Publications

• A Biconvex Formulation for Stable Transport of Mixture Models with a Unique Solution
Y Marghi, K Jin, U Sümbül
NeurIPS, 2027

• Interpretable time series analysis with Gumbel dynamics
Y Wang, TD Kim, E Shea-Brown, U Sümbül
NeurIPS, 2027

• Identifying Connectivity Distributions from Neural Dynamics Using Flows
TD Kim, U Pereira-Obilinovic, Y Wang, E Shea-Brown, U Sümbül
ICML, 2026

• Connecting single-cell transcriptomes to projectomes in the mouse visual cortex
SA Sorensen, NW Gouwens, Y Wang, M Mallory, A Budzillo, R Dalley, BR Lee, O Gliko, H Kuo, X Kuang, R Mann, L Ahmadinia, L Alfiler, F Baftizadeh, KS Baker, S Bannick, D Bertagnolli, K Bickley, P Bohn, J Bomben, C Bowman, G Boyer, K Brouner, D Brown, A Cahoon, N Chen, C Chen, K Chen, M Chvilicek, F Collman, TL Daigle, T Dawes, R de Frates, N Dee, M DePartee, T Egdorf, L El-Hifnawi, R Enstrom, L Esposito, C Farrell, R Gala, C Gamlin, A Gary, A Glomb, O Gerasymchuk, J Goldy, H Gu, K Hadley, M Hawrylycz, A Henry, D Hill, KE Hirokawa, Z Huang, K Johnson, Z Juneau, S Kebede, L Kim, L Kruse, C Lee, AL Leon, P Lesnar, Q Lheureux, A Li, Y Li, E Liang, K Link, M Maxwell, M McGraw, DA McMillen, A Mukora, L Ng, T Ochoa, A Oldre, D Park, CA Pom, Z Popovich, L Potekhina, R Rajanbabu, S Ransford, MR Reding, A Ruiz, D Sandman, M Schroedter, J Sevigny, L Shulga, L Siverts, CR Slaughterbeck, KA Smith, M Stoecklin, J Sulc, SM Sunkin, M Tieu, JT Ting, J Trinh, R Velasco, S Vargas, D Vumbaco, M Walker, M Wang, A Wanner, J Waters, M Wells, G Williams, JA Wilson, W Xiong, ES Lein, J Berg, BE Kalmbach, S Yao, H Gong, Q Luo, Q Wang, L Ng, U Sümbül, Z Yao, T Jarsky, B Tasic, H Zeng
Nature, 2026

• SPINT: Spatial Permutation-Invariant Neural Transformer for Consistent Intracortical Motor Decoding
T Le, H Fang, J Li, T Nguyen, L Mi, A Orsborn, U Sümbül, E Shlizerman
NeurIPS, 2025

• Evidence from spatial transcriptomics for the mosaic hypothesis and pure cell types in the cortex
Y Wang, C Koch, U Sümbül
Cell Reports, 2025

• Efficient Connectivity-Preserving Instance Segmentation with Supervoxel-Based Loss Function
A Grim, J Chandrashekar, U Sümbül
AAAI, 2025

• Layer-specific input to medial prefrontal cortex is linked to stress susceptibility
ST Solakoglu, SE Erdener, O Gliko, A Can, U Sümbül, E Eren-Kocak
Translational Psychiatry, 2025

• NetFormer: An interpretable model for recovering dynamical connectivity in neuronal population dynamics
Z Lu, W Zhang, T Le, H Wang, U Sümbül, E Shea-Brown, L Mi
ICLR, 2025

• Joint inference of discrete cell types and continuous type-specific variability in single-cell datasets with MMIDAS
Y Marghi, R Gala, F Baftizadeh, U Sümbül
Nature Computational Science, 2024

• High-throughput analysis of dendrite and axonal arbors reveals transcriptomic correlates of neuroanatomy
O Gliko, M Mallory, R Dalley, R Gala, J Gornet, H Zeng, SA Sorensen, U Sümbül
Nature Communications, 2024

• Learning Time-Invariant Representations for Individual Neurons from Population Dynamics
L Mi, T Le, T He, E Shlizerman, U Sümbül
NeurIPS, 2023

• Predictive and robust gene selection for spatial transcriptomics
I Covert, R Gala, T Wang, K Svoboda, U Sümbül*, S-I Lee*
Nature Communications, 2023

• Biologically-plausible backpropagation through arbitrary timespans via local neuromodulators
YH Liu, SJ Smith, S Mihalas, E Shea-Brown, U Sümbül
NeurIPS, 2022

• Single-neuron models linking electrophysiology, morphology, and transcriptomics across cortical cell types
A Nandi, T Chartrand, W Van Geit, A Buchin, Z Yao, SY Lee, Y Wei, B Kalmbach, B Lee, E Lein, J Berg, U Sümbül, C Koch, B Tasic, C Anastassiou
Cell Reports, 2022

• Cell-type–specific neuromodulation guides synaptic credit assignment in a spiking neural network
YH Liu, SJ Smith, S Mihalas, E Shea-Brown, U Sümbül
PNAS, 2021

• Consistent cross-modal identification of cortical neurons with coupled autoencoders
R Gala, A Budzillo, F Baftizadeh, J Miller, N Gouwens, A Arkhipov, G Murphy, B Tasic, H Zeng, M Hawrylycz, U Sümbül
Nature Computational Science, 2021

• Integrated morphoelectric and transcriptomic classification of cortical GABAergic cells
NW Gouwens, SA Sorensen, F Baftizadeh, A Budzillo, BR Lee, T Jarsky, L Alfiler, K Baker, E Barkan, K Berry, D Bertagnolli, K Bickley, J Bomben, T Braun, K Brouner, T Casper, K Crichton, TL Daigle, R Dalley, RA de Frates, N Dee, T Desta, SD Lee, N Dotson, T Egdorf, L Ellingwood, R Enstrom, L Esposito, C Farrell, D Feng, O Fong, R Gala, C Gamlin, A Gary, A Glandon, J Goldy, M Gorham, L Graybuck, H Gu, K Hadley, MJ Hawrylycz, AM Henry, D Hill, M Hupp, S Kebede, TK Kim, L Kim, M Kroll, C Lee, KE Link, M Mallory, R Mann, M Maxwell, M McGraw, D McMillen, A Mukora, L Ng, L Ng, K Ngo, PR Nicovich, A Oldre, D Park, H Peng, O Penn, T Pham, A Pom, Z Popovic, L Potekhina, R Rajanbabu, S Ransford, D Reid, C Rimorin, M Robertson, K Ronellenfitch, A Ruiz, D Sandman, K Smith, J Sulc, SM Sunkin, A Szafer, M Tieu, A Torkelson, J Trinh, H Tung, W Wakeman, K Ward, G Williams, Z Zhou, JT Ting, A Arkhipov, U Sümbül, ES Lein, C Koch, Z Yao, B Tasic, J Berg, GJ Murphy, H Zeng
Cell, 2020

• New Light on Cortical Neuropeptides and Synaptic Network Plasticity
SJ Smith, M Hawrylycz, J Rossier, U Sümbül
Current Opinion in Neurobiology, 2020

• Whole-Neuron Synaptic Mapping Reveals Spatially Precise Excitatory/Inhibitory Balance Limiting Dendritic and Somatic Spiking
DM Iascone, Y Li, U Sümbül, M Doron, H Chen, V Andreu, F Goudy, I Segev, H Peng, F Polleux
Neuron, 2020

• A coupled autoencoder approach for multi-modal analysis of cell types
R Gala, N Gouwens, Z Yao, A Budzillo, O Penn, B Tasic, G Murphy, H Zeng, U Sümbül
NeurIPS, 2019

• Single-cell transcriptomic evidence for dense intracortical neuropeptide networks
SJ Smith, U Sümbül, LT Graybuck, F Collman, S Seshamani, R Gala, O Gliko, L Elabbady, J Miller, T Bakken, J Rossier, Z Yao, E Lein, H Zeng, B Tasic, M Hawrylycz
eLife, 2019

• Reconstructing neuronal anatomy from whole-brain images
J Gornet, KU Venkataraju, A Narasimhan, K Lee, N Turner, HS Seung, P Osten, U Sümbül
ISBI, 2019