Publications

2025

"Data Heterogeneity Limits the Scaling Effect of Pretraining Neural Data Transformers," Linxing Preston Jiang, Shirui Chen, Emmanuel Tanumihardja, Xiaochuang Han, Weijia Shi, Eric Shea-Brown, Rajesh P. N. Rao, bioRxiv, https://doi.org/10.1101/2025.05.12.653551

"Correlates of head-fixed orienting movements in mouse superior colliculus and substantia nigra pars reticulata," Ted K. Doykos, Taylor Yamauchi, Anna Buteau, Spencer Hanson, Joshua T. Dudman, Gidon Felsen, Elizabeth A. Stubblefield, bioRxiv, https://doi.org/10.1101/2025.05.02.651955

"In vitro 2 In vivo : Bidirectional and High-Precision Generation of In Vitro and In Vivo Neuronal Spike Data,"  View ORCID ProfileMasanori Shimono, bioRxiv, https://doi.org/10.1101/2025.03.26.645366

"DREDge: robust motion correction for high-density extracellular recordings across species," Charlie Windolf, Han Yu, Angelique C. Paulk, Domokos Meszéna, William Muñoz, Julien Boussard, Richard Hardstone, Irene Caprara, Mohsen Jamali, Yoav Kfir, Duo Xu, Jason E. Chung, Kristin K. Sellers, Zhiwen Ye, Jordan Shaker, Anna Lebedeva, RT Raghavan, Eric Trautmann, Max Melin, João Couto, Samuel Garcia, Brian Coughlin, Margot Elmaleh, David Christianson, Erdem Varol, et al., Nature Methods (2025), https://doi.org/10.1038/s41592-025-02614-5

"AIRUS: a simple workflow for AI-assisted exploration of scientific data”, Kenneth Harris, bioRxiv, https://doi.org/10.1101/2025.02.23.639768

"Quantifying Differences in Neural Population Activity With Shape Metrics," Joao Barbosa,  Amin Nejatbakhsh, Lyndon Duong, Sarah E. Harvey, Scott L. Brincat, Markus Siegel, Earl K. Miller, Alex H. Williams, bioRxiv, https://doi.org/10.1101/2025.01.10.632411

2024

"Rarely categorical, always high-dimensional: how the neural code changes along the cortical hierarchy," Lorenzo Posani, Shuqi Wang, Samuel P. Muscinelli, Liam Paninski, Stefano Fusi, bioRxiv, https://doi.org/10.1101/2024.11.15.623878

"Marked point process variational autoencoder with applications to unsorted spiking activities," Ryohei Shibue, Tomoharu Iwata, PLOS, https://doi.org/10.1371/journal.pcbi.1012620

"A Prefrontal Cortex Map based on Single Neuron Activity,"Pierre Le Merre, Katharina Heining, Marina Slashcheva, Felix Jung, Eleni Moysiadou, Nicolas Guyon, Ram Yahya, Hyunsoo Park, Fredrik Wernstal, Marie Carlén, bioRxiv, https://doi.org/10.1101/2024.11.06.622308

"Temporal regularities shape perceptual decisions and striatal dopamine signals," Matthias Fritsche, Antara Majumdar, Lauren Strickland, Samuel Liebana Garcia, Rafal Bogacz & Armin Lak, Nature Communications 15: 7093 (2024), https://doi.org/10.1038/s41467-024-51393-8

"Dimensionality reduction beyond neural subspaces with slice tensor component analysis," Arthur Pellegrino, Heike Stein, N Alex Cayco-Gajic, Nature Neuroscience 27, 1199–1210 (2024), https://doi.org/10.1038/s41593-024-01626-2

"Spike sorting with Kilosort4," Marius Pachitariu, Shashwat Sridhar, Jacob Pennington & Carsen Stringer, Nature Methods 21, 914–921 (2024), https://doi.org/10.1038/s41593-024-01626-2