Rose, F., Michaluk, M., Blindauer, T., Ignatowska-Jankowska, B.M., O'Shaughnessy, L., Stephens, G.J., Pereira, T.D., Uusisaari, M.Y., Bozek, K. Deep Imputation for Skeleton data (DISK) for behavioral science. (2025) 自然方法. DOI: 10.1038/s41592-025-02893-y

Zhang, C.Y., Yang, Y., Sirbu, A., Abe, E.T.T., Wärnberg, E., Leonardis, E.J., Aldarondo, D.E., Lee, A., Prasad, A., Foat, J., Bian, K., Park, J., Bhatt, R., Saunders, H., Nagamori, A., Thanawalla, A.R., Huang, K.W., Plum, F., Beck, H.K., Flavell, S.W., Labonte, D., Richards, B.A., Brunton, B.W., Azim, E., Ölveczky, B.P., Pereira, T.D. MIMIC-MJX: Neuromechanical Emulation of Animal Behavior. (2025) arXiv.

Leonardis, E., Nagamori, A., Thanawalla, A., Yang, Y., Park, J., Saunders, H., Azim, E., Pereira, T. Massively Parallel Imitation Learning of Mouse Forelimb Musculoskeletal Reaching Dynamics. (2025) arXiv.

Mitelut, C., Diez Castro, M., Peterson, R.E., Gonçalves, M., Li, J., Gamer, M., Nilsson, S.R., Pereira, T.D., Sanes, D.H. Continuous monitoring and machine vision reveals that developing gerbils exhibit structured social behaviors prior to the emergence of autonomy. (2025) PLOS Biology. 23(9):e3003348. DOI: 10.1371/journal.pbio.3003348

Cheng, Y., Chen, Y., Kwak, M., Kempner, R.P., Singha, R., Winslow, J., Liu, R., Khan, U., Spangler, T., Khan, A., Pereira, T.D., Whiteway, M.R., Schaffer, E.S., Rungratsameetaweemana, N., Yang, N., Wu, H.Z. Asymmetric Social Representations in the Prefrontal Cortex for Cooperative Behavior. (2025) bioRxiv. DOI: 10.1101/2025.08.27.672249

Coley, A., Tye, K., Batra, K., Delahanty, J., Keyes, L., Pamintuan, R., Ramot, A., Hagemann, J., Lee, C., Liu, V., Adivikolanu, H., Cressy, J., Jia, C., Massa, F., LeDuke, D., Gabir, M., Durubeh, B., Linderhof, L., Patel, R., Wichmann, R., Li, H., Fischer, K., Pereira, T. Predicting Future Development of Stress-Induced Anhedonia From Cortical Dynamics and Facial Expression. (2025) Res Sq. DOI: 10.21203/rs.3.rs-5537951/v1

Duporge, I., Pereira, T., de Obeso, S.C., Ross, J.G.B., J Lee, S., G Hindle, A. The utility of animal models to inform the next generation of human space exploration. (2025) NPJ Microgravity. 11(1):7. DOI: 10.1038/s41526-025-00460-5

Weinreb, C., Pearl, J.E., Lin, S., Osman, M.A.M., Zhang, L., Annapragada, S., Conlin, E., Hoffmann, R., Makowska, S., Gillis, W.F., Jay, M., Ye, S., Mathis, A., Mathis, M.W., Pereira, T., Linderman, S.W., Datta, S.R. Keypoint-MoSeq: parsing behavior by linking point tracking to pose dynamics. (2024) 自然方法. 21(7):1329-1339. DOI: 10.1038/s41592-024-02318-2

Berrigan, E.M., Wang, L., Carrillo, H., Echegoyen, K., Kappes, M., Torres, J., Ai-Perreira, A., McCoy, E., Shane, E., Copeland, C.D., Ragel, L., Georgousakis, C., Lee, S., Reynolds, D., Talgo, A., Gonzalez, J., Zhang, L., Rajurkar, A.B., Ruiz, M., Daniels, E., Maree, L., Pariyar, S., Busch, W., Pereira, T.D. Fast and Efficient Root Phenotyping via Pose Estimation. (2024) Plant Phenomics. 6:0175. DOI: 10.34133/plantphenomics.0175

Mitelut, C., Diez Castro, M., Peterson, R.E., Goncalves, M., Li, J., Gamer, M.M., Nilsson, S.R.O., Pereira, T.D., Sanes, D.H. A behavioral roadmap for the development of agency in the rodent. (2024) bioRxiv. DOI: 10.1101/2023.11.10.566632

Tye, K., Patel, R., Patarino, M., Kim, K., Pamintuan, R., Taschbach, F., Li, H., Lee, C., Hoek, A., Castro, R., Cazares, C., Miranda, R., Jia, C., Delahanty, J., Batra, K., Keyes, L., Libster, A., Wichmann, R., Pereira, T., Benna, M. Social isolation recruits amygdala-cortical circuitry to escalate alcohol drinking. [Preprint] (2024) Res Sq. DOI: 10.21203/rs.3.rs-4033115/v1

Mitelut , C., Diez Castro, M., Peterson, R.E., Gonçalves , M., Gamer, M.M., Nilsson, S.R.O., Pereira, T.D., Sanes, D.H. Distinct developmental trajectories of autonomous behaviors and agency in rodents (2023) bioRxiv. DOI: https://doi.org/10.1101/2023.11.10.566632

Luxem, K., Sun, J.J., Bradley, S.P., Krishnan, K., Yttri, E., Zimmermann, J., Pereira, T.D., Laubach, M. Open-source tools for behavioral video analysis: Setup, methods, and best practices. (2023) Elife. 12. DOI: 10.7554/eLife.79305

Weinreb, C., Osman, M.A.M., Zhang, L., Lin, S., Pearl, J., Annapragada, S., Conlin, E., Gillis, W.F., Jay, M., Ye, S., Mathis, A., Mathis, M.W., Pereira, T., Linderman, S.W., Datta, S.R. Preprint - Keypoint-MoSeq: parsing behavior by linking point tracking to pose dynamics. (2023) bioRxiv. DOI: 10.1101/2023.03.16.532307

Prasad, A., Manor, U., Pereira, T. Exploring the role of image domain in self-supervised DNN models of rodent brains (2022) OpenReview.net.

Mills, F., Lee, C.R., Howe, J.R., Li, Shao, Keisler, M.N., Lemieux , M.E., Taschbach , F.H., Keyes, L.R., Borio, M., Chen, H.S., Patel, R.R., Gross, A.l., Delahanty , J., Cazares, C., Maree, L., Wichmann , R., Pereira , T.D., Benna, M.K., Root, C.M., Tye, K.M. Amygdalostriatal transition zone neurons encode sustained valence to direct conditioned behaviors (2022) bioRxiv. DOI: https://doi.org/10.1101/2022.10.28.514263

Wang, Z.Y., McKenzie-Smith, G.C., Liu, W., Cho, H.J., Pereira, T., Dhanerawala, Z., Shaevitz, J.W., Kocher, S.D. Isolation disrupts social interactions and destabilizes brain development in bumblebees. (2022) 当前生物学。. DOI: 10.1016/j.cub.2022.04.066

Pereira, T.D., Tabris, N., Matsliah, A., Turner, D.M., Li, J., Ravindranath, S., Papadoyannis, E.S., Normand, E., Deutsch, D.S., Wang, Z.Y., McKenzie-Smith, G.C., Mitelut, C.C., Castro, M.D., D'Uva, J., Kislin, M., Sanes, D.H., Kocher, S.D., Wang, S.S., Falkner, A.L., Shaevitz, J.W., Murthy, M. SLEAP: A deep learning system for multi-animal pose tracking. (2022) 自然方法. 19(4):486-495. DOI: 10.1038/s41592-022-01426-1

Gall, G.E.C., Pereira, T.D., Jordan, A., Meroz, Y. Fast estimation of plant growth dynamics using deep neural networks. (2022) Plant Methods. 18(1):21. DOI: 10.1186/s13007-022-00851-9

Pereira, T.D., Shaevitz, J.W., Murthy, M. Quantifying behavior to understand the brain. (2020) 自然神经科学. 23(12):1537-1549. DOI: 10.1038/s41593-020-00734-z

Deutsch, D., Pacheco, D., Encarnacion-Rivera, L., Pereira, T., Fathy, R., Clemens, J., Girardin, C., Calhoun, A., Ireland, E., Burke, A., 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, H.S., Murthy, M. The neural basis for a persistent internal state in females. (2020) Elife. 9. DOI: 10.7554/eLife.59502

Jones, J.M., Foster, W., Twomey, C.R., Burdge, J., Ahmed, O.M., Pereira, T.D., Wojick, J.A., Corder, G., Plotkin, J.B., Abdus-Saboor, I. A machine-vision approach for automated pain measurement at millisecond timescales. (2020) Elife. 9. DOI: 10.7554/eLife.57258

Charles, A.S., Falk, B., Turner, N., Pereira, T.D., Tward, D., Pedigo, B.D., Chung, J., Burns, R., Ghosh, S.S., Kebschull, J.M., Silversmith, W., Vogelstein, J.T. Toward Community-Driven Big Open Brain Science: Open Big Data and Tools for Structure, Function, and Genetics. (2020) 神经科学年度评论》。. 43:441-464. DOI: 10.1146/annurev-neuro-100119-110036

Pereira, T.D., Aldarondo, D.E., Willmore, L., Kislin, M., Wang, S.S., Murthy, M., Shaevitz, J.W. Fast animal pose estimation using deep neural networks. (2019) 自然方法. 16(1):117-125. DOI: 10.1038/s41592-018-0234-5

Badura, A., Verpeut, J.L., Metzger, J.W., Pereira, T.D., Pisano, T.J., Deverett, B., Bakshinskaya, D.E., Wang, S.S. Normal cognitive and social development require posterior cerebellar activity. (2018) Elife. 7. DOI: 10.7554/eLife.36401

Clemens, J., Coen, P., Roemschied, F.A., Pereira, T.D., Mazumder, D., Aldarondo, D.E., Pacheco, D.A., Murthy, M. Discovery of a New Song Mode in Drosophila Reveals Hidden Structure in the Sensory and Neural Drivers of Behavior. (2018) 当前生物学。. 28(15):2400-2412.e6. DOI: 10.1016/j.cub.2018.06.011

Pereira, T.D., Murthy, M. To Fight or Not to Fight. (2017) 神经元. 95(5):986-988. DOI: 10.1016/j.neuron.2017.08.029

Giovannucci, A., Badura, A., Deverett, B., Najafi, F., Pereira, T.D., Gao, Z., Ozden, I., Kloth, A.D., Pnevmatikakis, E., Paninski, L., De Zeeuw, C.I., Medina, J.F., Wang, S.S. Cerebellar granule cells acquire a widespread predictive feedback signal during motor learning. (2017) 自然神经科学. 20(5):727-734. DOI: 10.1038/nn.4531

Hobbs, E.T., Pereira, T., O'Neill, P.K., Erill, I. A Bayesian inference method for the analysis of transcriptional regulatory networks in metagenomic data. (2016) Algorithms Mol Biol. 11:19. DOI: 10.1186/s13015-016-0082-8