computational modeling (no new data)

Modality: 117 papers with a page, 97 of them with their authors' code.

Friday, 25 September 2026 (1 paper)

[1] 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)

[2] 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)

[3] 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)

[4] 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)

[5] 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)

[6] 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

[7] 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)

[8] 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)

[9] 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

[10] 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

[11] 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)

[12] 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)

[13] 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)

[14] 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)

[15] 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

[16] 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)

[17] 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

[18] 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

[19] 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

[20] 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)

[21] 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)

[22] 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

[23] 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

[24] 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)

[25] 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

[26] 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)

[27] 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)

[28] 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)

[29] 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)

[30] 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

[31] 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)

[32] 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

[33] 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)

[34] 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

[35] 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)

[36] 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

[37] 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

[38] 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)

[39] 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

[40] 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)

[41] 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

[42] 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)

[43] 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)

[44] 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)

[45] 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

[46] 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

[47] 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)

[48] 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)

[49] 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

[50] 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

[51] 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

[52] 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)

[53] 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)

[54] 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

[55] 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)

[56] 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

[57] 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)

[58] 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)

[59] 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)

[60] 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

[61] 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)

[62] 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)

[63] 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

[64] 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)

[65] 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)

[66] 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

[67] 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)

[68] 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

[69] 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)

[70] 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

[71] 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)

[72] 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)

[73] 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

[74] 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)

[75] 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)

[76] 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

[77] 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)

[78] 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

[79] 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)

[80] 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)

[81] 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)

[82] 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, 64 files readable, 1 match

Friday, 15 May 2026 (1 paper)

[83] 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)

[84] 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)

[85] 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

[86] 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)

[87] 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)

[88] 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

[89] 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

[90] 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)

[91] 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)

[92] 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)

[93] 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

Monday, 20 April 2026 (2 papers)

[94] 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

[95] 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)

[96] 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)

[97] 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)

[98] 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)

[99] 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

[100] 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

[101] 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

[102] 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)

[103] 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

[104] 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)

[105] 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)

[106] 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)

[107] 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)

[108] 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)

[109] 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)

[110] 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)

[111] 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)

[112] 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

[113] 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

[114] 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)

[115] 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)

[116] 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

[117] 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