MURTHY LAB PUBLICATIONS (2010-2024):
#indicates that paper first appeared on bioRxiv - the Murthy lab is committed to openness and since 2017 has published all articles on bioRxiv at the time of first submission to a journal
2025
Bates AS*, Phelps JS*, Kim M, Yang HH, Matsliah A, Ajabi Z, Perlman E, Delgado KM, Osman MAM, Salmon CK, Gager J, Silverman B, Renauld S, Collie MF, Fan J, Pacheco DA, Zhao Y, Patel J, Zhang W, Serratosa Capdevilla L, Roberts RJV, Munnelly EJ, Griggs N, Langley H, Moya-Llamas B, Maloney RT, Yu SC, Sterling AR, Sorek M, Kruk K, Serafetinidis N, Dhawan S, Stürner T, Klemm F, Brooks P, Lesser E, Jones JM, Pierce-Lundgren SE, Lee SY, Luo Y, Cook AP, McKim TH, Kophs EC, Falt T, Negrón Morales AM, Burke A, Hebditch J, Willie KP, Willie R, Popovych S, Kemnitz N, Ih D, Lee K, Lu R, Halageri A, Bae JA, Jourdan B, Schwartzman G, Demarest DD, Behnke E, Bland D, Kristiansen A, Skelton J, Stocks T, Garner D, Salman F, Daly KC, Hernandez A, Kumar S; BANC-FlyWire Consortium; Dorkenwald S, Collman F, Suver MP, Fenk LM, Pankratz MJ, Jefferis GSXE, Eichler K, Seeds AM, Hampel S, Agrawal S, Zandawala M, Macrina T, Adjavon DY, Funke J, Tuthill JC, Azevedo A, Seung HS, de Bivort BL, Murthy M*, Drugowitsch J*, Wilson RI*, Lee WA*. Distributed control circuits across a brain-and-cord connectome. bioRxiv 2025 doi: 10.1101/2025.07.31.667571. *co-corresponding authors
Yu, S-C, Bae, A, Matsliah, A, Dorkenwald, S, Gager, J, Hebditch, J, Silverman, B, Willie, KP, Willie, R, Burke, A, Macrina, T, Seung, HS, Murthy, M. New Synapse Detection in the Whole-Brain Connectome of Drosophila. bioRxiv 2025 doi.org/10.1101/2025.07.11.664377
Gauthey, W, Lin, A, Ahmed, O, Leifer, A*, Murthy, M*, Thiberge, S*. *co-leads High-speed whole-brain imaging in Drosophila. bioRxiv 2025 doi.org/10.1101/2025.06.18.660371 *co-corresponding authors
Deutsch, D, Matsliah, A, Wang, K, Dorkenwald, S, Mondal, A, Burke, A, Hebditch, J, Gager, J, Yu S-C, Sterling, A, McKellar, C, Schlegel, P, Gerhard, S, Sterne, G, Costa, M, Eichler, K, Yin, Y, Jefferis, GSXE, Dickson, B, Seung, HS, Murthy, M. Sexually-dimorphic neurons in the Drosophila whole-brain connectome. bioRxiv 2025. doi.org/1101/2025.06.10.658788
Stürner, T, Brooks, P, Capdevila, LS, Morris, BJ, Javier, A, Fang, S, Gkantia, M, Cachero, S, Beckett, IR, Marin, EC, Schlegel, P, Champion, AS, Moitra, I, Richards, A, Klemm, F, Kugel, L, Namiki, S, Cheong, HSJ, Kovalyak, J, Tenshaw, E, Parekh, R, Phelps, JS, Mark, B, Dorkenwald, S, Bates, AS, Matsliah, A, Yu, S-C, McKellar, CE, Sterling, A, Seung, HS, Murthy, M, Tuthill, JC, Lee, W-C A, Card, GM, Costa, M, Jefferis GSXE, Eichler, K. Comparative connectomics of Drosophila descending and ascending neurons. Nature 2025 643, 158–172. doi.org/10.1038/s41586-025-08925-z #
Pang R, Baker C, Murthy M*, Pillow J*. *co-leads Inferring neural dynamics of memory during naturalistic social communication. 2025 Vol. 122 (21) PNAS 2025 e2417733122. doi.org/10.1073/pnas.2417733122 #
2024
Brezovec, LE, Berger, AB, Hao, YA, Lin, A, Ahmed, OM, Pacheco, DA, Thiberge, SY, Murthy, M*, Clandinin, TR*. *co-corresponding authors. BIFROST: a method for registering diverse imaging datasets. PNAS 2024. Nov 19, Vol. 121, No. 47.
doi.org/10.1073/pnas.2322687121 #FlyWire Connectome Paper Package
Dorkenwald, S, Matsliah, A, Sterling, AR, Schlegel, P Yu, S-C, McKellar, CE, Lin, A, Costa, M, Eichler, K, Yin, Y, Silversmith, W, Schneider-Mizell, C, Jordan, CS, Brittain, D, Halageri, A, Kuehner, K, Ogedengbe, O, Morey, R, Gager, J, Kruk, K, Perlman, E, Yang, R, Deutsch, D, Bland, D, Sorek, M, Lu, R, Macrina, T, Lee, K, Bae, JA, Mu, S, Nehoran, B, Mitchell, E, Popovych, S, Wu, J, Jia, Z, Castro, M, Kemnitz, N, Ih, D, Bates, AS, Eckstein, N, Funke, J, Collman, F, Bock, DD, Jefferis, GSXE, Seung, HS*, Murthy, M*, and the FlyWire Consortium. *co-leads Neuronal wiring diagram of an adult brain. Nature 2024. 634, 124–138. doi.org/10.1038/s41586-024-07558-y #
Schlegel, P, Yin, Y, Bates, AS, Dorkenwald,S, Eichler, K, Brooks, P, Han, DS, Gkantia, M, dos Santos, M, Munnelly, EJ, Badalamente, G, Capdevila, LS, Sane, VA, Pleijzier, MW, Tamimi, IFM, Dunne, CR, Salgarella, I, Javier, A, Fang, S, Perlman, E, Kazimiers, T, Jagannathan, SR, Matsliah, A, Sterling, AR, Yu, S-C, McKellar, CE, the FlyWire Consortium, Costa, M, Seung, HS, Murthy, M, Hartenstein, V, Bock, DD, and Jefferis, GSXE. Whole-brain annotation and multi-connectome cell typing quantifies circuit stereotypy in Drosophila. Nature 2024. 634, 139–152. doi.org/10.1038/s41586-024-07686-5 #
Lin, A, Yang, R, Dorkenwald, S, Matsliah, A, Sterling, AR, Schlegel, P, Yu, S-C, McKellar, CE, Costa, M, Eichler, K, Bates, AS, Eckstein, N, Funke, J, Jefferis, GSXE, and Murthy, M. Network Statistics of the Whole-Brain Connectome of Drosophila. Nature 2024. 634, 153–165. doi.org/10.1038/s41586-024-07968-y #
Matsliah A, Yu SC, Kruk K, Bland D, Burke A, Gager J, Hebditch J, Silverman B, Willie K, Willie R, Sorek M, Sterling AR, Kind E, Garner D, Sancer G, Wernet M, Kim SS, Murthy M, Seung HS, and the FlyWire Consortium. Neuronal "parts list" and wiring diagram for a visual system. Nature 2024. 634, 166–180. doi.org/10.1038/s41586-024-07981-1 #
Shiu, PK, Sterne, GR, Spiller, N, Franconville, R, Sandoval, A, Zhou, J, Simha, N, Kang, CH, Yu, S, Kim, J, Dorkenwald, S, Matsliah, A, Sterling, AR, Yu, S-C, McKellar, CE, Schlegel, P, Costa, M, Eichler, K, Jefferis, GSXE, Murthy, M, Bates, AS, Eckstein, N, Funke, J , Bidaye, SS, Hampel, S, Seeds, AM, and Scott, K. A leaky integrate-and-fire computational model based on the connectome of the entire adult Drosophila brain reveals insights into sensorimotor processing. Nature 2024. 634, 210–219. doi.org/10.1038/s41586-024-07763-9 #
Popisil, D, Aragon, M, … Murthy, M, Pillow, JW. From connectome to effectome: learning the causal interaction map of the fly brain. Nature 2024. 634, 201–209. doi.org/10.1038/s41586-024-07982-0 #
Cowley, BR, Calhoun, AJ, Rangarajan, N, Turner, M, Pillow, JW, Murthy, M. Mapping model units to visual neurons reveals population code for social behaviour. Nature 2024 629, 1100–1108. https://doi.org/10.1038/s41586-024-07451-8 #
Baker CA, Guan X-J, Choi M, Murthy M. The role of fruitless in specifying courtship behaviors differs across Drosophila species. Science Advances 2024 13 Mar Vol 10, Issue 11 10.1126/sciadv.adk1273 #
Eckstein, N, Bates, AS, Champion, A, Du, M, Yin, Y, Schlegel, P, Lu, A, Rymer, T, Finley-May, S, Paterson, T, Parekh, R, Dorkenwald, S, Matsliah, A, Sterling, AR, Yu, S-C, McKellar, CE, Eichler, K, Costa, M, Seung, HS, Murthy, M, Hartenstein, V, Jefferis, GSXE, and Funke, J. Neurotransmitter Classification from Electron Microscopy Images at Synaptic Sites in Drosophila melanogaster. Cell 2024 Vol 187, Iss 10, 2574-2594 May 09. doi.org/10.1016/j.cell.2024.03.016 #
2023
Roemschied, F, Pacheco, DA, Aragon, MA, Ireland, EC, Li, X, Thieringer K, Pang, R, and Murthy, M. Flexible Circuit Mechanisms for Context-Dependent Song Sequencing. Nature 2023 doi.org/10.1038/s41586-023-06632-1 #
Princeton homepage: Fruit fly serenade
Ahmed OM, Crocker A, Murthy M. Transcriptional profiling of Drosophila male-specific P1 (pC1) neurons. bioRxiv 2023 Nov 10:2023.11.07.566045. doi: 10.1101/2023.11.07.566045.
2022
Baker, C, McKellar, C, Pang, R, Nern, A, Dorkenwald, S, Pacheco, DA, Eckstein, N, Funke, J, Dickson, BJ, and Murthy, M. Neural network organization for courtship-song feature detection in Drosophila. Current Biology 2022. 32, 3317–3333, August 8. #
Simons Foundation News: New efforts to relate brain structure and function
Pereira, TD, Tabris, N, Matsliah, A, Turner, DM, Li, J, Ravindranath, S, Papadoyannis, ES, Normand, E, Deutsch, DS, Wang, ZY, McKenzie-Smith, GC, Mitelut, CC, Castro, MD, D’Uva, J, Kislin, M, Sanes, DH, Kocher, SD, Wang, SSH, Falkner, AL, Shaevitz, JW, Murthy, M. SLEAP: A deep learning system for multi-animal pose tracking. Nature Methods 2022. Vol 19 April 486–495. doi.org/10.1038/s41592-022-01426-1. #
News&Views: Tracking together: estimating social poses
Dorkenwald, S, McKellar, C, Macrina, T, Kemnitz, N, Lee, K, Lu, R, Wu, J, Popovych, S, Mitchell, E, Nehoran, B, Jia, Z, Bae, JA, Mu, S, Ih, D, Castro, M, Ogedengbe, O, Halageri, A, Kuehner, K, Sterling, A, Ashwood, Z, Zung, J, Brittain, D, Collman, F, Schneider-Mizell, C, Jordan, C, Silversmith, W, Baker, C, Deutsch, D, Encarnacion-Rivera, L, Kumar, S, Burke, A, Bland, D, Gager, J, Hebditch, J, Koolman, S, Moore, M, Morejohn, S, Silverman, B, Willie, K, Willie, R, Yu, S-C, Murthy, M*, and Seung, HS*. FlyWire: Online community for whole-brain connectomics. Nature Methods 2022. Jan;19(1):119-128. doi: 10.1038/s41592-021-01330-0.Epub 2021 Dec 23. *co-leads #
2020
Deutsch, D, Pacheco, DA, Encarnacion-Rivera, L, Pereira, T, Fathy, R, Calhoun, A, Ireland, EC, Burke, AT, Dorkenwald, S, McKellar, C, Macrina, T, Lu, R, Lee, K, Kemnitz, N, Ih, D, Castro, M, Halageri, A, Jordan, C, Silversmith, W, Wu, J, Seung, HS, and Murthy, M. The Neural Basis for a Persistent Internal State in Drosophila Females. eLife 2020. https://elifesciences.org/articles/59502. #
Pacheco, DA, Thiberge, SY, Pnevmatikakis, E, and Murthy, M. Auditory Activity is Diverse and Widespread Throughout the Central Brain of Drosophila. Nature Neuroscience 2020. 23 Nov. https://doi.org/10.1038/s41593-020-00743-y #
Pereira, TD, Shaevitz, JW, and Murthy, M. Quantifying behavior to understand the brain. Nature Neuroscience 2020. Nov 9, 23, 1537–1549. doi.org/10.1038/s41593-020-00734-z.
2019
Calhoun, AJ, Pillow, JW, and Murthy, M. Unsupervised identification of the internal states that shape natural behavior. Nature Neuroscience 2019. Nov 25. #
News&Views: Opening the black box of social behavior
Princeton Discovery Magazine: Neuroscientists develop models to identify internal states of the brain
Nature: Inside the Mind of an Animal
Ahmed, O. and Murthy, M. Neuroscience: Tantalized Flies Are Primed for Satiety. Current Biology 2019. Dispatch. Vol. 29, Issue 21, pg 1146-1148. Nov 4. doi.org/10.1016/j.cub.2019.09.029.
Deutsch, D, Clemens, J, Thiberge, SY, Guan, G., Murthy, M. Shared Song Detector Neurons in Drosophila Male and Female Brains Drive Sex-Specific Behaviors. Current Biology 2019. Oct 7. vol 29, 1–16. #
Baker, CA, Clemens, J and Murthy, M. Acoustic Pattern Recognition and Courtship Songs: Insights from Insects. Annual Review of Neuroscience 2019. Feb 20. doi: 10.1146/annurev-neuro-080317-061839.
Pereira, T, Aldarondo, D, Willmore, L, Kislin, M, Wang, SS, Murthy, M*, Shaevitz, JW*. Fast animal pose estimation using deep neural networks. Nature Methods 2019. volume 16, pages117–125. *co-leads #
Princeton University homepage: Translating the Language of Behavior
The Scientist: AI Tools Capture Animal Movement
2018
Clemens, J, Coen, P, Roemschied, FA, Pereira, T, Mazumder, D, Aldarondo, D, Pacheco, D, and Murthy, M. Discovery of a new song mode in Drosophila reveals hidden structure in the sensory and neural drivers of behavior. Current Biology 2018. Aug 6. vol 28 issue 15, p2400-2412. #
Clemens, J, Ozeri-Engelhard, N, and Murthy, M. Fast Intensity Adaptation Enhances the Encoding of Sound in Drosophila. Nature Communications 2018. vol. 9 (1) p. 134. doi:10.1038/s41467-017-02453-9. #
2017
Calhoun, AJ and Murthy, M. Quantifying Behavior To Solve Sensorimotor Transformations: Advances from Worms and Flies. Current Opinion in Neurobiology 2017. Volume 46, October, pgs 90-98. doi.org/10.1016/j.conb.2017.08.006.
Pereira, TD and Murthy, M. To Fight or Not to Fight. Neuron 2017. Aug 30;95(5):986-988. doi: 10.1016/j.neuron.2017.08.029.
Stern, D, Clemens, J, Coen, P, Calhoun, AJ, Hogenesch, J, Arthur, B, and Murthy, M. Experimental and statistical reevaluation provides no evidence for Drosophila courtship song rhythms. PNAS 2017. vol 89 doi/10.1073/pnas.1707471114. #
Clemens J, and Murthy M. The use of computational modeling to link sensory processing with behavior in Drosophila. Springer International Publishing AG 2017. From: Decoding Neural Circuit Structure and Function, Eds. Celik and Wernet, doi:10.1007/978-3-319-57363-2_9.
2016
Crocker, A, Guan, XJ, Murphy, CT, and Murthy, M. Cell Type-Specific Transcriptome Analysis in the Drosophila Mushroom Body Reveals Memory-Related Changes in Gene Expression. Cell Reports 2016. May 17; 15, 1-17. doi: 10.1016/j.celrep.2016.04.046.
Princeton Journal Watch: Study of individual neurons in flies reveals memory-related changes in gene activity
Coen, P and Murthy, M. Singing on the Fly: Sensorimotor Integration and Acoustic Communication in Drosophila. Current Opinion in Neurobiology 2016. Feb 10;38:38-45. doi: 10.1016/j.conb.2016.01.013. Curr Opin Neurobiol website
Coen, P, Xie, M, Clemens, J, and Murthy, M. Sensorimotor transformations underlying variability in song intensity during Drosophila courtship. Neuron 2016. Feb 3; 89(3): 629-644. Neuron website
Preview: Can You Hear Me Now?
Cell Press: Fruit flies adjust their courtship song based on distance
Science Update: Singing Fruit Flies
2015
Clemens, J, Girardin, C, Coen, P, Guan, XJ, Dickson, BJ, and Murthy, M. Connecting neural codes with behavior in the auditory system of Drosophila. Neuron 2015. Sep 23; 87:1-12. Neuron website
Princeton University Website: PU Homepage
LaRue, K, Clemens, J, Berman, GJ, and Murthy, M. Acoustic duetting in Drosophila virilis relies on the integration of auditory and tactile signals. eLife 2015. June 5. doi: 10.7554/eLife.07277 eLife Website
2014
Coen, P, Clemens, J, Weinstein, A, Pacheco, D, Deng, Y, and Murthy, M. Dynamic sensory cues shape song structure in Drosophila. Nature 2014. March 13. doi:10.1038/nature13131 Nature Website
News and Views: Neuroscience: Ordered Randomness in Fly Love Songs
Princeton University Website: PU Homepage
2010-2013
Sun XR, Badura A, Pacheco DA, Lynch LA, Schneider ER, Taylor MP, Hogue IB, Enquist LW, Murthy M, and Wang SS. Fast GCaMPs for improved tracking of neuronal activity. Nature Communications. 2013 Jul 17;4:2170.
Arthur, BJ, Sunayama-Morita, T, Coen, P, Murthy, M* and Stern, DL*. Multi-channel acoustic recording and automated analysis of Drosophila courtship songs. BMC Biology. 2013. January vol. 11(1): 11. *co-corresponding authors BMC Biology website
Tayler TD, Pacheco DA, Hergarden AC, Murthy M, and Anderson DJ. A neuropeptide circuit that coordinates sperm transfer and copulation duration in Drosophila. Proc Natl Acad Sci U S A. 2012 Dec 11;109(50):20697-702.
Tootoonian, S, Coen, P, Kawai, R, and Murthy, M. Neural representations of courtship song in the Drosophila brain. Journal of Neuroscience. 2012. January vol. 32(3): 787-798. J Neurosci website
Murthy, M. Unraveling the Auditory System of Drosophila. Current Opinion in Neurobiology 2010. June 20(30): 281-287. Curr Opin Neurobiol website
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Mala's Previous Publications:
Murthy, M, Fiete, I, and Laurent, G. Testing odor response stereotypy in the Drosophila mushroom body. Neuron. 2008 Sep 25;59(6):1009-23.
Murthy, M and Turner, G. In vivo whole-cell recordings in the Drosophila brain. Drosophila Neurobiology: A Laboratory Manual. Ed. Zhang B, Freeman MR, Waddell S. CSHL Press. June 2010.
Murthy, M*, Teodoro, R*, Miller, TP, and Schwarz, TL. Sec5, a member of the exocyst complex, mediates Drosophila embryo cellularization. Development. 2010 Aug;137(16):2773-83. *equal authors
Menon, K, Andrews, S, Murthy, M, Gavis, E, and Zinn, K. The translational repressors Nanos and Pumilio have divergent effects on presynatic terminal growth and postsynaptic glutamate receptor subunit composition. Journal of Neuroscience. 2009 Apr;29(17):5558 –5572.
Langevin J, Morgan MJ, Sibarita JB, Aresta S, Murthy M, Schwarz T, Camonis J, Bellaiche Y. Drosophila exocyst components Sec5, Sec6, and Sec15 regulate DE-Cadherin trafficking from recycling endosomes to the plasma membrane.Developmental Cell. 2005 Sep;9(3):355-76.
Murthy, M, Ranjan, R, Denef, N, Higashi, M, Schupbach, T, and Schwarz TL. Sec6 mutations and the Drosophila exocyst complex. Journal of Cell Science. 2005 Mar 15;118(Pt 6):1139-50.
Murthy, M and Schwarz, TL. The exocyst component sec5 is required for membrane traffic and polarity in the Drosophila ovary. Development. 2004 Jan 131(02): 377-388.
Murthy, M, Garza, D, Scheller, RH, and Schwarz, TL. Mutations in the exocyst component sec5 disrupt neuronal membrane traffic, but neurotransmitter release persists. Neuron. 2003 Feb 6;37(3):433-47.
Chen, YA, Scales, SJ, Duvvuri, V, Murthy, M, Patel, SM, Schulman, H, and Scheller, RH. Calcium regulation of exocytosis in PC12 cells. Journal of Biological Chemistry. 2001 Jul 13;276(28):26680-7.
Kennedy, BK, Gotta, M, Sinclair, DA, Mills, K, McNabb, DS, Murthy, M, Pak, SM, Laroche, T, Gasser, SM, and Guarente, L. Redistribution of silencing proteins from telomeres to the nucleolus is associated with extension of life span in S. cerevisae. Cell. 1997 May 2;89(3):381-91.