none (in silico)

Organism: 60 papers with a page, 45 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

Thursday, 17 September 2026 (1 paper)

[3] Code ↔ Paper doi:10.1007/s00422-026-01063-3 [paper, repository]

Increased firing rates monotonically expand neuronal coding bandwidth.

Journal: Biological cybernetics

Authors' code: bendalab/punitmodel (GPL-3.0), doi.gin.g-node.org/10.12751/g-node.5b08du (no license)

Status: code verified, 11 files readable, 10 matches

Saturday, 5 September 2026 (1 paper)

[4] 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

Friday, 4 September 2026 (1 paper)

[5] Code ↔ Paper doi:10.1126/sciadv.aeg6797 [paper, repository]

Dorsoventral gradient of theta sweeps in the medial entorhinal cortex.

Journal: Science advances

Authors' code: Zenodo 21427119 (CC-BY-4.0), zilongji/topographythetasweeps (no license)

Status: code verified, 39 files readable, 9 matches

Thursday, 27 August 2026 (1 paper)

[6] 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

Friday, 21 August 2026 (1 paper)

[7] 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

Friday, 7 August 2026 (4 papers)

[8] Code ↔ Paper doi:10.1007/s00422-026-01048-2 [paper, repository]

A quality measure for repeating multiple-unit spike patterns.

Journal: Biological cybernetics

Authors' code: Zenodo 18424512 (CC-BY-4.0)

Status: code verified, 5 files readable, 1 match

[9] 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

[10] 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

[11] Code ↔ Paper doi:10.3389/fnbeh.2026.1871826 [paper, repository]

Effects of repetitive scanning ultrasound on the intraneuronal dendritic signalling of CA1 pyramidal neurons.

Journal: Frontiers in behavioral neuroscience

Authors' code: somogyia/Intraneuronal-dendritic-signalling (no license)

Status: code verified, 4 files readable

Wednesday, 5 August 2026 (1 paper)

[12] 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

Tuesday, 28 July 2026 (2 papers)

[13] Code ↔ Paper doi:10.1371/journal.pcbi.1013487 [paper, repository]

Flexible navigation with neuromodulated cognitive maps.

Journal: PLoS computational biology

Authors' code: iKiru-hub/PCNN (no license)

Status: code verified, 7 files readable

[14] 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)

[15] 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

[16] 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 (1 paper)

[17] 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 (1 paper)

[18] 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 (1 paper)

[19] 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

Wednesday, 15 July 2026 (1 paper)

[20] Code ↔ Paper doi:10.1038/s41467-026-75402-0 [paper, repository]

Efficient Gillespie algorithms for spreading phenomena in large and heterogeneous higher-order networks.

Journal: Nature communications

Authors' code: gisc-ufv/hyperSIS (LGPL-3.0), Zenodo 20548808 (LGPL-3.0)

Status: code verified, 62 files readable

Tuesday, 7 July 2026 (1 paper)

[21] Code ↔ Paper doi:10.1093/nc/niag029 [paper, repository]

A data-driven approach to identifying and evaluating connectivity-based neural correlates of conscious visual perception.

Journal: Neuroscience of consciousness

Authors' code: anniegbryant/MEG_functional_connectivity (no license)

Status: code verified, 289 files readable, 17 matches

Monday, 29 June 2026 (2 papers)

[22] 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

[23] 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

Wednesday, 24 June 2026 (1 paper)

[24] 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, 16 June 2026 (1 paper)

[25] doi:10.1021/acsomega.5c11807 [paper, data]

Repurposing <i>T‑614</i> for Gout: An In Silico Framework Integrating Network Pharmacology, Mendelian Randomization, and Single-Cell and Molecular Dynamics Analyses.

Journal: ACS omega

Status: code on request, 4 datasets cited

Saturday, 13 June 2026 (1 paper)

[26] doi:10.1186/s12983-026-00620-7 [paper, data]

In silico screening for safe and potent essential oils against mosquito neural targets.

Journal: Frontiers in zoology

Status: data only, 4 datasets cited

Wednesday, 10 June 2026 (1 paper)

[27] Code ↔ Paper doi:10.1371/journal.pcbi.1014378 [paper, repository]

A mean-field model of neural networks with PV and SOM interneurons reveals connectivity-based mechanisms of gamma oscillations.

Journal: PLoS computational biology

Authors' code: Zenodo 20391404 (CC-BY-4.0), Zenodo 20391405 (CC-BY-4.0)

Status: code verified, 2 files readable

Tuesday, 9 June 2026 (1 paper)

[28] Code ↔ Paper doi:10.1371/journal.pcbi.1014391 [paper, repository]

Multi-stable oscillations in cortical networks with two classes of inhibition.

Journal: PLoS computational biology

Authors' code: Arnabds/Comp-Neuro-Research-Project-1--Multi-stable-oscillations-in-cortical-networks-with-two-classes (no license)

Status: code verified, 6 files readable

Friday, 5 June 2026 (2 papers)

[29] Code ↔ Paper doi:10.1162/imag.a.1249 [paper, repository]

Global search metaheuristics for neural mass model calibration.

Journal: Imaging neuroscience (Cambridge, Mass.)

Authors' code: domdunstan/Global_NMM_parameter_inference (MIT)

Status: code verified, 12 files readable, 7 matches

[30] 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)

[31] 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 (3 papers)

[32] 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

[33] Code ↔ Paper doi:10.3389/fncom.2026.1753444 [paper, repository]

NMDA receptor kinetics drive distinct routes to chaotic firing in pyramidal neurons.

Journal: Frontiers in computational neuroscience

Authors' code: borjkhani/Bifurcation_NMDA_FCN (MIT)

Status: code verified, 11 files readable, 26 matches

[34] doi:10.3389/fphys.2026.1727491 [paper, data]

A compartmental model for simulating the gut-brain axis in gastric function regulation.

Journal: Frontiers in physiology

Status: data only, 1 dataset cited

Monday, 1 June 2026 (4 papers)

[35] Code ↔ Paper doi:10.1093/bioinformatics/btag328 [paper, repository]

eFEL: electrophysiology feature extraction library.

Journal: Bioinformatics (Oxford, England)

Authors' code: berenslab/ephyspy (GPL-3.0), AllenInstitute/ipfx (BSD-2-Clause), openbraininstitute/eFEL (GPL-3.0), Zenodo 8283490 (Apache-2.0), Zenodo 14002264 (LGPL-3.0), bluebrain/bluepyefe (LGPL-3.0), bluebrain/bluepyemodel (Apache-2.0)

Status: code verified, 759 files readable, 10 matches

[36] Code ↔ Paper doi:10.1038/s41565-026-02180-7 [paper, repository]

Intracellular neuronal recordings across DNA tiles.

Journal: Nature nanotechnology

Authors' code: shulanx1/dnatiles (no license), shulanx1/DNAtiles_analysis (no license), Zenodo 18702671 (CC-BY-4.0), Zenodo 18702664 (CC-BY-4.0)

Status: code verified, 142 files readable, 1 match

[37] doi:10.1016/j.dib.2026.112926 [paper, data]

Synthetic dataset of PLGA and liposome nanocarrier formulations for brain-cancer-relevant drug delivery, release, blood-brain-barrier transport, and paired cell-viability proxies.

Journal: Data in brief

Status: data only, 3 datasets cited

[38] 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 (2 papers)

[39] Code ↔ Paper doi:10.1038/s41598-026-50423-3 [paper, repository]

Theoretical analysis of low power synergistic sono-optogenetic control of calcium-dependent synaptic plasticity.

Journal: Scientific reports

Authors' code: Zenodo 18297611 (CC-BY-4.0)

Status: empty repository

[40] Code ↔ Paper doi:10.1162/imag.a.1250 [paper, repository]

Dynamics-informed priors (DIP) for neural mass modelling.

Journal: Imaging neuroscience (Cambridge, Mass.)

Authors' code: AlessiaCaccamo/Figures_DIP_DCM_25 (GPL-3.0), AlessiaCaccamo/DIP_DCM_25 (GPL-3.0)

Status: code verified, 104 files readable, 4 matches

Thursday, 28 May 2026 (1 paper)

[41] 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

Tuesday, 26 May 2026 (1 paper)

[42] Code ↔ Paper doi:10.1162/imag.a.1247 [paper, repository]

Evaluating BOLD functional MRI biophysical simulation approaches: Impact of vascular geometry, magnetic field calculations, and water diffusion models.

Journal: Imaging neuroscience (Cambridge, Mass.)

Authors' code: jacobchausse/BOLDswimsuite (GPL-3.0)

Status: code verified, 20 files readable, 1 match

Tuesday, 19 May 2026 (1 paper)

[43] Code ↔ Paper doi:10.1038/s41598-026-53152-9 [paper, repository]

Layer-specific feature preference in a trained AlexNet model revealed by stylized image analysis.

Journal: Scientific reports

Authors' code: pytorch/examples (BSD-3-Clause), naoto0804/pytorch-AdaIN (MIT)

Status: code verified, 126 files readable, 3 matches

Wednesday, 13 May 2026 (2 papers)

[44] Code ↔ Paper doi:10.1111/cobi.70323 [paper, repository]

Integrating fossil data in ecological niche models to improve predictions of future habitat of Caribbean corals.

Journal: Conservation biology : the journal of the Society for Conservation Biology

Authors' code: supp:PMC13613574/COBI-40-e70323-s014.R (no license)

Status: code verified, 1 file readable, 2 matches

[45] 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

Tuesday, 12 May 2026 (1 paper)

[46] 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 (1 paper)

[47] 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

Wednesday, 6 May 2026 (1 paper)

[48] 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

Sunday, 3 May 2026 (1 paper)

[49] doi:10.1038/s41598-026-49043-8 [paper, data]

Physics-informed Koopman learning approach for fixed-time synchronization of stochastic neural dynamics.

Journal: Scientific reports

Status: data only, 1 dataset cited

Friday, 24 April 2026 (1 paper)

[50] Code ↔ Paper doi:10.1162/imag.a.1214 [paper, repository]

Replicability of representational similarity and its role in successful memory retrieval.

Journal: Imaging neuroscience (Cambridge, Mass.)

Authors' code: OSF zuyna (no license)

Status: code verified, 21 files readable, 1 match

Monday, 20 April 2026 (1 paper)

[51] 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

Wednesday, 15 April 2026 (4 papers)

[52] 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

[53] 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

[54] 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

[55] 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

Monday, 13 April 2026 (1 paper)

[56] 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, 3 April 2026 (1 paper)

[57] doi:10.1038/s41598-026-38002-y [paper]

Tsunami inversion using deep neural representations.

Journal: Scientific reports

Status: code on request

Wednesday, 1 April 2026 (3 papers)

[58] doi:10.1186/s12860-026-00584-w [paper, data]

A role for PaxB in regulating blebbing: experimental insights and theoretical perspectives from Dictyostelium discoideum.

Journal: BMC molecular and cell biology

Status: data only, 1 dataset cited

[59] doi:10.2147/jpr.s566042 [paper]

Quantum Mechanical Mechanisms in the Therapeutic Effects of Spinal Cord Stimulation to Treat Chronic Neuropathic Pain: A Quantum Computational Model.

Journal: Journal of pain research

Status: code on request

[60] 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