Papers citing Virtual Fly Brain

A curated selection of published work that used Virtual Fly Brain, with a short note on what each paper used it for. It is not a complete citation count — it is a sample showing how VFB is used in practice, from retrieving a single template to cross-linking transcriptomic and connectome data.

If you have used VFB in a paper we have missed, please get in touch. See how to cite us for the citations to use.

Research papers

1. Shen D et al. — Cell Reports, 2025

Cross-linked transcriptomic and connectome data using the query tool.

Shen D, Vincent A, Udine E, Buhidma Y, Anoar S, Tsintzas E, Maeland M, Xu D, Carcolé M, Osumi-Sutherland D, Aleyakpo B, Hull A, Martínez Corrales G, Woodling N, Rademakers R, Isaacs AM, Frigerio C, van Blitterswijk M, Lashley T, Niccoli T. Cell Reports (2025). doi:10.1016/j.celrep.2025.115459 Last author: Teresa Niccoli, UCL, UK

2. Zhang T et al. — PLoS Biology, 2025

Explored connectivity by brain region.

Zhang T, Wu Z, Song Y, Ryu TH, Zhang X, Li W, Sun Y, Wong K, Schweizer J, Nguyen KH, Kwan A, Yu K, Kim WJ. PLoS Biology (2025). doi:10.1371/journal.pbio.3003330 Last author: Woo Jae Kim, University of Ottawa, Canada

3. Dürr B et al. — Cell Reports, 2025

Compared morphology in light- and electron-microscopy data.

Dürr B, Bertolini E, Takagi S, Pascual J, Abuin L, Lucarelli G, Benton R, Auer T. Cell Reports (2025). doi:10.1016/j.celrep.2025.115615 Last author: Thomas Auer, University of Fribourg, Switzerland

4. Mohamed A et al. — Frontiers in Physiology, 2023

Explored morphology and connectivity.

Mohamed A, Malekou I, Sim T, O’Kane CJ, Maait Y, Scullion B, Masuda-Nakagawa LM. Frontiers in Physiology (2023). doi:10.3389/fphys.2023.1111244 Last author: Liria M. Masuda-Nakagawa, University of Cambridge, UK

5. Yamakoshi H et al. — iScience, 2025

Compared morphology.

Yamakoshi H, Horigome M, Yamamoto S, Iwanami S, Iwami S, Tanaka R, Ishikawa Y, Kamikouchi A. iScience (2025). doi:10.1016/j.isci.2025.113232 Last author: Azusa Kamikouchi, Nagoya University, Japan

6. Song Y et al. — PLoS Biology, 2025

Explored morphology and expression pattern.

Song Y, Zhang T, Ryu TH, Wong K, Wu Z, Wei Y, Schweizer J, Nguyen KH, Kwan A, Zhang X, Yu K, Kim WJ. PLoS Biology (2025). doi:10.1371/journal.pbio.3003345 Last author: Woo Jae Kim, University of Ottawa, Canada

7. Goldschmidt D et al. — bioRxiv, 2023

Explored morphology and expression pattern.

Goldschmidt D, Tastekin I, Münch D, Park J-Y, Haberkern H, Serra L, Baltazar C, Jayaraman V, Rubin GM, Ribeiro C. bioRxiv (2023). doi:10.1101/2023.07.19.549514 Last author: Carlos Ribeiro, Champalimaud, Portugal

8. Cheong HSJ et al. — eLife, 2026

Retrieved tract meshes.

Cheong HSJ, Eichler K, Stürner T, Asinof SK, Champion AS, Marin EC, Oram TB, Sumathipala M, Venkatasubramanian L, Namiki S, Siwanowicz I, Costa M, Berg S, Janelia FlyEM Project Team, Jefferis GSXE, Card GM. eLife (2026). doi:10.7554/eLife.96084 Last author: Gwyneth M. Card, Columbia University, USA

9. Davidson AM et al. — eNeuro, 2023

Explored morphology and expression pattern.

Davidson AM, Kaushik S, Hige T. eNeuro (2023). doi:10.1523/ENEURO.0275-23.2023 Last author: Toshihide Hige, University of North Carolina at Chapel Hill, USA

10. Imoto K et al. — iScience, 2024

Visualised morphology.

Imoto K, Ishikawa Y, Aso Y, Funke J, Tanaka R, Kamikouchi A. iScience (2024). doi:10.1016/j.isci.2024.110266 Last author: Azusa Kamikouchi, Nagoya University, Japan

11. Castaneda AN et al. — PLoS Genetics, 2024

Identified tracts.

Castaneda AN, Huda A, Whitaker IBM, Reilly JE, Shelby GS, Bai H, Ni L. PLoS Genetics (2024). doi:10.1371/journal.pgen.1011190 Last author: Lina Ni, Virginia Tech, USA

12. O’Hara MK et al. — Sleep, 2024

Examined regional expression of GAL4 lines.

O’Hara MK, Saul C, Handa A, Cho B, Zheng X, Sehgal A, Williams JA. Sleep (2024). doi:10.1093/sleep/zsae096 Last author: Julie A. Williams, University of Pennsylvania, USA

13. Sakr R et al. — EMBO Reports, 2026

Visualised neurons and brain regions.

Sakr R, Monticelli S, Kizhakkenottiyath Shasthadevan S, Delaporte C, Zhang G, Tabiat T, Giangrande A, Cattenoz PB. EMBO Reports (2026). doi:10.1038/s44319-026-00728-1 Last author: Pierre B. Cattenoz, CNRS Illkirch, France

14. Jiang H et al. — bioRxiv, 2025

Used brain templates.

Jiang H, Walker LA, Li Y, Duan B, Niu X, Hsieh JC, Cheng MC, Su H, Sheng K, Tang JP, Athukorala K, Greene S, Pan R, Parlapalli A, Yin P, Cui M, Cai D. bioRxiv (2025). doi:10.1101/2025.05.31.657163 Last author: Dawen Cai, University of Michigan, USA

15. Olivera RA et al. — Neuroinformatics, 2026

Retrieved neuron names, aliases and neurotransmitter expression.

Olivera RA. Neuroinformatics (2026). doi:10.1007/s12021-026-09783-4 Last author: R. A. Olivera, NST Mangalore, India

16. Palmieri E et al. — bioRxiv, 2026

Confirmed gene expression.

Palmieri E, Coon M, Sobukunola A, Sutton L, Vonhoff FJ. bioRxiv (2026). doi:10.64898/2026.04.22.720032 Last author: Fernando J. Vonhoff, University of Maryland, Baltimore County, USA

17. Wright N et al. — Bioinformatics Advances, 2023

Visualised brain regions and neurons.

Wright N, Rowlands CJ. Bioinformatics Advances (2023). doi:10.1093/bioadv/vbad182 Last author: Christopher J. Rowlands, Imperial College London, UK

18. Münch D et al. — Nature, 2022

Retrieved registered neurons for analysis.

Münch D, Goldschmidt D, Ribeiro C. Nature (2022). doi:10.1038/s41586-022-04909-5 Last author: Carlos Ribeiro, Champalimaud, Portugal

19. Jetti SK et al. — Neuron, 2023

Explored morphology and connectivity.

Jetti SK, Crane AB, Akbergenova Y, Aponte-Santiago NA, Cunningham KL, Whittaker CA, Littleton JT. Neuron (2023). doi:10.1016/j.neuron.2023.07.019 Last author: J. Troy Littleton, MIT, USA

20. Xie T et al. — Cell Reports, 2018

Retrieved templates and GAL4 expression patterns.

Xie T, Ho MCW, Liu Q, Horiuchi W, Lin CC, Task D, Luan H, White BH, Potter CJ, Wu MN. Cell Reports (2018). doi:10.1016/j.celrep.2018.03.068 Last author: Mark N. Wu, Johns Hopkins, USA

21. May CE et al. — eLife, 2020

Visualised neurons.

May CE, Rosander J, Gottfried J, Dennis E, Dus M. eLife (2020). doi:10.7554/eLife.54530 Last author: Monica Dus, University of Michigan, USA

22. Goulard R et al. — PLoS Computational Biology, 2021

Retrieved connectivity data.

Goulard R, Buehlmann C, Niven JE, Graham P, Webb B. PLoS Computational Biology (2021). doi:10.1371/journal.pcbi.1009383 Last author: Barbara Webb, University of Edinburgh, UK

23. Coates KE et al. — Journal of Neuroscience, 2020

Compared morphology and expression pattern.

Coates KE, Calle-Schuler SA, Helmick LM, Knotts VL, Martik BN, Salman F, Warner LT, Valla SV, Bock DD, Dacks AM. Journal of Neuroscience (2020). doi:10.1523/JNEUROSCI.0552-20.2020 Last author: Andrew M. Dacks, West Virginia University, USA

24. Gkanias E et al. — eLife, 2022

Visualised neurons.

Gkanias E, McCurdy LY, Nitabach MN, Webb B. eLife (2022). doi:10.7554/eLife.75611 Last author: Barbara Webb, University of Edinburgh, UK

25. Chen KF et al. — eLife, 2019

Retrieved GAL4 expression patterns.

Chen KF, Lowe S, Lamaze A, Krätschmer P, Jepson J. eLife (2019). doi:10.7554/eLife.38114 Last author: James Jepson, UCL, UK

26. Odell SR et al. — Scientific Reports, 2022

Explored morphology and connectivity.

Odell SR, Clark D, Zito N, Jain R, Gong H, Warnock K, Carrion-Lopez R, Maixner C, Prieto-Godino L, Mathew D. Scientific Reports (2022). doi:10.1038/s41598-022-20147-1 Last author: Dennis Mathew, University of Nevada, Reno, USA

27. Tsuji M et al. — Nature Communications, 2023

Explored morphology, expression patterns and connectivity.

Tsuji M, Nishizuka Y, Emoto K. Nature Communications (2023). doi:10.1038/s41467-023-39667-z Last author: Kazuo Emoto, University of Tokyo, Japan

28. Hartenstein V et al. — Developmental Biology, 2015

Identified tracts.

Hartenstein V, Younossi-Hartenstein A, Lovick JK, Kong A, Omoto JJ, Ngo KT, Viktorin G. Developmental Biology (2015). doi:10.1016/j.ydbio.2015.06.021 Last author: Volker Hartenstein, UCLA, USA

29. Hildebrandt K et al. — Developmental Biology, 2022

Assigned expression to structures and lineages.

Hildebrandt K, Klöppel C, Gogel J, Hartenstein V, Walldorf U. Developmental Biology (2022). doi:10.1016/j.ydbio.2022.09.006 Last author: Uwe Walldorf, Saarland University, Germany

30. Afkhami M et al. — Journal of Neurogenetics, 2024

Compared morphology and expression pattern.

Afkhami M. Journal of Neurogenetics (2024). doi:10.1080/01677063.2024.2396352 Last author: Mehrnaz Afkhami, University of Oklahoma, USA

31. Mollá-Albaladejo R et al. — eLife, 2025

Retrieved skeletons and aligned them to a template.

Mollá-Albaladejo R, Jiménez-Caballero M, Sanchez-Alcaniz JA. eLife (2025). doi:10.7554/eLife.100947 Last author: Juan Antonio Sanchez-Alcaniz, Institute of Neuroscience, Alicante, Spain

32. Chen YD et al. — Journal of Experimental Biology, 2019

Ran a morphology screen for candidate driver lines.

Chen YD, Ahmad S, Amin K, Dahanukar A. Journal of Experimental Biology (2019). doi:10.1242/jeb.210724 Last author: Anupama Dahanukar, University of California Riverside, USA

33. Aimon S et al. — PLoS Biology, 2019

Visualised brain regions and neurons.

Aimon S, Katsuki T, Jia T, Grosenick L, Broxton M, Deisseroth K, Sejnowski TJ, Greenspan RJ. PLoS Biology (2019). doi:10.1371/journal.pbio.2006732 Last author: Ralph J. Greenspan, UCSD, USA

34. Zheng Z et al. — Cell, 2018

Used a mesh in the template brain to trim skeletons of EM- and LM-reconstructed neurons.

Zheng Z, Lauritzen JS, Perlman E, Robinson CG, Nichols M, Milkie D, Torrens O, Price J, Fisher CB, Sharifi N, Calle-Schuler SA, Kmecova L, Ali IJ, Karsh B, Trautman ET, Bogovic JA, Hanslovsky P, Jefferis GSXE, Kazhdan M, Khairy K, Saalfeld S, Fetter RD, Bock DD. Cell (2018). doi:10.1016/j.cell.2018.06.019 Last author: Davi D. Bock, HHMI Janelia, USA

35. Liang Q et al. — bioRxiv, 2026

Analysed brain-region morphology of neurons.

Liang Q, Liu Q, Ning J, Lv Q, Zhang X, Wang K, Sun Y. bioRxiv (2026). doi:10.64898/2026.05.29.728103 Last author: Yi Sun, Westlake University, Zhejiang, China

36. Bates AS et al. — Current Biology, 2020

Retrieved reconstructions of neurons from EM data.

Bates AS, Schlegel P, Roberts RJV, Drummond N, Tamimi IFM, Turnbull R, Zhao X, Marin EC, Popovici PD, Dhawan S, Jamasb A, Javier A, Serratosa Capdevila L, Li F, Rubin GM, Waddell S, Bock DD, Costa M, Jefferis GSXE. Current Biology (2020). doi:10.1016/j.cub.2020.06.042 Last author: Gregory S. X. E. Jefferis, LMB and University of Cambridge, UK

37. Okuno T et al. — bioRxiv, 2025

Retrieved a brain-region atlas.

Okuno T, Woodward A, Okano H, Hata J. bioRxiv (2025). doi:10.1101/2025.07.01.662601 Last author: Junichi Hata, Tokyo Metropolitan University, Japan

38. Otsuna H et al. — bioRxiv, 2018

Retrieved reconstructions of neurons from EM data.

Otsuna H, Ito M, Kawase T. bioRxiv (2018). doi:10.1101/318006 Last author: Takashi Kawase, HHMI Janelia, USA

39. Mann K et al. — Current Biology, 2017

Used a template and brain-region atlas to align calcium-imaging data.

Mann K, Gallen CL, Clandinin TR. Current Biology (2017). doi:10.1016/j.cub.2017.06.076 Last author: Thomas R. Clandinin, Stanford University, USA

40. Yu HH et al. — Current Biology, 2013

Explored morphology and expression pattern.

Yu HH, Awasaki T, Schroeder MD, Long F, Yang JS, He Y, Ding P, Kao JC, Wu GY, Peng H, Myers G, Lee T. Current Biology (2013). doi:10.1016/j.cub.2013.02.057 Last author: Tzumin Lee, HHMI Janelia and University of Massachusetts, USA

41. Lee YJ et al. — eLife, 2020

Explored morphology and expression pattern.

Lee YJ, Yang CP, Miyares RL, Huang YF, He Y, Ren Q, Chen HM, Kawase T, Ito M, Otsuna H, Sugino K, Aso Y, Ito K, Lee T. eLife (2020). doi:10.7554/eLife.53518 Last author: Tzumin Lee, HHMI Janelia, USA

42. Marquis M et al. — Current Biology, 2022

Cross-referenced cell-type names against VFB exemplars.

Marquis M, Wilson RI. Current Biology (2022). doi:10.1016/j.cub.2022.11.008 Last author: Rachel I. Wilson, Harvard Medical School, USA

43. Scheffer LK et al. — eLife, 2020

Retrieved neuron names and synonyms.

Scheffer LK, Xu CS, Januszewski M, Lu Z, Takemura SY, Hayworth KJ, Huang GB, Shinomiya K, Maitlin-Shepard J, Berg S, Clements J, Hubbard PM, Katz WT, et al.. eLife (2020). doi:10.7554/eLife.57443 Last author: Stephen M. Plaza, HHMI Janelia, USA

Honourable mentions

Reviews, book chapters and papers that discuss VFB as a resource rather than using it for a specific analysis.

Fiala A et al. — Learning & Memory (2024)

Cited VFB as a platform connecting connectome neurons to existing Drosophila resources, and as an example of the collaborative infrastructure behind 25 years of mushroom body research.

Fiala A, Kaun KR. Learning & Memory (2024). doi:10.1101/lm.053827.123 Last author: Karla R. Kaun, Brown University, USA

Forrest H et al. — In: Home Cage Monitoring in Rodents: A Global Effort, Springer (2026)

Held up VFB’s provenance system as an example of effective data integration, linking entries to original sources with machine-readable metadata.

Forrest H, Huzard D, Restivo L, Baran SW, Petit-Demoulière B. In: Home Cage Monitoring in Rodents: A Global Effort, Springer (2026). doi:10.1007/978-3-032-19781-8_10 Last author: Benoit Petit-Demoulière, University of Strasbourg, France

Heinze S et al. — eLife (2021)

Described VFB as the main repository for Drosophila anatomical data and the model for what a unified insect-neuroscience platform should provide.

Heinze S, El Jundi B, Berg BG, Homberg U, Menzel R, Pfeiffer K, Hensgen R, Zittrell F, Dacke M, Warrant E, Pfuhl G, Rybak J, Tedore K. eLife (2021). doi:10.7554/eLife.65376 Last author: Kevin Tedore, Lund University, Sweden