A complete, current list is on ORCID. *Equal contribution.
Featured papers
Sensory receptor expansion and neural accommodation in butterfly color vision
Gao K, Ainsworth J, Donati A, Zhao Y, Ragsac MF, Genduso C, Andre Z, Tomlinson A, Perry MW
Science Advances 12(41):eaei7570 (2026).
Butterflies see more colors than flies in part because they added a second R7 photoreceptor to every unit of the compound eye. We traced the extra cell to a change in the fate of neighboring R3/4 photoreceptors, recreated it in a “butterfly-fly,” and found that the developing brain was ready for it: Dm8 neurons that would normally die are rescued and wired to the new input.
Regulatory changes underlying the evolution of skylight navigation
Roth H, Sarfert M, Simdianova A, Balke J, Perry MW, Nowick K, Wernet MF
iScience 29(7):116313 (2026).
Nearly all insects read the polarization of skylight with the dorsal rim area, a strip of specialized ommatidia along the top of the eye. In Drosophila the transcription factor Homothorax specifies it, but with the Wernet lab we found that Homothorax plays this role only in the higher flies, suggesting it was inserted into an older regulatory network.
Evolution and integration of a novel cell type in the housefly Love Spot
Donati A, Zhao Y, Terner E, Konstantinides N, Perry MW
bioRxiv (2026). In review.
Male house flies chase females in flight using a specialized patch of the eye, the Love Spot. Its R7 photoreceptors start out as ordinary color-vision cells, then take on a hybrid identity under the control of Doublesex and Spineless and connect to motion-vision circuits instead: a new cell type built from existing parts.
Cell fate ratios are encoded by transcriptional dynamics in the Drosophila retina
Ainsworth J*, Zhao Y*, Gao K, Gravina NM, Goldberg ZH, Pinkerton C, Rifkin SA, Ernst AM, Garcia HG, Perry MW
Current Biology 35(12):2946-2959.e5 (2025).
In the fly retina, each R7 photoreceptor makes a random choice to turn on the transcription factor Spineless, and about 70% do. By imaging spineless transcription live and swapping its core promoter at the endogenous locus, we found that the ratio is set by the timing of transcriptional bursts: longer gaps between bursts mean fewer cells turn Spineless on.
Deep conservation complemented by novelty and innovation in the insect eye ground plan
Gao K, Donati A, Ainsworth J, Wu D, Terner ER, Perry MW
Proceedings of the National Academy of Sciences 122(1):e2416562122 (2025).
Using single-cell profiling of developing retinas from insects separated by more than 300 million years, we found that photoreceptor types and the regulatory logic that specifies them are deeply conserved. Diversity comes from changes layered on top of this shared ground plan: shifted ratios, added regions and receptor types, and fixed maps in place of random patterning.
Preprints
Evolution and integration of a novel cell type in the housefly Love Spot
Donati A, Zhao Y, Terner E, Konstantinides N, Perry MW
bioRxiv (2026). In review.
Transcriptome analysis of the winter tick (Dermacentor albipictus) reveals sex-specific expression patterns
Edwards RTM, Antoshechkin I, Hill E, Perry MW, Olafson PU, Saelao P, Lohmeyer KH, Akbari OS
bioRxiv (2025).
All papers
Sensory receptor expansion and neural accommodation in butterfly color vision
Gao K, Ainsworth J, Donati A, Zhao Y, Ragsac MF, Genduso C, Andre Z, Tomlinson A, Perry MW
Science Advances 12(41):eaei7570 (2026).
Regulatory changes underlying the evolution of skylight navigation
Roth H, Sarfert M, Simdianova A, Balke J, Perry MW, Nowick K, Wernet MF
iScience 29(7):116313 (2026).
Cell fate ratios are encoded by transcriptional dynamics in the Drosophila retina
Ainsworth J*, Zhao Y*, Gao K, Gravina NM, Goldberg ZH, Pinkerton C, Rifkin SA, Ernst AM, Garcia HG, Perry MW
Current Biology 35(12):2946-2959.e5 (2025).
Deep conservation complemented by novelty and innovation in the insect eye ground plan
Gao K, Donati A, Ainsworth J, Wu D, Terner ER, Perry MW
Proceedings of the National Academy of Sciences 122(1):e2416562122 (2025).
CRISPR mediated transactivation in the human disease vector Aedes aegypti
Bui M, Dalla Benetta E, Dong Y, Zhao Y, Yang T, Li M, Antoshechkin IA, Buchman A, Bottino-Rojas V, James AA, Perry MW, Dimopoulos G, Akbari OS
PLOS Pathogens 19(1):e1010842 (2023).
Human retinal ganglion cell neurons generated by synchronous BMP inhibition and transcription factor mediated reprogramming
Agarwal D*, Dash N*, Mazo KW, …, Perry MW, …, Wahlin KJ
npj Regenerative Medicine 8(1):55 (2023).
Cortex cis-regulatory switches establish scale colour identity and pattern diversity in Heliconius
Livraghi L, Hanly JJ, Van Bellghem SM, …, Perry MW, …, Jiggins CD
eLife 10:e68549 (2021).
A transposable element insertion is associated with an alternative life history strategy
Woronik A, Tunström K, Perry MW, Neethiraj R, Stefanescu C, Celorio-Mancera MP, Brattström O, Hill J, Lehmann P, Käkelä R, Wheat CW
Nature Communications 10(1) (2019).
A matter of timing
Perry MW, Desplan C
eLife 8:e41523 (2019).
Patterning the insect eye: From stochastic to deterministic mechanisms
Ebadi H, Perry MW, Short K, Klemm K, Desplan C, Stadler PF, Mehta A
PLOS Computational Biology 14(11):e1006363 (2018).
Generation and Evolution of Neural Cell Types and Circuits: Insights from the Drosophila Visual System
Perry MW, Konstantinides N, Pinto-Teixeira F, Desplan C
Annual Review of Genetics 51(1):501-527 (2017).
An Engineered orco Mutation Produces Aberrant Social Behavior and Defective Neural Development in Ants
Yan H, Opachaloemphan C, Mancini G, …, Perry MW, …, Desplan C
Cell 170(4):736-747.e9 (2017).
Genetic Basis of Melanin Pigmentation in Butterfly Wings
Zhang L, Martin A, Perry MW, van der Burg KRL, Matsuoka Y, Monteiro A, Reed RD
Genetics 205(4):1537-1550 (2017).
Molecular logic behind the three-way stochastic choices that expand butterfly colour vision
Perry MW, Kinoshita M, Saldi G, Huo L, Arikawa K, Desplan C
Nature 535(7611):280-284 (2016).
Love spots
Perry MW, Desplan C
Current Biology 26(12):R484-R485 (2016).
Enhancer additivity and non-additivity are determined by enhancer strength in the Drosophila embryo
Bothma JP, Garcia HG, Ng S, Perry MW, Gregor T, Levine M
eLife 4:e07956 (2015).
The evolutionary diversity of insect retinal mosaics: common design principles and emerging molecular logic
Wernet MF, Perry MW, Desplan C
Trends in Genetics 31(6):316-328 (2015).
Opposing Feedbacks on Ras Tune Receptor Tyrosine Kinase Signaling
Perry MW, Desplan C
Science Signaling 6(300) (2013).
Precision of Hunchback Expression in the Drosophila Embryo
Perry MW, Bothma JP, Luu RD, Levine M
Current Biology 22(23):2247-2252 (2012).
Neural-specific elongation of 3′ UTRs during Drosophila development
Hilgers V, Perry MW, Hendrix D, Stark A, Levine M, Haley B
Proceedings of the National Academy of Sciences 108(38):15864-15869 (2011).
Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo
Perry MW, Boettiger AN, Levine M
Proceedings of the National Academy of Sciences 108(33):13570-13575 (2011).
Shadow Enhancers Foster Robustness of Drosophila Gastrulation
Perry MW, Boettiger AN, Bothma JP, Levine M
Current Biology 20(17):1562-1567 (2010).
Evolution of Insect Dorsoventral Patterning Mechanisms
Perry MW, Cande JD, Boettiger AN, Levine M
Cold Spring Harbor Symposia on Quantitative Biology 74:275-279 (2009).
Patterns on the insect wing
Parchem RJ, Perry MW, Patel NH
Current Opinion in Genetics & Development 17(4):300-308 (2007).