Research papers

Papers using BrainX.

Recent publications that use BrainX ecosystem tools — from large-scale brain dynamics simulation to differentiable modeling and brain-inspired learning. Listed newest first and grouped by year. If you've used BrainX in your work and don't see your paper here, let us know and we'll add it.

2026

Massimo Trusel, Junfeng Zuo, Danyal H. Alam, others

Holistic motor control of zebra finch song syllable sequences

Nature

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Shan Zhao, Heying Shan, Xiao Liu, Yu Qian, Jingyao Huang, Yi-Ran Liu, Zhenfei Jiao, Lichen Ye, Lin Cong, Xiaoou Wang, Zhi-Yuan Wang, Danyang Li, Ming-Quan Chen, Kai Wang, Ling Fu, Xu-Fei Du, Si Wu, Yu Mu

A thalamus–brainstem attractor network drives history-biased decisions

Nature

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Jinzhao Wei, Licong Li, Jieshuo Zhang, Jianli Yang, Xiuling Liu

Computational modeling investigates the neural mechanisms underlying working memory updating impairments in depression

Brain Research Bulletin

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Aur Shalev Merin

Massive Redundancy in Gradient Transport Enables Sparse Online Learning

arXiv:2603.15195

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Baiyu Chen, Yujie Wu, Siyuan Xu, Peng Qu, Dehua Wu, Xu Chu, Haodong Bian, Shuo Zhang, Bo Xu, Youhui Zhang, Zhengyu Ma, Guoqi Li

BrainFuse: a unified infrastructure integrating realistic biological modeling and core AI methodology

arXiv:2601.21407

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Roel Koopman, Sebastian Otte, Sander M. Bohté

SpikingGamma: Surrogate-Gradient Free and Temporally Precise Online Training of Spiking Neural Networks with Smoothed Delays

arXiv:2602.01978

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Zilong Ji, Tianhao Chu, Xingsi Dong, Changmin Yu, Daniel Bush, Neil Burgess, Si Wu

Dynamical modulation of hippocampal replay through firing rate adaptation

Nature Communications

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Shinya Ito, Darrell Haufler, Javier Galván Fraile, Kael Dai, Joseph Aman, Guozhang Chen, Claudio Mirasso, Wolfgang Maass, Anton Arkhipov

Deep-learning-assisted simulation of a cortical circuit: integrating anatomy, physiology and function

bioRxiv: 2026–03

Jinzhao Wei, Licong Li, Jieshuo Zhang, Jianli Yang, Xiuling Liu

Computational modeling investigates the neural mechanisms underlying working memory updating impairments in depression

Brain Research Bulletin: 111773

Shunmin Yao, Ziyang Wang, Rui Zhu, Wen Cheng, Yuan Chai

A coupling network for brain computing: EI balanced embedding in dual-attractor dynamics systems

Brain Research Bulletin: 111788

Mario Senden, Leonardo Dalla Porta, Jan Fousek, Jorge F Mejias, Gorka Zamora-López

Functional Whole-Brain Models: A New Framework for Unifying Brain Structure and Cognitive Function

arXiv preprint arXiv:2605.18118

2025

Xuexing Du, K Tian Zhong-qi, Songting Li, Douglas Zhou

A generalized Spiking Locally Competitive Algorithm for multiple optimization problems

Neurocomputing, 624: 129392

Zilong Ji, Tianhao Chu, Si Wu, others

A systems model of alternating theta sweeps via firing rate adaptation

Current Biology

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Changmin Yu, Zilong Ji, Jake Ormond

Hippocampal theta sweeps indicate goal direction

bioRxiv

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Lining Yin, Lanyun Cui, Ying Yu, Qingyun Wang

A Heterogeneous Attractor Model for Neural Dynamical Mechanism of Movement Preparation

International Journal of Neural Systems

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Anonymous

Controlling Epileptic Seizures through Hippocampal Regulation: A Complex Network Analysis

IEEE Transactions on Neural Systems and Rehabilitation Engineering

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Z. Ge, Xu He, Lingfei Mo, others

Boosting Brain-inspired Path Integration Efficiency via Learning-based Replication of Continuous Attractor Neurodynamics

arXiv:2511.17687

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Sicheng Shen, Dongcheng Zhao, Linghao Feng, others

STEP: A Unified Spiking Transformer Evaluation Platform for Fair and Reproducible Benchmarks

arXiv:2505.11151

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Zilong Ji, Eleonora Lomi, Kate Jeffery, Anna S Mitchell, Neil Burgess

Phase Precession Relative to Turning Angle in Theta-Modulated Head Direction Cells

Hippocampus, 35(2): e70008

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Xuexing Du, Jennifer Crodelle, Victor James Barranca, Songting Li, Yunzhu Shi, Shangbang Gao, Douglas Zhou

Biophysical modeling and experimental analysis of the dynamics of C. elegans body-wall muscle cells

PLoS Computational Biology, 21(1): e1012318

Xuexing Du, K Tian Zhong-qi, Songting Li, Douglas Zhou

A generalized Spiking Locally Competitive Algorithm for multiple optimization problems

Neurocomputing, 624: 129392

Qinglai Wei, Qizhi Yang, Liyuan Han, Tielin Zhang

Physics-informed spiking neural networks for continuous-time dynamic systems

Neurocomputing: 132192

Renato Paredes, Juan B Cabral, Peggy Seriès

Scikit-neuromsi: a generalized framework for modeling multisensory integration

Neuroinformatics, 23(3): 40

2024

Tianhao Chu, Zilong Ji, Junfeng Zuo, Yuanyuan Mi, Wen-hao Zhang, Tiejun Huang, Daniel Bush, Neil Burgess, Si Wu

Firing rate adaptation affords place cell theta sweeps, phase precession, and procession

Elife, 12: RP87055

Code

Shangyang Li, Chaoming Wang, Si Wu

Spindle oscillations emerge at the critical state of electrically coupled networks in the thalamic reticular nucleus

Cell Reports, 43(10)

Chaoming Wang, Muyang Lyu, Tianqiu Zhang, Sichao He, Si Wu

A differentiable approach to multi-scale brain modeling

arXiv preprint arXiv:2406.19708

Hongru Jiang, Xiangdong Bu, Xiaohong Sui, Huajin Tang, Xiaochuan Pan, Yao Chen

Spike Neural network of motor cortex model for arm reaching control

2024 46th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC): 1–4

Papers using BrainX.

2026

Holistic motor control of zebra finch song syllable sequences

A thalamus–brainstem attractor network drives history-biased decisions

Computational modeling investigates the neural mechanisms underlying working memory updating impairments in depression

Massive Redundancy in Gradient Transport Enables Sparse Online Learning

BrainFuse: a unified infrastructure integrating realistic biological modeling and core AI methodology

SpikingGamma: Surrogate-Gradient Free and Temporally Precise Online Training of Spiking Neural Networks with Smoothed Delays

Dynamical modulation of hippocampal replay through firing rate adaptation

Deep-learning-assisted simulation of a cortical circuit: integrating anatomy, physiology and function

Computational modeling investigates the neural mechanisms underlying working memory updating impairments in depression

A coupling network for brain computing: EI balanced embedding in dual-attractor dynamics systems

Functional Whole-Brain Models: A New Framework for Unifying Brain Structure and Cognitive Function

2025

A generalized Spiking Locally Competitive Algorithm for multiple optimization problems

A systems model of alternating theta sweeps via firing rate adaptation

Hippocampal theta sweeps indicate goal direction

A Heterogeneous Attractor Model for Neural Dynamical Mechanism of Movement Preparation

Controlling Epileptic Seizures through Hippocampal Regulation: A Complex Network Analysis

Boosting Brain-inspired Path Integration Efficiency via Learning-based Replication of Continuous Attractor Neurodynamics

STEP: A Unified Spiking Transformer Evaluation Platform for Fair and Reproducible Benchmarks

Phase Precession Relative to Turning Angle in Theta-Modulated Head Direction Cells

Biophysical modeling and experimental analysis of the dynamics of C. elegans body-wall muscle cells

A generalized Spiking Locally Competitive Algorithm for multiple optimization problems

Physics-informed spiking neural networks for continuous-time dynamic systems

Scikit-neuromsi: a generalized framework for modeling multisensory integration

2024

Firing rate adaptation affords place cell theta sweeps, phase precession, and procession

Spindle oscillations emerge at the critical state of electrically coupled networks in the thalamic reticular nucleus

A differentiable approach to multi-scale brain modeling

Spike Neural network of motor cortex model for arm reaching control

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