Interpolating Between Periodicity and Discreteness Through the Fractional Fourier Transform. - Haldun M. Özaktas; Uygar Sümbül (IEEE Trans. Signal Process., 2006)

Improved Time Series Reconstruction for Dynamic Magnetic Resonance Imaging. - Uygar Sümbül; Juan M. Santos; John M. Pauly (IEEE Trans. Medical Imaging, 2009)

A Practical Acceleration Algorithm for Real-Time Imaging. - Uygar Sümbül; Juan M. Santos; John M. Pauly (IEEE Trans. Medical Imaging, 2009)

Automated scalable segmentation of neurons from multispectral images. - Uygar Sümbül; Douglas H. Roossien; Dawen Cai; Fei Chen; Nicholas Barry; John P. Cunningham; Edward S. Boyden; Liam Paninski (NIPS, 2016)

Reconstructing Neuronal Anatomy from Whole-Brain Images. - James Gornet; Kannan Umadevi Venkataraju; Arun Narasimhan; Nicholas L. Turner; Kisuk Lee; H. Sebastian Seung; Pavel Osten; Uygar Sümbül (ISBI, 2019)

A coupled autoencoder approach for multi-modal analysis of cell types. - Rohan Gala; Nathan W. Gouwens; Zizhen Yao; Agata Budzillo; Osnat Penn; Bosiljka Tasic; Gabe Murphy; Hongkui Zeng; Uygar Sümbül (NeurIPS, 2019)

Joint Learning of Discrete and Continuous Variability with Coupled Autoencoding Agents. - Yeganeh M. Marghi; Rohan Gala; Uygar Sümbül (CoRR, 2020)

Consistent cross-modal identification of cortical neurons with coupled autoencoders. - Rohan Gala; Agata Budzillo; Fahimeh Baftizadeh; Jeremy A. Miller; Nathan W. Gouwens; Anton Arkhipov; Gabe Murphy; Bosiljka Tasic; Hongkui Zeng; Michael Hawrylycz; Uygar Sümbül (Nat. Comput. Sci., 2021)

Biologically-plausible backpropagation through arbitrary timespans via local neuromodulators. - Yuhan Helena Liu; Stephen Smith; Stefan Mihalas; Eric Shea-Brown; Uygar Sümbül (NeurIPS, 2022)

Learning Time-Invariant Representations for Individual Neurons from Population Dynamics. - Lu Mi; Trung Le 002; Tianxing He; Eli Shlizerman; Uygar Sümbül (NeurIPS, 2023)

Joint inference of discrete cell types and continuous type-specific variability in single-cell datasets with MMIDAS. - Yeganeh M. Marghi; Rohan Gala; Fahimeh Baftizadeh; Uygar Sümbül (Nat. Comput. Sci., 2024)

Publisher Correction: Joint inference of discrete cell types and continuous type-specific variability in single-cell datasets with MMIDAS. - Yeganeh M. Marghi; Rohan Gala; Fahimeh Baftizadeh; Uygar Sümbül (Nat. Comput. Sci., 2024)

Author Correction: Joint inference of discrete cell types and continuous type-specific variability in single-cell datasets with MMIDAS. - Yeganeh M. Marghi; Rohan Gala; Fahimeh Baftizadeh; Uygar Sümbül (Nat. Comput. Sci., 2024)

Efficient Connectivity-Preserving Instance Segmentation with Supervoxel-Based Loss Function. - Anna Grim; Jayaram Chandrashekar; Uygar Sümbül (AAAI, 2025)

NetFormer: An interpretable model for recovering dynamical connectivity in neuronal population dynamics. - Ziyu Lu; Wuwei Zhang; Trung Le 002; Hao Wang; Uygar Sümbül; Eric Todd Shea-Brown; Lu Mi (ICLR, 2025)

SPINT: Spatial Permutation-Invariant Neural Transformer for Consistent Intracortical Motor Decoding. - Trung Le 002; Hao Fang; Jingyuan Li; Tung Nguyen; Lu Mi; Amy L. Orsborn; Uygar Sümbül; Eli Shlizerman (CoRR, 2025)