequence context-dependent transcription factor binding in early Drosophila development

Stringham, J. L., Brown, A. S., Drewell, R. A., & Dresch, J. M. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-298 · Cited by 17 · see citing works

Transcriptional regulation of metabolism in disease: From transcription factors to epigenetics

Hawkins, L. J., Al-attar, R., & Storey, K. B. (2018) · PeerJ · doi:10.7717/peerj.5062 · Cited by 16 · see citing works

Modularity of CHIP/LDB transcription complexes regulates cell differentiation

Bronstein, R., & Segal, D. (2011) · Fly · doi:10.4161/fly.5.3.14854 · Cited by 14 · see citing works

Endocrinology: Advances through omics and related technologies

García‐Reyero, N., Tingaud‐Sequeira, A., Cao, M., Zhu, Z., Perkins, E. J., & Hu, W. (2014) · General and Comparative Endocrinology · doi:10.1016/j.ygcen.2014.03.042 · Cited by 13 · see citing works

Common motifs shared by conserved enhancers of Drosophila midline glial genes

Fulkerson, E., & Estes, P. A. (2010) · Journal of Experimental Zoology Part B Molecular and Developmental Evolution · doi:10.1002/jez.b.21382 · Cited by 10 · see citing works

The Evo-Devo Puzzle of Human Hair Patterning

Held, L. I. (2010) · Evolutionary Biology · doi:10.1007/s11692-010-9085-4 · Cited by 10 · see citing works

In vivo mapping of mutagenesis sensitivity of human enhancers

Kosicki, M., Zhang, B., Hecht, V. C., Pampari, A., Cook, L., Slaven, N., Akiyama, J. A., Plajzer-Frick, I., Novak, C. S., Kato, M., et al. (2025) · Nature · doi:10.1038/s41586-025-09182-w · Cited by 9 · see citing works

The folded k-spectrum kernel: A machine learning approach to detecting transcription factor binding sites with gapped nucleotide dependencies

Elmas, A., Wang, X., & Dresch, J. M. (2017) · PLoS ONE · doi:10.1371/journal.pone.0185570 · Cited by 8 · see citing works

Color-Patterns to Architecture Conversion through Conditional Generative Adversarial Networks

Navarro-Mateu, D., Carrasco, O. L., & Nieves, P. C. (2021) · Biomimetics · doi:10.3390/biomimetics6010016 · Cited by 8 · see citing works

Natural selection drives rapid evolution of mouse embryonic heart enhancers

Liao, B., & Weng, M. (2012) · BMC Systems Biology · doi:10.1186/1752-0509-6-s2-s1 · Cited by 8 · see citing works

The evolutionary geometry of human anatomy: Discovering our inner fly

Held, L. I. (2010) · Evolutionary Anthropology Issues News and Reviews · doi:10.1002/evan.20287 · Cited by 5 · see citing works

Phylogenetic Approach to Studying Developmental Evolution: A Model Clade Approach

Howarth, D. G., & Dunn, M. P. (2016) · Elsevier eBooks · doi:10.1016/b978-0-12-800049-6.00137-2 · Cited by 5 · see citing works

Microevolution of cis-Regulatory Elements: An Example from the Pair-Rule Segmentation Gene fushi tarazu in the Drosophila melanogaster Subgroup

Bakkali, M. (2011) · PLoS ONE · doi:10.1371/journal.pone.0027376 · Cited by 4 · see citing works

Spacer sequences separating transcription factor binding motifs set enhancer quality and strengthPreprint

Guéroult-Bellone, M., Nitta, K. R., Kari, W., Jacox, E. H., Dauzat, R. B., Vincentelli, R., Diarra, C., Rothbächer, U., Dantec, C., Cambillau, C., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/098830 · Cited by 4 · see citing works

Transcriptional regulation of neuropeptide receptors underlies context‐dependent adaptation in Drosophila melanogaster

Ryu, S., Wei, Y., Wu, Z., Zhang, T., Lee, D., Najafi, H., & Kim, W. J. (2025) · FEBS Open Bio · doi:10.1002/2211-5463.70107 · Cited by 3 · see citing works

CBS: an open platform that integrates predictive methods and epigenetics information to characterize conserved regulatory features in multiple Drosophila genomes

Blanco, E., & Corominas, M. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-688 · Cited by 3 · see citing works

Cis acting variation is common, can propagates across multiple regulatory layers, but is often buffered in developmental programsPreprint

Floc’hlay, S., Wong, E. S. W., Zhao, B., Viales, R. R., Thomas‐Chollier, M., Thieffry, D., Garfield, D. A., & Furlong, E. E. M. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.05.21.107961 · Cited by 3 · see citing works

Two coacting shadow enhancers regulate twin of eyeless expression during early Drosophila development

Dresch, J. M., Nourie, L., Conrad, R. D., Carlson, L. T., Tchantouridze, E. I., Tesfaye, B., Verhagen, E., Gupta, M., Borges-Rivera, D., & Drewell, R. A. (2024) · Genetics · doi:10.1093/genetics/iyae176 · Cited by 2 · see citing works

Rapid and efficient purification of Drosophila homeodomain transcription factors for biophysical characterization

Orlomoski, R. J., Bogle, A., Loss, J., Simons, R., Dresch, J. M., Drewell, R. A., & Spratt, D. E. (2019) · Protein Expression and Purification · doi:10.1016/j.pep.2019.02.001 · Cited by 2 · see citing works

Transcription Factor Binding Site Redundancy in Embryonic Enhancers of the Drosophila Bithorax Complex

Drewell, R. A. (2011) · G3 Genes Genomes Genetics · doi:10.1534/g3.111.001404 · Cited by 1 · see citing works

Transcriptional Protein-Protein Cooperativity in POU/HMG/DNA Complexes Revealed by Normal Mode Analysis

Wang, D. D., & Yan, H. (2013) · Computational and Mathematical Methods in Medicine · doi:10.1155/2013/854710 · Cited by 1 · see citing works

Cell-specific Gene Expression: Pylorus Morphogenesis and Hedgehog-regulated Enhancers.

Udager, A. M. (2012) · Deep Blue (University of Michigan)

Differential Use of Paralogous Genes via Evolution of Cis-Regulatory Elements for Divergent Expression Specificities

Ochi, H., Kawaguchi, A., & Ogino, H. (2014) · Springer eBooks · doi:10.1007/978-4-431-54634-4_21

Transcriptional cooperativity in molecular dynamics based on normal mode analysis

Wang, D. D., Yan, H., & Be, Q. (2012) · International Conference on Machine Learning and Cybernetics · doi:10.1109/icmlc.2012.6359491

Identifying developmental enhancers: changing perspectives with advancing techniques

Gongal, P. (2013) · Postdoc Journal · doi:10.14304/surya.jpr.v1n10.1

Deciphering the developmental program in the ascidian Ciona intestinalis just prior to gastrulationPreprint

Harada, Y. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/137166

Watching gene expression in color

Simpson, J. H. (2019) · eLife · doi:10.7554/elife.49414

Exploring a Drosophila Transcription Factor Interaction Network to Identify Cis-Regulatory Modules

Mahmud, A. K. M. F., Yang, D., Stenberg, P., Ioshikhes, I. P., & Nandi, S. (2019) · Journal of Computational Biology · doi:10.1089/cmb.2018.0160

Gene expression and regulation relative to specific tissues and functions

Smith, M. (2023) · Elsevier eBooks · doi:10.1016/b978-0-443-15352-5.00004-2

A Phylogenetic Approach to Studying Developmental Evolution: A Model Clade Approach

Sengupta, A., Dunn, M. P., & Howarth, D. G. (2024) · Elsevier eBooks · doi:10.1016/b978-0-443-15750-9.00081-1

Mechanism of regulatory evolution : studies on the gain and diversification of wing pigmentation patterns in Drosphila

Su, K. (2011) · theses.fr (ABES) · doi:10.70675/b18a55a9z9caez40e6z85c9z1a9363096edb

Signatures nucléotidiques de l'activité des enhancers développementaux chez l'ascidie Ciona intestinalis

Guéroult-Bellone, M. (2016) · theses.fr (ABES) · doi:10.70675/59604ff1z809az4462zb8f9z6a8870b33001

Mise en place de l'identité musculaire durant la myogenèse embryonnaire chez la drosophile

Carayon, A. (2018) · doi:10.70675/e22450c4z6ee9z49eczabdcz080f041eecd8

Computational analysis and modelling of regulatory networks controlling embryonic development

Floc’hlay, S. (2020) · doi:10.70675/8d0e3a18z3294z4502z870dz9c18564e6415

Characterising the function and evolution of enhancers in Drosophila

Buffry, A. D. (2019) · Radar (Oxford Brookes University) · doi:10.24384/re1v-5k80

Assessing modularity of developmental enhancers in Drosophila melanogaster

Martin, T. L. (2014) · Digital Access to Scholarship at Harvard (DASH) (Harvard University)

Functional Evolution of a cis-Regulatory Module

Ludwig, M. Z., Pálsson, A., Alekseeva, E. A., Bergman, C., Nathan, J., & Kreitman, M. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030093 · Cited by 207 · see citing works

A Closer Look at the eve Stripe 2 Enhancers of Drosophila and Themira

Crocker, J., & Erives, A. J. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000276 · Cited by 23 · see citing works

Enhancer Interactions in Developmental Gene Regulation

Biette, K. M. (2019) · Digital Access to Scholarship at Harvard (DASH) (Harvard University)