Every paper, by date: page 82

44,644 papers with a page: 24,189 with their authors' code, 4,955 with code on request, 15,495 with data only. The most recent first, 224 a page. Page 82 of 200: 15 April 2025 to 8 April 2025.

Tuesday, 15 April 2025 (44 papers, 8 on this page)

[18145] doi:10.3389/fnagi.2025.1549518 [paper, data]

Decoding immune cell dynamics in ischemic stroke: insights from single-cell RNA sequencing analysis.

Journal: Frontiers in aging neuroscience

Status: data only, 1 dataset cited

[18146] doi:10.3389/fnins.2025.1547010 [paper, repository]

Relations between neurometabolism and clinical biomarkers in patients with metabolic disease.

Journal: Frontiers in neuroscience

Authors' code: IHEP-Brain-Imaging/Spatial-Normalization-of-Brain-PET-Images (GPL-3.0)

Status: code verified, 28 files readable, 2 matches

[18147] doi:10.3758/s13428-025-02653-y [paper, repository]

Silicon Spike: An Arduino-based low-cost and open-access triggerbox to precisely control TMS devices.

Journal: Behavior research methods

Authors' code: Ippolz/SiliconSpike (MIT)

Status: code verified, 5 files readable, 2 matches

[18148] doi:10.7554/elife.100492 [paper, repository]

An anatomical and physiological basis for flexible coincidence detection in the auditory system.

Journal: eLife

Authors' code: modeldb:2018259 (no license)

Status: code verified

[18149] doi:10.7554/elife.101841 [paper, repository]

Neural mechanisms of credit assignment for delayed outcomes during contingent learning.

Journal: eLife

Authors' code: OSF b9m6q (no license)

Status: code verified, 7 files readable

[18150] doi:10.7554/elife.105013 [paper, repository]

Non-allometric expansion and enhanced compartmentalization of Purkinje cell dendrites in the human cerebellum.

Journal: eLife

Authors' code: Zenodo 15066697 (CC-BY-4.0)

Status: code verified, 2 files readable, 4 matches

[18151] doi:10.7554/elife.91150 [paper, repository]

UFMTrack, an Under-Flow Migration Tracker enabling analysis of the entire multi-step immune cell extravasation cascade across the blood-brain barrier in microfluidic devices.

Journal: eLife

Authors' code: neworldemancer/UFMSegm (Apache-2.0), neworldemancer/UFMTrack (Apache-2.0)

Status: code verified, 32 files readable, 3 matches

[18152] doi:10.7717/peerj.19270 [paper, data]

Identification of single nucleotide polymorphisms (SNPs) potentially associated with residual feed intake in Qinchuan beef cattle by hypothalamus and duodenum RNA-Seq data.

Journal: PeerJ

Status: data only, 1 dataset cited

Monday, 14 April 2025 (33 papers)

[18153] doi:10.1002/adma.202418524 [paper, repository]

Flexible 3D Kirigami Probes for In Vitro and In Vivo Neural Applications.

Journal: Advanced materials (Deerfield Beach, Fla.)

Authors' code: jcouto/labcams (GPL-3.0)

Status: code verified, 30 files readable

[18154] doi:10.1007/s12035-025-04900-x [paper, data]

Deregulated mRNA and microRNA Expression Patterns in the Prefrontal Cortex of the BTBR Mouse Model of Autism.

Journal: Molecular neurobiology

Status: data only, 1 dataset cited

[18155] doi:10.1016/j.ebiom.2025.105700 [paper, data]

HMGA1 deficiency: a pathogenic link between tau pathology and insulin resistance.

Journal: EBioMedicine

Status: data only, 1 dataset cited

[18156] doi:10.1016/j.isci.2025.112423 [paper]

Substantia nigra modulates breathing rate via locus coeruleus.

Journal: iScience

Status: code on request

[18157] doi:10.1016/j.nicl.2025.103779 [paper, repository]

Sequential patterning of dynamic brain states distinguish Parkinson's disease patients with mild cognitive impairments.

Journal: NeuroImage. Clinical

Authors' code: kempaaron/seq2pat_notebook (Apache-2.0)

Status: code verified, 3 files readable, 1 match

[18158] doi:10.1016/j.ynirp.2025.100259 [paper, repository]

Deep learning identification of reward-related neural substrates of preadolescent irritability: A novel 3D CNN application for fMRI.

Journal: Neuroimage. Reports

Authors' code: DCAN-Labs/abcd-hcp-pipeline (BSD-3-Clause)

Status: code verified, 8 files readable, 3 matches

[18159] doi:10.1021/acschemneuro.4c00632 [paper, repository]

Multi-Frequency Interpolation X-talk Removal Algorithm: Enabling Combinations of Concurrent Optogenetics and Lock-in Amplification Fiber Photometry via Removal of Optogenetic Stimulation Crosstalk.

Journal: ACS chemical neuroscience

Authors' code: maxbrkstone/mufix (no license)

Status: code verified, 26 files readable, 1 match

[18160] doi:10.1038/s41398-025-03350-2 [paper]

An orexin-sensitive subpopulation of layer 6 neurons regulates cortical excitability and anxiety behaviour.

Journal: Translational psychiatry

Status: code on request

[18161] doi:10.1038/s41467-025-57636-6 [paper, repository]

A genetically informed brain atlas for enhancing brain imaging genomics.

Journal: Nature communications

Authors' code: Zenodo 14549178 (MIT), JingxuanBao/GIANT (MIT)

Status: code verified, 10 files readable, 3 matches

[18162] doi:10.1038/s41467-025-58459-1 [paper, repository]

Relationships between brain activity, tryptophan-related gut metabolites, and autism symptomatology.

Journal: Nature communications

Authors' code: Zenodo 14834325 (apgl-v3), Zenodo 14834337 (apgl-v3), cenec/disgustfmri (AGPL-3.0), cenec/ment_ppi (AGPL-3.0)

Status: code verified, 30 files readable, 2 matches

[18163] doi:10.1038/s41593-025-01928-z [paper, repository]

Hippocampal output suppresses orbitofrontal cortex schema cell formation.

Journal: Nature neuroscience

Authors' code: OSF 78gy4 (no license)

Status: code verified, 367 files readable, 6 matches

[18164] doi:10.1038/s41598-025-97053-9 [paper]

A simplified preparation method for single-nucleus RNA-sequencing using long-term frozen brain tumor tissues.

Journal: Scientific reports

Status: data only

[18165] doi:10.1038/s41598-025-97333-4 [paper, data]

Identification and validation of LY6H and GRM3 as candidate biomarkers for Glioma-related epilepsy.

Journal: Scientific reports

Status: data only, 1 dataset cited

[18166] doi:10.1038/s41598-025-97515-0 [paper, data]

Unveiling the neural network involved in mentally projecting the self through episodic autobiographical memories.

Journal: Scientific reports

Status: data only, 1 dataset cited

[18167] doi:10.1038/s42003-025-08011-0 [paper, repository]

Representational shifts from feedforward to feedback rhythms index phenomenological integration in naturalistic vision.

Journal: Communications biology

Authors' code: OSF xjnrt (no license)

Status: code verified, 5 files readable, 4 matches

[18168] doi:10.1073/pnas.2416106122 [paper, data]

Molecular design of a therapeutic LSD analogue with reduced hallucinogenic potential.

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

Status: data only, 1 dataset cited

[18169] doi:10.1101/2025.04.10.648210 [paper, repository]

Working memory impairments in Neurofibromatosis Type 1 are explained by disrupted functional connectivity and network controllability

Journal: bioRxiv (preprint)

Authors' code: MCLit/NF1-FC (no license)

Status: dead link

[18170] doi:10.1101/2025.04.11.643415 [paper, repository]

PsiConnect: A Multimodal Neuroimaging Study of Psilocybin-Induced Changes in Brain and Behaviour

Journal: bioRxiv (preprint)

Authors' code: razilab (no license), NSBLab/BrainEigenmodes (Apache-2.0)

Status: code verified, 297 files readable, 5 matches

[18171] doi:10.1101/gr.279159.124 [paper, repository]

Assessing DNA methylation detection for primary human tissue using Nanopore sequencing.

Journal: Genome research

Authors' code: nanoporetech/modkit (GPL-3.0), NIH-CARD/CARDlongread_meth_R.9vs10 (no license)

Status: code verified, 142 files readable

[18172] doi:10.1101/gr.279318.124 [paper, data]

Optical genome mapping identifies rare structural variants in neural tube defects.

Journal: Genome research

Status: data only, 1 dataset cited

[18173] doi:10.1101/gr.280060.124 [paper, repository]

Deciphering the largest disease-associated transcript isoforms in the human neural retina with advanced long-read sequencing approaches.

Journal: Genome research

Authors' code: erikdevrieze/USH_retina (GPL-3.0), cmbi/Neural-Retina-Atlas (GPL-3.0)

Status: code verified, 113 files readable, 9 matches

[18174] doi:10.1186/s12888-025-06817-0 [paper, repository]

Classification of schizophrenia spectrum disorder using machine learning and functional connectivity: reconsidering the clinical application.

Journal: BMC psychiatry

Authors' code: lichao312214129/SSD_classification (MIT)

Status: code verified, 47 files readable, 8 matches

[18175] doi:10.1186/s13073-025-01451-7 [paper, repository]

Epigenetic timing effects on child developmental outcomes: a longitudinal meta-regression of findings from the Pregnancy And Childhood Epigenetics Consortium.

Journal: Genome medicine

Authors' code: aneumann-science/epigenetic_timing_effects (GPL-3.0)

Status: code verified, 21 files readable

[18176] doi:10.1371/journal.pcbi.1012303 [paper, repository]

On the validity of electric brain signal predictions based on population firing rates.

Journal: PLoS computational biology

Authors' code: torbjone/kernel_validity_paper (no license)

Status: code verified, 12 files readable, 7 matches

[18177] doi:10.1371/journal.pone.0320360 [paper, repository]

c-Triadem: A constrained, explainable deep learning model to identify novel biomarkers in Alzheimer's disease.

Journal: PloS one

Authors' code: Sherlyn-J/KU-BMED2 (no license)

Status: code verified, 2 files readable, 2 matches

[18178] doi:10.21203/rs.3.rs-4676122/v1 [paper, data]

Dynamic basal ganglia output signals license and suppress forelimb movements

Journal: Research Square (preprint)

Status: data only, 1 dataset cited

[18179] doi:10.3389/fmed.2025.1523535 [paper, data]

Nomogram establishment for gastrointestinal bleeding prediction in ICU patients with traumatic brain injury based on the MIMIC-IV database.

Journal: Frontiers in medicine

Status: data only, 1 dataset cited

[18180] doi:10.3389/fneur.2025.1527434 [paper, data]

Prefrontal cortex activity during binocular color fusion and rivalry: an fNIRS study.

Journal: Frontiers in neurology

Status: data only, 1 dataset cited

[18181] doi:10.3389/fnins.2025.1549163 [paper]

Sound-evoked plasticity differentiates tinnitus from non-tinnitus mice.

Journal: Frontiers in neuroscience

Status: code on request

[18182] doi:10.3390/biomedinformatics5020020 [paper, data]

Strategies to Improve the Robustness and Generalizability of Deep Learning Segmentation and Classification in Neuroimaging.

Journal: BioMedInformatics

Status: data only, 1 dataset cited

[18183] doi:10.3390/brainsci15040396 [paper, repository]

Neurocomputational Mechanisms of Sense of Agency: Literature Review for Integrating Predictive Coding and Adaptive Control in Human-Machine Interfaces.

Journal: Brain sciences

Authors' code: Siagnos/ICRA2025 (no license)

Status: code verified, 4 files readable, 6 matches

[18184] doi:10.7554/elife.100941 [paper, data]

Somatodendritic orientation determines tDCS-induced neuromodulation of Purkinje cell activity in awake mice.

Journal: eLife

Status: data only, 1 dataset cited

[18185] doi:10.7554/elife.105059 [paper, repository]

Food intake enhances hippocampal sharp wave-ripples.

Journal: eLife

Authors' code: figshare 28691093 (CC-BY-4.0)

Status: code verified, 4 files readable, 1 match

Sunday, 13 April 2025 (10 papers)

[18186] doi:10.1002/mc.23922 [paper, data]

Four-gene Prognostic Signature and Risk of Brain Metastasis of Lung Adenocarcinoma.

Journal: Molecular carcinogenesis

Status: data only, 1 dataset cited

[18187] doi:10.1016/j.nicl.2025.103785 [paper, repository]

Tell me why: A scoping review on the fundamental building blocks of fMRI-based network analysis.

Journal: NeuroImage. Clinical

Authors' code: Schrantee-lab/GIN_networks_review (no license)

Status: code verified, 3 files readable, 2 matches

[18188] doi:10.1016/j.nicl.2025.103786 [paper, repository]

Differential patterns of axonal loss associated with threat-related adversity in atypical depression and non-atypical depression.

Journal: NeuroImage. Clinical

Authors' code: pnlbwh/pnlNipype (other)

Status: code verified, 28 files readable, 3 matches

[18189] doi:10.1038/s41467-025-58675-9 [paper, repository]

Multimodal fusion of radio-pathology and proteogenomics identify integrated glioma subtypes with prognostic and therapeutic opportunities.

Journal: Nature communications

Authors' code: Zaoqu-Liu/MOFS (GPL-3.0)

Status: code verified, 79 files readable, 28 matches

[18190] doi:10.1038/s41531-025-00928-x [paper]

Linking Parkinson's disease and melanoma: the impact of copper-driven cuproptosis and related mechanisms.

Journal: NPJ Parkinson's disease

Status: code on request

[18191] doi:10.1038/s41598-025-94677-9 [paper, data]

Hybrid of DSR-GAN and CNN for Alzheimer disease detection based on MRI images.

Journal: Scientific reports

Status: data only, 1 dataset cited

[18192] doi:10.1101/2025.04.11.648398 [paper, repository]

Anterior cingulate cortex mixes retrospective cognitive signals and ongoing movement signatures during decision-making

Journal: bioRxiv (preprint)

Authors' code: churchlandlab/chipmunk (no license), jcouto/fit_psychometric (GPL-3.0), churchlandlab/chiCa (no license), jcouto/labdata-tools (GPL-3.0), jcouto/wfield (GPL-3.0), LukasOesch/Oesch (no license)

Status: code verified, 193 files readable, 15 matches

[18193] doi:10.1155/da/9505414 [paper, repository]

Enhanced Performance Monitoring as a Transdiagnostic Risk Marker of the Anxiety and Obsessive-Compulsive Spectrum: The Role of Disorder Category, Clinical Status, Family Risk, and Anxiety Dimensions.

Journal: Depression and anxiety

Authors' code: OSF 7dcm3 (no license)

Status: code verified, 1 file readable

[18194] doi:10.1186/s13578-025-01389-8 [paper, data]

Dysregulated ac4C modification of mRNA in a mouse model of early-stage Alzheimer's disease.

Journal: Cell & bioscience

Status: data only, 2 datasets cited

[18195] doi:10.7150/thno.107345 [paper, repository]

Shh agonist enhances maturation in homotypic Lgr5-positive inner ear organoids.

Journal: Theranostics

Authors' code: SegataLab/hclust2 (MIT)

Status: code verified, 5 files readable

Saturday, 12 April 2025 (13 papers)

[18196] doi:10.1007/s10633-025-10017-2 [paper, repository]

The ERGtools2 package: a toolset for processing and analysing visual electrophysiology data.

Journal: Documenta ophthalmologica. Advances in ophthalmology

Authors' code: moritzlindner/ERGtools2 (no license)

Status: code verified, 48 files readable, 3 matches

[18197] doi:10.1016/j.gendis.2025.101643 [paper, data]

CCDC86-BHLHE40-ATF3 axis promotes aerobic glycolysis and tumor development in glioma.

Journal: Genes & diseases

Status: data only, 1 dataset cited

[18198] doi:10.1016/j.neuroimage.2025.121215 [paper]

Adults on the autism spectrum differ from neurotypical peers when self-generating but not passively-experiencing somatosensation: a high-density electrophysiological (EEG) mapping and virtual reality study.

Journal: NeuroImage

Status: code on request

[18199] doi:10.1038/s41380-025-02961-x [paper]

Neuroimaging-derived biological brain age and its associations with glial reactivity and synaptic dysfunction cerebrospinal fluid biomarkers.

Journal: Molecular psychiatry

Status: code on request

[18200] doi:10.1038/s41467-025-58708-3 [paper, data]

Myeloid lineage C3 induces reactive gliosis and neuronal stress during CNS inflammation.

Journal: Nature communications

Status: data only, 1 dataset cited

[18201] doi:10.1038/s41467-025-58786-3 [paper, repository]

Hand position fields of neurons in the premotor cortex of macaques during natural reaching.

Journal: Nature communications

Authors' code: caoshenghao/pmd_position_cell (MIT)

Status: code verified, 15 files readable, 2 matches

[18202] doi:10.1038/s41597-025-04967-0 [paper, data]

Simultaneous EEG and fNIRS recordings for semantic decoding of imagined animals and tools.

Journal: Scientific data

Status: data only, 2 datasets cited

[18203] doi:10.1038/s41598-025-85989-x [paper, data]

Neurobiological correlates of personality dimensions in borderline personality disorder using graph analysis of functional connectivity.

Journal: Scientific reports

Status: data only, 1 dataset cited

[18204] doi:10.1038/s41598-025-95759-4 [paper]

Cortico force coherence of the finger and toe with slight rhythmic pressure on force sensors using electroencephalography.

Journal: Scientific reports

Status: code on request

[18205] doi:10.1038/s41598-025-97320-9 [paper, repository]

Trait dissociation is associated with dissociative experiences arising from disrupted multisensory integration.

Journal: Scientific reports

Authors' code: OSF qh543 (no license)

Status: code verified

[18206] doi:10.1093/lifemeta/loaf012 [paper, repository]

Brain-body mitochondrial distribution patterns lack coherence and point to tissue-specific regulatory mechanisms.

Journal: Life metabolism

Authors' code: mitopsychobio (no license)

Status: code verified

[18207] doi:10.1101/2025.04.11.25324538 [paper, repository]

Mitochondrial DNA copy number is associated with cognitive function, cognitive decline, and dementia: a longitudinal study in UK Biobank

Journal: medRxiv (preprint)

Authors' code: n-mounier/Mrlap (GPL-2.0), qlu-lab/SUPERGNOVA (MIT), bulik/ldsc (GPL-3.0)

Status: code verified, 48 files readable, 3 matches

[18208] doi:10.3390/cancers17081303 [paper]

Tertiary Lymphoid Structures Are Associated with Progression-Free Survival of Peripheral Neuroblastic Tumor Patients.

Journal: Cancers

Status: data only

Friday, 11 April 2025 (36 papers)

[18209] doi:10.1002/ijc.35441 [paper, repository]

A strategy for multimodal integration of transcriptomics, proteomics, and radiomics data for the prediction of recurrence in patients with IDH-mutant gliomas.

Journal: International journal of cancer

Authors' code: gitlab.inria.fr/cetchega/transcan_idh-mutant_lgg_radiomics (no license)

Status: code verified, 10 files readable, 5 matches

[18210] doi:10.1016/j.celrep.2025.115526 [paper, repository]

A population representation of the confidence in a decision in the parietal cortex.

Journal: Cell reports

Authors' code: arielzylberberg/LIP_Confidence_CellReports2025 (GPL-3.0)

Status: code verified, 442 files readable, 2 matches

[18211] doi:10.1016/j.celrep.2025.115570 [paper, repository]

Disuse-driven plasticity in the human thalamus and putamen.

Journal: Cell reports

Authors' code: zenodo.com (no license), Zenodo 14975944 (CC-BY-4.0), roscha/subcortical-cast (no license)

Status: code verified

[18212] doi:10.1016/j.crmeth.2025.101024 [paper]

Human MAPT knockin mouse models of frontotemporal dementia for the neurodegenerative research community.

Journal: Cell reports methods

Status: code on request

[18213] doi:10.1016/j.neuroimage.2025.121211 [paper, repository]

Comparison of structural connectomes for modeling deep brain stimulation pathway activation.

Journal: NeuroImage

Authors' code: OSF byhgk (no license)

Status: code verified, 12 files readable, 4 matches

[18214] doi:10.1016/j.neuroimage.2025.121212 [paper, repository]

Quantifying axonal features of human superficial white matter from three-dimensional multibeam serial electron microscopy data assisted by deep learning.

Journal: NeuroImage

Authors' code: NYU-DiffusionMRI/RaW-seg (MIT)

Status: code verified, 11 files readable, 1 match

[18215] doi:10.1016/j.neuroimage.2025.121213 [paper, repository]

Bayesian deconvolution for computational cognitive modeling of fMRI data.

Journal: NeuroImage

Authors' code: jonhowlett/bayesian-deconvolution (no license), Zenodo 15091508 (CC-BY-4.0)

Status: code verified, 8 files readable

[18216] doi:10.1016/j.neuroimage.2025.121214 [paper, repository]

Blending into naturalistic scenes: Cortical regions serving visual search are more strongly activated in congruent contexts.

Journal: NeuroImage

Authors' code: coins.trendscenter.org (no license)

Status: code verified

[18217] doi:10.1016/j.xpro.2025.103764 [paper]

Protocol for extraction and characterization of mouse brain-derived extracellular matrix for neuronal cell culture.

Journal: STAR protocols

Status: code on request

[18218] doi:10.1021/acsomega.5c00535 [paper, data]

Trelagliptin Ameliorates Memory Decline in Diabetic Rats through the AMPK/AKT/GSK-3β Pathway in the Cerebral Cortex.

Journal: ACS omega

Status: data only, 1 dataset cited

[18219] doi:10.1038/s41398-025-03357-9 [paper]

Auditory cortical neurons are recruited to encode fear signals and anxiety by neuroligin-3-mediated synapse formation.

Journal: Translational psychiatry

Status: code on request

[18220] doi:10.1038/s41420-025-02448-2 [paper, data]

Zic3 enables bimodal regulation of tyrosine hydroxylase expression in olfactory bulb and midbrain-derived neurons.

Journal: Cell death discovery

Status: data only, 1 dataset cited

[18221] doi:10.1038/s41467-025-58688-4 [paper, repository]

Brain-wide microstrokes affect the stability of memory circuits in the hippocampus.

Journal: Nature communications

Authors' code: drive.google.com/drive/folders (no license), Zenodo 14906653 (LGPL-2.1), wahl-lab/heiser_brainwidemicrostrokes (LGPL-2.1)

Status: code verified, 23 files readable, 21 matches

[18222] doi:10.1038/s41467-025-58707-4 [paper, repository]

Dynamic categorization rules alter representations in human visual cortex.

Journal: Nature communications

Authors' code: mmhenderson/shapeDim (GPL-3.0)

Status: code verified, 186 files readable, 15 matches

[18223] doi:10.1038/s41467-025-58817-z [paper, repository]

A comprehensive suite for extracting neuron signals across multiple sessions in one-photon calcium imaging.

Journal: Nature communications

Authors' code: doi:10.5061/dryad.crjdfn3ck (no license), CaliAli-PV/CaliAli (GPL-3.0), Zenodo 14934924 (GPL-3.0)

Status: code verified, 1,342 files readable, 11 matches

[18224] doi:10.1038/s41597-025-04822-2 [paper, repository]

A multi-site, multi-modal travelling-heads resource for brain MRI harmonisation.

Journal: Scientific data

Authors' code: spmic-uon/on-harmony_ukbb_pipeline (other), SPMIC-UoN/ON-Harmony (no license)

Status: code verified, 130 files readable, 7 matches

[18225] doi:10.1038/s41598-025-97565-4 [paper, data]

Privacy-preserving federated learning for collaborative medical data mining in multi-institutional settings.

Journal: Scientific reports

Status: data only, 3 datasets cited

[18226] doi:10.1038/s41746-025-01612-3 [paper]

Classification of intracranial pressure epochs using a novel machine learning framework.

Journal: NPJ digital medicine

Status: code on request

[18227] doi:10.1038/s42003-025-07991-3 [paper, repository]

Neural models for detection and classification of brain states and transitions.

Journal: Communications biology

Authors' code: arnaumarin/LFPDeepStates (GPL-3.0), Zenodo 15066751 (GPL-3.0)

Status: code verified, 8 files readable, 9 matches

[18228] doi:10.1038/s42004-025-01504-3 [paper]

A modular click ligand-directed approach to label endogenous dopamine D<sub>1</sub> receptors in live cells.

Journal: Communications chemistry

Status: code on request

[18229] doi:10.1038/s43587-025-00851-z [paper, repository]

Pre-symptomatic Parkinson's disease blood test quantifying repetitive sequence motifs in transfer RNA fragments.

Journal: Nature aging

Authors' code: NimrodMd/PD_motif_codes (no license)

Status: code verified, 25 files readable, 15 matches

[18230] doi:10.1073/pnas.2424521122 [paper, repository]

Global subnational estimates of migration of scientists reveal large disparities in internal and international flows.

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

Authors' code: Zenodo 15047101 (GPL-3.0), Zenodo 15047102 (GPL-3.0), akbaritabar/internal-and-international-migration-of-scientists (GPL-3.0)

Status: code verified, 38 files readable, 8 matches

[18231] doi:10.1101/2025.04.11.648375 [paper, repository]

Reduced occurrence of alpha waves during resting state predicts high ADHD traits in young adults

Journal: bioRxiv (preprint)

Authors' code: OSF yef9z (no license)

Status: empty repository

[18232] doi:10.1126/sciadv.adp8504 [paper, repository]

Astrocytic RNA editing regulates the host immune response to alpha-synuclein.

Journal: Science advances

Authors' code: Zenodo 14242993 (CC-BY-4.0), RHReynolds/RNAseqProcessing (no license), Zenodo 10608267 (CC-BY-4.0), karishdsa/ipscAstrNeurCocul (GPL-3.0), Zenodo 14024385 (CC-BY-4.0), aaronwagen/Astrocytes_editing (other), Zenodo 14164792 (CC-BY-4.0)

Status: code verified, 121 files readable, 17 matches

[18233] doi:10.1126/sciadv.ads5750 [paper, repository]

Distinct transmission sites within a synapse for strengthening and homeostasis.

Journal: Science advances

Authors' code: Zenodo 14450657 (MIT)

Status: code verified, 12 files readable, 6 matches

[18234] doi:10.1128/mra.00841-24 [paper, data]

Draft genome sequences of <i>Salmonella enterica</i> subsp. <i>enterica</i> serovar Give sequence type 516 isolated from blood and brain abscess of a child from North India.

Journal: Microbiology resource announcements

Status: data only, 3 datasets cited

[18235] doi:10.1371/journal.pcbi.1012911 [paper, repository]

Virtual epilepsy patient cohort: Generation and evaluation.

Journal: PLoS computational biology

Authors' code: BalanceKey/virtual_epilepsy_patient_cohort (no license), HuifangWang/VEP_atlas_shared (no license)

Status: code verified, 43 files readable, 21 matches

[18236] doi:10.1371/journal.pcbi.1012969 [paper, repository]

Biases in neural population codes with a few active neurons.

Journal: PLoS computational biology

Authors' code: vrossumlab/bias24 (no license), vanrossumlab/bias24 (no license)

Status: code verified, 7 files readable

[18237] doi:10.1371/journal.pcbi.1012994 [paper, repository]

Dynamic brain connectivity predicts emotional arousal during naturalistic movie-watching.

Journal: PLoS computational biology

Authors' code: hyssong/NarrativeEngagement (no license), jinke828/AffectPrediction (no license)

Status: code verified, 18 files readable, 4 matches

[18238] doi:10.21203/rs.3.rs-5614024/v1 [paper]

Facial Muscle Mapping and Expression Prediction using a Conformal Surface-Electromyography Platform

Journal: Research Square (preprint)

Status: code on request

[18239] doi:10.2176/jns-nmc.2024-0269 [paper, data]

Favorable Response to Conventional Chemoradiotherapy in Radiation-induced Glioma Harboring Coamplification of PDGFRA, KIT, and KDR: A Case Report and Literature Review.

Journal: NMC case report journal

Status: data only, 1 dataset cited

[18240] doi:10.3389/fonc.2025.1512739 [paper, data]

EnSLDe: an enhanced short-range and long-range dependent system for brain tumor classification.

Journal: Frontiers in oncology

Status: data only, 2 datasets cited

[18241] doi:10.3390/ijms26083608 [paper, repository]

Resting-State fMRI and Post-Ischemic Stroke Functional Recovery: Unraveling Causality and Predicting Therapeutic Targets.

Journal: International journal of molecular sciences

Authors' code: chr1swallace/coloc (no license)

Status: code verified, 41 files readable, 3 matches

[18242] doi:10.3758/s13415-025-01289-x [paper, data]

Modulating interhemispheric prefrontal dynamics of aggressive behavior: Sex differences and the association with personal disposition.

Journal: Cognitive, affective & behavioral neuroscience

Status: code on request, 1 dataset cited

[18243] doi:10.7554/elife.95618 [paper, repository]

Diverging roles of TRPV1 and TRPM2 in warm-temperature detection.

Journal: eLife

Authors' code: hummuscience/neuroimgr (Apache-2.0), heidata.uni-heidelberg.de (no license)

Status: code verified, 9 files readable, 1 match

[18244] doi:10.7554/elife.97334 [paper, repository]

Dynamic gamma modulation of hippocampal place cells predominates development of theta sequences.

Journal: eLife

Authors' code: WNunc/Dynamic_gamma_modulation (GPL-3.0)

Status: code verified, 369 files readable, 3 matches

Thursday, 10 April 2025 (35 papers)

[18245] doi:10.1002/advs.202413195 [paper, repository]

FREQ-NESS Reveals the Dynamic Reconfiguration of Frequency-Resolved Brain Networks During Auditory Stimulation.

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

Authors' code: mattiaRosso92/Frequency-resolved_brain_network_estimation_via_source_separation_FREQ-NESS (no license), Zenodo 14939325 (CC-BY-4.0)

Status: code verified, 231 files readable, 13 matches

[18246] doi:10.1016/j.celrep.2025.115546 [paper, repository]

Multi-site investigation of gut microbiota in CDKL5 deficiency disorder mouse models: Targeting dysbiosis to improve neurological outcomes.

Journal: Cell reports

Authors' code: Zenodo 14756355 (CC-BY-4.0), Zenodo 5776770 (CC-BY-4.0), Zenodo 14761357 (GPL-3.0)

Status: code verified, 11 files readable

[18247] doi:10.1016/j.eclinm.2025.103187 [paper]

Qualitative and quantitative educational disparities and brain signatures in healthy aging and dementia across global settings.

Journal: EClinicalMedicine

Status: code on request

[18248] doi:10.1016/j.neuroimage.2025.121190 [paper, repository]

FetDTIAlign: A deep learning framework for affine and deformable registration of fetal brain dMRI.

Journal: NeuroImage

Authors' code: blibli/fetdtialign (GPL-3.0)

Status: code verified, 17 files readable

[18249] doi:10.1016/j.xpro.2025.103756 [paper, repository]

Protocol to predict time perception bias from cortical neurite microstructures in healthy older adults.

Journal: STAR protocols

Authors' code: code.stanford.edu/cbrain/mvpa-regression (no license)

Status: code verified

[18250] doi:10.1038/s41398-025-03347-x [paper, repository]

Blood-brain barrier biomarkers modulate the associations of peripheral immunity with Alzheimer's disease.

Journal: Translational psychiatry

Authors' code: JiaHuiHou666/ADNI_BBB_peripheral-immunity_AD (no license)

Status: empty repository

[18251] doi:10.1038/s41398-025-03355-x [paper, repository]

Prediction of antipsychotic drug efficacy for schizophrenia treatment based on neural features of the resting-state functional connectome.

Journal: Translational psychiatry

Authors' code: nitrc.org/projects/bioimagesuite (no license)

Status: code verified

[18252] doi:10.1038/s41467-025-57119-8 [paper, repository]

Contralesional hippocampal spreading depolarization promotes functional recovery after stroke.

Journal: Nature communications

Authors' code: Zenodo 8303055 (CC-BY-4.0), leomol/spreading-depolarization (no license)

Status: code verified, 28 files readable, 5 matches

[18253] doi:10.1038/s41467-025-58252-0 [paper, data]

Plasma-to-tumour tissue integrated proteomics using nano-omics for biomarker discovery in glioblastoma.

Journal: Nature communications

Status: data only, 1 dataset cited

[18254] doi:10.1038/s41540-025-00499-w [paper]

A mechanism for the emergence of low-dimensional structures in brain dynamics.

Journal: NPJ systems biology and applications

Status: code on request

[18255] doi:10.1038/s41556-025-01641-w [paper, data]

Multipotent neural stem cells originating from neuroepithelium exist outside the mouse central nervous system.

Journal: Nature cell biology

Status: data only, 1 dataset cited

[18256] doi:10.1038/s41597-025-04926-9 [paper, repository]

A dataset of synthetic, maturation-informed magnetic resonance images of the human fetal brain.

Journal: Scientific data

Authors' code: Zenodo 10170034 (BSD-3-Clause), Zenodo 10171333 (BSD-3-Clause), Zenodo 4392788 (BSD-3-Clause), medical-image-analysis-laboratory/fabian (BSD-3-Clause), medical-image-analysis-laboratory/mialsuperresolutiontoolkit (BSD-3-Clause)

Status: code verified, 307 files readable, 12 matches

[18257] doi:10.1038/s41598-025-86709-1 [paper]

Optimized driver fatigue detection method using multimodal neural networks.

Journal: Scientific reports

Status: code on request

[18258] doi:10.1038/s41598-025-95496-8 [paper, data]

The spatial transcriptome of the late-stage embryonic and postnatal mouse brain reveals spatiotemporal molecular markers.

Journal: Scientific reports

Status: data only, 1 dataset cited

[18259] doi:10.1038/s41598-025-96884-w [paper, data]

Transcriptome signatures of human neural stem cells derived from LRRK2 gene therapeutic cells.

Journal: Scientific reports

Status: data only, 1 dataset cited

[18260] doi:10.1038/s43856-025-00811-z [paper, repository]

Respiratory modulations of cortical excitability and interictal spike timing in focal epilepsy: a case report.

Journal: Communications medicine

Authors' code: OSF z4xgp (no license)

Status: code verified, 4 files readable, 7 matches

[18261] doi:10.1073/pnas.2410698122 [paper, data]

Inactivation of microglial LXRβ in early postnatal mice impairs microglia homeostasis and causes long-lasting cognitive dysfunction.

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

Status: data only, 1 dataset cited

[18262] doi:10.1073/pnas.2417400122 [paper, data]

Astrocytic Ryk signaling coordinates scarring and wound healing after spinal cord injury.

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

Status: data only, 1 dataset cited

[18263] doi:10.1088/1741-2552/adb180 [paper, repository]

Multi-gesture drag-and-drop decoding in a 2D iBCI control task.

Journal: Journal of neural engineering

Authors' code: jgusman/drag-and-drop (other)

Status: code verified, 72 files readable, 11 matches

[18264] doi:10.1101/2025.04.08.25325384 [paper, repository]

The genetic landscape of heterogeneity in human functional brain connectivity

Journal: medRxiv (preprint)

Authors' code: dutchconnectomelab.nl/cato (no license), fuma.ctglab.nl (no license), ctg.cncr.nl/software/magma (no license), bulik/ldsc (GPL-3.0), cog-genomics.org/plink (no license), gabraham/flashpca (GPL-3.0), Marijn-Schipper/FLAMES (MIT), christianbenner.com (no license)

Status: code verified, 86 files readable, 3 matches

[18265] doi:10.1101/2025.04.08.647770 [paper, repository]

VP-CLEM-Kit: An accessible pipeline for visual proteomics using super resolution volume correlative light and electron microscopy (SR-vCLEM)

Journal: bioRxiv (preprint)

Authors' code: Zenodo 13151252 (BSD-3-Clause), Zenodo 3773450 (other-open), Zenodo 15029515 (BSD-3-Clause), multiview-stitcher/multiview-stitcher (BSD-3-Clause), napari/napari (BSD-3-Clause), zarr-developers/zarr-python (MIT)

Status: code verified, 2,593 files readable, 2 matches

[18266] doi:10.1101/2025.04.09.25325556 [paper, repository]

Examining the relationship between plasma pTau181 and cognitive decline, structural brain integrity, and biological ageing in midlife

Journal: medRxiv (preprint)

Authors' code: danbelsky/DunedinPACE (GPL-3.0)

Status: code verified, 7 files readable

[18267] doi:10.1101/2025.04.10.648162 [paper, repository]

A conserved differentiation program facilitates inhibitory neuron production in the developing mouse and human cerebellum

Journal: bioRxiv (preprint)

Authors' code: AHBrand-Lab/DamID_scripts (no license), BayinLab/Christensen_et_al_2025 (MIT)

Status: code verified, 21 files readable, 12 matches

[18268] doi:10.1162/imag_a_00534 [paper, data]

Novel insights into vascular dysfunction in cuprizone-induced demyelination through functional ultrasound imaging.

Journal: Imaging neuroscience (Cambridge, Mass.)

Status: data only, 1 dataset cited

[18269] doi:10.1186/s12885-025-13979-3 [paper, repository]

Investigating potential drug targets for the treatment of glioblastoma: a Mendelian randomization study.

Journal: BMC cancer

Authors' code: MRCIEU/TwoSampleMR (other)

Status: code verified, 73 files readable, 4 matches

[18270] doi:10.1242/dev.204347 [paper, data]

Insulin-like growth factor 2 as a driving force for exponential expansion and differentiation of the neonatal thymus.

Journal: Development (Cambridge, England)

Status: data only, 1 dataset cited

[18271] doi:10.1242/jeb.250015 [paper, repository]

Context-dependent coordination of movement in Tribolium castaneum larvae.

Journal: The Journal of experimental biology

Authors' code: Zenodo 11520087 (CC-BY-4.0)

Status: code verified

[18272] doi:10.1371/journal.pbio.3002499 [paper, repository]

Modulation of NMDA receptor signaling and zinc chelation prevent seizure-like events in a zebrafish model of SLC13A5 epilepsy.

Journal: PLoS biology

Authors' code: Zenodo 14853182 (CC-BY-4.0), ankita86/bulkrnaseq_kurrasch_lab (no license)

Status: code verified, 8 files readable, 7 matches

[18273] doi:10.1371/journal.pbio.3002688 [paper, repository]

Top-down and bottom-up interactions rely on nested brain oscillations to shape rhythmic visual attention sampling.

Journal: PLoS biology

Authors' code: Zenodo 14836618 (CC-BY-4.0), jelenatrajkovic-hub/brain-interactions-rely-on-nested-brain-oscillations. (no license)

Status: code verified, 8 files readable, 4 matches

[18274] doi:10.1371/journal.pbio.3003099 [paper, repository]

MSP-tracker: A versatile vesicle tracking software tool used to reveal the spatial control of polarized secretion in Drosophila epithelial cells.

Journal: PLoS biology

Authors' code: gurdon-institute/egg_chamber_analysis (GPL-3.0)

Status: code verified, 3 files readable

[18275] doi:10.1371/journal.pcbi.1012926 [paper, repository]

A comprehensive investigation of intracortical and corticothalamic models of the alpha rhythm.

Journal: PLoS computational biology

Authors' code: GriffithsLab/Bastiaens2025_AlphaModels (MIT)

Status: code verified, 31 files readable, 5 matches

[18276] doi:10.1371/journal.pgen.1011658 [paper, repository]

Exploring the molecular basis of the genetic correlation between body mass index and brain morphological traits.

Journal: PLoS genetics

Authors' code: bulik/ldsc (GPL-3.0)

Status: code verified, 27 files readable, 1 match

[18277] doi:10.1371/journal.pntd.0013002 [paper, data]

Correlation of serum screening and neuroimaging studies: A comparative analysis for diagnostic evaluation of neurocysticercosis among people with epilepsy attending mental health clinics in selected district hospitals of Tanzania.

Journal: PLoS neglected tropical diseases

Status: data only, 1 dataset cited

[18278] doi:10.1371/journal.pone.0319936 [paper, repository]

Novel brain biomarkers of obesity in young adult women based on statistical measurements of white matter tracts.

Journal: PloS one

Authors' code: mathworks.com/matlabcentral/fileexchange (no license)

Status: code verified

[18279] doi:10.3390/ijms26083569 [paper]

An Improved SHANEL Procedure for Clearing and Staining Brain Tissue from Multiple Species.

Journal: International journal of molecular sciences

Status: code on request

Wednesday, 9 April 2025 (58 papers)

[18280] doi:10.1002/mds.30192 [paper, repository]

Repeat Expansions with Small TTTCA Insertions in MARCHF6 Cause Familial Myoclonus without Epilepsy.

Journal: Movement disorders : official journal of the Movement Disorder Society

Authors' code: kilpert/FAME3_analyses (no license)

Status: code verified, 13 files readable

[18281] doi:10.1016/j.celrep.2025.115439 [paper]

Activity-dependent synthesis of Emerin gates neuronal plasticity by regulating proteostasis.

Journal: Cell reports

Status: code on request

[18282] doi:10.1016/j.isci.2025.112399 [paper, repository]

Burst firing optimizes invariant coding of natural communication signals by electrosensory neural populations.

Journal: iScience

Authors' code: aminakhshi/burst_invariance (CC-BY-4.0), aminakhshi/spc_optim (CC-BY-4.0), Zenodo 7370358 (other-open), lmfit/lmfit-py (BSD-3-Clause)

Status: code verified, 232 files readable, 7 matches

[18283] doi:10.1016/j.jpha.2025.101295 [paper, repository]

Perturbation response scanning of drug-target networks: Drug repurposing for multiple sclerosis.

Journal: Journal of pharmaceutical analysis

Authors' code: CSB-SUDA/DTNPerturbome (MIT)

Status: code verified, 20 files readable, 6 matches

[18284] doi:10.1016/j.media.2025.103570 [paper, repository]

Integrated brain connectivity analysis with fMRI, DTI, and sMRI powered by interpretable graph neural networks.

Journal: Medical image analysis

Authors' code: GQ93/IBrainGNN_fMRI_DTI_sMRI (MIT)

Status: code verified, 26 files readable, 7 matches

[18285] doi:10.1038/s41398-025-03258-x [paper]

Layer-specific input to medial prefrontal cortex is linked to stress susceptibility.

Journal: Translational psychiatry

Status: code on request

[18286] doi:10.1038/s41398-025-03352-0 [paper]

Ready for translation: non-invasive auricular vagus nerve stimulation inhibits psychophysiological indices of stimulus-specific fear and facilitates responding to repeated exposure in phobic individuals.

Journal: Translational psychiatry

Status: code on request

[18287] doi:10.1038/s41467-025-57339-y [paper, repository]

Cell type-specific multi-omics analysis of cocaine use disorder in the human caudate nucleus.

Journal: Nature communications

Authors' code: lzillich/CN_multiome_cocaine (MIT), Zenodo 14615181 (MIT)

Status: code verified, 60 files readable, 22 matches

[18288] doi:10.1038/s41467-025-58276-6 [paper, repository]

Coding schemes in neural networks learning classification tasks.

Journal: Nature communications

Authors' code: figshare 26539129 (CC-BY-4.0)

Status: code verified

[18289] doi:10.1038/s41467-025-58585-w [paper, repository]

GRAMD1B is a regulator of lipid homeostasis, autophagic flux and phosphorylated tau.

Journal: Nature communications

Authors' code: eturkes/acosta-organoid-scRNAseq (GPL-3.0), Zenodo 15084587 (GPL-3.0)

Status: code verified, 70 files readable, 5 matches

[18290] doi:10.1038/s41467-025-58618-4 [paper, data]

Mutant huntingtin induces neuronal apoptosis via derepressing the non-canonical poly(A) polymerase PAPD5.

Journal: Nature communications

Status: code on request, 1 dataset cited

[18291] doi:10.1038/s41467-025-58620-w [paper, repository]

Natural language processing models reveal neural dynamics of human conversation.

Journal: Nature communications

Authors' code: Zenodo 14697221 (bsd-4-clause), jill620/sEEG_conversation (no license), nilearn/nilearn (BSD-3-Clause)

Status: code verified, 943 files readable, 7 matches

[18292] doi:10.1038/s41467-025-58667-9 [paper, repository]

Dual parallel stream-specific and generalized effects of corticogeniculate feedback on LGN neurons in primate and carnivore.

Journal: Nature communications

Authors' code: BriggsNeuro/Tuning-and-opto (no license)

Status: code verified, 11 files readable, 3 matches

[18293] doi:10.1038/s41467-025-58698-2 [paper, repository]

Multiplexed subspaces route neural activity across brain-wide networks.

Journal: Nature communications

Authors' code: petersaj/AP_histology (GPL-3.0), buschman-lab/MultiplexedSubspaces (no license), Zenodo 14721950 (CC-BY-4.0)

Status: code verified, 135 files readable, 2 matches

[18294] doi:10.1038/s41467-025-58763-w [paper, repository]

An unsupervised map of excitatory neuron dendritic morphology in the mouse visual cortex.

Journal: Nature communications

Authors' code: eckerlab.org/code/weis2021b (no license), eckerlab.org/code/weis2024 (no license)

Status: code verified

[18295] doi:10.1038/s41467-025-58781-8 [paper, repository]

Spike-phase coupling of subthalamic neurons to posterior perisylvian cortex predicts speech sound accuracy.

Journal: Nature communications

Authors' code: Brain-Modulation-Lab/Lead_MER (no license), Brain-Modulation-Lab/SpeechCodingApp (no license), Brain-Modulation-Lab/bml (no license), Brain-Modulation-Lab/code_SPC_ECoG_STN_Speech (MIT), Zenodo 12610957 (CC-BY-4.0)

Status: code verified, 354 files readable, 17 matches

[18296] doi:10.1038/s41556-025-01648-3 [paper, repository]

Nuclear pores safeguard the integrity of the nuclear envelope.

Journal: Nature cell biology

Authors' code: Zenodo 5921012 (other-open), turonova/novasta (GPL-3.0)

Status: code verified, 100 files readable, 1 match

[18297] doi:10.1038/s41586-024-07765-7 [paper, repository]

Perisomatic ultrastructure efficiently classifies cells in mouse cortex.

Journal: Nature

Authors' code: AllenInstitute/Guidebook (no license), AllenInstitute/Perisomatic_Based_CellTyping (no license), AllenInstitute/Extract_Somatic_Features (MIT), AllenInstitute/featureExtractionParty (BSD-2-Clause), AllenInstitute/pss_extraction_pipeline (BSD-2-Clause)

Status: code verified, 120 files readable, 14 matches

[18298] doi:10.1038/s41586-024-07780-8 [paper, repository]

Inhibitory specificity from a connectomic census of mouse visual cortex.

Journal: Nature

Authors' code: AllenInstitute/render-modules (BSD-2-Clause), AllenInstitute/Guidebook (no license), Zenodo 7641780 (cc-by-3.0-us), AllenInstitute/ColumnCensusCSM (BSD-3-Clause), seung-lab/CAVEclient (MIT), Zenodo 3710398 (Apache-2.0), sdorkenw/meshparty (Apache-2.0)

Status: code verified, 241 files readable, 14 matches

[18299] doi:10.1038/s41586-025-08660-5 [paper, repository]

NEURD offers automated proofreading and feature extraction for connectomics.

Journal: Nature

Authors' code: reimerlab/NEURD (no license), sdorkenw/MeshParty (Apache-2.0)

Status: code verified, 171 files readable, 2 matches

[18300] doi:10.1038/s41586-025-08790-w [paper, repository]

Functional connectomics spanning multiple areas of mouse visual cortex.

Journal: Nature

Authors' code: seung-lab/cloud-volume (BSD-3-Clause), cajal/pipeline (LGPL-3.0), AllenInstitute/render-modules (BSD-2-Clause), saalfeldlab/render (GPL-2.0), AllenInstitute/asap-modules (BSD-2-Clause), AllenInstitute/Guidebook (no license), seung-lab/neuroglancer (Apache-2.0), AllenInstitute/MicronsFunctionalConnectomics (BSD-3-Clause), CAVEconnectome (no license), Zenodo 5671443 (other-open)

Status: code verified, 2,219 files readable, 17 matches

[18301] doi:10.1038/s41586-025-08805-6 [paper, repository]

Connectomics of predicted Sst transcriptomic types in mouse visual cortex.

Journal: Nature

Authors' code: AllenInstitute/skeleton_keys (BSD-2-Clause), alleninstitute/scrattch.hicat (BSD-2-Clause), AllenInstitute/EM_MC_paper_figures (BSD-2-Clause), seung-lab/CAVEclient (MIT), CAVEconnectome/MeshParty (Apache-2.0)

Status: code verified, 187 files readable, 15 matches

[18302] doi:10.1038/s41586-025-08807-4 [paper, data]

Stress dynamically modulates neuronal autophagy to gate depression onset.

Journal: Nature

Status: data only, 1 dataset cited

[18303] doi:10.1038/s41586-025-08808-3 [paper, repository]

Human assembloid model of the ascending neural sensory pathway.

Journal: Nature

Authors' code: linnarsson-lab/developing-human-brain (BSD-2-Clause), Zenodo 13921410 (CC-BY-4.0), Zenodo 13921409 (CC-BY-4.0)

Status: code verified, 21 files readable, 2 matches

[18304] doi:10.1038/s41586-025-08829-y [paper, repository]

Foundation model of neural activity predicts response to new stimulus types.

Journal: Nature

Authors' code: cajal/fnn (MIT), cajal/foundation (LGPL-2.1), cajal/pipeline (LGPL-3.0)

Status: code verified, 736 files readable, 11 matches

[18305] doi:10.1038/s41586-025-08840-3 [paper, repository]

Functional connectomics reveals general wiring rule in mouse visual cortex.

Journal: Nature

Authors' code: cajal/pipeline (LGPL-3.0), seung-lab/neuroglancer (Apache-2.0), cajal/microns-funconn-2025 (MIT), Zenodo 7703278 (other-open), alleninstitute/pcg_skel (MIT)

Status: code verified, 1,168 files readable, 7 matches

[18306] doi:10.1038/s41586-025-08868-5 [paper, repository]

Goal-specific hippocampal inhibition gates learning.

Journal: Nature

Authors' code: singerlabgt/Inhibitory_Gating_Project (MIT)

Status: code verified, 114 files readable, 30 matches

[18307] doi:10.1038/s41592-024-02426-z [paper, repository]

CAVE: Connectome Annotation Versioning Engine.

Journal: Nature methods

Authors' code: seung-lab/zmesh (GPL-3.0), seung-lab/DracoPy (Apache-2.0), caveconnectome (no license), hub.docker.com/repositories/caveconnectome (no license), CAVEconnectome/CAVEpaper (MIT)

Status: code verified, 46 files readable, 1 match

[18308] doi:10.1038/s42003-025-07879-2 [paper, repository]

Plasticity in inhibitory networks improves pattern separation in early olfactory processing.

Journal: Communications biology

Authors' code: OSF 45tay (no license), bazhlab-ucsd/honeybee-learning (no license)

Status: code verified, 25 files readable, 2 matches

[18309] doi:10.1038/s44318-025-00427-y [paper, data]

Temporal refinement of Dach1 expression contributes to the development of somatosensory neurons.

Journal: The EMBO journal

Status: data only, 2 datasets cited

[18310] doi:10.1089/neu.2024.0421 [paper]

Contribution of Extracranial Injuries to GOSE Scores after Traumatic Brain Injury TBI: A TRACK-Traumatic Brain Injury Study.

Journal: Journal of neurotrauma

Status: code on request

[18311] doi:10.1098/rspb.2024.2566 [paper, repository]

Respiration shapes response speed and accuracy with a systematic time lag.

Journal: Proceedings. Biological sciences

Authors' code: doi:10.6084/m9.figshare.c.7741094 (no license)

Status: code found, still to be checked

[18312] doi:10.1101/2025.04.05.647340 [paper, repository]

A High-Precision Timing Method and Digital Interface for Closed-Loop TMS

Journal: bioRxiv (preprint)

Authors' code: Zenodo 14198232 (CC-BY-4.0)

Status: code verified, 4 files readable

[18313] doi:10.1101/2025.04.05.647342 [paper, repository]

NeuroSimo: an open-source software for closed-loop EEG- or EMG-guided TMS

Journal: bioRxiv (preprint)

Authors' code: neurosimo/neurosimo (GPL-3.0), Zenodo 14398633 (CC-BY-4.0), pybind/pybind11 (BSD-3-Clause), RobotWebTools/rosbridge_suite (BSD-3-Clause)

Status: code verified, 650 files readable, 1 match

[18314] doi:10.1101/2025.04.09.647733 [paper, repository]

MonoAlg3D: Enabling Cardiac Electrophysiology Digital Twins with an Efficient Open Source Scalable Solver on GPU Clusters

Journal: bioRxiv (preprint)

Authors' code: rsachetto/MonoAlg3D_C (MIT)

Status: code verified, 560 files readable, 4 matches

[18315] doi:10.1111/epi.18402 [paper, repository]

Surgical targeting of lateralized <sup>18</sup>F-fluorodeoxyglucose positron emission tomography hypometabolism relates to long-term epilepsy surgery outcomes.

Journal: Epilepsia

Authors' code: vmorgan-lab/pet-drs (MIT), aimn.it/brain-fdg (no license)

Status: code verified, 3 files readable, 2 matches

[18316] doi:10.1117/1.nph.12.2.025007 [paper, repository]

Beneath the surface: revealing deep-tissue blood flow in human subjects with massively parallelized diffuse correlation spectroscopy.

Journal: Neurophotonics

Authors' code: wumelissa/scatterBrains (BSD-2-Clause), OSF tj2wv (no license)

Status: code verified, 34 files readable, 4 matches

[18317] doi:10.1126/sciadv.adr8015 [paper, repository]

Neural mechanisms of resource allocation in working memory.

Journal: Science advances

Authors' code: doi:10.5061/dryad.0zpc8676x (no license), clayspacelab/wmPriority_shared (no license), Zenodo 15133656 (MIT)

Status: code verified, 22 files readable, 10 matches

[18318] doi:10.1126/sciadv.ads9150 [paper, repository]

MyoGestic: EMG interfacing framework for decoding multiple spared motor dimensions in individuals with neural lesions.

Journal: Science advances

Authors' code: nsquaredlab/myogestic (GPL-3.0), Zenodo 14020173 (CC-BY-4.0), Zenodo 15700021 (GPL-3.0)

Status: code verified, 264 files readable, 2 matches

[18319] doi:10.1126/sciadv.adt9693 [paper, repository]

Computer vision-guided rapid and precise automated cranial microsurgeries in mice.

Journal: Science advances

Authors' code: Zenodo 14596992 (CC-BY-4.0), bsbrl/cv-craniobot (no license)

Status: code verified, 13 files readable, 4 matches

[18320] doi:10.1159/000545692 [paper, data]

Clinical and Neurophysiological Effects of Robotically Delivered fMRI-Guided Personalized Transcranial Magnetic Stimulation Therapy for Depression.

Journal: Psychotherapy and psychosomatics

Status: data only, 1 dataset cited

[18321] doi:10.1162/imag_a_00529 [paper]

Neural emotion regulation during pregnancy: An fMRI study investigating a transdiagnostic mental health factor in healthy first-time pregnant women.

Journal: Imaging neuroscience (Cambridge, Mass.)

Status: code on request

[18322] doi:10.1162/imag_a_00537 [paper, repository]

Streamline tractography of the fetal brain in utero with machine learning.

Journal: Imaging neuroscience (Cambridge, Mass.)

Authors' code: liuweide01/MLFT (no license)

Status: code verified, 6 files readable, 1 match

[18323] doi:10.1186/s12889-025-22407-x [paper, repository]

Consumption of folic acid fortified foods among Hispanic women of reproductive age in the US: a systematic review.

Journal: BMC public health

Authors' code: OSF 7tx3a (no license)

Status: empty repository

[18324] doi:10.1371/journal.pcbi.1012918 [paper, repository]

Multiple patterns of persistent inward currents with multiple types of repetitive firings in medullary serotonergic neurons of mice: An experimental and modeling study.

Journal: PLoS computational biology

Authors' code: Cheng-ECNU/5-HT-model-PIC (GPL-3.0)

Status: code verified, 38 files readable

[18325] doi:10.1371/journal.pgen.1011407 [paper, repository]

Genetic risk for neurodegenerative conditions is linked to disease-specific microglial pathways.

Journal: PLoS genetics

Authors' code: aydanasg/cell_hmagma (no license)

Status: code verified, 16 files readable, 8 matches

[18326] doi:10.1371/journal.pone.0319519 [paper, data]

Machine learning approach for the prediction of 30-day mortality in patients with sepsis-associated delirium.

Journal: PloS one

Status: data only, 1 dataset cited

[18327] doi:10.1523/jneurosci.1846-24.2025 [paper, repository]

Rapid and Stimulus-Specific Deviance Detection in the Human Inferior Colliculus.

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

Authors' code: doi:10.12751/g-node.8vqj6h (no license)

Status: code verified

[18328] doi:10.1523/jneurosci.1978-24.2025 [paper, repository]

Hippocampal Place Cell Sequences Are Impaired in a Rat Model of Fragile X Syndrome.

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

Authors' code: mmdonahue/FMR1CircTrack_PublicShare (no license)

Status: code verified, 52 files readable, 20 matches

[18329] doi:10.1523/jneurosci.2269-24.2025 [paper, repository]

Response of Neuronal Populations to Phase-Locked Stimulation: Model-Based Predictions and Validation.

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

Authors' code: Bogacz-Group (no license)

Status: code verified

[18330] doi:10.3389/fbinf.2025.1532981 [paper, data]

Transcripts derived from AmnSINE1 repetitive sequences are depleted in the cortex of autism spectrum disorder patients.

Journal: Frontiers in bioinformatics

Status: data only, 1 dataset cited

[18331] doi:10.3389/fgene.2025.1533900 [paper, repository]

An <i>in vivo</i> systemic massively parallel platform for deciphering animal tissue-specific regulatory function.

Journal: Frontiers in genetics

Authors' code: pfenninglab/sysMPRA (no license), Zenodo 7527429 (other-open), pfenninglab/gmpra (no license)

Status: code verified, 39 files readable, 4 matches

[18332] doi:10.3389/fnhum.2025.1560558 [paper, data]

Neural speech tracking in a virtual acoustic environment: audio-visual benefit for unscripted continuous speech.

Journal: Frontiers in human neuroscience

Status: data only, 1 dataset cited

[18333] doi:10.3389/fninf.2025.1559335 [paper, data]

Recognition of MI-EEG signals using extended-LSR-based inductive transfer learning.

Journal: Frontiers in neuroinformatics

Status: data only, 1 dataset cited

[18334] doi:10.3389/fnins.2025.1542957 [paper, repository]

Age-related white matter alterations in children with neurofibromatosis type 1: a diffusion MRI tractography study.

Journal: Frontiers in neuroscience

Authors' code: vistalab/vistasoft (no license)

Status: code verified, 2,000 files readable, 1 match

[18335] doi:10.3389/fnins.2025.1572463 [paper, data]

Altered integrated and segregated states in cocaine use disorder.

Journal: Frontiers in neuroscience

Status: data only, 1 dataset cited

[18336] doi:10.3390/bios15040240 [paper]

Intra- and Inter-Regional Complexity in Multi-Channel Awake EEG Through Multivariate Multiscale Dispersion Entropy for Assessing Sleep Quality and Aging.

Journal: Biosensors

Status: code on request

[18337] doi:10.3390/ijms26083544 [paper, data]

Extracellular Competing Endogenous RNA Networks Reveal Key Regulators of Early Amyloid Pathology Propagation in Alzheimer's Disease.

Journal: International journal of molecular sciences

Status: data only, 2 datasets cited

Tuesday, 8 April 2025 (35 papers, 31 on this page)

[18338] doi:10.1007/s11357-025-01639-0 [paper, data]

Bilingualism and "brain reserve" in subregions of the hippocampal formation.

Journal: GeroScience

Status: data only, 1 dataset cited

[18339] doi:10.1016/j.celrep.2025.115556 [paper]

The dorsal column nuclei scale mechanical sensitivity in naive and neuropathic pain states.

Journal: Cell reports

Status: code on request

[18340] doi:10.1016/j.isci.2025.112380 [paper, data]

RNA splicing modulator for Huntington's disease treatment induces peripheral neuropathy.

Journal: iScience

Status: code on request, 2 datasets cited

[18341] doi:10.1016/j.isci.2025.112385 [paper]

Endosomal protein DENND10 promotes developmental competence of neurite extension.

Journal: iScience

Status: code on request

[18342] doi:10.1016/j.isci.2025.112386 [paper]

Ligand preference of EphB2 receptor is selectively regulated by N-glycosylation.

Journal: iScience

Status: code on request

[18343] doi:10.1016/j.isci.2025.112390 [paper, repository]

Agent-based modeling of neuronal mitochondrial dynamics using intrinsic variables of individual mitochondria.

Journal: iScience

Authors' code: sanderson-lab/MiDyS-agent-model (no license)

Status: empty repository, 1 file readable

[18344] doi:10.1016/j.xhgg.2025.100435 [paper]

Allele-specific silencing of a dominant SETX mutation in familial amyotrophic lateral sclerosis type 4.

Journal: HGG advances

Status: code on request

[18345] doi:10.1016/j.xpro.2025.103738 [paper, repository]

Protocol to analyze deep-learning-predicted functional scores for noncoding de novo variants and their correlation with complex brain traits.

Journal: STAR protocols

Authors' code: google-deepmind/deepmind-research (Apache-2.0), MortonLabBCH/brain-ncdnv-chd (MIT), Zenodo 14934079 (MIT)

Status: code verified, 556 files readable, 4 matches

[18346] doi:10.1038/s41467-025-58535-6 [paper, data]

Transcriptomic and morphologic vascular aberrations underlying FCDIIb etiology.

Journal: Nature communications

Status: data only, 1 dataset cited

[18347] doi:10.1038/s41467-025-58614-8 [paper, repository]

Single-nucleus and spatial transcriptomics identify brain landscape of gene regulatory networks associated with behavioral maturation in honeybees.

Journal: Nature communications

Authors' code: BGIResearch/SAW (GPL-3.0), aertslab/create_cisTarget_databases (no license), mumu8910/snRNA_NF (no license), Zenodo 14909482 (CC-BY-4.0)

Status: code verified, 65 files readable, 11 matches

[18348] doi:10.1038/s41467-025-58661-1 [paper, repository]

Discrete photoentrainment of mammalian central clock is regulated by bi-stable dynamic network in the suprachiasmatic nucleus.

Journal: Nature communications

Authors' code: chenwunci/motion_correction_2D (no license)

Status: code verified, 7 files readable

[18349] doi:10.1038/s41597-025-04861-9 [paper, repository]

Dataset combining EEG, eye-tracking, and high-speed video for ocular activity analysis across BCI paradigms.

Journal: Scientific data

Authors' code: QinXinlan/EEG-experiment-to-understand-differences-in-blinking (no license), NeuroTechX/moabb (BSD-3-Clause)

Status: code verified, 318 files readable, 22 matches

[18350] doi:10.1038/s41598-025-96355-2 [paper]

Identifying the human olfactory and chemosignaling neural networks using event related fMRI and graph theory.

Journal: Scientific reports

Status: code on request

[18351] doi:10.1038/s41598-025-96537-y [paper, repository]

Neurophysiological evidence for emotional attention modulation depending on goal relevance.

Journal: Scientific reports

Authors' code: OSF sjyw5 (no license)

Status: code found, still to be checked

[18352] doi:10.1038/s44324-025-00056-3 [paper, repository]

Ultra-processed food consumption affects structural integrity of feeding-related brain regions independent of and via adiposity.

Journal: npj metabolic health and disease

Authors' code: HoumanAzizi/UKB_DTI_Pipeline (no license), FilipMorys/UPF_study (no license)

Status: code verified, 12 files readable, 10 matches

[18353] doi:10.1039/d4bm01051e [paper, data]

Development of a VEGF-activated scaffold with enhanced angiogenic and neurogenic properties for chronic wound healing applications.

Journal: Biomaterials science

Status: data only, 1 dataset cited

[18354] doi:10.1073/pnas.2416423122 [paper, repository]

Cortical scaling of the neonatal brain in typical and altered development.

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

Authors' code: supp:PMC12012530/pnas.2416423122.sd02.r (no license)

Status: code verified, 1 file readable

[18355] doi:10.1073/pnas.2419449122 [paper, data]

Structural and functional characterization of the brain-specific dynamin superfamily member RNF112.

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

Status: data only, 4 datasets cited

[18356] doi:10.1073/pnas.2422331122 [paper, data]

Multiplexing of cognitive encoding by oculomotor networks leads to incidental gaze shifts.

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

Status: data only, 1 dataset cited

[18357] doi:10.1073/pnas.2426180122 [paper, data]

The fruit fly, <i>Drosophila melanogaster</i>, as a microrobotics platform.

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

Status: data only, 1 dataset cited

[18358] doi:10.1097/ee9.0000000000000379 [paper, repository]

Associations of prenatal exposure to residential greenspace and active living environments with cerebral palsy: A population-based cohort study in Ontario, Canada.

Journal: Environmental epidemiology (Philadelphia, Pa.)

Authors' code: ices.on.ca (no license)

Status: code verified

[18359] doi:10.1117/1.nph.12.2.025006 [paper, repository]

Co-localized optode-electrode design for multimodal functional near infrared spectroscopy and electroencephalography.

Journal: Neurophotonics

Authors' code: dejar14/Co-location-Method-fNIRS-EEG- (no license)

Status: code verified, 18 files readable, 3 matches

[18360] doi:10.1162/imag_a_00525 [paper, repository]

Alignment of auditory artificial networks with massive individual fMRI brain data leads to generalisable improvements in brain encoding and downstream tasks.

Journal: Imaging neuroscience (Cambridge, Mass.)

Authors' code: SIMEXP/load_confounds (MIT), brain-bzh/cNeuromod_encoding_2020 (no license), smallflyingpig/SoundNet_Pytorch (MIT)

Status: code verified, 123 files readable, 10 matches

[18361] doi:10.1162/imag_a_00532 [paper, repository]

Characterizing BOLD activation patterns in the human hippocampus with laminar fMRI.

Journal: Imaging neuroscience (Cambridge, Mass.)

Authors' code: viktor-pfaffenrot/hippocampus_laminarfMRI_code (no license)

Status: code verified, 71 files readable, 16 matches

[18362] doi:10.1162/imag_a_00536 [paper, repository]

Quantitative mapping of cerebrovascular reactivity amplitude and delay with breath-hold BOLD fMRI when end-tidal CO <sub>2</sub> quality is low.

Journal: Imaging neuroscience (Cambridge, Mass.)

Authors' code: BrightLab-ANVIL/PreProc_BRAIN (no license), BrightLab-ANVIL/Clements_BHCVR-PredictedCO2 (no license)

Status: code verified, 22 files readable, 10 matches

[18363] doi:10.1186/s13024-025-00829-w [paper, data]

ASO-mediated knock-down of GPNMB in mutant-GRN and in Grn-deficient peripheral myeloid cells disrupts lysosomal function and immune responses.

Journal: Molecular neurodegeneration

Status: data only, 2 datasets cited

[18364] doi:10.1371/journal.pbio.3003108 [paper, repository]

Active and passive touch are differentially represented in the mouse somatosensory thalamus.

Journal: PLoS biology

Authors' code: Zenodo 14691035 (CC-BY-4.0)

Status: code verified, 26 files readable, 5 matches

[18365] doi:10.1371/journal.pdig.0000682 [paper, data]

Reliability of online, remote neuropsychological assessment in people with and without subjective cognitive decline.

Journal: PLOS digital health

Status: data only, 1 dataset cited

[18366] doi:10.1371/journal.pntd.0012977 [paper, data]

Intestinal Lactobacillus johnsonii protects against neuroangiostrongyliasis in BALB/c mice through modulation of immune response.

Journal: PLoS neglected tropical diseases

Status: data only, 1 dataset cited

[18367] doi:10.1371/journal.pone.0321107 [paper, data]

Detection of motor-related mu rhythm desynchronization by ear EEG.

Journal: PloS one

Status: data only, 1 dataset cited

[18368] doi:10.21037/qims-24-1440 [paper, repository]

Brain white matter microstructural alterations in patients with diabetic retinopathy: an automated fiber-tract quantification study.

Journal: Quantitative imaging in medicine and surgery

Authors' code: jyeatman/AFQ (gnu)

Status: code verified, 165 files readable, 5 matches

Also: by category, author, journal, institution, tool or dataset; the search; the DOI lookup for any paper read, with or without a page.