A regulatory code for neurogenic gene expression in the Drosophila embryo

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The Drosophila embryo at single-cell transcriptome resolution

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Genomic Regulatory Networks and Animal Development

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Multiple enhancers ensure precision of gap gene-expression patterns in the <i>Drosophila</i> embryo

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Dorsoventral Axis Formation in the Drosophila Embryo—Shaping and Transducing a Morphogen Gradient

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Computational Models for Neurogenic Gene Expression in the Drosophila Embryo

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Enhancer grammar in development, evolution, and disease: dependencies and interplay

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Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer featuresPreprint

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Quantitative Models of Developmental Pattern Formation

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A conserved role for Snail as a potentiator of active transcriptionPreprint

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Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation

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A Combinatorial Code for Pattern Formation in Drosophila Oogenesis

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Whole-genome analysis of Drosophila gastrulation

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A systematic approach to identify functional motifs within vertebrate developmental enhancers

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Conservation of enhancer location in divergent insects

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cis-Regulatory networks during development: a view of Drosophila

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Pattern Formation by Graded and Uniform Signals in the Early Drosophila Embryo

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Localized repressors delineate the neurogenic ectoderm in the early Drosophila embryo

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Evolution of the Ventral Midline in Insect Embryos

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High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservationPreprint

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An ancient transcriptional regulatory linkage

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Enhancer architecture and chromatin accessibility constrain phenotypic space during Drosophila development

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Genome-wide analyses of Shavenbaby target genes reveals distinct features of enhancer organization

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Big Genomes Facilitate the Comparative Identification of Regulatory Elements

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Transcriptional Enhancers in Drosophila

Small, S., & Arnosti, D. N. (2020) · Genetics · doi:10.1534/genetics.120.301370 · Cited by 41 · 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

Brachyury, Foxa2 and the cis-Regulatory Origins of the Notochord

José‐Edwards, D. S., Oda‐Ishii, I., Kugler, J. E., Passamaneck, Y. J., Katikala, L., Nibu, Y., & Gregorio, A. D. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005730 · Cited by 42 · see citing works

Evidence for Deep Regulatory Similarities in Early Developmental Programs across Highly Diverged Insects

Kazemian, M., Suryamohan, K., Chen, J., Zhang, Y., Samee, M. A. H., Halfon, M. S., & Sinha, S. (2014) · Genome Biology and Evolution · doi:10.1093/gbe/evu184 · Cited by 40 · see citing works

Enhancer Responses to Similarly Distributed Antagonistic Gradients in Development

Zinzen, R. P., & Papatsenko, D. (2007) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030084 · Cited by 40 · see citing works

Autoregulatory Feedback Controls Sequential Action of cis-Regulatory Modules at the brinker Locus

Dunipace, L., Saunders, A., Ashe, H. L., & Stathopoulos, A. (2013) · Developmental Cell · doi:10.1016/j.devcel.2013.08.010 · Cited by 36 · see citing works

Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules

Boeva, V., Clément, J., Régnier, M., Абрамович, Р. М., & Makeev, V. J. (2007) · Algorithms for Molecular Biology · doi:10.1186/1748-7188-2-13 · Cited by 38 · see citing works

The mouth, the anus, and the blastopore—open questions about questionable openings

Hejnol, A., & Martindale, M. Q. (2009) · Animal Evolution · doi:10.1093/acprof:oso/9780199549429.003.0004 · Cited by 37 · see citing works

Su(H)-Mediated Repression Positions Gene Boundaries along the Dorsal-Ventral Axis of Drosophila Embryos

Özdemir, A., Ma, L., White, K. P., & Stathopoulos, A. (2014) · Developmental Cell · doi:10.1016/j.devcel.2014.08.005 · Cited by 35 · see citing works

Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis

Yavatkar, A. S., Lin, Y., Ross, J., Fann, Y. C., Brody, T., & Odenwald, W. F. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-106 · Cited by 33 · see citing works

Hairless induces cell death by downregulation of EGFR signalling activity

Protzer, C. E., Wech, I., & Nagel, A. C. (2008) · Journal of Cell Science · doi:10.1242/jcs.035014 · Cited by 30 · see citing works

Accurate Prediction of Gene Expression by Integration of DNA Sequence Statistics with Detailed Modeling of Transcription Regulation

Vilar, J. M. G. (2010) · Biophysical Journal · doi:10.1016/j.bpj.2010.08.006 · Cited by 28 · 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

Integrating sequence, evolution and functional genomics in regulatory genomics

Vingron, M., Brāzma, A., Coulson, R., van Helden, J., Manke, T., Palin, K., Sand, O., & Ukkonen, E. (2009) · Genome biology · doi:10.1186/gb-2009-10-1-202 · Cited by 28 · see citing works

The identification and functional characterisation of conserved regulatory elements in developmental genes

Dickmeis, T. (2005) · Briefings in Functional Genomics and Proteomics · doi:10.1093/bfgp/3.4.332 · Cited by 28 · see citing works

The animal in the genome: comparative genomics and evolution

Copley, R. R. (2008) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2007.2235 · Cited by 28 · see citing works

Redeployment of a conserved gene regulatory network during Aedes aegypti development

Suryamohan, K., Hanson, C. R., Andrews, E., Sinha, S., Duman‐Scheel, M., & Halfon, M. S. (2016) · Developmental Biology · doi:10.1016/j.ydbio.2016.06.031 · Cited by 27 · see citing works

Genomic Approaches to Understanding Hox Gene Function

Choo, S. W., & Russell, S. R. H. (2011) · Advances in genetics · doi:10.1016/b978-0-12-386481-9.00003-1 · Cited by 27 · see citing works

Signaling gradients in cascades of two-state reaction-diffusion systems

Berezhkovskii, A. M., Coppey, M., & Shvartsman, S. Y. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0811807106 · Cited by 27 · see citing works

Mechanisms of Groucho-mediated repression revealed by genome-wide analysis of Groucho binding and activity

Chambers, M., Turki-Judeh, W., Kim, M. W., Chen, K., Gallaher, S. D., & Courey, A. J. (2017) · BMC Genomics · doi:10.1186/s12864-017-3589-6 · Cited by 26 · see citing works

Developmental mechanisms and cis-regulatory codes

Ochoa‐Espinosa, A., & Small, S. (2006) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2006.02.014 · Cited by 26 · see citing works

cis-Decoder discovers constellations of conserved DNA sequences shared among tissue-specific enhancers

Brody, T., Rasband, W. S., Baler, K., Kuzin, A., Kundu, M., & Odenwald, W. F. (2007) · Genome biology · doi:10.1186/gb-2007-8-5-r75 · Cited by 26 · see citing works

Genomic, phylogenetic, and cell biological insights into metazoan origins

Nichols, S. A., Dayel, M. J., & King, N. (2009) · Animal Evolution · doi:10.1093/acprof:oso/9780199549429.003.0003 · Cited by 24 · see citing works

Stripe formation in the early fly embryo: principles, models, and networks

Papatsenko, D. (2009) · BioEssays · doi:10.1002/bies.200900096 · Cited by 23 · see citing works

Comparison of embryonic expression within multigene families using the flyexpress discovery platform reveals more spatial than temporal divergence

Konikoff, C. E., Karr, T. L., McCutchan, M., Newfeld, S. J., & Kumar, S. (2011) · Developmental Dynamics · doi:10.1002/dvdy.22749 · Cited by 24 · see citing works

RTK signaling modulates the Dorsal gradient

Helman, A., Lim, B., Andreu, M. J., Kim, Y., Shestkin, T., Lu, H., Jiménez, G., Shvartsman, S. Y., & Paroush, Z. (2012) · Development · doi:10.1242/dev.075812 · Cited by 23 · see citing works

Identifying synonymous regulatory elements in vertebrate genomes

Ovcharenko, I., & Nóbrega, M. A. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki466 · Cited by 23 · see citing works

Causal Gene Regulatory Network Modeling and Genomics: Second-Generation Challenges

Rothenberg, E. V. (2019) · Journal of Computational Biology · doi:10.1089/cmb.2019.0098 · Cited by 20 · see citing works

Cis‐regulatory mechanisms of gene expression in an olfactory neuron type in Caenorhabditis elegans

Nokes, E. B., van der Linden, A. M., Winslow, C., Mukhopadhyay, S., Ma, K., & Sengupta, P. (2009) · Developmental Dynamics · doi:10.1002/dvdy.22147 · Cited by 19 · see citing works

Mitosis-associated repression in developmentPreprint

Esposito, E., Lim, B., Guessous, G., Falahati, H., & Levine, M. (2016) · Genes & Development · doi:10.1101/gad.281188.116 · Cited by 22 · see citing works

Uncoupling neurogenic gene networks in the Drosophila embryoPreprint

Rogers, W. A., Goyal, Y., Yamaya, K., Shvartsman, S. Y., & Levine, M. (2017) · Genes & Development · doi:10.1101/gad.297150.117 · Cited by 19 · see citing works

A directional recombination cloning system for restriction- and ligation-free construction of GFP, DsRed, and lacZ transgenic Drosophila reporters

Swanson, C. I., Hinrichs, T., Johnson, L. A., Zhao, Y., & Barolo, S. (2007) · Gene · doi:10.1016/j.gene.2007.11.003 · Cited by 17 · see citing works

Notch-dependent and -independent transcription are modulated by tissue movements at gastrulation

Sanjuan, J. F., & Bray, S. J. (2022) · eLife · doi:10.7554/elife.73656 · Cited by 16 · see citing works

Improvement of molecular phylogenetic inference and the phylogeny of Bilateria

Lartillot, N., & Philippe, H. (2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.003.0012 · Cited by 15 · see citing works

Identification of new Anopheles gambiae transcriptional enhancers using a cross‐species prediction approach

Schember, I., & Halfon, M. S. (2021) · Insect Molecular Biology · doi:10.1111/imb.12705 · Cited by 14 · see citing works

The 3D Genome Shapes the Regulatory Code of Developmental Genes

Mozziconacci, J., Merle, M., & Lesne, A. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.10.017 · Cited by 13 · 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

Computational Models for Neurogenic Gene Expression in the Drosophila Embryo

Zinzen, R. P., Senger, K., Levine, M., & Papatsenko, D. (2006) · Current Biology · doi:10.1016/j.cub.2006.05.044 · Cited by 165 · see citing works

Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the <i>Drosophila</i> embryo

Papatsenko, D., & Levine, M. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409414102 · Cited by 82 · see citing works

The molecular evolution of the Drosophila neurogenic ectodermal enhancers.

Crocker, J. (2010) · doi:10.1349/ddlp.386

Design flexibility in cis-regulatory control of gene expression: Synthetic and comparative evidence

Liberman, L. M., & Stathopoulos, A. (2009) · Developmental Biology · doi:10.1016/j.ydbio.2008.12.020 · Cited by 76 · see citing works