Publications

Chintaluri C.*, Podlaski W.*, Bozelos P.A., Gonçalves P.J., Lueckmann J.-M., Macke J.H., Vogels T.P. (2025) Ion channel omnimodel for standardized biophysical neuron modelling. (bioRxiv) 

Deistler M., Boelts J., Steinbach P., Moss G., Moreau T., Gloeckler M., Rodrigues P.L.C., Linhart J., Lappalainen J.K., Miller B.K.,  Gonçalves P.J., Lueckmann J.M., Schröder C., Macke J.H. (2025) Simulation-Based Inference: A Practical Guide. (arXiv)

Confavreux B., Harrington Z., Kania M., Ramesh P., Krouglova A.N., Bozelos P., Macke J.H., Saxe A.M., Gonçalves P.J., Vogels T.P. (2025) Memory by a thousand rules: Automated discovery of functional multi-type plasticity rules reveals variety and degeneracy at the heart of learning. (bioRxiv)

Gao R., Deistler M., Schulz A., Gonçalves P.J., Macke J.H. (2024) Deep inverse modeling reveals dynamic-dependent invariances in neural circuit mechanisms. (bioRxiv)

Gerken F.,* Darcher A.*,  Gonçalves P.J., Rapp R., Elezi I., Niediek J., Kehl M.S., Reber T.P., Liebe S., Macke J.H.*, Mormann F.*, Leal-Taixé L.* (2024) Decoding movie content from neuronal population activity in the human medial temporal lobe. (bioRxiv)

Ramesh P., Confavreux B., Gonçalves P.J.*, Vogels T.P.*, Macke J.H.* (2023) Indistinguishable network dynamics can emerge from unalike plasticity rules. (bioRxiv)

Darcher A.*, Gerken F.,* Niediek J., Kehl M.S., Reber T.P., Liebe S., Nett L., Racz A., Kunz L., Staresina B., Rapp R., Gonçalves P.J., Elezi I., Borger V., Surges R., Leal-Taixé L.*, Macke J.H.*, Mormann F.* (2026) Human neuron activity during an 83-minute movie from 2,286 neurons and 29 patients. Sci Data, 13, 1105.

Schiltz E., Broux M., Aydin C, Gonçalves P.J., Haesler S. (2026) Experience shapes the transformation of olfactory representations along the cortico-hippocampal pathway. eLife, 13, RP103373.

Krouglova A.N., Johnson H.R., Confavreux B., Deistler M.,  Gonçalves P.J. (2026) Multifidelity Simulation-based Inference for Computationally Expensive Simulators. International Conference on Learning Representations (ICLR)

Deistler M., Kadhim K.L., Pals M., Beck J., Huang Z., Gloeckler M., Lappalainen J.K., Schröder C., Berens P.,  Gonçalves P.J., Macke J.H. (2025) JAXLEY: differentiable simulation enables large-scale training of detailed biophysical models of neural dynamics. Nature Methods.

Boelts J., Deistler M., Gloeckler M., Tejero-Cantero A., Lueckmann J.-M., Moss G., Steinbach P., Moreau T., Muratore F., Linhart J., Durkan C., Vetter J., Miller B.K., Herold M., Ziaeemehr A., Pals M., Gruner T., Bischoff S., Krouglova N., Gao R., Lappalainen J.K., Mucsányi B., Pei F., Schulz A., Stefanidi Z., Rodrigues P., Schröder C., Abu Zaid F., Beck J., Kapoor J., Greenberg D.S., Gonçalves P.J., Macke J.H. (2025) sbi reloaded: a toolkit for simulation-based inference workflows. Journal of Open Source Software, 10(108), 7754.

Bernaerts Y., Deistler M., Gonçalves P.J., Beck J., Stimberg M., Scala F., Tolias A.S., Macke J.H., Kobak D., Berens P. (2025) Combined statistical-mechanistic modeling links ion channel genes to physiology of cortical neuron types. Patterns.

Zucca S.*, Schulz A.*, Gonçalves P.J., Macke J.H., Saleem A.B.*, Solomon S.G.* (2025) Visual loom caused by self-movement or object-movement elicits distinct responses in mouse superior colliculus. Current Biology.

Manzano-Patron J.P., Deistler M., Schröder C., Kypraios T., Gonçalves P.J., Macke J.H., Sotiropoulos S.H. (2025) Uncertainty mapping and probabilistic tractography using Simulation-based Inference in diffusion MRI: A comparison with classical Bayes. Medical Image Analysis, 103580.

Schulz A., Vetter J., Gao R., Morales D., Lobato-Rios V., Ramdya P., Gonçalves P.J.*, Macke J.H.* (2025) Modeling conditional distributions of neural and behavioral data with masked variational autoencoders. Cell Reports, Volume 44, Issue 3, 115338.

Schiltz E., Broux M., Aydin C, Gonçalves P.J., Haesler S. (2024) Experience shapes the transformation of olfactory representations along the cortico-hippocampal pathway. eLife, 13, RP103373

Caenepeel C.*, Falony G.*, Machiels K., Verstockt B., Gonçalves P.J., Ferrante M., Sabino J., Raes J., Vieira-Silva S.*, Vermeire S.* (2023) Dysbiosis and associated stool features improve prediction of response to biological therapy in inflammatory bowel disease. Gastroenterology.

Confavreux B., Ramesh P., Gonçalves P.J., Macke J.H., Vogels T.P. (2023) Meta-learning families of plasticity rules in recurrent spiking networks using simulation-based inference. Advances in Neural Information Processing Systems (NeurIPS).

Deistler M., Macke J.H.*, Gonçalves P.J.* (2022) Energy efficient network activity from disparate circuit parameters. Proc. Natl. Acad. Sci. U.S.A. 119 (44) e2207632119.

Deistler M., Gonçalves P.J.*, Macke J.H.* (2022) Truncated proposals for scalable and hassle-free simulation-based inference. Advances in Neural Information Processing Systems (NeurIPS).

Calaim N.*, Dehmelt F.A.*, Gonçalves P.J.*, Machens C.K. (2022) The geometry of robustness in spiking neural networks. eLife, 11, e73276.

Ramesh P., Lueckmann J.-M., Boelts J., Tejero-Cantero A., Greenberg D.S., Gonçalves P.J., Macke J.H. (2022) GATSBI: Generative Adversarial Training for Simulation-Based Inference. International Conference on Learning Representations (ICLR).

Valle A.F., Gonçalves P.J.@, Seelig J.D.@ (2021) Integration of sleep homeostasis and navigation in Drosophila. PLoS Computational Biology, 17(7): e1009088.

Llorens-Rico V., Vieira-Silva S., Gonçalves P.J., Falony G., Raes J. (2021) Benchmarking microbiome transformations favors experimental, quantitative approaches to address compositionality and sampling depth biases. Nature Communications, 12, 3562.

Lueckmann J.-M., Boelts J., Greenberg D.S., Gonçalves P.J., Macke J.H. (2021) Benchmarking simulation-based inference. In The 24th International Conference on Artificial Intelligence and Statistics (AISTATS), PMLR 130:343-351.

Gonçalves P.J.*, Lueckmann J.*, Deistler M.*, Nonnenmacher M., Oecal K., Bassetto G., Chintaluri C., Podlaski W.F., Haddad S.A., Vogels T.P., Greenberg D.S., Macke J.H. (2020) Training deep neural density estimators to identify mechanistic models of neural dynamics. eLife, 9, e56261.

Gothner T.*, Gonçalves P.J.*, Sahani M., Linden J.F., Hildebrandt K.J. (2020) Sustained Activation of PV+ Interneurons in Auditory Cortex Enables Robust Divisive Gain Control for Complex and Naturalistic Stimuli. Cerebral Cortex.

Tejero-Cantero A., Boelts J., Deistler M., Lueckmann J.-M., Durkan C., Gonçalves P.J., Greenberg D.S., Macke J.H. (2020) sbi -- a toolkit for simulation-based inference. Journal of Open Source Software, 5(52), 2505.

Lueckmann J.*, Gonçalves P.J.*, Bassetto G., Oecal K., Nonnenmacher M., Macke J.H. (2017) Flexible statistical inference for mechanistic models of neural dynamics. Advances in Neural Information Processing Systems, pages 1289–1299.

Gonçalves P.J.*, Arrenberg A.B.*, Hablitzel B., Baier H. and Machens C.K. (2014). Optogenetic perturbations reveal the dynamics of an oculomotor integrator. Frontiers in Neural Circuits 8:10.

Boelts J., Lueckmann J.M., Gonçalves P.J., Sprekeler H., Macke J.H. Comparing neural simulations by neural density estimation. Conference on Cognitive Computational Neuroscience (2019)

*equal contributions, @corresponding author(s)