computational modeling (no new data)

Modality: 1,122 papers with a page, 913 of them with their authors' code.

Tuesday, 10 November 2026 (1 paper)

[1] Code ↔ Paper doi:10.1186/s12874-026-03050-5 [paper, repository]

A comprehensive simulation study evaluating the predictive performance of Cox proportional hazards model and machine learning methods for time-to-event data.

Journal: BMC medical research methodology

Authors' code: Josline90/Cox-vs-ML-models-for-time-to-event-data_A-simulation-study (no license)

Status: code verified, 9 files readable, 4 matches

Sunday, 1 November 2026 (1 paper)

[2] Code ↔ Paper doi:10.1111/cogs.70271 [paper, repository]

Computation or Weight Adaptation? Rethinking the Role of Plasticity in Learning.

Journal: Cognitive science

Authors' code: colab.research.google.com/drive/1llf_gxk9zq4yl6c7f3gnaz7fqsateimf (no license)

Status: code verified

Wednesday, 28 October 2026 (2 papers)

[3] Code ↔ Paper doi:10.1038/s41467-026-78769-2 [paper, repository]

Computational modeling and preclinical evaluation support targeting somatic instability for Huntington's disease treatment.

Journal: Nature communications

Authors' code: LatusBio/HD_Model_NatComm_Publication (no license), Zenodo 22118021 (CC-BY-4.0), Zenodo 22118020 (CC-BY-4.0)

Status: code verified, 15 files readable, 7 matches

[4] doi:10.1371/journal.pone.0360036 [paper, data]

The diminishing returns of distance: Computational analysis of approach-avoidance behavior under threat of predation.

Journal: PloS one

Status: data only, 1 dataset cited

Tuesday, 27 October 2026 (3 papers)

[5] Code ↔ Paper doi:10.1038/s42003-026-11157-0 [paper, repository]

A NEST-based framework unlocks massively parallel simulation of networks of multi-compartment neurons with customizable subcellular dynamics.

Journal: Communications biology

Authors' code: Zenodo 22878144 (CC-BY-4.0), willemwybo/wta-states (no license), jugit.fz-juelich.de/w.wybo/ca-adex (no license), Zenodo 10125416 (GPL-2.0), Zenodo 20757797 (GPL-2.0)

Status: code verified, 16 files readable, 5 matches

[6] Code ↔ Paper doi:10.1371/journal.pcbi.1014879 [paper, repository]

Evolutionary and dynamic constraints converge on a conserved coupling sector in thermally adapted GH1 β-glucosidases.

Journal: PLoS computational biology

Authors' code: zh-l-t/GH1--Glucosidase (no license)

Status: code verified, 117 files readable, 4 matches

[7] Code ↔ Paper doi:10.1371/journal.pone.0360636 [paper, repository]

Causality-enhanced and symmetry-preserving PINNs for damped elastodynamic PDEs.

Journal: PloS one

Authors' code: shahbaz1982/Symmetry-PINNs- (MIT)

Status: code verified, 6 files readable, 3 matches

Wednesday, 21 October 2026 (1 paper)

[8] Code ↔ Paper doi:10.7554/elife.109757 [paper, repository]

A mechanistic theory of planning in prefrontal cortex.

Journal: eLife

Authors' code: KrisJensen/pysta (MIT)

Status: code verified, 50 files readable, 12 matches

Friday, 25 September 2026 (1 paper)

[9] Code ↔ Paper doi: [paper, repository]

Going deeper with morphologically detailed neural networks by simulation-based gradient propagation

Journal: Frontiers in computational neuroscience

Authors' code: MS-GEB/DeepDendrite-modularization (Apache-2.0)

Status: code verified, 1,731 files readable

Friday, 18 September 2026 (1 paper)

[10] Code ↔ Paper doi:10.1007/s00422-026-01061-5 [paper, repository]

Modeling synaptic interactions between mammalian breathing and swallowing central pattern generators.

Journal: Biological cybernetics

Authors' code: ptolmachev/SimplifiedModel_rCPG_swCPG_interaction (MIT)

Status: code verified, 45 files readable, 5 matches

Wednesday, 16 September 2026 (1 paper)

[11] Code ↔ Paper doi:10.1371/journal.pcbi.1014752 [paper, repository]

Hierarchical feature binding in a spiking neural network model of the primate ventral visual pathway.

Journal: PLoS computational biology

Authors' code: BCGardner/feature_binding (AGPL-3.0)

Status: code verified, 187 files readable, 18 matches

Tuesday, 8 September 2026 (1 paper)

[12] Code ↔ Paper doi:10.1371/journal.pcbi.1014701 [paper, repository]

Computer models predict differential dendritic vulnerability with ischemia and spreading depression.

Journal: PLoS computational biology

Authors' code: modeldb:244688 (no license), modeldb:185858 (no license), modeldb:2017004 (no license)

Status: code verified

Saturday, 5 September 2026 (1 paper)

[13] Code ↔ Paper doi:10.1093/nc/niag046 [paper, repository]

Awareness of being: a computational neurophenomenological model of mindfulness, mind-wandering, and meta-attentional control.

Journal: Neuroscience of consciousness

Authors' code: h-idei/mbhrnn (Apache-2.0)

Status: code verified, 6 files readable

Wednesday, 2 September 2026 (2 papers)

[14] Code ↔ Paper doi:10.1126/sciadv.aef2894 [paper, repository]

Human cortical networks trade communication efficiency for computational reliability.

Journal: Science advances

Authors' code: fabridamicelli.github.io/echoes (no license), netneurotools.readthedocs.io (no license), netneurolab.github.io/neuromaps (no license), kuffmode/yanat (MIT)

Status: code verified, 5 files readable

[15] Code ↔ Paper doi:10.1371/journal.pcbi.1014730 [paper, repository]

A unified model of short- and long-term plasticity: Effects on network connectivity and information capacity.

Journal: PLoS computational biology

Authors' code: IiroAhokainen/SL-STDP (Apache-2.0), Zenodo 22011941 (CC-BY-4.0)

Status: code verified, 58 files readable, 8 matches

Tuesday, 1 September 2026 (1 paper)

[16] Code ↔ Paper doi:10.1021/acs.jcim.6c01299 [paper, repository]

Targeting BCL-2 through Deep Learning-Based Drug Repurposing: A Multimodal Approach Combining Diffusion-Based Generative Modeling, Neural Relational Inference, and In Vitro Validation.

Journal: Journal of chemical information and modeling

Authors' code: DurdagiLab/Neuralplexer_Ligand_Scoring (MIT), DurdagiLab/Automate-Neural-relational-inference-NRI- (MIT)

Status: code verified, 17 files readable, 1 match

Thursday, 27 August 2026 (3 papers)

[17] doi:10.1085/jgp.202513926 [paper, data]

Characterization of an open-channel structure and lateral conduction pathway in the cation-selective pentameric ligand-gated ion channel, ELIC.

Journal: The Journal of general physiology

Status: data only, 1 dataset cited

[18] Code ↔ Paper doi:10.1073/pnas.2616911123 [paper, repository]

Cerebellar microcircuits enable robust evidence-based decisions through cortico-cerebellar coupling.

Journal: Proceedings of the National Academy of Sciences of the United States of America

Authors' code: yyb177/cerebellar-decision-making (no license)

Status: code verified, 4 files readable

[19] Code ↔ Paper doi:10.1371/journal.pcbi.1014653 [paper, repository]

Noisy models of the ventral stream reveal the impact of recurrence and learned representations on information processing timescales.

Journal: PLoS computational biology

Authors' code: Saravaretti/hierarchical-cnn-rnn (no license)

Status: code verified, 9 files readable, 1 match

Friday, 21 August 2026 (1 paper)

[20] Code ↔ Paper doi:10.1371/journal.pcbi.1014617 [paper, repository]

An in silico framework for dissecting the mechanistic origins of in vivo recorded neuronal activity.

Journal: PLoS computational biology

Authors' code: mpinb.github.io/in_silico_framework (no license), pypi.org/project/isf-pandas-msgpack (no license)

Status: code verified

Wednesday, 19 August 2026 (1 paper)

[21] Code ↔ Paper doi:10.1038/s41467-026-76104-3 [paper, repository]

Sensorimotor remapping drives task specialization in prefrontal cortex.

Journal: Nature communications

Authors' code: HTissot42/Sensorimotor-remapping-drives-task-specialization (no license)

Status: code verified, 59 files readable, 21 matches

Tuesday, 18 August 2026 (1 paper)

[22] Code ↔ Paper doi:10.1371/journal.pone.0355402 [paper, repository]

Disentangling sensory contributions to postural control regulation through sample entropy and neural modeling: A preliminary study.

Journal: PloS one

Authors' code: nonlinear-analysis-core/nonanlibrary (BSD-3-Clause)

Status: code verified, 183 files readable, 2 matches

Monday, 17 August 2026 (2 papers)

[23] Code ↔ Paper doi:10.7554/elife.104262 [paper, repository]

A behavioral architecture for realistic simulations of <i>Drosophila</i> larva locomotion and foraging.

Journal: eLife

Authors' code: larvaworld.readthedocs.io (no license)

Status: code verified

[24] Code ↔ Paper doi:10.1038/s41467-026-75704-3 [paper, repository]

A minimal model of working memory in neural systems and neuromorphic circuits.

Journal: Nature communications

Authors' code: GabrieleCasagrande/MinimalNeuro_WorkingMemo (no license)

Status: code verified, 11 files readable, 3 matches

Friday, 7 August 2026 (4 papers)

[25] Code ↔ Paper doi:10.1371/journal.pcbi.1014585 [paper, repository]

Decoding behavior with minimal and interpretable agent models.

Journal: PLoS computational biology

Authors' code: giorgionicoletti/FSC-inference-MAPSO (no license)

Status: code verified, 19 files readable, 6 matches

[26] Code ↔ Paper doi:10.1016/j.neuron.2026.07.016 [paper, repository]

Inferring brain-wide interactions using data-constrained recurrent neural network models.

Journal: Neuron

Authors' code: HarveyLab/Acquisition2P_class (MIT), OSF u3kcp (no license), rajanlab/CURBD (GPL-3.0)

Status: code verified, 165 files readable, 8 matches

[27] Code ↔ Paper doi:10.1038/s41526-026-00644-7 [paper, repository]

A computational model of altered neuronal activity in altered gravity.

Journal: NPJ microgravity

Authors' code: camillegontier/neuron_microgravity (MIT)

Status: code verified, 13 files readable, 2 matches

[28] Code ↔ Paper doi:10.1007/s11571-026-10522-3 [paper, repository]

Acetylcholine enhances deviance detection in Hodgkin-Huxley neuronal networks.

Journal: Cognitive neurodynamics

Authors' code: Zenodo 17072341 (MIT)

Status: code verified

Thursday, 6 August 2026 (1 paper)

[29] Code ↔ Paper doi:10.7759/cureus.114096 [paper, repository]

Serious Games: Human-AI Interaction, Evolution, and Co-evolution.

Journal: Cureus

Authors' code: Zenodo 21428706 (CC-BY-NC-ND-4.0)

Status: code verified, 1 file readable

Wednesday, 5 August 2026 (3 papers)

[30] Code ↔ Paper doi:10.1371/journal.pone.0354021 [paper, repository]

A genetic algorithm for self-supervised models of oscillatory neurodynamics.

Journal: PloS one

Authors' code: HNXJ/GSDR (no license), supp:PMC13440876/pone.0354021.s002.zip (no license)

Status: code verified, 36 files readable, 7 matches

[31] Code ↔ Paper doi:10.1016/j.celrep.2026.117793 [paper, repository]

Clustered inputs engage dendritic nonlinearities and calcium signaling to support efficient place-field formation in CA1 pyramidal neurons.

Journal: Cell reports

Authors' code: Zenodo 20738191 (GPL-3.0), zenodo.com (no license), poirazi-lab/tasciotti_et_al_2026 (GPL-3.0)

Status: code verified, 128 files readable, 22 matches

[32] Code ↔ Paper doi:10.1038/s41467-026-76102-5 [paper, repository]

The inherent capacity of neurons to learn order relations and support abstract reasoning.

Journal: Nature communications

Authors' code: superrrpotato/Relationship-learning (MIT), Zenodo 20729243 (MIT)

Status: code verified, 30 files readable, 4 matches

Monday, 3 August 2026 (2 papers)

[33] Code ↔ Paper doi:10.1371/journal.pcbi.1014590 [paper, repository]

Real-time GPU-accelerated coupled cardiac system: Integrating bidirectional interactions between living optogenetic monolayers and computational simulations.

Journal: PLoS computational biology

Authors' code: younesvalibeigi/Coupled-Cardiac-System (MIT)

Status: code verified, 1,593 files readable, 3 matches

[34] Code ↔ Paper doi:10.3389/fncir.2026.1783892 [paper, repository]

Representations of facial features and surface quality in monkey area TE compared to neural network models.

Journal: Frontiers in neural circuits

Authors' code: rgeirhos/Stylized-ImageNet (MIT)

Status: code verified, 14 files readable, 1 match

Saturday, 1 August 2026 (1 paper)

[35] Code ↔ Paper doi:10.1093/bioinformatics/btag553 [paper, repository]

Spatial-spectral fusion enables drug repositioning by capturing indirect and long-range associations in biological networks.

Journal: Bioinformatics (Oxford, England)

Authors' code: Juniper-cola/BIO_SSF (MIT)

Status: code verified, 14 files readable, 2 matches

Thursday, 30 July 2026 (1 paper)

[36] Code ↔ Paper doi:10.1371/journal.pcbi.1014577 [paper, repository]

Combining sampling and attractor dynamics in spiking models of head direction systems.

Journal: PLoS computational biology

Authors' code: michnard/sampl_attract_HD (GPL-3.0)

Status: code verified, 7 files readable

Wednesday, 29 July 2026 (1 paper)

[37] Code ↔ Paper doi:10.1113/jp290729 [paper, repository]

Modelling the memory of unmyelinated axons: Integration of a data-driven approach with physiological memory concept.

Journal: The Journal of physiology

Authors' code: Zenodo 17182121 (CC-BY-4.0), digital-c-fiber/modelling-of-memory-in-unmyelinated-axons (BSD-3-Clause)

Status: code verified, 15 files readable

Tuesday, 28 July 2026 (2 papers)

[38] Code ↔ Paper doi:10.1371/journal.pcbi.1014575 [paper, repository]

Remembering the "when": Hebbian memory models for the time of past events.

Journal: PLoS computational biology

Authors' code: jbrea/RememberingTheWhen.jl (no license)

Status: code verified, 4 files readable, 1 match

[39] Code ↔ Paper doi:10.1038/s41467-026-75924-7 [paper, repository]

Data-driven reduced modeling of neural dynamics.

Journal: Nature communications

Authors' code: haller-group/SSMTool-2.4 (GPL-3.0), haller-group/SSMLearn (AGPL-3.0), alicemarr/RNN-paper (MIT), Zenodo 20623670 (MIT)

Status: code verified, 189 files readable, 4 matches

Thursday, 23 July 2026 (2 papers)

[40] Code ↔ Paper doi:10.1007/s00422-026-01047-3 [paper, repository]

Frequency-dependent coupling in response to oscillatory inputs in minimal networks of electrically coupled nodes: Gap junction networks and spatially extended neurons.

Journal: Biological cybernetics

Authors' code: BioDatanamics-Lab/Coupling_Coefficient-25_05 (no license)

Status: dead link

[41] Code ↔ Paper doi:10.3390/biomimetics11080522 [paper, repository]

Mechanics-AI: A Bio-Inspired Physics Intelligence Pipeline for Cross-Domain Engineering Prediction and Sustainable Design.

Journal: Biomimetics (Basel, Switzerland)

Authors' code: [your-account]/Mechanics-AI (no license)

Status: dead link

Tuesday, 21 July 2026 (2 papers)

[42] Code ↔ Paper doi:10.1371/journal.pcbi.1014523 [paper, repository]

Coordinative structures as scale-free networks: Cascade and percolation dynamics in motor learning with empirical validation.

Journal: PLoS computational biology

Authors' code: pcw8531/Coordinative-structures-scale-free-networks (MIT), Zenodo 20694466 (MIT)

Status: code verified, 12 files readable, 14 matches

[43] Code ↔ Paper doi:10.1038/s42256-026-01254-4 [paper, repository]

Neural sampling from cognitive maps enables goal-directed imagination and planning.

Journal: Nature machine intelligence

Authors' code: LH-cbicr/GCML (MIT), Zenodo 19370442 (MIT)

Status: code verified, 12 files readable, 2 matches

Monday, 20 July 2026 (3 papers)

[44] Code ↔ Paper doi:10.3758/s13428-026-03122-w [paper, repository]

Modeling intraindividual variability in affect (MIVA): Formalized theoretical approach, computational model, and parameter recovery study.

Journal: Behavior research methods

Authors' code: OSF spxf8 (no license)

Status: code verified, 5 files readable, 5 matches

[45] Code ↔ Paper doi:10.1038/s41467-026-75705-2 [paper, repository]

Redundant prefrontal hemispheres adapt storage strategy to working memory demands.

Journal: Nature communications

Authors' code: Zenodo 20513995 (CC-BY-4.0), melanietschiersch/redundantprefrontalhemispheres (no license)

Status: code verified, 70 files readable, 16 matches

[46] doi:10.3389/fncom.2026.1799705 [paper, data]

Structural synaptogenesis superior to functional modulation in a pruning-based recurrent network model of OCD.

Journal: Frontiers in computational neuroscience

Status: data only, 1 dataset cited

Friday, 17 July 2026 (2 papers)

[47] Code ↔ Paper doi:10.1016/j.isci.2026.116776 [paper, repository]

Selective perturbation of mirror and non-mirror neurons in an in silico model of the action observation network.

Journal: iScience

Authors' code: lucaguglielmi97/AON_RNN (MIT), tensorflow.org/;rrid:scr_016345 (no license)

Status: code verified, 4 files readable

[48] doi:10.3389/fncom.2026.1869643 [paper, data]

Spiking neurons-based facial emotion recognition: a comparative analysis of leaky and a quadratic integrated neuron for the unprocessed dataset.

Journal: Frontiers in computational neuroscience

Status: data only, 1 dataset cited

Friday, 10 July 2026 (2 papers)

[49] doi:10.1038/s41598-026-55178-5 [paper, data]

Novel approach to early prediction of alzheimer's disease progression using integrated deep regulatory genetic neural network and optimized deep belief networks.

Journal: Scientific reports

Status: data only, 1 dataset cited

[50] Code ↔ Paper doi:10.1016/j.isci.2026.116705 [paper, repository]

Spatiotemporal characteristics of visual cortical responses to transpalpebral electrical stimulation.

Journal: iScience

Authors' code: Zenodo 20730362 (CC-BY-4.0)

Status: code verified, 37 files readable

Thursday, 9 July 2026 (1 paper)

[51] Code ↔ Paper doi:10.1371/journal.pcbi.1014432 [paper, repository]

Spiking neurons as predictive controllers of linear systems.

Journal: PLoS computational biology

Authors' code: gitlab.socsci.ru.nl/2023-phd-paolo-agliati/spiking-neurons-as-predictive-controllers-of-linear-systems (CC-BY-4.0)

Status: code verified, 11 files readable, 8 matches

Tuesday, 7 July 2026 (1 paper)

[52] Code ↔ Paper doi:10.1038/s41467-026-74460-8 [paper, repository]

Spike-based alignment learning solves the weight transport problem.

Journal: Nature communications

Authors' code: zalandoresearch/fashion-mnist (MIT), unibe-cns/sal-code (MIT)

Status: code verified, 86 files readable, 10 matches

Monday, 6 July 2026 (3 papers)

[53] Code ↔ Paper doi:10.1371/journal.pcbi.1014435 [paper, repository]

Predictive coding explains asymmetric connectivity in the brain: A neural network study.

Journal: PLoS computational biology

Authors' code: khanrom/Feedback_Grasping (CC-BY-4.0)

Status: code verified, 67 files readable, 7 matches

[54] Code ↔ Paper doi:10.1371/journal.pcbi.1013235 [paper, repository]

Population sparseness determines strength of Hebbian plasticity for maximal memory lifetime in associative networks.

Journal: PLoS computational biology

Authors' code: itbgit.biologie.hu-berlin.de/auer/sparseness_plasticity_lifetime (no license)

Status: code verified

[55] Code ↔ Paper doi:10.3389/fcimb.2026.1785750 [paper, repository]

gNODE: gLV model-informed neural ordinary differential equations for modeling microbial community dynamics.

Journal: Frontiers in cellular and infection microbiology

Authors' code: tanxiaoxiu/gNODE (GPL-3.0)

Status: code verified, 9 files readable

Saturday, 4 July 2026 (1 paper)

[56] doi:10.1038/s41467-026-74791-6 [paper, data]

Visual learning at fast and slow timescales is driven by distinct plasticity rules in primate inferotemporal cortex.

Journal: Nature communications

Status: code on request, 1 dataset cited

Wednesday, 1 July 2026 (4 papers)

[57] doi:10.1111/cbdd.70354 [paper, data]

In Silico Drug Repositioning Identifies SYK Kinase Inhibitors as Potential Neuroprotective Agents for Ataxia-Telangiectasia.

Journal: Chemical biology & drug design

Status: data only, 2 datasets cited

[58] Code ↔ Paper doi:10.1038/s41593-026-02365-2 [paper, repository]

Hippocampal theta sweeps indicate goal direction during navigation.

Journal: Nature neuroscience

Authors' code: changmin-yu/goal_directed_theta_sweeps_honeycomb_maze (Apache-2.0)

Status: code verified, 7 files readable, 2 matches

[59] Code ↔ Paper doi:10.1093/molbev/msag157 [paper, repository]

Severe bottleneck of ancient Homo populations: insights from computational modeling and relevant fossil evidence.

Journal: Molecular biology and evolution

Authors' code: Zenodo 19435195 (CC-BY-4.0)

Status: code verified

[60] Code ↔ Paper doi:10.1111/ejn.70604 [paper, repository]

The Role of the Glutamate-Glutamine Cycle in Synaptic Transmission During Ischemia and Recovery.

Journal: The European journal of neuroscience

Authors' code: HannahvanSusteren3/GGsyntrans (no license)

Status: code verified, 7 files readable, 6 matches

Tuesday, 30 June 2026 (1 paper)

[61] Code ↔ Paper doi:10.3389/fphys.2026.1827577 [paper, repository]

The all-or-none repolarization in cardiac ventricular myocytes: an <i>in silico</i> characterization of a relevant biomarker of ventricular action potential.

Journal: Frontiers in physiology

Authors' code: Zenodo 19666107 (CC-BY-4.0)

Status: code verified, 1 file readable

Monday, 29 June 2026 (2 papers)

[62] doi:10.1021/acs.jpclett.6c01632 [paper, data]

Spiking without Resets: Continuous Integrate-and-Fire Dynamics in Neuronal Circuits.

Journal: The journal of physical chemistry letters

Status: data only, 2 datasets cited

[63] Code ↔ Paper doi:10.1371/journal.pcbi.1014458 [paper, repository]

Neuronal excitability and parameter variability in the Hodgkin-Huxley model.

Journal: PLoS computational biology

Authors' code: alon67/HodgkinHuxleyVariability (no license)

Status: code verified, 24 files readable, 14 matches

Thursday, 25 June 2026 (2 papers)

[64] Code ↔ Paper doi:10.7554/elife.99611 [paper, repository]

Intrinsic properties link a network model to zebra finch song.

Journal: eLife

Authors' code: doi:10.5061/dryad.wdbrv162x (no license)

Status: code verified

[65] Code ↔ Paper doi:10.1038/s41467-026-74357-6 [paper, repository]

Hippocampo-neocortical interaction as compressive retrieval-augmented generation.

Journal: Nature communications

Authors' code: ellie-as/hippocampal-neocortical-RAG (MIT), Zenodo 20215885 (MIT)

Status: code verified, 73 files readable, 29 matches

Wednesday, 24 June 2026 (1 paper)

[66] Code ↔ Paper doi:10.1038/s41586-026-10670-w [paper, repository]

Zero-shot design of drug-binding proteins via neural iterative selection-expansion.

Journal: Nature

Authors' code: polizzilab/LASErMPNN (MIT), polizzilab/nise (MIT), benf549/CARPdock (MIT), Zenodo 18308430 (CC-BY-4.0)

Status: code verified, 59 files readable, 13 matches

Tuesday, 23 June 2026 (1 paper)

[67] doi:10.3389/fimmu.2026.1852083 [paper, data]

Astrocyte-derived HMGB1 compromises the integrity of the blood-brain barrier through the CaM/CaMKII/AQP4 pathway and the protective function of trifluoperazine.

Journal: Frontiers in immunology

Status: data only, 1 dataset cited

Tuesday, 16 June 2026 (2 papers)

[68] Code ↔ Paper doi:10.7554/elife.109313 [paper, repository]

Linear and categorical coding units in the mouse gustatory cortex drive population dynamics and behavior in taste decision-making.

Journal: eLife

Authors' code: llang6/linear-categorical (MIT)

Status: code verified, 101 files readable, 15 matches

[69] Code ↔ Paper doi:10.1038/s41467-026-74354-9 [paper, repository]

Stabilizing stiffness is the most limiting factor in human force exertion.

Journal: Nature communications

Authors' code: figshare 30135883 (CC-BY-4.0), ftessari23/GimbalForceAnalysis (MIT), Zenodo 20076777 (MIT)

Status: code verified, 6 files readable, 1 match

Monday, 8 June 2026 (1 paper)

[70] Code ↔ Paper doi:10.1038/s41598-026-55225-1 [paper, repository]

Benchmarking criteria to determine latent linear dimensionality in neural data.

Journal: Scientific reports

Authors' code: francescovaccari/Dimensionality-estimation (MIT), francescovaccari/Dimensionality-estimation-upper-bound (MIT)

Status: code verified, 23 files readable, 19 matches

Friday, 5 June 2026 (2 papers)

[71] Code ↔ Paper doi:10.1038/s41467-026-73347-y [paper, repository]

A week in the life of the human brain reveals stable states punctuated by chaotic-like transitions.

Journal: Nature communications

Authors' code: MNobodyWang/WeekLongBrain (no license), Zenodo 18718538 (CC-BY-4.0)

Status: code verified, 70 files readable, 8 matches

[72] Code ↔ Paper doi:10.1016/j.isci.2026.116116 [paper, repository]

Learning stable radiation boundaries for wave simulations via passive neural state-space models.

Journal: iScience

Authors' code: Blizzard-Passage-Lab/NP-SSM_CRBC (no license), Blizzard-Passage-Lab/NP-SSM–CRBC.•Any (no license)

Status: dead link

Thursday, 4 June 2026 (1 paper)

[73] doi:10.1038/s41598-026-55218-0 [paper]

Amorphous metal-oxide semiconductor thin-film neuron, synapse, and neuromorphic system.

Journal: Scientific reports

Status: code on request

Wednesday, 3 June 2026 (2 papers)

[74] doi:10.1007/s10237-026-02070-w [paper]

Modification of a poroelastic model for zero porosity: finite element implementation and investigation of fluid mechanics in the perivascular space.

Journal: Biomechanics and modeling in mechanobiology

Status: code on request

[75] Code ↔ Paper doi:10.1007/s10237-026-02067-5 [paper, repository]

Sparse polynomial surrogates for F-actin networks with compliant crosslinkers.

Journal: Biomechanics and modeling in mechanobiology

Authors' code: jpsferreira/UMAT-ABAQUS_library (no license)

Status: code verified, 712 files readable, 3 matches

Tuesday, 2 June 2026 (2 papers)

[76] Code ↔ Paper doi:10.1371/journal.pcbi.1014364 [paper, repository]

A comparative study of simulation-based inference methods for epidemic models with identifiability considerations.

Journal: PLoS computational biology

Authors' code: geunsoojang/EpiSBI (no license)

Status: code verified, 63 files readable, 7 matches

[77] Code ↔ Paper doi:10.1371/journal.pcbi.1014325 [paper, repository]

Assessing the importance of sex and disease-specific anatomy in electrophysiology and mechanical simulations with a newly developed public virtual cohort of four-chamber heart models.

Journal: PLoS computational biology

Authors' code: OpenHeartDevelopers/cemrg-heartbuilder (no license), Zenodo 4593739 (CC-BY-4.0)

Status: code verified, 126 files readable, 11 matches

Monday, 1 June 2026 (2 papers)

[78] Code ↔ Paper doi:10.1111/jnc.70470 [paper, repository]

Calcium Buffering in Astrocytes and Its Relevance for Experimental Data Interpretation and Computational Modeling.

Journal: Journal of neurochemistry

Authors' code: kerstinlenk/calciumbuffering (GPL-3.0)

Status: code verified, 3 files readable, 1 match

[79] Code ↔ Paper doi: [paper, repository]

Limit-Cycle Proliferation Under Parametric Delayed Feedback in a Conductance-Based Neuron: Bifurcation Landscape, Orbit Catalog, and Capacity Analysis

Journal: Entropy (Basel, Switzerland)

Authors' code: malhawarat/HH-DFC-OrbitMemory (MIT)

Status: code verified, 11 files readable, 36 matches

Friday, 29 May 2026 (1 paper)

[80] Code ↔ Paper doi:10.1038/s43856-026-01695-3 [paper, repository]

Predict neuromuscular performance in human epidural electrical stimulation: phase 1 trial interim results.

Journal: Communications medicine

Authors' code: yunyuewei/HdSafeBO (no license)

Status: code verified, 35 files readable

Thursday, 28 May 2026 (2 papers)

[81] Code ↔ Paper doi:10.1371/journal.pcbi.1013138 [paper, repository]

Hierarchical recurrent temporal prediction as a model of the mammalian dorsal visual pathway.

Journal: PLoS computational biology

Authors' code: sebbkw/hierarchical_temporal_prediction (no license)

Status: code verified, 35 files readable, 8 matches

[82] Code ↔ Paper doi:10.1371/journal.pcbi.1014341 [paper, repository]

Accurate computation of ionic concentrations in the synaptic cleft requires the full Poisson-Nernst-Planck (PNP) equations.

Journal: PLoS computational biology

Authors' code: karolihj/PNP-synapse-FDM-2026 (GPL-3.0)

Status: code verified, 25 files readable

Wednesday, 27 May 2026 (1 paper)

[83] Code ↔ Paper doi:10.1038/s41540-026-00749-5 [paper, repository]

A novel approach to quantify out-of-distribution uncertainty in Neural and Universal Differential Equations.

Journal: NPJ systems biology and applications

Authors' code: cosbi-research/UQNU (other)

Status: code verified, 663 files readable, 1 match

Friday, 22 May 2026 (2 papers)

[84] Code ↔ Paper doi:10.1371/journal.pcbi.1014283 [paper, repository]

Spatial richness of neural magnetic fields.

Journal: PLoS computational biology

Authors' code: figshare 32061105 (CC-BY-4.0)

Status: code verified, 410 files readable, 5 matches

[85] Code ↔ Paper doi:10.1162/imag.a.1234 [paper, repository]

Multiscale parcellation of dynamic causal models of the brain.

Journal: Imaging neuroscience (Cambridge, Mass.)

Authors' code: tszarghami/Parcellation (AGPL-3.0)

Status: code verified, 24 files readable, 9 matches

Thursday, 21 May 2026 (2 papers)

[86] Code ↔ Paper doi:10.1371/journal.pcbi.1014337 [paper, repository]

Fast reconstruction of degenerate populations of conductance-based neuron models from spike times.

Journal: PLoS computational biology

Authors' code: Zenodo 16912160 (CC-BY-4.0), julienbrandoit/automatic-degenerate-cbm (no license), julienbrandoit/Spike2Pop---Bridging-Experimental-Neuroscience-and-Computational-Modeling (MIT)

Status: code verified, 53 files readable, 14 matches

[87] doi:10.1038/s41598-026-54384-5 [paper, data]

Optimization of connectome weights for a neural network model generating both forward and backward locomotion in C. elegans.

Journal: Scientific reports

Status: data only, 1 dataset cited

Wednesday, 20 May 2026 (1 paper)

[88] Code ↔ Paper doi:10.1038/s41586-026-10528-1 [paper, repository]

A critical initialization for biological neural networks.

Journal: Nature

Authors' code: mouseland/critical_init (GPL-3.0), Zenodo 19322086 (GPL-3.0)

Status: code verified, 44 files readable, 13 matches

Tuesday, 19 May 2026 (1 paper)

[89] Code ↔ Paper doi:10.3389/fncom.2026.1771884 [paper, repository]

NEURONpyxl: fast, flexible, Python-integrated simulation of biophysical neural networks with complex plastic synapses.

Journal: Frontiers in computational neuroscience

Authors' code: CWRUChielLab/neuronpyxl (GPL-3.0), CWRUChielLab/NEURONpyxl-2026-figures (no license)

Status: code verified, 42 files readable, 13 matches

Monday, 18 May 2026 (1 paper)

[90] Code ↔ Paper doi:10.1038/s41598-026-53415-5 [paper, repository]

Computational design and immunoinformatics validation of a T cell multi-epitope vaccine targeting glioblastoma stem cells.

Journal: Scientific reports

Authors' code: sokrypton/colabfold (MIT)

Status: code verified, 74 files readable, 1 match

Friday, 15 May 2026 (1 paper)

[91] Code ↔ Paper doi:10.1038/s41467-026-73032-0 [paper, repository]

Fast efficient coding and sensory adaptation in gain-adaptive recurrent networks.

Journal: Nature communications

Authors' code: OSF wa7hm (no license)

Status: code verified, 2 files readable, 4 matches

Thursday, 14 May 2026 (1 paper)

[92] Code ↔ Paper doi:10.1088/1741-2552/ae5fd7 [paper, repository]

Metric validation for detection of delayed and directed coupling.

Journal: Journal of neural engineering

Authors' code: hermandarrowlab (no license), pwollstadt/IDTxl (GPL-3.0), hermandarrowlab/ec-metrics-validation (no license)

Status: code verified, 190 files readable, 7 matches

Wednesday, 13 May 2026 (2 papers)

[93] Code ↔ Paper doi:10.1007/s10827-026-00936-7 [paper, repository]

When can neuronal activity-dependent homeostatic plasticity maintain circuit-level properties?

Journal: Journal of computational neuroscience

Authors' code: Zenodo 18509900 (bsd-2-clause-netbsd), ljstolting/adhp-maintains-pyloricness (BSD-2-Clause)

Status: code verified, 36 files readable, 2 matches

[94] Code ↔ Paper doi:10.1007/s10827-026-00935-8 [paper, repository]

A biophysically grounded model of glutamatergic synaptic transmission integrating glutamate transport, receptor kinetics, and electrotonic effects.

Journal: Journal of computational neuroscience

Authors' code: antonvchizhov/EAAT-paper (no license)

Status: code verified, 5 files readable, 3 matches

Tuesday, 12 May 2026 (1 paper)

[95] Code ↔ Paper doi:10.3389/fpsyg.2026.1654139 [paper, repository]

Whole-to-parts causation mechanism.

Journal: Frontiers in psychology

Authors' code: Yoshiyuki-Ohmura/DownwardCausation (no license)

Status: code verified, 17 files readable, 1 match

Monday, 11 May 2026 (3 papers)

[96] Code ↔ Paper doi:10.7554/elife.107905 [paper, repository]

Adult-neurogenesis allows for representational stability and flexibility in early olfactory system.

Journal: eLife

Authors' code: MAGICzhen/neurogenesis_model (MIT)

Status: code verified, 11 files readable

[97] Code ↔ Paper doi:10.1038/s42003-026-10064-8 [paper, repository]

The hippocampal CA3 area implements sequence learning of discontinuous episodes.

Journal: Communications biology

Authors' code: bobazok/Sequence-learning-in-the-hippocampal-CA3 (no license)

Status: code verified, 20 files readable, 2 matches

[98] doi:10.1016/j.jbc.2026.113136 [paper, data]

Photoreceptor outer segment disk rim curvature relies on a tetraspanin interaction web.

Journal: The Journal of biological chemistry

Status: data only, 1 dataset cited

Wednesday, 6 May 2026 (1 paper)

[99] Code ↔ Paper doi:10.1038/s41598-026-51212-8 [paper, repository]

Uncertainty aware machine learning for bridging simulation and experiment in high throughput materials characterization.

Journal: Scientific reports

Authors' code: jcj7292/USEM (no license)

Status: code verified, 2 files readable, 2 matches

Tuesday, 5 May 2026 (1 paper)

[100] Code ↔ Paper doi:10.1038/s41598-026-50523-0 [paper, repository]

Mechanistic multiscale modeling identifies putative natural tri-target candidates of MAO-B, LRRK2 and A₂A for Parkinson's disease.

Journal: Scientific reports

Authors' code: khibech/Parkinson-s-Disease (no license)

Status: code verified, 3 files readable

Saturday, 2 May 2026 (1 paper)

[101] Code ↔ Paper doi:10.1038/s41598-026-48239-2 [paper, repository]

LigGen-a GEN-AI based ligand generation approach for de-novo drug design.

Journal: Scientific reports

Authors' code: neurocare-iiitd/LigGen (no license)

Status: code verified, 19 files readable, 12 matches

Thursday, 30 April 2026 (1 paper)

[102] Code ↔ Paper doi:10.1371/journal.pcbi.1014214 [paper, repository]

Evolutionary Kuramoto dynamics unravels origins of chimera states in neural populations.

Journal: PLoS computational biology

Authors' code: tzdyrski.github.io/egt-kuramoto (no license), tzdyrski/egt-kuramoto (GPL-3.0), Zenodo 19582421 (GPL-3.0)

Status: code verified, 66 files readable, 6 matches

Tuesday, 28 April 2026 (3 papers)

[103] doi:10.1007/s00422-026-01043-7 [paper]

Fluctuation-response relations for a two-stage population of spiking neurons stimulated by common noise.

Journal: Biological cybernetics

Status: code on request

[104] Code ↔ Paper doi:10.1038/s41467-026-71918-7 [paper, repository]

Developmental disinhibition gates language lateralization in childhood.

Journal: Nature communications

Authors' code: Minarose/WBMLangBetaERDS (no license), griffithslab/whobpyt (MIT)

Status: code verified, 73 files readable, 26 matches

[105] Code ↔ Paper doi:10.1038/s41598-026-50758-x [paper, repository]

Telecommunication-inspired network models of healthy and diseased brains.

Journal: Scientific reports

Authors' code: medusamedusa/time_series_from_AD_fMRI_ (no license), medusamedusa/fMRI_telecommunications (no license)

Status: code verified, 30 files readable, 6 matches

Monday, 27 April 2026 (2 papers)

[106] Code ↔ Paper doi:10.1371/journal.pcbi.1013113 [paper, repository]

Systems biology analysis of vasodynamics in mouse cerebral arterioles during resting state and functional hyperemia.

Journal: PLoS computational biology

Authors' code: hesfandi/Mouse-cerebral-Arteriolar-vasodynamics_Model (no license)

Status: code verified, 42 files readable

[107] Code ↔ Paper doi:10.1371/journal.pcbi.1014216 [paper, repository]

Diversity in emergent cell locomotion from the coupling cytosolic and cortical Marangoni flows with reaction-diffusion dynamics.

Journal: PLoS computational biology

Authors' code: blejzara/CellRDA-LS (MIT), Zenodo 18824137 (CC-BY-4.0)

Status: code verified, 8 files readable

Friday, 24 April 2026 (1 paper)

[108] Code ↔ Paper doi:10.1038/s42003-026-10094-2 [paper, repository]

E/I imbalance and internal noise cause weak neural representations and face recognition challenges in ASD.

Journal: Communications biology

Authors' code: xthomaswang/ASD_FaceReg_Modeling_CNN (MIT)

Status: code verified, 29 files readable, 4 matches

Thursday, 23 April 2026 (1 paper)

[109] Code ↔ Paper doi:10.1038/s41467-026-72152-x [paper, repository]

Centralized brain networks controlling antennal grooming coordination.

Journal: Nature communications

Authors' code: gizemozd/anipose (BSD-2-Clause), NeLy-EPFL/kinematics3d (Apache-2.0), NeLy-EPFL/antennal-grooming (Apache-2.0)

Status: code verified, 89 files readable, 40 matches

Wednesday, 22 April 2026 (2 papers)

[110] doi:10.1113/jp290395 [paper]

Spinal motor neuron pools may be partly driven by impulsive common inputs.

Journal: The Journal of physiology

Status: code on request

[111] Code ↔ Paper doi:10.1038/s41467-026-71759-4 [paper, repository]

CellNiche represents cellular microenvironments in atlas-scale spatial omics data with contrastive learning.

Journal: Nature communications

Authors' code: QIFEIDKN/STGATE_pyG (no license), Super-LzzZ/CellNiche (MIT), Zenodo 19143524 (MIT)

Status: code verified, 12 files readable, 11 matches

Monday, 20 April 2026 (2 papers)

[112] doi:10.1021/acs.jctc.6c00146 [paper, data]

qNEP: A Highly Efficient Neuroevolution Potential with Dynamic Charges for Large-Scale Atomistic Simulations.

Journal: Journal of chemical theory and computation

Status: data only, 2 datasets cited

[113] doi:10.1371/journal.pone.0347532 [paper, data]

Deciphering the molecular network of Trichostatin A in regulating Alzheimer's disease screening of core genes and mechanistic investigation based on multidimensional bioinformatics and molecular simulation.

Journal: PloS one

Status: data only, 1 dataset cited

Saturday, 18 April 2026 (1 paper)

[114] Code ↔ Paper doi:10.1038/s42003-026-10032-2 [paper, repository]

Data-driven mouse motor thalamus model reveals topography and spatial weight scaling govern spindle dynamics.

Journal: Communications biology

Authors' code: Zenodo 15198488 (CC-BY-4.0), Zenodo 15198487 (CC-BY-4.0)

Status: code verified, 66 files readable, 18 matches

Friday, 17 April 2026 (1 paper)

[115] Code ↔ Paper doi:10.1371/journal.pcbi.1014164 [paper, repository]

'Backpropagation and the brain' realized in cortical error neuron microcircuits.

Journal: PLoS computational biology

Authors' code: Zenodo 16909564 (CC-BY-4.0), kma-code/error-neuron-microcircuits (no license)

Status: code verified, 44 files readable, 2 matches

Thursday, 16 April 2026 (1 paper)

[116] doi:10.1186/s42238-025-00363-y [paper, data]

In silico receptor binding and ex vivo nasal epithelial membrane permeation studies of selected phytocannabinoids.

Journal: Journal of cannabis research

Status: data only, 1 dataset cited

Wednesday, 15 April 2026 (4 papers)

[117] Code ↔ Paper doi:10.1371/journal.pcbi.1013382 [paper, repository]

On the role of L-type Ca2+ and BK channels in a biophysical model of cartwheel interneurons.

Journal: PLoS computational biology

Authors' code: researchdata.cab.unipd.it/1615 (no license)

Status: code verified

[118] Code ↔ Paper doi:10.1371/journal.pcbi.1014177 [paper, repository]

Activity-dependent neuromodulation and calcium homeostasis cooperate to produce robust and modulable neuronal function.

Journal: PLoS computational biology

Authors' code: arthur-fyon/BIOCONTROL_2025 (MIT), Zenodo 17827990 (MIT)

Status: code verified, 69 files readable, 5 matches

[119] Code ↔ Paper doi:10.1038/s41598-026-48748-0 [paper, repository]

GPU-accelerated modeling of biological regulatory networks.

Journal: Scientific reports

Authors' code: miilusaskvido/scientificreports-codes](https: (no license)

Status: dead link

[120] Code ↔ Paper doi:10.1093/nc/niag013 [paper, repository]

Intrinsic units: identifying a system's causal grain.

Journal: Neuroscience of consciousness

Authors' code: Zenodo 11211435 (GPL-3.0), csc-uw/marshall-intrinsic-units (GPL-3.0)

Status: code verified, 30 files readable, 1 match

Tuesday, 14 April 2026 (2 papers)

[121] Code ↔ Paper doi:10.1186/s12866-026-04991-z [paper, repository]

Gut microbial metabolic disorder in depression: insights from computational modeling and mediation analysis.

Journal: BMC microbiology

Authors' code: zyc134/Depression (no license)

Status: code verified, 1 file readable

[122] Code ↔ Paper doi:10.1007/s12021-025-09766-x [paper, repository]

The Neural Analysis Toolkit Unifies Semi-Analytical Techniques to Simplify, Understand, and Simulate Dendrites.

Journal: Neuroinformatics

Authors' code: jugit.fz-juelich.de/w.wybo/neatpaper (no license), Zenodo 12191059 (GPL-2.0)

Status: code verified

Monday, 13 April 2026 (1 paper)

[123] Code ↔ Paper doi:10.1038/s42003-026-10044-y [paper, repository]

Astrocyte-mediated higher-order control of synaptic plasticity.

Journal: Communications biology

Authors' code: Zenodo 19260114 (CC-BY-4.0)

Status: code verified, 1 file readable, 1 match

Friday, 10 April 2026 (1 paper)

[124] Code ↔ Paper doi:10.1371/journal.pcbi.1013252 [paper, repository]

Dynamic cholinergic signaling differentially desynchronizes cortical microcircuits dependent on modulation rate and network connectivity.

Journal: PLoS computational biology

Authors' code: RichLabUConn/DynamicACh (GPL-3.0), Zenodo 15641814 (GPL-3.0)

Status: code verified, 26 files readable, 5 matches

Thursday, 9 April 2026 (1 paper)

[125] doi:10.1007/s00285-026-02386-2 [paper]

A multiscale theory for network advection- reaction-diffusion.

Journal: Journal of mathematical biology

Status: code on request

Tuesday, 7 April 2026 (1 paper)

[126] Code ↔ Paper doi:10.1371/journal.pcbi.1014157 [paper, repository]

Modeling spatial contrast sensitivity in responses of primate retinal ganglion cells to natural movies.

Journal: PLoS computational biology

Authors' code: gollischlab/SpatiotemporalSCModel (MIT), dimokaramanlis/KiloSortMEA (GPL-2.0)

Status: code verified, 135 files readable, 23 matches

Monday, 6 April 2026 (1 paper)

[127] Code ↔ Paper doi:10.1371/journal.pcbi.1014123 [paper, repository]

Subunit-specific behavioral modulation of sensory tuning in the visual cortex.

Journal: PLoS computational biology

Authors' code: Mlynarski-Group/behavioral-visual-tuning (no license)

Status: code verified, 2 files readable

Sunday, 5 April 2026 (1 paper)

[128] doi:10.1038/s41598-026-45845-y [paper, data]

Identification of natural FGFR3 inhibitor for glioma using integrated computational and microRNA regulatory analysis.

Journal: Scientific reports

Status: data only, 1 dataset cited

Saturday, 4 April 2026 (1 paper)

[129] Code ↔ Paper doi:10.1038/s42003-026-09938-8 [paper, repository]

Representation Transfer via Invariant Input-driven Continuous Attractors for Fast Domain Adaptation.

Journal: Communications biology

Authors' code: Zenodo 16441066 (CC-BY-4.0)

Status: code verified

Friday, 3 April 2026 (3 papers)

[130] Code ↔ Paper doi:10.1038/s43856-026-01555-0 [paper, repository]

Mechanistically driven transnidal hemodynamic manipulations enhance simulated endovascular transvenous treatments for brain AVMs.

Journal: Communications medicine

Authors' code: kellenvu/massoud-avm (no license)

Status: code verified, 2 files readable, 5 matches

[131] Code ↔ Paper doi:10.1371/journal.pcbi.1014022 [paper, repository]

Emergence of multifrequency activity in a laminar neural mass model.

Journal: PLoS computational biology

Authors' code: dsb-lab/LaNMM (CC0-1.0)

Status: code verified, 6 files readable

[132] doi:10.3390/ijms27073253 [paper, data]

S-equol Modulates T3-Induced Transcription and Neurite Outgrowth in Neuronal Cells.

Journal: International journal of molecular sciences

Status: data only, 1 dataset cited

Thursday, 2 April 2026 (1 paper)

[133] doi:10.1371/journal.pone.0345287 [paper, data]

Directional leads applied to spinal cord stimulation: A computational modelling study.

Journal: PloS one

Status: data only, 1 dataset cited

Wednesday, 1 April 2026 (2 papers)

[134] Code ↔ Paper doi:10.1038/s41586-026-10301-4 [paper, repository]

Dopaminergic mechanisms of dynamical social specialization.

Journal: Nature

Authors' code: Zenodo 17121126 (CC-BY-4.0)

Status: code verified, 10 files readable, 3 matches

[135] doi:10.3390/cimb48040369 [paper]

Elucidating the Multi-Target Anti-Pruritic Mechanism of <i>Polygonatum odoratum</i> via Integrated Network Pharmacology, Molecular Simulations, and GEO Dataset Validation.

Journal: Current issues in molecular biology

Status: data only

Tuesday, 31 March 2026 (1 paper)

[136] Code ↔ Paper doi:10.1016/j.bpj.2026.03.028 [paper, repository]

Astral architecture can enhance mechanical strength of cytoskeletal networks by modulating percolation thresholds.

Journal: Biophysical journal

Authors' code: Zenodo 18970832 (GPL-3.0), Zenodo 18970060 (CC-BY-4.0), bcberg/berg_astralmikado (no license), bcberg/cytosim-bcb (GPL-3.0)

Status: code verified, 1,143 files readable, 9 matches

Monday, 30 March 2026 (1 paper)

[137] Code ↔ Paper doi:10.1117/1.nph.13.2.025003 [paper, repository]

Monte Carlo simulations of time-resolved blood flow index: times-of-flight beyond ∼1 ns are necessary for brain-dominated measurements.

Journal: Neurophotonics

Authors' code: CoMind-Technologies/mc_analysis (MIT)

Status: code verified, 30 files readable, 7 matches

Friday, 27 March 2026 (1 paper)

[138] Code ↔ Paper doi:10.1073/pnas.2517661123 [paper, repository]

Physics-constrained neural ordinary differential equation models to discover and predict microbial community dynamics.

Journal: Proceedings of the National Academy of Sciences of the United States of America

Authors' code: VenturelliLab/Thompson_et_al_2025 (no license)

Status: code verified, 14 files readable

Friday, 20 March 2026 (1 paper)

[139] Code ↔ Paper doi:10.1038/s41598-026-44588-0 [paper, repository]

Visualization and simulation of full-scale point-neuron circuits via the Neural Circuit Visualizer web platform.

Journal: Scientific reports

Authors' code: modeldb:267531 (no license), cnr-ibf-pa/NeuralCircuitVisualizer (no license)

Status: code verified, 29 files readable, 6 matches

Thursday, 19 March 2026 (3 papers)

[140] doi:10.1007/s10827-026-00929-6 [paper, repository]

Inhibitory-stabilization is sufficient for history-dependent computation in a randomly connected attractor network.

Journal: Journal of computational neuroscience

Authors' code: Zenodo 17470740 (no license)

Status: dead link

[141] doi:10.1073/pnas.2525051123 [paper, repository]

Autogenic spinal excitatory circuit ensures skilled hand movements in primates.

Journal: Proceedings of the National Academy of Sciences of the United States of America

Authors' code: Zenodo 18229897 (CC-BY-4.0), Zenodo 18229898 (CC-BY-4.0), animalmodel/kim_pnas_2026 (no license)

Status: code verified, 27 files readable, 2 matches

[142] doi:10.1038/s41467-026-70920-3 [paper, repository]

Intrinsic stabilization of synaptic plasticity improves learning and robustness in artificial neural networks.

Journal: Nature communications

Authors' code: figshare 31146457 (Apache-2.0)

Status: code verified, 10 files readable

Tuesday, 17 March 2026 (5 papers)

[143] doi:10.1038/s41467-026-70065-3 [paper, repository]

Local lateral connectivity is sufficient for replicating cortex-like topographical organization in deep neural networks.

Journal: Nature communications

Authors' code: pytorch/pytorch (BSD-3-Clause), neuroailab/TDANN (no license), BashivanLab/LLCNN (no license)

Status: code verified, 2,184 files readable, 3 matches

[144] doi:10.1371/journal.pcbi.1014026 [paper, repository]

Separating random and deterministic sources of computational noise in explore-exploit decisions.

Journal: PLoS computational biology

Authors' code: wangxsiyu/Paper_PlosCB_2026_RandomDeterministicNoise (no license)

Status: code verified, 484 files readable, 1 match

[145] doi:10.1371/journal.pcbi.1013251 [paper, repository]

Learning, sleep replay and consolidation of contextual fear memories: A neural network model.

Journal: PLoS computational biology

Authors' code: Zenodo 15546751 (MIT), larswe/fear_memory_plos (MIT)

Status: code verified, 52 files readable, 9 matches

[146] doi:10.1038/s41467-026-70267-9 [paper, repository]

Neural circuit models for evidence accumulation through choice-selective sequences.

Journal: Nature communications

Authors' code: lindseysbrown/evidence_accumulation_through_sequences (AGPL-3.0), Zenodo 18040040 (apgl-v3), Zenodo 5498992 (CC0-1.0)

Status: code verified, 518 files readable, 25 matches

[147] doi:10.3389/fnins.2026.1780751 [paper, repository]

Computational modeling of spatiotemporal afterimage visual perception with spiking neural networks.

Journal: Frontiers in neuroscience

Authors' code: NBELab/afterimage (no license)

Status: code verified, 10 files readable, 9 matches

Saturday, 14 March 2026 (1 paper)

[148] doi:10.1038/s41467-026-70659-x [paper, repository]

Noradrenaline causes a spread of association in the hippocampal cognitive map.

Journal: Nature communications

Authors' code: p-rakriti/koolschijn_et_al (no license)

Status: code verified, 3 files readable

Friday, 13 March 2026 (3 papers)

[149] doi:10.1371/journal.pcbi.1013342 [paper, repository]

Towards model-based characterization of individual electrically stimulated nerve fibers.

Journal: PLoS computational biology

Authors' code: Zenodo 15848230 (CC-BY-4.0)

Status: code verified, 1 file readable

[150] doi:10.1038/s41467-026-70347-w [paper, repository]

Desegregation of neuronal predictive processing.

Journal: Nature communications

Authors' code: BinW3233/HDPC_code (no license)

Status: code verified, 8 files readable

[151] doi:10.1038/s41598-026-40961-1 [paper, data]

Efficient cosine-windowed cross-correlation for intermediate deformable image registration.

Journal: Scientific reports

Status: data only, 1 dataset cited

Thursday, 12 March 2026 (2 papers)

[152] doi:10.1371/journal.pone.0343614 [paper, repository]

pH-dependent structural dynamics of neuropeptide Y in aqueous solution.

Journal: PloS one

Authors' code: maltesie/bridge2 (no license), Zenodo 14069542 (CC-BY-4.0)

Status: code verified, 27 files readable, 4 matches

[153] doi:10.1038/s41467-026-70354-x [paper, repository]

Global error signal guides local optimization in mismatch calculation.

Journal: Nature communications

Authors' code: johnhongyumeng/DuetPredictiveCoding_Plasticity (no license)

Status: code verified, 23 files readable, 2 matches

Wednesday, 11 March 2026 (3 papers)

[154] doi:10.1038/s44271-026-00436-5 [paper, repository]

Behavioral evidence for the hierarchical execution of sequential movements.

Journal: Communications psychology

Authors' code: figshare 31169632 (CC-BY-4.0)

Status: code verified, 22 files readable, 5 matches

[155] doi:10.1038/s41593-026-02205-3 [paper, repository]

Competitive interactions shape mammalian brain network dynamics and computation.

Journal: Nature neuroscience

Authors' code: Imperial-MIND-lab/integrated-info-decomp (BSD-3-Clause), netneurolab/conn2res (BSD-3-Clause), Hana-Ali/competitive-cooperative-hopf (no license), sites.google.com/site/bctnet (no license), neurospin/pypreclin (CECILL-2.1), jlizier/jidt (gpl)

Status: code verified, 768 files readable, 2 matches

[156] doi:10.3389/fncom.2026.1745836 [paper, repository]

Role of spinal sensorimotor circuits in triphasic muscle command: a simulation approach using goal exploration process.

Journal: Frontiers in computational neuroscience

Authors' code: cattaert/rgep (no license)

Status: code verified, 42 files readable, 5 matches

Tuesday, 10 March 2026 (1 paper)

[157] doi:10.1038/s41598-026-43529-1 [paper, repository]

A spiking neural network inspired by neuroscience and psychology for Western mode- and key-conditioned music learning and composition.

Journal: Scientific reports

Authors' code: lqnankai/Music-Dataset (MIT), braincog-x/brain-cog (Apache-2.0)

Status: code verified, 547 files readable, 1 match

Monday, 9 March 2026 (5 papers)

[158] doi:10.1371/journal.pcbi.1014085 [paper, repository]

The integrated information Φ of an integrate and fire network.

Journal: PLoS computational biology

Authors' code: mdanilczuk/IITfire (no license)

Status: code verified, 8 files readable, 1 match

[159] doi:10.1371/journal.pcbi.1012966 [paper, repository]

How the dynamic interplay of cortico-basal ganglia-thalamic pathways shapes the time course of deliberation and commitment.

Journal: PLoS computational biology

Authors' code: CoAxLab/CBGTPy (no license)

Status: code verified, 33 files readable, 8 matches

[160] doi:10.1371/journal.pcbi.1014001 [paper, repository]

Burst firing creates an attractor in synaptic weight dynamics.

Journal: PLoS computational biology

Authors' code: KJacquerie/Burst-Attractor (no license)

Status: code verified, 42 files readable

[161] doi:10.1371/journal.pcbi.1013958 [paper, repository]

Computing the effects of excitatory-inhibitory balance on neuronal input-output properties.

Journal: PLoS computational biology

Authors' code: AlexDReyes/ReyesPlosCompBio2025 (MIT)

Status: code verified, 4 files readable, 1 match

[162] doi:10.3758/s13415-026-01417-1 [paper, repository]

Computational signatures of exertion and rest underlie moment-to-moment dynamics of subjective perceptions of effort and fatigue.

Journal: Cognitive, affective & behavioral neuroscience

Authors' code: OSF sb9jf (no license)

Status: code verified, 2 files readable

Sunday, 8 March 2026 (1 paper)

[163] doi:10.1186/s13054-026-05929-7 [paper]

Reporting practices and impact of withdrawal of life-sustaining treatment on outcomes in acute brain injury clinical trials: a literature review and simulation study.

Journal: Critical care (London, England)

Status: code on request

Friday, 6 March 2026 (2 papers)

[164] doi:10.1038/s41540-026-00677-4 [paper]

Neuro-Dynamic Quantitative Systems Pharmacology (QSP) model describing Alzheimer's disease pathophysiology and treatment effects.

Journal: NPJ systems biology and applications

Status: code on request

[165] doi:10.1016/j.bpj.2026.03.010 [paper]

Chlorpromazine inhibits EAG1 channels by altering the interdomain coupling.

Journal: Biophysical journal

Status: code on request

Thursday, 5 March 2026 (1 paper)

[166] doi:10.1038/s41598-026-42421-2 [paper, repository]

Robustness of interstitial photodynamic therapy treatment planning under power and positional uncertainties in light delivery.

Journal: Scientific reports

Authors' code: fullmonte.org (no license), FullMonte (no license)

Status: code verified

Monday, 2 March 2026 (3 papers)

[167] doi:10.1073/pnas.2530340123 [paper, data]

Persistent adaptation through dual-timescale regulation of ion channel properties.

Journal: Proceedings of the National Academy of Sciences of the United States of America

Status: data only, 1 dataset cited

[168] doi:10.1038/s41598-026-40513-7 [paper, repository]

Protein trafficking and synaptic demand configure complex and dynamic synaptome architectures of individual neurons.

Journal: Scientific reports

Authors' code: oksankas/Sushi_belt_PSD95 (CC-BY-4.0), digitalresearchservices.ed.ac.uk/resources/eddie (no license)

Status: code verified, 104 files readable, 6 matches

[169] doi:10.1063/5.0308450 [paper, repository]

Computational modeling of human vagus nerve stimulation with three-dimensional fascicular morphology.

Journal: APL bioengineering

Authors' code: wmglab-duke/3D_nerve_pipeline (GPL-2.0), Zenodo 8298703 (GPL-2.0), Zenodo 18475038 (CC-BY-4.0), wmglab-duke/ascent (GPL-2.0)

Status: code verified, 329 files readable, 4 matches

Sunday, 1 March 2026 (1 paper)

[170] doi:10.1093/bib/bbag118 [paper, repository]

Drug screening for α-synuclein aggregation inhibitors via multimodal graph neural network.

Journal: Briefings in bioinformatics

Authors' code: JiaCZ-Computational-Biology/M-GAT-GraphSAGE (no license)

Status: code verified, 44 files readable, 6 matches

Saturday, 28 February 2026 (1 paper)

[171] doi:10.1007/s00422-025-01032-2 [paper, repository]

A spiking neural network model for fractional proprioceptive encoding of limb posture and movement in insects.

Journal: Biological cybernetics

Authors' code: Zenodo 13827523 (CC-BY-4.0), thomasvanderveen/stickinsectproprioception (MIT)

Status: code verified, 22 files readable, 4 matches

Thursday, 26 February 2026 (1 paper)

[172] doi:10.1117/1.jbo.31.2.026004 [paper, repository]

Learning to simulate realistic human diffuse reflectance spectra.

Journal: Journal of biomedical optics

Authors' code: IMSY-DKFZ/mcmlnet (MIT), IMSY-DKFZ/mcmlgpu (GPL-3.0)

Status: code verified, 128 files readable, 24 matches

Tuesday, 24 February 2026 (2 papers)

[173] doi:10.1038/s41598-026-37063-3 [paper, repository]

Differentiable multiphase flow model for physics-informed machine learning in reservoir pressure management.

Journal: Scientific reports

Authors' code: hrashid10/DiffMultiPhaseflowPresMngmnt (no license)

Status: code verified, 20 files readable, 4 matches

[174] doi:10.1073/pnas.2510334123 [paper, repository]

Understanding human metacontrol and its pathologies using deep neural networks.

Journal: Proceedings of the National Academy of Sciences of the United States of America

Authors' code: Zenodo 15359298 (GPL-3.0), kjsandbrink/learning-metacontrol (GPL-3.0)

Status: code verified, 75 files readable, 1 match

Monday, 23 February 2026 (3 papers)

[175] doi:10.1038/s41593-026-02216-0 [paper, repository]

Convolutional neural network models describe the encoding subspace of local circuits in auditory cortex.

Journal: Nature neuroscience

Authors' code: lbhb/baphy (no license), LBHB/laminar_tools (no license), LBHB/NEMS (GPL-3.0)

Status: code verified, 2,157 files readable, 13 matches

[176] doi:10.3389/fneur.2026.1766089 [paper, repository]

A neutrosophic explainable AI framework for modeling uncertainty in immersive stereotactic neurosurgical simulation.

Journal: Frontiers in neurology

Authors' code: Zenodo 17905071 (CC-BY-4.0)

Status: code verified, 3 files readable, 7 matches

[177] doi:10.3389/fncom.2026.1753417 [paper, repository]

Population-level neural rejuvenation dynamics in addiction: a computational framework for understanding developmental plasticity reactivation.

Journal: Frontiers in computational neuroscience

Authors' code: Zenodo 18489543 (MIT)

Status: code verified, 4 files readable, 16 matches

Friday, 20 February 2026 (2 papers)

[178] doi:10.1371/journal.pcbi.1013966 [paper, repository]

Carba-NAD binding activates SIR2 by reshaping conformational plasticity and rewiring long-range allosteric networks.

Journal: PLoS computational biology

Authors' code: Zenodo 17247434 (CC-BY-4.0)

Status: code verified, 14 files readable, 4 matches

[179] doi:10.1073/pnas.2515371123 [paper, repository]

Robust input disentanglement through dendritic calcium-mediated action potentials.

Journal: Proceedings of the National Academy of Sciences of the United States of America

Authors' code: simahashemi/Single-Cell-Synaptic-Clustering (GPL-3.0)

Status: code verified, 47 files readable, 1 match

Thursday, 19 February 2026 (1 paper)

[180] doi:10.1038/s43588-026-00956-4 [paper, repository]

A neural network for modeling human concept formation, understanding and communication.

Journal: Nature computational science

Authors' code: Hiroid/CATS_Net (Apache-2.0), Zenodo 18136642 (Apache-2.0)

Status: code verified, 204 files readable, 16 matches

Wednesday, 18 February 2026 (1 paper)

[181] doi:10.1038/s41598-025-33709-w [paper, repository]

Toward cardiac electrophysiology digital twins with an efficient open source scalable solver on GPU clusters.

Journal: Scientific reports

Authors' code: rsachetto/MonoAlg3D_C (MIT), Zenodo 15041476 (CC-BY-4.0)

Status: code verified, 560 files readable, 4 matches

Tuesday, 17 February 2026 (4 papers)

[182] doi:10.1038/s41467-026-69380-6 [paper, repository]

Inferring latent behavioral strategy from the representational geometry of prefrontal cortex activity.

Journal: Nature communications

Authors' code: YQian2333/Inferring-WM-Strategies (Apache-2.0)

Status: code verified, 21 files readable, 12 matches

[183] doi:10.1038/s41589-026-02147-8 [paper, repository]

A two-step clockwork mechanism opens a proteo-lipidic pore in PIEZO2.

Journal: Nature chemical biology

Authors' code: lynaluo-lab/piezo2 (no license), hanlab-computchem/hanlab (no license), Zenodo 17644912 (CC-BY-4.0), Zenodo 17958235 (CC-BY-4.0)

Status: code verified, 92 files readable, 9 matches

[184] doi:10.3758/s13423-026-02857-z [paper, repository]

Crossmodal interaction of flashes and beeps across time and number follows Bayesian causal inference.

Journal: Psychonomic bulletin & review

Authors' code: OSF bqt9e (no license)

Status: code verified, 2 files readable

[185] doi:10.1007/s00366-026-02287-4 [paper, repository]

Near real-time adaptive isotropic and anisotropic image-to-mesh conversion for cerebral aneurysm simulations.

Journal: Engineering with computers

Authors' code: intel/lmbench (GPL-2.0)

Status: code verified, 80 files readable

Thursday, 12 February 2026 (1 paper)

[186] doi:10.1371/journal.pcbi.1013926 [paper, repository]

Plastic Arbor: A modern simulation framework for synaptic plasticity-From single synapses to networks of morphological neurons.

Journal: PLoS computational biology

Authors' code: Zenodo 18088337 (CC-BY-4.0), arbor-sim/arbor (BSD-3-Clause), jlubo/simulatorcomparison (no license), Shirin1993/Arbor_diffusion (no license), Zenodo 7415130 (BSD-3-Clause), Zenodo 4429195 (other-open), jlubo/brian_synaptic_plasticity_stc (no license), jlubo/arbor_2N1S (no license), jlubo/arbor_network_consolidation (Apache-2.0), jlubo/brian_network_plasticity (no license), jlubo/arbor_network_consolidation_mc (Apache-2.0), tetzlab/FIPPA (no license), jlubo/coreneuron_busyring (BSD-3-Clause), jlubo/memory-consolidation-stc (Apache-2.0)

Status: code verified, 746 files readable, 17 matches

Wednesday, 11 February 2026 (3 papers)

[187] doi:10.1371/journal.pcbi.1013959 [paper, repository]

Invariant visual object and face learning in the ventral cortical visual pathway: A biologically plausible model.

Journal: PLoS computational biology

Authors' code: oxcns.org (no license)

Status: code verified

[188] doi:10.1371/journal.pone.0338873 [paper, repository]

Abnormal calcium release and delayed afterdepolarizations: A comparison of two mathematical models for human ventricular myocytes.

Journal: PloS one

Authors' code: Zenodo 14360369 (CC-BY-4.0)

Status: code verified, 121 files readable, 3 matches

[189] doi:10.1038/s41598-026-35102-7 [paper, repository]

A physics-informed graph neural network to approximate docking-based binding affinity for DYRK2 in Alzheimer's drug repurposing.

Journal: Scientific reports

Authors' code: starnnt/physdual-gcn](https: (no license)

Status: dead link

Tuesday, 10 February 2026 (1 paper)

[190] doi:10.1073/pnas.2506040123 [paper, data]

Allosteric coupling between PIP<sub>2</sub> and Ca<sup>2+</sup> binding sites gates TMEM16A channels.

Journal: Proceedings of the National Academy of Sciences of the United States of America

Status: data only, 2 datasets cited

Friday, 6 February 2026 (1 paper)

[191] doi:10.1007/s11571-026-10415-5 [paper, repository]

A brain-constrained neural model of cognition and language with NEST: transitioning from the Felix framework.

Journal: Cognitive neurodynamics

Authors' code: MaximeCarriere/cogninest (no license)

Status: code verified, 38 files readable, 8 matches

Wednesday, 4 February 2026 (1 paper)

[192] doi:10.1371/journal.pcbi.1013937 [paper, repository]

Modeling human visuomotor adaptation with a disturbance observer framework.

Journal: PLoS computational biology

Authors' code: thartbm/PyVMEC2 (no license)

Status: code verified, 5 files readable

Tuesday, 3 February 2026 (1 paper)

[193] doi:10.1016/j.jmccpl.2026.100834 [paper, repository]

Response of human iPSC-cardiomyocytes to adrenergic drugs assessed by high-throughput pericellular oxygen measurements and computational modeling.

Journal: Journal of molecular and cellular cardiology plus

Authors' code: Zenodo 18410201 (MIT), aminforouzandehmehr (no license), aminforouzandehmehr/forouzandehmehr2026-hipsc-cms-model (MIT)

Status: code verified, 22 files readable, 6 matches

Monday, 2 February 2026 (4 papers)

[194] doi:10.1371/journal.pone.0341965 [paper, data]

Discovery of a novel Keap1 inhibitor for neurodegeneration through virtual screening and molecular dynamics simulations.

Journal: PloS one

Status: data only, 1 dataset cited

[195] doi:10.3390/molecules31030522 [paper, repository]

De Novo Generation-Based Design of Potential Computational Hits Targeting the GluN1-GluN2A Receptor.

Journal: Molecules (Basel, Switzerland)

Authors' code: kotori-y/gmx_batch (MIT)

Status: code verified, 3 files readable

[196] doi:10.3389/fncom.2025.1731161 [paper, repository]

Arbor-TVB: a novel multi-scale co-simulation framework with a case study on neural-level seizure generation and whole-brain propagation.

Journal: Frontiers in computational neuroscience

Authors' code: arbor-contrib/arbor-tvb-cosim (BSD-3-Clause)

Status: code verified, 8 files readable, 3 matches

[197] doi:10.3389/fninf.2025.1726374 [paper, repository]

Macular: a multi-scale simulation platform for the retina and the primary visual system.

Journal: Frontiers in neuroinformatics

Authors' code: gitlab.inria.fr/macular/macular (GPL-3.0)

Status: code verified, 227 files readable, 12 matches

Sunday, 1 February 2026 (1 paper)

[198] doi:10.1167/jov.26.2.11 [paper, repository]

Deep neural networks trained for estimating reflectance and illumination achieve lightness constancy differently than human observers.

Journal: Journal of vision

Authors' code: albanflachot/iid4constancy (MIT)

Status: code verified, 60 files readable, 3 matches

Saturday, 31 January 2026 (2 papers)

[199] doi:10.1038/s41467-026-68806-5 [paper, repository]

Recurrent connections facilitate occluded object recognition by explaining-away.

Journal: Nature communications

Authors' code: Zenodo 17655370 (CC-BY-4.0), kangbyungwoo/occlusion_public_repo (no license)

Status: code verified, 57 files readable, 9 matches

[200] doi:10.3390/ijms27031427 [paper, repository]

In Silico Prediction and Validation of the Permeability of Small Molecules Across the Blood-Brain Barrier.

Journal: International journal of molecular sciences

Authors' code: ELambden/bbb-permeability (no license)

Status: code verified, 6 files readable, 1 match

Friday, 23 January 2026 (1 paper)

[201] doi:10.1021/acs.jcim.5c02855 [paper, repository]

Combined Modeling Approaches for Assessing Sodium-Iodide Symporter Inhibition.

Journal: Journal of chemical information and modeling

Authors' code: PharminfoVienna/NIS_model_notebook (no license)

Status: code verified, 2 files readable, 3 matches

Tuesday, 20 January 2026 (4 papers)

[202] doi:10.7554/elife.99688 [paper, repository]

Modeling and simulation of neocortical micro- and mesocircuitry (Part I, anatomy).

Journal: eLife

Authors' code: Zenodo 8165004 (CC-BY-4.0)

Status: code verified

[203] doi:10.1371/journal.pcbi.1013273 [paper, repository]

Therapeutic targeting of oligodendrocytes in an agent-based model of multiple sclerosis.

Journal: PLoS computational biology

Authors' code: Georgia-Weatherley/MS_ABM_Weatherley (MIT)

Status: code verified, 28 files readable, 2 matches

[204] doi:10.3390/ijms27021008 [paper, data]

Design, Synthesis, and Biological Evaluation of Novel Acetylcholinesterase and β-Secretase 1 Inhibitors.

Journal: International journal of molecular sciences

Status: data only, 2 datasets cited

[205] doi:10.3390/molecules31020366 [paper, repository]

Computational Identification of Blood-Brain Barrier-Permeant Microbiome Metabolites with Binding Affinity to Neurotransmitter Receptors in Neurodevelopmental Disorders.

Journal: Molecules (Basel, Switzerland)

Authors' code: figshare 30494093 (MIT)

Status: code verified, 2 files readable

Monday, 19 January 2026 (2 papers)

[206] doi:10.1038/s41467-026-68453-w [paper, repository]

Model-agnostic linear-memory online learning in spiking neural networks.

Journal: Nature communications

Authors' code: chaobrain/braintrace-snn-experiments (no license), braintrace.readthedocs.io (no license), chaobrain/fitting_drosophila_whole_brain_spiking_model (no license), chaobrain/braintrace-shd-experiments (no license), Zenodo 17847403 (CC-BY-4.0), Zenodo 17892849 (CC-BY-4.0), Zenodo 17791424 (CC-BY-4.0)

Status: code verified, 96 files readable, 14 matches

[207] doi:10.3390/cells15020177 [paper, repository]

Cell-Based Computational Models of Organoids: A Systematic Review.

Journal: Cells

Authors' code: sysbio-curie/PhysiBoSS (no license)

Status: code verified, 261 files readable, 4 matches

Wednesday, 14 January 2026 (1 paper)

[208] doi:10.1523/jneurosci.1133-25.2025 [paper, repository]

Orientation Maps in Mouse Superior Colliculus Explained by Population Model of Non-Orientation Selective Neurons.

Journal: The Journal of neuroscience : the official journal of the Society for Neuroscience

Authors' code: austinchkuo/mousesc-ori-model (CC0-1.0)

Status: code verified, 24 files readable, 11 matches

Monday, 12 January 2026 (2 papers)

[209] doi:10.1371/journal.pbio.3003587 [paper, data]

Synaptic input variation enhances rate coding at the expense of temporal precision in cochlear nucleus neurons.

Journal: PLoS biology

Status: data only, 1 dataset cited

[210] doi:10.1038/s41467-025-67657-w [paper, repository]

Parietal alpha frequency shapes own-body perception by modulating the temporal integration of bodily signals.

Journal: Nature communications

Authors' code: OSF ytga5 (no license), OSF s5p4v (no license)

Status: code verified, 30 files readable, 9 matches

Thursday, 8 January 2026 (2 papers)

[211] doi:10.7554/elife.103512 [paper, repository]

Barcode activity in a recurrent network model of the hippocampus enables efficient memory binding.

Journal: eLife

Authors' code: chingf/barcodes (no license)

Status: code verified, 40 files readable, 1 match

[212] doi:10.1162/netn.a.38 [paper]

On the virtues and limitations of Granger-causal brain connectivity estimate: Critical analysis using neural mass models.

Journal: Network neuroscience (Cambridge, Mass.)

Status: code on request

Wednesday, 7 January 2026 (2 papers)

[213] doi:10.1007/s00422-025-01030-4 [paper, repository]

Task success in trained spiking neural network models coincides with emergence of cross-stimulus-modulated inhibition.

Journal: Biological cybernetics

Authors' code: doi:10.12751/nncn.bc2024.313 (no license), doi:10.12751/nncn.bc2024.128 (no license)

Status: code verified

[214] doi:10.1038/s44387-025-00053-3 [paper, repository]

Uncertainty-aware genomic deep learning with knowledge distillation.

Journal: NPJ artificial intelligence

Authors' code: zrcjessica/ensemble_distillation (MIT)

Status: code verified, 108 files readable, 15 matches

Tuesday, 6 January 2026 (1 paper)

[215] doi:10.1371/journal.pcbi.1013866 [paper, repository]

Biologically-constrained spiking neural network for neuromodulation in locomotor recovery after spinal cord injury.

Journal: PLoS computational biology

Authors' code: rchia16/balancing-locomotor-networks (no license)

Status: code verified, 4 files readable, 2 matches

Monday, 5 January 2026 (1 paper)

[216] doi:10.1371/journal.pone.0339326 [paper, repository]

Integrating simulated and experimental data to identify mitochondrial bioenergetic defects in Parkinson's Disease models.

Journal: PloS one

Authors' code: sandeepred/mitoexperiments_interpret (no license)

Status: code verified, 21 files readable, 9 matches

Saturday, 3 January 2026 (1 paper)

[217] doi:10.1038/s41598-025-34304-9 [paper, data]

Alchemilla vulgaris cytoprotection against methyl methanesulfonate by experimental and molecular docking approaches.

Journal: Scientific reports

Status: data only, 1 dataset cited

Thursday, 1 January 2026 (4 papers)

[218] doi:10.1111/desc.70099 [paper, repository]

Computationally Probing the Role of Time-Limited Neuronal Plasticity in Early Visual Development.

Journal: Developmental science

Authors' code: marin-oz/TimeLimitedPlasticity (no license)

Status: code verified, 9 files readable, 2 matches

[219] doi:10.3390/diagnostics16010139 [paper, data]

AI-Guided Inference of Morphodynamic Attractor-like States in Glioblastoma.

Journal: Diagnostics (Basel, Switzerland)

Status: code on request, 1 dataset cited

[220] doi:10.1111/micc.70049 [paper]

Modeling Pressure-Dependent Wave and Vessel Compliance in the Brain Following Middle Cerebral Artery Occlusion.

Journal: Microcirculation (New York, N.Y. : 1994)

Status: code on request

[221] doi:10.1177/23312165261421708 [paper, repository]

Benefits of Enhanced Phase-Locking for Binaural Coding of Amplitude-Modulated Sounds.

Journal: Trends in hearing

Authors' code: pinkbox-models/SBC2025 (no license)

Status: code verified, 6 files readable, 6 matches

Tuesday, 30 December 2025 (1 paper)

[222] doi:10.1016/j.nbd.2025.107253 [paper, repository]

Spinal circuit mechanisms constrain therapeutic windows for ALS intervention: A computational modeling study.

Journal: Neurobiology of disease

Authors' code: Zenodo 18185871 (MIT), Zenodo 10125416 (GPL-2.0), allodi-lab/cpg_modeling_als (MIT)

Status: code verified, 68 files readable, 12 matches

Monday, 29 December 2025 (2 papers)

[223] doi:10.1038/s41467-025-67076-x [paper, repository]

Biomimetic model of corticostriatal micro-assemblies discovers a neural code.

Journal: Nature communications

Authors' code: neuroblox.ai (no license), Neuroblox/corticostriatal-circuit-notebook (no license), neuroblox/neuroblox.jl (other)

Status: code verified, 5 files readable, 2 matches

[224] doi:10.1371/journal.pcbi.1013838 [paper, repository]

Ion dynamics underlying the seizure delay effect of low-frequency electrical stimulation.

Journal: PLoS computational biology

Authors' code: GuillaumeGirier/Low-Frequency-Electrical-Stimulation-and-Seizure-Delay (gnu), OSF 8j49w (no license)

Status: code verified, 8 files readable, 4 matches

Friday, 26 December 2025 (1 paper)

[225] doi:10.1038/s41467-025-66666-z [paper, repository]

Backpropagation through space, time and the brain.

Journal: Nature communications

Authors' code: greydanus/mnist1d (Apache-2.0), neurobench/neurobench (Apache-2.0), unibe-cns/gle-code (GPL-3.0)

Status: code verified, 170 files readable, 7 matches

Tuesday, 23 December 2025 (1 paper)

[226] doi:10.7554/elife.103324 [paper, repository]

DendroTweaks, an interactive approach for unraveling dendritic dynamics.

Journal: eLife

Authors' code: Poirazi-Lab/DendroTweaks (MPL-2.0), Poirazi-Lab/DendroTweaksApp (MPL-2.0)

Status: code verified, 220 files readable, 15 matches

Wednesday, 17 December 2025 (1 paper)

[227] doi:10.3389/fnins.2025.1639092 [paper, repository]

Simulated auditory nerve response evoked by lateral-wall and peri-modiolar electrode arrays inserted in scala tympani or scala vestibuli.

Journal: Frontiers in neuroscience

Authors' code: MPh-py/MPh (MIT), doi:10.12751/nncn.bc2023.262 (no license)

Status: code verified, 40 files readable, 1 match

Tuesday, 16 December 2025 (1 paper)

[228] doi:10.3390/molecules30244789 [paper, data]

Synthesis and Anti-Tumor Evaluation of Carboranyl BMS-202 Analogues-A Case of Carborane Not as Phenyl Ring Mimetic.

Journal: Molecules (Basel, Switzerland)

Status: data only, 1 dataset cited

Monday, 15 December 2025 (1 paper)

[229] doi:10.1371/journal.pcbi.1013674 [paper, repository]

Computational origins of shape perception.

Journal: PLoS computational biology

Authors' code: buildingamind/ShapeBasedVision_HumanAdult (MIT)

Status: code verified, 38 files readable, 4 matches

Saturday, 13 December 2025 (3 papers)

[230] doi:10.1038/s42003-025-09184-4 [paper, repository]

Optimal stochastic tracking control for brain network dynamics.

Journal: Communications biology

Authors' code: mb-bca/pymou (Apache-2.0), Kangli-Dong (no license)

Status: code verified, 5 files readable, 4 matches

[231] doi:10.1038/s41598-025-31950-x [paper, repository]

Episodic-like memory in a simulation of cuttlefish behavior.

Journal: Scientific reports

Authors' code: jkrichma/EpisodicLikeMemoryModel (GPL-3.0)

Status: code verified, 4 files readable, 1 match

[232] doi:10.1038/s41467-025-67137-1 [paper, repository]

Reshaping reservoirs with unsupervised Hebbian adaptation.

Journal: Nature communications

Authors' code: Zenodo 1342401 (other-open), Zenodo 4654722 (CC-BY-4.0), codeocean:3241639 (no license)

Status: code verified, 9 files readable

Friday, 12 December 2025 (3 papers)

[233] doi:10.7554/elife.106194 [paper, repository]

Virtual Brain Inference (VBI), a flexible and integrative toolkit for efficient probabilistic inference on whole-brain models.

Journal: eLife

Authors' code: ins-amu/vbi (Apache-2.0)

Status: code verified, 128 files readable, 31 matches

[234] doi:10.1371/journal.pcbi.1013764 [paper, repository]

PyFibers: An open-source NEURON-Python package to simulate responses of model nerve fibers to electrical stimulation.

Journal: PLoS computational biology

Authors' code: Zenodo 17068760 (CC-BY-4.0), Zenodo 5136631 (MIT), Zenodo 10608262 (GPL-2.0), Zenodo 15825841 (GPL-2.0), Zenodo 22921429 (CC-BY-4.0), Zenodo 22904322 (CC-BY-4.0), Zenodo 19595192 (CC-BY-4.0), Zenodo 22708608 (CC-BY-4.0), Zenodo 22697954 (CC-BY-4.0), Zenodo 21499046 (CC-BY-4.0), Zenodo 22030929 (CC-BY-4.0), Zenodo 21966787 (CC-BY-4.0), Zenodo 18774046 (CC-BY-4.0), Zenodo 17967056 (CC-BY-4.0)

Status: code verified, 1,569 files readable, 25 matches

[235] doi:10.1073/pnas.2513319122 [paper, repository]

Spiking world model with multicompartment neurons for model-based reinforcement learning.

Journal: Proceedings of the National Academy of Sciences of the United States of America

Authors' code: Brain-Cog-Lab/Spiking-WM (Apache-2.0)

Status: code verified, 15 files readable

Monday, 8 December 2025 (2 papers)

[236] doi:10.1038/s41598-025-31783-8 [paper, repository]

Simulation-assisted multimodal deep learning (Sim-MDL) fusion models for the evaluation of thermal barrier coatings using infrared thermography and Terahertz imaging.

Journal: Scientific reports

Authors' code: SKrishkp/Sim-MDL (no license)

Status: code verified, 3 files readable

[237] doi:10.1038/s41551-025-01536-z [paper, repository]

Long-term unsupervised recalibration of cursor-based intracortical brain-computer interfaces using a hidden Markov model.

Journal: Nature biomedical engineering

Authors' code: guyhwilson/nonstationarities (no license), guyhwilson/PRI-T (other)

Status: code verified, 25 files readable, 4 matches

Friday, 5 December 2025 (1 paper)

[238] doi:10.1007/s10687-025-00521-8 [paper, repository]

Neural Bayes estimation and selection of complex bivariate extremal dependence models.

Journal: Extremes

Authors' code: lidiamandre/NBE_classifier_depmodels (no license)

Status: code verified, 2 files readable

Tuesday, 2 December 2025 (3 papers)

[239] doi:10.1007/s10565-025-10109-4 [paper, data]

Exploring potential targets and molecular mechanisms of traumatic brain injury exacerbated by Benzo(a)pyrene via network toxicology and molecular dynamics simulation.

Journal: Cell biology and toxicology

Status: data only, 1 dataset cited

[240] doi:10.1007/s11538-025-01557-4 [paper, repository]

Astrocyte Reprogramming Drives Tumor Progression and Chemotherapy Resistance in Agent-Based Models of Breast Cancer Brain Metastases.

Journal: Bulletin of mathematical biology

Authors' code: RupleenK/AstroTumor-ABM (MIT)

Status: code verified, 220 files readable, 14 matches

[241] doi:10.1016/j.csbj.2025.12.001 [paper, repository]

Model-based evaluation of connexin hemichannel permeability.

Journal: Computational and structural biotechnology journal

Authors' code: thr3iog/detectron2-hela-cells-data-extractor (no license)

Status: code verified, 19 files readable, 4 matches

Monday, 1 December 2025 (4 papers)

[242] doi:10.1007/s00285-025-02317-7 [paper, repository]

A 3D-1D-0D multiscale model of the neuro-glial-vascular unit for synaptic and vascular dynamics in the dorsal vagal complex.

Journal: Journal of mathematical biology

Authors' code: alhermann/ngvu-multiscale-3d1d0d (GPL-3.0)

Status: code verified, 397 files readable, 10 matches

[243] doi:10.1038/s41598-025-28304-y [paper, data]

Molecular modeling to simulation: insights into Gaussian QSAR, molecular docking, and DFT for identification of HDAC3 inhibitors for neurocognitive vascular dementia.

Journal: Scientific reports

Status: data only, 1 dataset cited

[244] doi:10.1097/md.0000000000046463 [paper, data]

Research on the potential mechanisms of propofol in treating depression after brain injury based on network pharmacology.

Journal: Medicine

Status: data only, 1 dataset cited

[245] doi:10.18699/vjgb-25-110 [paper, repository]

Self-learning virtual organisms in a physics simulator: on the optimal resolution of their visual system, the architecture of the nervous system and the computational complexity of the problem.

Journal: Vavilovskii zhurnal genetiki i selektsii

Authors' code: DerpyFox/organism_simulator (no license)

Status: empty repository, 1 file readable

Friday, 28 November 2025 (3 papers)

[246] doi:10.7554/elife.107301 [paper, repository]

Center-surround inhibition in expectation and its underlying computational and artificial neural network models.

Journal: eLife

Authors' code: OSF 5tj8c (no license)

Status: code found, still to be checked

[247] doi:10.1038/s41467-025-66745-1 [paper, repository]

Contribution of amygdala to dynamic model arbitration under uncertainty.

Journal: Nature communications

Authors' code: DartmouthCCNL/woo_etal_amygdala (MIT), Zenodo 17480631 (MIT)

Status: code verified, 59 files readable, 7 matches

[248] doi:10.1186/s12984-025-01818-2 [paper, repository]

A model of the cerebellum generates gait adaptations in a reflex-based neuromusculoskeletal model during split-belt walking.

Journal: Journal of neuroengineering and rehabilitation

Authors' code: simtk.org/projects/splitbelt (no license)

Status: code verified

Wednesday, 26 November 2025 (2 papers)

[249] doi:10.1038/s41586-025-09805-2 [paper, repository]

Building compositional tasks with shared neural subspaces.

Journal: Nature

Authors' code: Zenodo 17274345 (CC-BY-4.0)

Status: code verified, 246 files readable, 8 matches

[250] doi:10.3389/fncom.2025.1647462 [paper, repository]

A neural network model combining the successor representation and actor-critic methods reveals effective biological use of the representation.

Journal: Frontiers in computational neuroscience

Authors' code: tkyktrm/frontiers (no license)

Status: code verified, 4 files readable

Monday, 24 November 2025 (2 papers)

[251] doi:10.1038/s41598-025-25418-1 [paper, data]

Believing in simulated virtual scents produces reported olfactory sensations.

Journal: Scientific reports

Status: data only, 1 dataset cited

[252] doi:10.3390/ijms262311347 [paper, repository]

Transferrin-Functionalized Liposomes Enhance MAPT-ASO Transport Across a 3D Blood-Brain Barrier Microvascular Network Model.

Journal: International journal of molecular sciences

Authors' code: S-Konig/Konig_Fluo_Signal_Quant_BBB_Microvascular_networks (MIT), Zenodo 17047899 (MIT)

Status: code verified, 4 files readable

Friday, 21 November 2025 (1 paper)

[253] doi:10.1371/journal.pcbi.1013644 [paper, repository]

Emergence of sparse coding, balance and decorrelation from a biologically-grounded spiking neural network model of learning in the primary visual cortex.

Journal: PLoS computational biology

Authors' code: marko-ruslim/bio-spiking-v1-learning (no license)

Status: code verified, 6 files readable, 3 matches

Thursday, 20 November 2025 (2 papers)

[254] doi:10.1371/journal.pcbi.1013712 [paper, repository]

How cortico-basal ganglia-thalamic subnetworks can shift decision policies to increase reward rate.

Journal: PLoS computational biology

Authors' code: coaxlab/cbgtpy (no license)

Status: code verified, 33 files readable, 4 matches

[255] doi:10.1162/netn.a.35 [paper, repository]

Coming up short: Generative network models fail to accurately capture long-range connectivity.

Journal: Network neuroscience (Cambridge, Mass.)

Authors' code: StuartJO/ComingUpShort (no license)

Status: code verified, 70 files readable, 9 matches

Wednesday, 19 November 2025 (3 papers)

[256] doi:10.1038/s42003-025-08971-3 [paper, repository]

Probabilistic inference of social presence across brain scales reveals enhanced synaptic efficacy.

Journal: Communications biology

Authors' code: ins-amu/SoFa-PI (no license)

Status: code verified, 18 files readable, 8 matches

[257] doi:10.1038/s41586-025-09778-2 [paper, repository]

Integrator dynamics in the cortico-basal ganglia loop for flexible motor timing.

Journal: Nature

Authors' code: inagaki-lab/Yang_et_al_2024 (no license), Zenodo 17343841 (CC-BY-4.0)

Status: code verified, 19 files readable, 2 matches

[258] doi:10.1039/d5ra06959a [paper, data]

Advances in predicting human olfactory perception: from data acquisition to computational models.

Journal: RSC advances

Status: data only, 2 datasets cited

Tuesday, 18 November 2025 (1 paper)

[259] doi:10.3390/cimb47110958 [paper, data]

In Silico Characterization of ADAR1: Structure, Dynamics, and Functional Implications.

Journal: Current issues in molecular biology

Status: data only, 1 dataset cited

Monday, 17 November 2025 (3 papers)

[260] doi:10.7554/elife.97274 [paper, repository]

Local, calcium- and reward-based synaptic learning rule that enhances dendritic nonlinearities can solve the nonlinear feature binding problem.

Journal: eLife

Authors' code: zahradd/dSPN-learning-rule (GPL-3.0)

Status: code verified, 51 files readable, 2 matches

[261] doi:10.1371/journal.pcbi.1012713 [paper, repository]

Benchmarking the predictive capability of human gait simulations.

Journal: PLoS computational biology

Authors' code: MaartenAfschrift/PredSim_gait_conditions (no license), kuleuvenneuromechanics/predsim (AGPL-3.0)

Status: code verified, 794 files readable, 12 matches

[262] doi:10.1038/s41562-025-02340-0 [paper, repository]

A habit and working memory model as an alternative account of human reward-based learning.

Journal: Nature human behaviour

Authors' code: AnneCollins/WMH (MIT)

Status: code verified, 27 files readable, 9 matches

Friday, 14 November 2025 (1 paper)

[263] doi:10.1038/s41598-025-22955-7 [paper, repository]

Identification of novel neuraminidase 1 modulators as potential therapeutics for Alzheimer's disease using virtual screening and molecular dynamics simulations.

Journal: Scientific reports

Authors' code: supp:PMC12618679/41598_2025_22955_MOESM4_ESM.sh (no license)

Status: code verified, 1 file readable

Tuesday, 11 November 2025 (1 paper)

[264] doi:10.1038/s41540-025-00596-w [paper, repository]

Digital dementia and testing of cognitive intervention for degenerating neural networks.

Journal: NPJ systems biology and applications

Authors' code: tigmoore/cog_therapy (no license)

Status: code verified, 6 files readable

Monday, 10 November 2025 (2 papers)

[265] doi:10.1371/journal.pcbi.1013681 [paper, repository]

A Bayesian neural ordinary differential equations framework to study the effects of chemical mixtures on survival.

Journal: PLoS computational biology

Authors' code: virgile-baudrot/maxim_TK_NeuralODEs_TD (no license), supp:PMC12674509/pcbi.1013681.s002.zip (no license)

Status: code verified, 54 files readable, 5 matches

[266] doi:10.1038/s41467-025-64976-w [paper, repository]

Fluctuation-learning relationship in recurrent neural networks.

Journal: Nature communications

Authors' code: labyrinth2shell/natcomm2025 (no license), Zenodo 17075784 (CC-BY-4.0)

Status: code verified, 10 files readable, 2 matches

Friday, 7 November 2025 (1 paper)

[267] doi:10.1002/dvdy.70072 [paper, repository]

Mathematical modeling predicts novel mechanisms of stream confinement from Trail/Colec12/Dan in the collective migration of cranial neural crest cells.

Journal: Developmental dynamics : an official publication of the American Association of Anatomists

Authors' code: SWSJChCh/leaderFollower (no license)

Status: code verified, 17 files readable, 3 matches

Wednesday, 5 November 2025 (1 paper)

[268] doi:10.1371/journal.pcbi.1013629 [paper, repository]

Null models for comparing information decomposition across complex systems.

Journal: PLoS computational biology

Authors' code: alberto-liardi/NuMIT (BSD-3-Clause)

Status: code verified, 398 files readable, 1 match

Monday, 3 November 2025 (2 papers)

[269] doi:10.1186/s12951-025-03748-6 [paper, data]

Apigenin regulates CCR5/JAK1/STAT1/MMPs signaling to alleviate secondary brain injury after intracerebral hemorrhage and its enhanced delivery via targeted nanoparticles.

Journal: Journal of nanobiotechnology

Status: data only, 1 dataset cited

[270] doi:10.7554/elife.98798 [paper, repository]

Characterization of binding kinetics and intracellular signaling of new psychoactive substances targeting cannabinoid receptor using transition-based reweighting method.

Journal: eLife

Authors' code: shuklagroup/dutta_shukla_cannabinoid_2023a (MIT)

Status: code verified, 19 files readable, 6 matches

Saturday, 1 November 2025 (3 papers)

[271] doi:10.1016/j.neuron.2025.09.037 [paper, repository]

Diverse perceptual biases emerge from Hebbian plasticity in a recurrent neural network model.

Journal: Neuron

Authors' code: OSF msbuh (no license)

Status: code verified, 1 file readable, 1 match

[272] doi:10.1093/cercor/bhaf295 [paper, repository]

Building on models-a perspective for computational neuroscience.

Journal: Cerebral cortex (New York, N.Y. : 1991)

Authors' code: INM-6/microcircuit-PD14-model (CC-BY-4.0), INM-6/multi-area-model (CC-BY-NC-SA-4.0), INM-6/human-multi-area-model (GPL-3.0), osb: (no license), OpenSourceBrain/PotjansDiesmann2014 (GPL-3.0)

Status: code verified, 269 files readable, 10 matches

[273] doi:10.1111/cns.70662 [paper, data]

Tetrahydrocurcumin Ameliorates Cerebral Ischemia-Reperfusion Injury and Restores Blood-Brain Barrier Dysfunction by Inhibiting Ferroptosis.

Journal: CNS neuroscience & therapeutics

Status: data only, 1 dataset cited

Friday, 31 October 2025 (2 papers)

[274] doi:10.1371/journal.pone.0335919 [paper, repository]

A method for quantifying parallel growth between neuronal dendritic branches in vitro.

Journal: PloS one

Authors' code: inbar2748/SOA-2.0 (no license)

Status: code verified, 3 files readable, 2 matches

[275] doi:10.1371/journal.pcbi.1013645 [paper, repository]

Subthreshold moment analysis of neuronal populations driven by synchronous synaptic inputs.

Journal: PLoS computational biology

Authors' code: MathNeuro/AONCB_moments (no license)

Status: code verified, 21 files readable, 3 matches

Tuesday, 28 October 2025 (1 paper)

[276] doi:10.1007/s42113-025-00258-4 [paper, repository]

Recurrent Neural Network Exploration Strategies During Reinforcement Learning Depend on Network Capacity.

Journal: Computational brain & behavior

Authors' code: OSF h76qr (no license), deniztu/p1_generalization (no license), deniztu/p1 (no license)

Status: code verified, 63 files readable, 3 matches

Monday, 27 October 2025 (1 paper)

[277] doi:10.1038/s41540-025-00595-x [paper, repository]

ROS-induced voltage-gated ion channel expression and electrophysiological remodeling in malignant human cells.

Journal: NPJ systems biology and applications

Authors' code: supp:PMC12559232/41540_2025_595_MOESM13_ESM.py (no license)

Status: code verified, 1 file readable, 4 matches

Sunday, 26 October 2025 (1 paper)

[278] doi:10.3390/bioengineering12111163 [paper]

A Computational Model of the Respiratory CPG for the Artificial Control of Breathing.

Journal: Bioengineering (Basel, Switzerland)

Status: code on request

Saturday, 25 October 2025 (1 paper)

[279] doi:10.1093/nsr/nwaf457 [paper, repository]

Artificial intelligence as a surrogate brain: bridging neural dynamical models and data.

Journal: National science review

Authors' code: ncclab-sustech/Review_Surrogate_Brain (no license)

Status: code verified, 10 files readable, 5 matches

Friday, 24 October 2025 (2 papers)

[280] doi:10.1038/s41467-025-64470-3 [paper, repository]

Modeling macroscopic brain dynamics with brain-inspired computing architecture.

Journal: Nature communications

Authors' code: GnohzZ/Brain-Dynamics-Modeling-Acceleration (no license), Zenodo 17104941 (CC-BY-4.0)

Status: code verified, 96 files readable, 13 matches

[281] doi:10.1186/s12883-025-04460-6 [paper, data]

Exploring the pathophysiological relationship between bisphenol A exposure and ischemic stroke risk using network toxicology and machine learning.

Journal: BMC neurology

Status: data only, 1 dataset cited

Thursday, 23 October 2025 (1 paper)

[282] doi:10.1021/acschemneuro.5c00734 [paper, data]

Aberrant S293 Phosphorylation Drives Oligomerization of Tau Repeat R2: Insights from Molecular Dynamics Simulations.

Journal: ACS chemical neuroscience

Status: data only, 1 dataset cited

Wednesday, 22 October 2025 (4 papers)

[283] doi:10.1021/acschemneuro.5c00635 [paper, repository]

The Effect of SARS-COV-2 Protein Fragments on the Dimerization of α-Synuclein.

Journal: ACS chemical neuroscience

Authors' code: ouhansmannlab/alpha_synuclein (no license)

Status: empty repository, 1 file readable

[284] doi:10.1371/journal.pcbi.1013500 [paper, repository]

Inferring effective networks of spiking neurons using a continuous-time estimator of transfer entropy.

Journal: PLoS computational biology

Authors' code: jlizier/jidt (gpl), Zenodo 17169511 (CC-BY-4.0), davidshorten/te_network_inference (no license)

Status: code verified, 594 files readable, 1 match

[285] doi:10.1038/s41598-025-20811-2 [paper, repository]

Layered structure of cortex explains reversal dynamics in bistable perception.

Journal: Scientific reports

Authors' code: ccnmaastricht/LCM-BS (GPL-3.0)

Status: code verified, 5 files readable, 1 match

[286] doi:10.3389/fncom.2025.1601641 [paper, repository]

Sudden restructuring of memory representations in recurrent neural networks with repeated stimulus presentations.

Journal: Frontiers in computational neuroscience

Authors' code: jonhowlett/hopfield-jumps (no license)

Status: code verified, 6 files readable, 6 matches

Tuesday, 21 October 2025 (2 papers)

[287] doi:10.1371/journal.pcbi.1013609 [paper, repository]

Homeostatic bidirectional plasticity in upbound and downbound micromodules in a model of the olivocerebellar loop.

Journal: PLoS computational biology

Authors' code: eliasmateo95/CerebellarLoop (no license)

Status: code verified, 6 files readable, 1 match

[288] doi:10.1038/s41598-025-20619-0 [paper, repository]

Isometric representations in neural networks improve robustness.

Journal: Scientific reports

Authors' code: KBeshkov/HIsometricNets (no license)

Status: code verified, 14 files readable, 1 match

Monday, 20 October 2025 (1 paper)

[289] doi:10.3390/ijms262010188 [paper, data]

Inhibition of Casein Kinase 1<i>δ</i> as a Novel Therapeutic Strategy for Amyotrophic Lateral Sclerosis: A Theoretical Study.

Journal: International journal of molecular sciences

Status: data only, 1 dataset cited

Friday, 17 October 2025 (5 papers)

[290] doi:10.1002/advs.202406440 [paper, repository]

TVB C++: A Fast and Flexible Back-End for The Virtual Brain.

Journal: Advanced science (Weinheim, Baden-Wurttemberg, Germany)

Authors' code: neich/tvb-root-cpp (Apache-2.0)

Status: code verified, 130 files readable, 13 matches

[291] doi:10.1371/journal.pcbi.1013573 [paper, repository]

Statistical regularities in natural scenes that support figure-ground segregation by neural populations.

Journal: PLoS computational biology

Authors' code: eacooper/FigureGround (MIT)

Status: code verified, 82 files readable, 8 matches

[292] doi:10.1038/s41467-025-63817-0 [paper, repository]

Explicit error coding can mediate gain recalibration in continuous bump attractor networks.

Journal: Nature communications

Authors' code: LIMBSlab/secer2025_expliciterror (no license)

Status: code verified, 99 files readable

[293] doi:10.1038/s41598-025-20245-w [paper, repository]

Recurrent issues with deep neural network models of visual recognition.

Journal: Scientific reports

Authors' code: dicarlolab/CORnet (GPL-3.0), TimManiquet/recurrent_issues_DNNs (MIT)

Status: code verified, 16 files readable, 4 matches

[294] doi:10.1038/s41598-025-20315-z [paper]

Analyzing the normal and epileptic output of a neural mass model based on cyclic-small gain theorem.

Journal: Scientific reports

Status: code on request

Thursday, 16 October 2025 (1 paper)

[295] doi:10.1038/s41467-025-63994-y [paper, repository]

The neural basis for uncertainty processing in hierarchical decision making.

Journal: Nature communications

Authors' code: Zenodo 13152289 (CC-BY-4.0), brabeeba/coglink-network (no license)

Status: code verified, 26 files readable, 3 matches

Monday, 13 October 2025 (3 papers)

[296] doi:10.1371/journal.pcbi.1012986 [paper, repository]

Understanding the mechanism of facilitation in hoverfly TSDNs.

Journal: PLoS computational biology

Authors' code: anindyaghosh/TSDN_facilitation (no license)

Status: code verified, 7 files readable, 10 matches

[297] doi:10.1038/s41467-025-64676-5 [paper, repository]

Allocentric flocking.

Journal: Nature communications

Authors' code: figshare 28925888 (CC-BY-4.0)

Status: code verified, 1 file readable

[298] doi:10.1038/s41598-025-19664-6 [paper, repository]

Streamlined and efficient patient-specific modeling for lumbar spine segmentation and finite element analysis.

Journal: Scientific reports

Authors' code: Zenodo 17051686 (CC-BY-4.0)

Status: code verified, 735 files readable, 18 matches

Friday, 10 October 2025 (3 papers)

[299] doi:10.1371/journal.pcbi.1013543 [paper, repository]

Learning spatial hearing via innate mechanisms.

Journal: PLoS computational biology

Authors' code: YangTrue/Learning-spatial-hearing-via-innate-mechanisms (BSD-3-Clause)

Status: code verified, 45 files readable, 8 matches

[300] doi:10.1038/s42003-025-08858-3 [paper, repository]

Temporal recurrence as a general mechanism to explain neural responses in the auditory system.

Journal: Communications biology

Authors' code: urancon/deepSTRF (GPL-3.0)

Status: code verified, 141 files readable, 19 matches

[301] doi:10.1063/5.0288838 [paper, repository]

When <i>in vitro</i> is not enough: <i>In silico</i> strategies to investigate functional and dynamical properties of large-scale neuronal assemblies.

Journal: APL bioengineering

Authors' code: dbbs-lab/bsb (GPL-3.0)

Status: code verified, 377 files readable

Thursday, 9 October 2025 (2 papers)

[302] doi:10.1098/rsta.2024.0423 [paper, repository]

Variational quantum and neural quantum states algorithms for the linear complementarity problem.

Journal: Philosophical transactions. Series A, Mathematical, physical, and engineering sciences

Authors' code: shravanvn/CV-quantum4ccp (no license), oliverknitter/VNLS_CSR (Apache-2.0), Zenodo 16780399 (Apache-2.0)

Status: code verified, 74 files readable, 2 matches

[303] doi:10.1021/acsomega.5c07084 [paper, data]

Silodosin as a Novel Inhibitor of Acetylcholinesterase, Butyrylcholinesterase, and BETA-Secretase 1: In Vitro and In Silico Studies.

Journal: ACS omega

Status: data only, 3 datasets cited

Wednesday, 8 October 2025 (2 papers)

[304] doi:10.1098/rsos.242062 [paper, repository]

An open-source neurodynamic model of the lower urinary tract.

Journal: Royal Society open science

Authors' code: Zenodo 16961553 (MIT), MoveR-Digital-Health-and-Care-Hub/lower-urinary-tract-sim (MIT), doi:10.6084/m9.figshare.c.8057289 (no license)

Status: code verified, 14 files readable, 13 matches

[305] doi:10.1016/j.jbc.2025.110804 [paper, data]

Transmembrane domain interactions underlie NSG1 regulation of sortilin ectodomain shedding.

Journal: The Journal of biological chemistry

Status: data only, 1 dataset cited

Tuesday, 7 October 2025 (2 papers)

[306] doi:10.1038/s41598-025-18776-3 [paper, repository]

Cholinergic modulation enables scalable action selection learning in a computational model of the striatum.

Journal: Scientific reports

Authors' code: EduardoRosLab/STR_DA_ACh (GPL-3.0)

Status: code verified, 352 files readable, 3 matches

[307] doi:10.1038/s41598-025-21460-1 [paper, repository]

Incremental self-organization of spatio-temporal spike pattern detection.

Journal: Scientific reports

Authors' code: MohammadDehghaniH/Incremental_Self-Organization_of_Spatio-Temporal_Spike_Pattern_Detection (MIT)

Status: code verified, 13 files readable, 3 matches

Monday, 6 October 2025 (1 paper)

[308] doi:10.1038/s41467-025-64234-z [paper, repository]

Predictive Coding Light.

Journal: Nature communications

Authors' code: neuromorphicsystems/IEBCS (GPL-3.0), comsee-research/Predictive-Coding-Light (no license)

Status: code verified, 73 files readable, 6 matches

Wednesday, 1 October 2025 (1 paper)

[309] doi:10.1111/micc.70027 [paper, repository]

Blood Flow Simulation and Uncertainty Quantification in Extensive Microvascular Networks: Application to Brain Cortical Networks.

Journal: Microcirculation (New York, N.Y. : 1994)

Authors' code: neuro8000/NetInf (GPL-3.0), Zenodo 15373376 (CC-BY-4.0)

Status: code verified, 33 files readable, 4 matches

Tuesday, 30 September 2025 (2 papers)

[310] doi:10.1038/s41467-025-63821-4 [paper, repository]

A doubly stochastic renewal framework for partitioning spiking variability.

Journal: Nature communications

Authors' code: engellab/DSRP (MIT)

Status: code verified, 12 files readable, 3 matches

[311] doi:10.1038/s41598-025-14619-3 [paper, repository]

Temporal single spike coding for effective transfer learning in spiking neural networks.

Journal: Scientific reports

Authors' code: SRKH/S4NN (GPL-3.0), hamidehmoghadasi/TS4TL (no license)

Status: code verified, 4 files readable, 4 matches

Wednesday, 24 September 2025 (3 papers)

[312] doi:10.1371/journal.pcbi.1013504 [paper, repository]

Elucidating reaction dynamics in a model of human brain energy metabolism.

Journal: PLoS computational biology

Authors' code: JolivetLab (no license), patsatzisdim/humBEMm_CSP (MIT)

Status: code verified, 5 files readable

[313] doi:10.1038/s42003-025-08728-y [paper, repository]

In silico reconstructions underpin aberrant trafficking dynamics in deficient axons of Dst knockout and Dst/Nefl double-knockout mice.

Journal: Communications biology

Authors' code: zongminliu9/igcps (no license), Zenodo 16579992 (CC-BY-4.0)

Status: code verified, 34 files readable, 2 matches

[314] doi:10.1038/s41586-025-09544-4 [paper, repository]

Arousal as a universal embedding for spatiotemporal brain dynamics.

Journal: Nature

Authors' code: allensdk.readthedocs.io (no license), ryraut/arousal_dynamics (MIT)

Status: code verified, 17 files readable, 13 matches

Tuesday, 23 September 2025 (1 paper)

[315] doi:10.7554/elife.103660 [paper, repository]

Neural dynamics of reversal learning in the prefrontal cortex and recurrent neural networks.

Journal: eLife

Authors' code: chrismkkim/learntoreverse (MIT)

Status: code verified, 6 files readable, 1 match

Friday, 19 September 2025 (3 papers)

[316] doi:10.1371/journal.pcbi.1013503 [paper, repository]

Modeling neuron-astrocyte interactions in neural networks using distributed simulation.

Journal: PLoS computational biology

Authors' code: Zenodo 13757202 (GPL-3.0), nest-simulator.readthedocs.io (no license), INM-6/beNNch (GPL-3.0), heplesser/astrocyte-surrogate-module (no license), Zenodo 17334796 (GPL-3.0)

Status: code verified, 16 files readable, 2 matches

[317] doi:10.1038/s41467-025-64152-0 [paper, repository]

Thalamus enables active dendritic coupling of inputs arriving at different cortical layers.

Journal: Nature communications

Authors' code: mpinb/in_silico_framework_hot_zone (GPL-3.0)

Status: code verified, 179 files readable, 8 matches

[318] doi:10.1016/j.isci.2025.113602 [paper, repository]

Rotating visual spaces induce behavioral biases consistent with recalibrated heading integration in humans.

Journal: iScience

Authors' code: Zenodo 16777254 (CC-BY-4.0), akeinath/HumanVR_HD_2025 (no license)

Status: code verified, 2 files readable, 1 match

Wednesday, 17 September 2025 (3 papers)

[319] doi:10.1371/journal.pbio.3002993 [paper, data]

Sensitive red fluorescent indicators for real-time visualization of potassium ion dynamics in vivo.

Journal: PLoS biology

Status: data only, 1 dataset cited

[320] doi:10.1371/journal.pcbi.1013462 [paper, repository]

Reconstructing noisy gene regulation dynamics using extrinsic-noise-driven neural stochastic differential equations.

Journal: PLoS computational biology

Authors' code: JianchengZ/Neural-SDE-GeneDynamics (no license)

Status: code verified, 13 files readable

[321] doi:10.1038/s41586-025-09528-4 [paper, repository]

Transitions in dynamical regime and neural mode during perceptual decisions.

Journal: Nature

Authors' code: Brody-Lab/decision_dynamics_commitment (Apache-2.0), Brody-Lab/findr (Apache-2.0), Brody-Lab/fhmddm (Apache-2.0), Brody-Lab/tzl_spglm (no license)

Status: code verified, 2,091 files readable, 16 matches

Tuesday, 16 September 2025 (2 papers)

[322] doi:10.1371/journal.pcbi.1013484 [paper, repository]

Dynamical mean-field theory for a highly heterogeneous neural population with graded persistent activity of the entorhinal cortex.

Journal: PLoS computational biology

Authors' code: fuuta/multiD_hetero_DMFT (no license)

Status: code verified, 30 files readable

[323] doi:10.1371/journal.pone.0330607 [paper, repository]

Neural SDE-based spike control of noisy neurons.

Journal: PloS one

Authors' code: ogura-lab/neuron-program (no license)

Status: code verified, 6 files readable

Friday, 12 September 2025 (2 papers)

[324] doi:10.1371/journal.pcbi.1013452 [paper, repository]

Simulation insights on the compound action potential in multifascicular nerves.

Journal: PLoS computational biology

Authors' code: Zenodo 15848037 (CC-BY-4.0), joseph-tharayil/vagusNerve (Apache-2.0), joseph-tharayil/vagusOptimization (Apache-2.0)

Status: code verified, 101 files readable, 6 matches

[325] doi:10.1371/journal.pcbi.1013403 [paper, repository]

Competition and cooperation of assembly sequences in recurrent neural networks.

Journal: PLoS computational biology

Authors' code: tristanstoeber/sequence_competition_cooperation (CC-BY-4.0)

Status: code verified, 29 files readable, 3 matches

Wednesday, 10 September 2025 (1 paper)

[326] doi:10.7554/elife.102269 [paper, data]

The flexible stalk domain of sTREM2 modulates its interactions with brain-based phospholipids.

Journal: eLife

Status: data only, 1 dataset cited

Monday, 8 September 2025 (2 papers)

[327] doi:10.1371/journal.pcbi.1013282 [paper, repository]

Microtubule-based nucleation results in a large sensitivity to cell geometry of the plant cortical array.

Journal: PLoS computational biology

Authors' code: corticalsim/corticalsim (MPL-2.0), Zenodo 16282498 (MPL-2.0), Zenodo 801852 (MPL-2.0), Zenodo 16282497 (MPL-2.0)

Status: code verified, 68 files readable, 5 matches

[328] doi:10.1371/journal.pcbi.1013269 [paper, repository]

Understanding thromboembolus transport patterns in the brain for stroke in the presence of carotid artery stenosis.

Journal: PLoS computational biology

Authors' code: shaddenlab.berkeley.edu/software.html (no license)

Status: code verified

Friday, 5 September 2025 (2 papers)

[329] doi:10.1073/pnas.2500938122 [paper, repository]

A mosquito-inspired theoretical framework for acoustic signal detection.

Journal: Proceedings of the National Academy of Sciences of the United States of America

Authors' code: jfaber3/Fig-Files-A-mosquito-inspired-theoretical-framework (no license)

Status: code verified, 6 files readable, 2 matches

[330] doi:10.1038/s41467-025-63493-0 [paper, repository]

Covariant spatio-temporal receptive fields for spiking neural networks.

Journal: Nature communications

Authors' code: jegp/nrf (GPL-3.0), Zenodo 16651826 (CC-BY-4.0)

Status: code verified, 21 files readable, 4 matches

Thursday, 4 September 2025 (1 paper)

[331] doi:10.3389/fimmu.2025.1632891 [paper, data]

Structural modifications to pregnane neurosteroids alter inhibition of LPS/Lipid A binding at the MD-2 activation site within the TLR4 signaling complex.

Journal: Frontiers in immunology

Status: data only, 1 dataset cited

Tuesday, 2 September 2025 (2 papers)

[332] doi:10.1371/journal.pone.0330681 [paper, repository]

An open-source replication for fast and accessible light propagation modeling in brain tissue.

Journal: PloS one

Authors' code: Zenodo 15490385 (no license)

Status: dead link

[333] doi:10.1038/s41598-025-10526-9 [paper, repository]

Implicit Runge-Kutta based sparse identification of governing equations in biologically motivated systems.

Journal: Scientific reports

Authors' code: anvari94/IRK-SINDy (MIT)

Status: code verified, 17 files readable, 2 matches

Monday, 1 September 2025 (2 papers)

[334] doi:10.1002/pro.70271 [paper, repository]

A multi-pore model of the blood-brain barrier tight junction strands recapitulates the permeability features of wild-type and mutant claudin-5.

Journal: Protein science : a publication of the Protein Society

Authors' code: membrane.urmc.rochester.edu/content/wham (no license)

Status: code verified

[335] doi:10.1111/cns.70609 [paper, data]

Network Pharmacology-Based and Experimental Validation Elucidate the Target Mechanism of Vinorine in Ameliorating Secondary Brain Injury After Intracerebral Hemorrhage.

Journal: CNS neuroscience & therapeutics

Status: data only, 1 dataset cited

Thursday, 28 August 2025 (1 paper)

[336] doi:10.7554/elife.104456 [paper, repository]

A neural network model that generates salt concentration memory-dependent chemotaxis in <i>Caenorhabditis elegans</i>.

Journal: eLife

Authors' code: 118-Oganesson/c_elegans_chemotaxis (MIT)

Status: code verified, 34 files readable

Wednesday, 20 August 2025 (1 paper)

[337] doi:10.1098/rsos.250491 [paper, repository]

A mathematical model of human oesophageal motility function.

Journal: Royal Society open science

Authors' code: miuraTakashi/EsophagealPeristalsisModel (GPL-3.0), Zenodo 15854411 (GPL-3.0), doi:10.6084/m9.figshare.c.7953936 (no license)

Status: code verified, 8 files readable, 5 matches

Tuesday, 19 August 2025 (1 paper)

[338] doi:10.1038/s42003-025-08690-9 [paper, repository]

Local homeostasis preserves global neural dynamics compensating for structural loss during human lifespan aging.

Journal: Communications biology

Authors' code: cbdl/agingmdmf (no license)

Status: code verified, 13 files readable, 5 matches

Monday, 18 August 2025 (2 papers)

[339] doi:10.1371/journal.pcbi.1013371 [paper, repository]

Stochastic activity in low-rank recurrent neural networks.

Journal: PLoS computational biology

Authors' code: fmastrogiuseppe/StochasticLowRank (no license)

Status: code verified, 15 files readable

[340] doi:10.1371/journal.pcbi.1013398 [paper, repository]

Heterogeneous synaptic homeostasis: A novel mechanism boosting information propagation in the cortex.

Journal: PLoS computational biology

Authors' code: Zenodo 15753856 (GPL-3.0), Zenodo 15753882 (GPL-3.0), fraziphy/heterogeneous_synaptic_homeostasis (GPL-3.0), fraziphy/iquanta (GPL-3.0)

Status: code verified, 36 files readable, 14 matches

Thursday, 14 August 2025 (1 paper)

[341] doi:10.1038/s41467-025-61466-x [paper, repository]

A decision-space model explains context-specific decision-making.

Journal: Nature communications

Authors' code: dirkbeck/dm_space_model (no license), Zenodo 15433189 (CC-BY-4.0), Zenodo 15433188 (CC-BY-4.0)

Status: code verified, 330 files readable, 16 matches

Wednesday, 13 August 2025 (3 papers)

[342] doi:10.1038/s42003-025-08599-3 [paper, repository]

Decomposed Linear Dynamical Systems (dLDS) models reveal instantaneous, context-dependent dynamic connectivity in C. elegans.

Journal: Communications biology

Authors' code: OSF 35hy2 (no license), dLDS-Decomposed-Linear-Dynamics (no license), dLDS-Decomposed-Linear-Dynamics/dLDS-Discrete-Matlab-Model (no license)

Status: code verified, 1,301 files readable, 4 matches

[343] doi:10.1186/s12987-025-00692-3 [paper, repository]

Advection versus diffusion in brain ventricular transport.

Journal: Fluids and barriers of the CNS

Authors' code: Zenodo 15194757 (CC-BY-4.0), Zenodo 10447666 (CC-BY-4.0)

Status: code verified, 28 files readable, 17 matches

[344] doi:10.3389/fncom.2025.1662598 [paper, repository]

The improved thalamo-cortical spiking network model of deep brain stimulation.

Journal: Frontiers in computational neuroscience

Authors' code: aafarokh/TCM_DBS (no license)

Status: dead link

Friday, 8 August 2025 (1 paper)

[345] doi:10.1371/journal.pone.0327386 [paper, data]

In Silico identification and modelling of FDA-approved drugs targeting T-type calcium channels.

Journal: PloS one

Status: data only, 1 dataset cited

Thursday, 7 August 2025 (2 papers)

[346] doi:10.3389/fninf.2025.1572782 [paper, repository]

Decoupling model descriptions from execution: a modular paradigm for extensible neurosimulation with EDEN.

Journal: Frontiers in neuroinformatics

Authors' code: eden-simulator.org/links/paper-backends-2025-material (no license)

Status: code verified

[347] doi:10.3390/biomimetics10080516 [paper, repository]

NeuroQ: Quantum-Inspired Brain Emulation.

Journal: Biomimetics (Basel, Switzerland)

Authors' code: colab.research.google.com/drive/1h1aslywmd_cnjd5daso3lw27_kvudj7y (no license)

Status: code verified

Wednesday, 6 August 2025 (1 paper)

[348] doi:10.1371/journal.pcbi.1013306 [paper, repository]

Excitatory/inhibitory ratio disruption modulates neural synchrony and flow directions in a cortical microcircuit.

Journal: PLoS computational biology

Authors' code: figshare 28715867 (CC-BY-4.0)

Status: code verified, 44 files readable, 1 match

Tuesday, 5 August 2025 (2 papers)

[349] doi:10.1007/s10827-025-00911-8 [paper, repository]

A simplified model of NMDA-receptor-mediated dynamics in leaky integrate-and-fire neurons.

Journal: Journal of computational neuroscience

Authors' code: janskaar/approximate_NMDA_model (no license), Zenodo 12624784 (GPL-2.0)

Status: code verified, 14 files readable, 1 match

[350] doi:10.3389/fnsyn.2025.1621352 [paper, repository]

Morphological variability may limit single-cell specificity to electric field stimulation.

Journal: Frontiers in synaptic neuroscience

Authors' code: alleninstitute/allensdk (BSD-2-Clause), djtrotter/morph-var (no license)

Status: code verified, 1,008 files readable, 1 match

Monday, 4 August 2025 (1 paper)

[351] doi:10.1038/s41467-025-62251-6 [paper, repository]

A multisynaptic spiking neuron for simultaneously encoding spatiotemporal dynamics.

Journal: Nature communications

Authors' code: Event-AHU/HARDVS (Apache-2.0), fanliangwei/Multisynaptic-spiking-neurons (no license)

Status: code verified, 308 files readable, 13 matches

Friday, 1 August 2025 (1 paper)

[352] doi:10.1038/s41598-025-12611-5 [paper, repository]

Short-term plasticity influences episodic memory recall: an interplay of synaptic traces in a spiking neural network model.

Journal: Scientific reports

Authors' code: Nikolaos-Chrysanthidis/Short-term-plasticity-influences-episodic-memory-recall (no license)

Status: code verified, 1 file readable

Wednesday, 30 July 2025 (2 papers)

[353] doi:10.1038/s41467-025-62202-1 [paper, repository]

Spiking dynamics of individual neurons reflect changes in the structure and function of neuronal networks.

Journal: Nature communications

Authors' code: ruocheny/neuronal-networks-spiking (MIT)

Status: code verified, 18 files readable, 5 matches

[354] doi:10.1038/s42003-025-08497-8 [paper, repository]

Text-related functionality and dynamics of visual human pre-frontal activations revealed through neural network convergence.

Journal: Communications biology

Authors' code: OSF a2bjg (no license), Zenodo 7813404 (CC-BY-4.0)

Status: code verified, 17 files readable, 2 matches

Tuesday, 29 July 2025 (2 papers)

[355] doi:10.1371/journal.pcbi.1013291 [paper, repository]

A Bayesian hierarchical model of trial-to-trial fluctuations in decision criterion.

Journal: PLoS computational biology

Authors' code: robinvloeberghs/hMFC (MIT)

Status: code verified, 33 files readable, 3 matches

[356] doi:10.1162/netn_a_00455 [paper, repository]

The exponential distance rule-based network model predicts topology and reveals functionally relevant properties of the <i>Drosophila</i> projectome.

Journal: Network neuroscience (Cambridge, Mass.)

Authors' code: bpentek/EDRmodel (no license), navis-org/fafbseg-py (GPL-3.0), navis-org/fafbseg-py):JFRC2 (no license), navis-org/fafbseg-py).EDR (no license)

Status: code verified, 15 files readable, 1 match

Monday, 28 July 2025 (2 papers)

[357] doi:10.1523/eneuro.0143-25.2025 [paper, repository]

Reinforced Odor Representations in the Anterior Olfactory Nucleus Can Serve as Memory Traces for Conspecifics.

Journal: eNeuro

Authors' code: clinster/Linsteretal2025 (no license)

Status: code verified, 15 files readable

[358] doi:10.1371/journal.pcbi.1013244 [paper, repository]

Recurrent neural networks as neuro-computational models of human speech recognition.

Journal: PLoS computational biology

Authors' code: christianbrodbeck/Eelbrain (BSD-3-Clause), christianbrodbeck/TRF-Tools (MIT), comp-cogneuro-lang/EARSHOT-MEG (no license)

Status: code verified, 352 files readable, 6 matches

Friday, 25 July 2025 (1 paper)

[359] doi:10.1038/s41598-025-11613-7 [paper]

A multi-stage auditory model for binaural sound localization using the locally competitive algorithm.

Journal: Scientific reports

Status: code on request

Thursday, 24 July 2025 (3 papers)

[360] doi:10.1523/eneuro.0383-24.2025 [paper, repository]

Spiking Neural Network Models of Interaural Time Difference Extraction via a Massively Collaborative Process.

Journal: eNeuro

Authors' code: comob-project/snn-sound-localization (MIT), neural-reckoning.github.io/cosyne-tutorial-2022 (no license), Zenodo 7044500 (other-open), neural-reckoning/cosyne-tutorial-2022 (MIT)

Status: code verified, 36 files readable, 10 matches

[361] doi:10.1088/1741-2552/adef7f [paper, data]

A primary mechanism for efficacy of the ketogenic diet may be energy repletion at the tripartite synapse.

Journal: Journal of neural engineering

Status: data only, 1 dataset cited

[362] doi:10.1007/s12021-025-09738-1 [paper, repository]

Scikit-NeuroMSI: A Generalized Framework for Modeling Multisensory Integration.

Journal: Neuroinformatics

Authors' code: renatoparedes/scikit-neuromsi (BSD-3-Clause), renatoparedes/NeuroMSI-Network (no license)

Status: code verified, 81 files readable, 24 matches

Wednesday, 23 July 2025 (1 paper)

[363] doi:10.3389/fninf.2025.1590968 [paper, repository]

Sensitivity analysis of a mathematical model of Alzheimer's disease progression unveils important causal pathways.

Journal: Frontiers in neuroinformatics

Authors' code: git.valeria.science/medics/models (no license)

Status: code verified

Tuesday, 22 July 2025 (1 paper)

[364] doi:10.1021/acsomega.5c03682 [paper, data]

<i><b>In Silico</b></i> Investigation of BTK as a Potent Immunomodulatory Target: Exploring Novel Therapeutic Approaches for Multiple Sclerosis.

Journal: ACS omega

Status: data only, 1 dataset cited

Monday, 21 July 2025 (2 papers)

[365] doi:10.1117/1.jbo.30.7.075002 [paper]

Evaluation of layered tissue scattering properties: a time-domain spatially resolved spectroscopy approach.

Journal: Journal of biomedical optics

Status: code on request

[366] doi:10.3389/fncir.2025.1542332 [paper, repository]

Bayesian estimation of orientation and direction tuning captures parameter uncertainty.

Journal: Frontiers in neural circuits

Authors' code: VH-Lab/vhlab-bayesoridir-matlab (other), MATLABCommunity-Toolboxes-at-INCF/Brain-Observatory-Toolbox (no license)

Status: code verified, 91 files readable, 11 matches

Friday, 18 July 2025 (1 paper)

[367] doi:10.3389/fnins.2025.1569397 [paper, repository]

Efficient implementation of the Hodgkin-Huxley potassium channel via a single volatile memristor.

Journal: Frontiers in neuroscience

Authors' code: llandsmeer/frontiers_nbox_k (no license)

Status: code verified, 17 files readable

Wednesday, 16 July 2025 (1 paper)

[368] doi:10.1098/rsos.250697 [paper, repository]

Enzyme inhibitory activity of marine alkaloid aaptamines for neurodegenerative diseases: an <i>in silico</i> study.

Journal: Royal Society open science

Authors' code: doi:10.5061/dryad.4f4qrfjqh (no license), doi:10.6084/m9.figshare.c.7888744 (no license)

Status: code verified

Wednesday, 9 July 2025 (1 paper)

[369] doi:10.1038/s41467-025-61458-x [paper, repository]

Computational models reveal that intuitive physics underlies visual processing of soft objects.

Journal: Nature communications

Authors' code: CNCLgithub/Woven (MIT), CNCLgithub/cloth-intuitive-physics_psiturk (no license), CNCLgithub/cloth-intuitive-physics_analysis (MIT), Zenodo 15555479 (CC-BY-4.0), Zenodo 15556559 (CC-BY-4.0), Zenodo 15555453 (CC-BY-4.0)

Status: code verified, 1,172 files readable, 10 matches

Monday, 7 July 2025 (4 papers)

[370] doi:10.1007/s00422-025-01017-1 [paper, repository]

Incorporating buccal mass planar mechanics and anatomical features improves neuromechanical modeling of Aplysia feeding behavior.

Journal: Biological cybernetics

Authors' code: CMU-BORG/Aplysia_Feeding_Neuromechanical_Model_Bennington_et_al (no license), Zenodo 15699753 (CC-BY-4.0)

Status: code verified, 37 files readable, 19 matches

[371] doi:10.1371/journal.pcbi.1013267 [paper, repository]

Selective inhibition in CA3: A mechanism for stable pattern completion through heterosynaptic plasticity.

Journal: PLoS computational biology

Authors' code: kgt1220/Hippocampus_SNN (no license)

Status: code verified, 36 files readable, 1 match

[372] doi:10.1371/journal.pcbi.1012733 [paper, repository]

Jaxkineticmodel: Neural ordinary differential equations inspired parameterization of kinetic models.

Journal: PLoS computational biology

Authors' code: AbeelLab/jaxkineticmodel (Apache-2.0), data.4tu.nl/datasets/3662eca5-7077-4ca3-8f66-d051e2c79cbe (no license)

Status: code verified, 61 files readable, 7 matches

[373] doi:10.1073/pnas.2419733122 [paper, data]

Adaptive arousal regulation: Pharmacologically shifting the peak of the Yerkes-Dodson curve by catecholaminergic enhancement of arousal.

Journal: Proceedings of the National Academy of Sciences of the United States of America

Status: data only, 1 dataset cited

Saturday, 5 July 2025 (1 paper)

[374] doi:10.1038/s41598-025-03672-7 [paper, data]

Design of a novel multiepitope vaccine against glioblastoma by in silico approaches.

Journal: Scientific reports

Status: data only, 4 datasets cited

Friday, 4 July 2025 (2 papers)

[375] doi:10.1038/s41467-025-61399-5 [paper, repository]

Self-supervised predictive learning accounts for cortical layer-specificity.

Journal: Nature communications

Authors' code: neuralml/neoSSL (MIT), Zenodo 15359568 (MIT)

Status: code verified, 66 files readable, 1 match

[376] doi:10.1186/s12984-025-01686-w [paper, data]

A PRISMA systematic review through time on predictive musculoskeletal simulations.

Journal: Journal of neuroengineering and rehabilitation

Status: data only, 1 dataset cited

Thursday, 3 July 2025 (1 paper)

[377] doi:10.1371/journal.pcbi.1012156 [paper, repository]

Cooperative coding of continuous variables in networks with sparsity constraint.

Journal: PLoS computational biology

Authors' code: NatalieSchieferstein/CoopCodeSpiking (GPL-3.0), Zenodo 15553757 (GPL-3.0), PaulZOnGit/CoopCodingRate (MIT), Zenodo 15555348 (MIT)

Status: code verified, 22 files readable, 7 matches

Wednesday, 2 July 2025 (3 papers)

[378] doi:10.1038/s41586-025-09142-4 [paper, repository]

Discovering cognitive strategies with tiny recurrent neural networks.

Journal: Nature

Authors' code: psuthaharan/covid19paranoia (no license), jil095/tinyRNN (no license)

Status: code verified, 274 files readable, 11 matches

[379] doi:10.1038/s41586-025-09215-4 [paper, repository]

A foundation model to predict and capture human cognition.

Journal: Nature

Authors' code: huggingface.co/marcelbinz/llama-3.1-centaur-70b-adapter (no license), marcelbinz/Llama-3.1-Centaur-70B (Apache-2.0)

Status: code verified, 74 files readable, 16 matches

[380] doi:10.1038/s41598-025-99501-y [paper, data]

A quantum-inspired neural fuzzy sliding mode control framework for fractional-order modeling of intraocular pressure regulation and optic nerve damage in glaucoma.

Journal: Scientific reports

Status: data only, 1 dataset cited

Tuesday, 1 July 2025 (4 papers)

[381] doi:10.1038/s41467-025-60878-z [paper, repository]

Advancing spatio-temporal processing through adaptation in spiking neural networks.

Journal: Nature communications

Authors' code: IGITUGraz/SE-adlif (CC-BY-SA-4.0), Zenodo 15364925 (CC-BY-4.0)

Status: code verified, 26 files readable, 9 matches

[382] doi:10.1038/s42003-025-08297-0 [paper, repository]

Higher dopamine D1 receptor expression in prefrontal parvalbumin neurons underlies higher distractibility in marmosets versus macaques.

Journal: Communications biology

Authors' code: tsvet-ivanov/marm-mac-D1R (no license)

Status: code verified, 5 files readable, 6 matches

[383] doi:10.1038/s41467-025-60511-z [paper, repository]

A normative principle governing memory transfer in cerebellar motor learning.

Journal: Nature communications

Authors' code: codeocean:3208717 (no license)

Status: code found, still to be checked

[384] doi:10.1167/jov.25.8.9 [paper, repository]

Computational evidence for an inverse relationship between retinal and brain complexity.

Journal: Journal of vision

Authors' code: mitchellslapik/retina (no license)

Status: code verified, 20 files readable, 5 matches

Monday, 30 June 2025 (2 papers)

[385] doi:10.1371/journal.pcbi.1012883 [paper, repository]

Investigate channel rectifications and neural dynamics by an electrodiffusive Gauss-Nernst-Planck approach.

Journal: PLoS computational biology

Authors' code: ND-ED/electrodiffusive-GNP-model-data (no license), ND-ED/electrodiffusive-GNP-model (no license)

Status: code verified, 18 files readable

[386] doi:10.1371/journal.pcbi.1013199 [paper, repository]

H- and m-channel overexpression promotes seizure-like events by impairing the ability of inhibitory neurons to process correlated inputs.

Journal: PLoS computational biology

Authors' code: RichLabUConn/HMChannelopathies (GPL-3.0), Zenodo 15012480 (GPL-3.0)

Status: code verified, 94 files readable, 3 matches

Thursday, 26 June 2025 (2 papers)

[387] doi:10.1098/rstb.2024.0114 [paper, repository]

Why did the human brain size evolve? A way forward.

Journal: Philosophical transactions of the Royal Society of London. Series B, Biological sciences

Authors' code: doi:10.6084/m9.figshare.c.7834282.v1 (no license)

Status: code found, still to be checked

[388] doi:10.1371/journal.pone.0326425 [paper, repository]

Metal coordination and enzymatic reaction of the glioma-target R132H isocitrate dehydrogenase 1: Insights by molecular simulations.

Journal: PloS one

Authors' code: mimic-project (no license), Zenodo 13862463 (CC-BY-4.0)

Status: code verified

Wednesday, 25 June 2025 (1 paper)

[389] doi:10.1038/s41586-025-09199-1 [paper, repository]

The dynamics and geometry of choice in the premotor cortex.

Journal: Nature

Authors' code: engellab/neuralflow (MIT), Zenodo 15426288 (CC-BY-4.0)

Status: code verified, 90 files readable, 19 matches

Tuesday, 24 June 2025 (1 paper)

[390] doi:10.1016/j.bpj.2025.06.029 [paper, repository]

Voltage gating and 4-aminopyridine inhibition in the Shaker Kv channel revealed by a closed-state model.

Journal: Biophysical journal

Authors' code: Zenodo 13958682 (CC-BY-4.0)

Status: code verified, 1 file readable, 1 match

Monday, 23 June 2025 (2 papers)

[391] doi:10.1113/ep092351 [paper, repository]

Computing muscle mechanical state variables from combined proprioceptive sensory feedback.

Journal: Experimental physiology

Authors' code: stephensjake72/spindlegrant (no license)

Status: code verified, 421 files readable, 2 matches

[392] doi:10.1038/s42256-025-01041-7 [paper, repository]

Dimensions underlying the representational alignment of deep neural networks with humans.

Journal: Nature machine intelligence

Authors' code: florianmahner/object-dimensions (GPL-3.0), Zenodo 14731440 (GPL-3.0)

Status: code verified, 93 files readable, 9 matches

Friday, 20 June 2025 (2 papers)

[393] doi:10.1007/s10827-025-00909-2 [paper, repository]

Modeling characteristics of neuronal firing in the thalamocortical network of connections in control and parkinsonian primates.

Journal: Journal of computational neuroscience

Authors' code: DrCaiola/PDModel (no license)

Status: code verified, 3 files readable

[394] doi:10.1371/journal.pcbi.1013075 [paper, repository]

Computations that sustain neural feature selectivity across processing stages.

Journal: PLoS computational biology

Authors' code: rjrowekamp/quad-quad (no license)

Status: code verified, 14 files readable, 7 matches

Thursday, 19 June 2025 (1 paper)

[395] doi:10.3389/fnins.2025.1570783 [paper, repository]

Modular architecture confers robustness to damage and facilitates recovery in spiking neural networks modeling <i>in vitro</i> neurons.

Journal: Frontiers in neuroscience

Authors' code: orlandi/netcal (MIT), orlandi/te-causality (gnu), akkeh/nc_sim (GPL-3.0), Zenodo 1119026 (MIT)

Status: code verified, 2,403 files readable, 2 matches

Monday, 16 June 2025 (1 paper)

[396] doi:10.1371/journal.pone.0326219 [paper, data]

Novel fungal metabolites as dual cholinesterase inhibitors: A computational approach for Alzheimer's disease therapy.

Journal: PloS one

Status: data only, 1 dataset cited

Friday, 13 June 2025 (1 paper)

[397] doi:10.1371/journal.pcbi.1013148 [paper, repository]

Unveiling the role of local metabolic constraints on the structure and activity of spiking neural networks.

Journal: PLoS computational biology

Authors' code: Wiss/edsnn (no license)

Status: code verified, 18 files readable

Thursday, 12 June 2025 (2 papers)

[398] doi:10.1371/journal.pbio.3003198 [paper, repository]

A unified framework to model synaptic dynamics during the sleep-wake cycle.

Journal: PLoS biology

Authors' code: Zenodo 15210933 (CC-BY-4.0), u963593d/synapse_boundary_simulation (no license)

Status: code verified, 136 files readable, 12 matches

[399] doi:10.1063/5.0250953 [paper, data]

Modeling nitric oxide diffusion and plasticity modulation in cerebellar learning.

Journal: APL bioengineering

Status: data only, 2 datasets cited

Wednesday, 11 June 2025 (4 papers)

[400] doi:10.1242/jcs.264093 [paper, repository]

A minimal mathematical model for polarity establishment and centralspindlin-independent cytokinesis.

Journal: Journal of cell science

Authors' code: omaxian/CElegansModel (no license)

Status: code verified, 22 files readable, 3 matches

[401] doi:10.1021/acs.jcim.5c00869 [paper, data]

Quantum Mechanics/Molecular Mechanics Simulations Distinguish Insulin-Regulated Aminopeptidase Substrate (Oxytocin) and Inhibitor (Angiotensin IV) and Reveal Determinants of Activity and Inhibition.

Journal: Journal of chemical information and modeling

Status: data only, 1 dataset cited

[402] doi:10.7554/elife.95243 [paper, repository]

Embedding stochastic dynamics of the environment in spontaneous activity by prediction-based plasticity.

Journal: eLife

Authors' code: TAsabuki/stochastic_transition (no license)

Status: code verified, 4 files readable, 1 match

[403] doi:10.1371/journal.pcbi.1013081 [paper, repository]

Balanced state of networks of winner-take-all units.

Journal: PLoS computational biology

Authors' code: rkp8000/balanced-wta (no license)

Status: code verified, 58 files readable, 3 matches

Tuesday, 10 June 2025 (2 papers)

[404] doi:10.3758/s13421-025-01731-y [paper, repository]

Dissociating voluntary mental imagery and mental simulation: Evidence from aphantasia.

Journal: Memory & cognition

Authors' code: OSF j9znu (no license)

Status: code verified, 5 files readable, 5 matches

[405] doi:10.1371/journal.pcbi.1013112 [paper, repository]

Energy optimization induces predictive-coding properties in a multi-compartment spiking neural network model.

Journal: PLoS computational biology

Authors' code: sbohte/SNN_PC_Multicomp (no license), Zenodo 13329388 (CC-BY-4.0)

Status: code verified, 8 files readable, 5 matches

Friday, 6 June 2025 (4 papers)

[406] doi:10.1021/acs.jcim.5c00858 [paper, data]

Mapping the Interactions Among Class IIa Histone Deacetylases and Myocyte Enhancer Factor 2s.

Journal: Journal of chemical information and modeling

Status: data only, 5 datasets cited

[407] doi:10.1038/s41562-025-02220-7 [paper, repository]

End-to-end topographic networks as models of cortical map formation and human visual behaviour.

Journal: Nature human behaviour

Authors' code: KietzmannLab/All-TNN (MIT)

Status: code verified, 44 files readable, 18 matches

[408] doi:10.1038/s41593-025-01944-z [paper, repository]

Spatial reasoning via recurrent neural dynamics in mouse retrosplenial cortex.

Journal: Nature neuroscience

Authors' code: jonnew/Oat (GPL-3.0), jvoigts/Voigts_Kanitscheider_et_al_2024 (no license), Zenodo 1098579 (other-open)

Status: code verified, 362 files readable, 1 match

[409] doi:10.1038/s41746-025-01703-1 [paper, repository]

Machine learning to predict penumbra core mismatch in acute ischemic stroke using clinical note data.

Journal: NPJ digital medicine

Authors' code: shaunk24/CTP_NLP (no license)

Status: code verified, 7 files readable, 3 matches

Thursday, 5 June 2025 (2 papers)

[410] doi:10.1007/s11064-025-04432-9 [paper, repository]

An Open-Science Computational Model of Organelle Acidification to Integrate Putative Mechanisms of Synaptic Vesicle Acidification and Filling.

Journal: Neurochemical research

Authors' code: colab.research.google.com/drive/1fmforaui4oyfxsihx-d_h8yn3kjaspt- (no license), Synthetic-Physiology-Lab/SynapticVesicles (no license), colab.research.google.com/drive/1etv4i53z5igd20yoesyrfgfmiqymw502 (no license), colab.research.google.com/drive/12dsun_rb9_chnkmmaeye6zlxl27rclar (no license), colab.research.google.com/drive/1ibtqupabykc0ho2lel6o_aiuebu8cd93 (no license), colab.research.google.com/drive/1xpfqspki8kry1wut5jfovrhgaxpjgvp0 (no license)

Status: code verified, 8 files readable, 5 matches

[411] doi:10.1371/journal.pcbi.1013105 [paper, repository]

A mathematical model suggests collectivity and inconstancy enhance the efficiency of neuronal migration in the adult brain.

Journal: PLoS computational biology

Authors' code: supp:PMC12140228/pcbi.1013105.s013.zip (no license)

Status: code verified, 3 files readable

Wednesday, 4 June 2025 (3 papers)

[412] doi:10.1007/s00422-025-01011-7 [paper, repository]

Decreased spinal inhibition leads to undiversified locomotor patterns.

Journal: Biological cybernetics

Authors' code: Zenodo 13981334 (CC-BY-4.0)

Status: code verified, 5 files readable, 7 matches

[413] doi:10.1371/journal.pcbi.1013099 [paper, repository]

GABAergic neurons can facilitate the propagation of cortical spreading depolarization: experiments in mouse neocortical slices and a novel neural field computational model.

Journal: PLoS computational biology

Authors' code: Zenodo 14230278 (CC-BY-4.0), emrebasp/a-neural-field-model-for-cortical-spreading-depression (CC0-1.0)

Status: code verified, 42 files readable, 2 matches

[414] doi:10.3389/fninf.2025.1544143 [paper, repository]

NESTML: a generic modeling language and code generation tool for the simulation of spiking neural networks with advanced plasticity rules.

Journal: Frontiers in neuroinformatics

Authors' code: Zenodo 7193351 (GPL-2.0)

Status: code verified

Tuesday, 3 June 2025 (1 paper)

[415] doi:10.1038/s41598-025-04347-z [paper, repository]

Navigation in brain networks is possible using only local measures.

Journal: Scientific reports

Authors' code: usidramki/usidramki1 (no license)

Status: code verified, 8 files readable

Monday, 2 June 2025 (1 paper)

[416] doi:10.1038/s41526-025-00478-9 [paper, data]

Reducing motion sickness during simulated astronaut post-spaceflight water landings using anticipatory cues or postural control.

Journal: NPJ microgravity

Status: data only, 1 dataset cited

Saturday, 31 May 2025 (1 paper)

[417] doi:10.3390/e27060589 [paper, data]

Information-Theoretical Analysis of a Transformer-Based Generative AI Model.

Journal: Entropy (Basel, Switzerland)

Status: data only, 1 dataset cited