Every paper, by date: page 87

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 87 of 200: 8 March 2025 to 1 March 2025.

Saturday, 8 March 2025 (14 papers, 13 on this page)

[19265] doi:10.1016/j.nicl.2025.103764 [paper, repository]

Detection of structural-functional coupling abnormalities using multimodal brain networks in Alzheimer's disease: A comparison of three computational models.

Journal: NeuroImage. Clinical

Authors' code: brain-networks/local_scfc (no license)

Status: code verified, 13 files readable

[19266] doi:10.1038/s41398-025-03284-9 [paper]

Fine-tuning of dopamine receptor signaling with aripiprazole counteracts ketamine's dissociative action, but not its antidepressant effect.

Journal: Translational psychiatry

Status: code on request

[19267] doi:10.1038/s41467-025-57685-x [paper, repository]

Reduced temporal and spatial stability of neural activity patterns predict cognitive control deficits in children with ADHD.

Journal: Nature communications

Authors' code: OSF 5apc8 (no license)

Status: code verified, 8 files readable

[19268] doi:10.1038/s41467-025-57810-w [paper, data]

Maternal behavior promotes resilience to adolescent stress in mice through a microglia-neuron axis.

Journal: Nature communications

Status: data only, 1 dataset cited

[19269] doi:10.1038/s41597-025-04744-z [paper, repository]

Human infant EEG recordings for 200 object images presented in rapid visual streams.

Journal: Scientific data

Authors' code: brain-products/LSL-LiveAmp (MIT)

Status: code verified, 8 files readable, 1 match

[19270] doi:10.1038/s41598-025-92721-2 [paper]

Brain and intracranial volumes are both enlarged and serve as potential risk factors in normal pressure hydrocephalus.

Journal: Scientific reports

Status: code on request

[19271] doi:10.1038/s41598-025-92776-1 [paper, data]

Automated multi-class MRI brain tumor classification and segmentation using deformable attention and saliency mapping.

Journal: Scientific reports

Status: data only, 1 dataset cited

[19272] doi:10.1038/s42003-025-07850-1 [paper, repository]

Perturbations in the microbiota-gut-brain axis shaped by social status loss.

Journal: Communications biology

Authors' code: Zenodo 14927861 (CC-BY-4.0)

Status: code verified, 9 files readable, 1 match

[19273] doi:10.1186/s12929-025-01126-w [paper, data]

IL-19 as a promising theranostic target to reprogram the glioblastoma immunosuppressive microenvironment.

Journal: Journal of biomedical science

Status: data only, 1 dataset cited

[19274] doi:10.1186/s12974-025-03388-5 [paper, data]

Neuroinflammation causes mitral cell dysfunction and olfactory impairment in a multiple sclerosis model.

Journal: Journal of neuroinflammation

Status: data only, 1 dataset cited

[19275] doi:10.3390/brainsci15030288 [paper, data]

Cross-Modal Interactions and Movement-Related Tactile Gating: The Role of Vision.

Journal: Brain sciences

Status: code on request, 1 dataset cited

[19276] doi:10.3390/bs15030333 [paper, data]

Prefrontal-Dependent and Gender-Specific Modulation of Guilt Emotion on Human Early Visual Perception.

Journal: Behavioral sciences (Basel, Switzerland)

Status: data only, 1 dataset cited

[19277] doi:10.3390/s25061669 [paper, repository]

Vocal Emotion Perception and Musicality-Insights from EEG Decoding.

Journal: Sensors (Basel, Switzerland)

Authors' code: OSF qakne (no license)

Status: code verified

Friday, 7 March 2025 (39 papers)

[19278] doi:10.1002/acn3.52286 [paper, repository]

Calcium modulating ligand confers risk for Parkinson's disease and impacts lysosomes.

Journal: Annals of clinical and translational neurology

Authors' code: r-project.org (no license), ChenPlotkinLab/CAMLG (MIT)

Status: code verified, 6 files readable, 4 matches

[19279] doi:10.1002/advs.202409642 [paper]

Dynamics of Cell Fate Decisions during Chemically Induced Multi-Lineage Trans-Differentiation at Single-Cell Level.

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

Status: data only

[19280] doi:10.1016/j.ajhg.2025.02.011 [paper, repository]

Single-cell analyses reveal increased gene expression variability in human neurodevelopmental conditions.

Journal: American journal of human genetics

Authors' code: suraj-upad/Transcriptional_variance_T21 (MIT)

Status: code verified, 6 files readable, 15 matches

[19281] doi:10.1016/j.bbrep.2025.101969 [paper]

Machine learning unravels the mysteries of glioma typing and treatment.

Journal: Biochemistry and biophysics reports

Status: data only

[19282] doi:10.1016/j.media.2025.103531 [paper, repository]

SpinFlowSim: A blood flow simulation framework for histology-informed diffusion MRI microvasculature mapping in cancer.

Journal: Medical image analysis

Authors' code: fragrussu/bodymritools (CC-BY-NC-SA-4.0)

Status: code verified, 17 files readable, 2 matches

[19283] doi:10.1016/j.mex.2025.103255 [paper, data]

Optimizing brain tumor detection in MRI scans through InceptionResNetV2 and deep stacked Autoencoders with SwiGLU activation and sparsity regularization.

Journal: MethodsX

Status: data only, 1 dataset cited

[19284] doi:10.1016/j.neuroimage.2025.121104 [paper]

Towards automatic US-MR fetal brain image registration with learning-based methods.

Journal: NeuroImage

Status: code on request

[19285] doi:10.1016/j.xcrm.2025.101998 [paper]

TRPM2 overactivation drives hyperlipidemia-induced dysfunction of myeloid cells and neurovascular units.

Journal: Cell reports. Medicine

Status: code on request

[19286] doi:10.1016/j.xcrm.2025.101999 [paper]

Single extracellular vesicle detection assay identifies membrane-associated α-synuclein as an early-stage biomarker in Parkinson's disease.

Journal: Cell reports. Medicine

Status: code on request

[19287] doi:10.1038/s41467-025-57347-y [paper, repository]

Locomotion-dependent auditory gating to the parietal cortex guides multisensory decisions.

Journal: Nature communications

Authors' code: seungheelee1789/PPC_Choi (no license)

Status: code verified, 38 files readable, 14 matches

[19288] doi:10.1038/s41467-025-57625-9 [paper, repository]

Spatiotemporally resolved transcriptomics reveals the cellular dynamics of human retinal development.

Journal: Nature communications

Authors' code: ZhaoXM-Lab/DevRetinaST (MIT), Zenodo 14862032 (MIT), zhang-jinglong/devretinast (MIT)

Status: code verified, 118 files readable, 24 matches

[19289] doi:10.1038/s41562-025-02105-9 [paper, repository]

A unified acoustic-to-speech-to-language embedding space captures the neural basis of natural language processing in everyday conversations.

Journal: Nature human behaviour

Authors' code: hassonlab/247-plotting (no license), hassonlab/247-pickling (no license), hassonlab/247-encoding (MIT)

Status: code verified, 58 files readable, 6 matches

[19290] doi:10.1038/s41598-025-90269-9 [paper, repository]

Bayesian prior uncertainty and surprisal elicit distinct neural patterns during sound localization in dynamic environments.

Journal: Scientific reports

Authors' code: OSF 9btze (no license)

Status: empty repository

[19291] doi:10.1038/s43587-025-00830-4 [paper, data]

A torpor-like state in mice slows blood epigenetic aging and prolongs healthspan.

Journal: Nature aging

Status: code on request, 1 dataset cited

[19292] doi:10.1038/s44319-025-00403-x [paper]

Auditory fear memory retrieval requires BLA-LS and LS-VMH circuitries via GABAergic and dopaminergic neurons.

Journal: EMBO reports

Status: data only

[19293] doi:10.1073/pnas.2404039122 [paper, repository]

Structure of activity in multiregion recurrent neural networks.

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

Authors' code: davidclark1/MultiregionDMFT (no license)

Status: code verified, 12 files readable, 4 matches

[19294] doi:10.1073/pnas.2408791122 [paper, repository]

Multilevel irreversibility reveals higher-order organization of nonequilibrium interactions in human brain dynamics.

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

Authors' code: rnartallo/multilevelirreversibility (no license), leonardob92/LBPD-1.0 (GPL-3.0)

Status: code verified, 202 files readable, 3 matches

[19295] doi:10.1073/pnas.2420091122 [paper, data]

Genetic ablation of the TET family in retinal progenitor cells impairs photoreceptor development and leads to blindness.

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

Status: data only, 2 datasets cited

[19296] doi:10.1101/2025.03.06.641926 [paper, repository]

Identification of drug candidates against glioblastoma with machine learning and high-throughput screening of heterogeneous cellular models

Journal: bioRxiv (preprint)

Authors' code: Zenodo 17100377 (CC-BY-4.0), Zenodo 17106111 (CC-BY-4.0), Zenodo 17100378 (CC-BY-4.0)

Status: code verified, 2 files readable

[19297] doi:10.1126/sciadv.adq2290 [paper, repository]

Contrasting genetic predisposition and diagnosis in psychiatric disorders: A multi-omic single-nucleus analysis of the human OFC.

Journal: Science advances

Authors' code: Zenodo 14541293 (CC-BY-4.0), github.molgen.mpg.de/mpip/singlenuclei_analysis_ofc.git (no license)

Status: code verified, 116 files readable, 26 matches

[19298] doi:10.1126/sciadv.adr0690 [paper, data]

Origin and cell type specificity of mitochondrial DNA mutations in <i>C9ORF72</i> ALS-FTLD human brain organoids.

Journal: Science advances

Status: data only, 1 dataset cited

[19299] doi:10.1126/sciadv.adt0780 [paper, repository]

Perirhinal cortex abnormalities impair hippocampal plasticity and learning in <i>Scn2a</i>, <i>Fmr1</i>, and <i>Cdkl5</i> autism mouse models.

Journal: Science advances

Authors' code: Zenodo 14510760 (apgl-v3)

Status: code verified, 6 files readable, 2 matches

[19300] doi:10.1126/sciadv.adt3724 [paper, data]

Paralemmin-1 controls the nanoarchitecture of the neuronal submembrane cytoskeleton.

Journal: Science advances

Status: data only, 2 datasets cited

[19301] doi:10.1162/imag_a_00500 [paper, repository]

V2C-Long: Longitudinal cortex reconstruction with spatiotemporal correspondence.

Journal: Imaging neuroscience (Cambridge, Mass.)

Authors' code: ai-med/Vox2Cortex (GPL-3.0)

Status: code verified, 56 files readable, 7 matches

[19302] doi:10.1162/imag_a_00502 [paper, repository]

Divergent and convergent creativity relate to different aspects of semantic control.

Journal: Imaging neuroscience (Cambridge, Mass.)

Authors' code: OSF dy37q (no license)

Status: code verified, 2 files readable

[19303] doi:10.1162/nol_a_00160 [paper, data]

Semantic and Phonological Abilities Inform Efficacy of Transcranial Magnetic Stimulation on Sustained Aphasia Treatment Outcomes.

Journal: Neurobiology of language (Cambridge, Mass.)

Status: data only, 1 dataset cited

[19304] doi:10.1186/s12883-025-04102-x [paper, data]

Exploring comorbidity networks in mild traumatic brain injury subjects through graph theory: a traumatic brain injury model systems study.

Journal: BMC neurology

Status: code on request, 1 dataset cited

[19305] doi:10.1186/s12888-025-06530-y [paper, data]

Effects of transcranial direct current stimulation combined with retrieval practice on semantic memory in patients with schizophrenia.

Journal: BMC psychiatry

Status: data only, 1 dataset cited

[19306] doi:10.1186/s12911-025-02950-8 [paper, repository]

Retinal vein occlusion risk prediction without fundus examination using a no-code machine learning tool for tabular data: a nationwide cross-sectional study from South Korea.

Journal: BMC medical informatics and decision making

Authors' code: taekeuntoo.github.io/rvo_risk_calc (no license)

Status: code verified

[19307] doi:10.1186/s40478-025-01968-3 [paper, data]

Antagonizing Il10 and Il4 signaling via intracerebral decoy receptor expression attenuates Aβ accumulation.

Journal: Acta neuropathologica communications

Status: data only, 1 dataset cited

[19308] doi:10.1371/journal.pcbi.1012795 [paper, repository]

DySCo: A general framework for dynamic functional connectivity.

Journal: PLoS computational biology

Authors' code: Mimbero/DySCo (no license)

Status: code verified, 25 files readable, 4 matches

[19309] doi:10.1371/journal.pcbi.1012870 [paper, data]

Exploring the transmission of cognitive task information through optimal brain pathways.

Journal: PLoS computational biology

Status: data only, 2 datasets cited

[19310] doi:10.1523/eneuro.0454-24.2025 [paper, repository]

A Common Stay-on-Goal Mechanism in the Anterior Cingulate Cortex for Information and Effort Choices.

Journal: eNeuro

Authors' code: izquierdolab (no license), gin.g-node.org/aizquie (no license)

Status: code verified

[19311] doi:10.3389/fneur.2025.1515432 [paper, repository]

Feedforward control in children with cerebral palsy and association with white matter integrity.

Journal: Frontiers in neurology

Authors' code: scilus/tractoflow (other), scilus/tractometry_flow (no license), scilus/noddi_flow (MIT), scilus/scilpy (MIT), surfer.nmr.mgh.harvard.edu (no license), scilus/freesurfer_flow (MIT)

Status: code verified, 609 files readable, 5 matches

[19312] doi:10.3390/cells14060393 [paper, data]

Role of Galactosylceramide Metabolism in Satellite Glial Cell Dysfunction and Neuron-Glia Interactions in Painful Diabetic Peripheral Neuropathy.

Journal: Cells

Status: data only, 1 dataset cited

[19313] doi:10.3390/geriatrics10020037 [paper, repository]

Aging Gut-Brain Interactions: Pro-Inflammatory Gut Bacteria Are Elevated in Fecal Samples from Individuals Living with Alzheimer's Dementia.

Journal: Geriatrics (Basel, Switzerland)

Authors' code: figshare 25151639 (CC-BY-4.0)

Status: code verified, 4 files readable, 3 matches

[19314] doi:10.7554/elife.90347 [paper, repository]

ThermoMaze behavioral paradigm for assessing immobility-related brain events in rodents.

Journal: eLife

Authors' code: misivoroslakos/3d_printed_designs (MIT), buzsakilab/buzcode (GPL-3.0)

Status: code verified, 2,002 files readable, 12 matches

[19315] doi:10.7554/elife.99545 [paper, repository]

Efficient coding in biophysically realistic excitatory-inhibitory spiking networks.

Journal: eLife

Authors' code: VeronikaKoren/efficient_EI (CC-BY-NC-SA-4.0), Zenodo 14628524 (CC-BY-4.0)

Status: code verified, 123 files readable, 2 matches

[19316] doi:10.7759/cureus.80200 [paper, data]

Extracellular Vesicle-Associated Angiopoietin-2 and Cell Migration-Inducing Protein in Lung Cancer Progression and Brain Metastases.

Journal: Cureus

Status: data only, 2 datasets cited

Thursday, 6 March 2025 (47 papers)

[19317] doi:10.1002/advs.202411191 [paper, repository]

Structural Diversity of Mitochondria in the Neuromuscular System across Development Revealed by 3D Electron Microscopy.

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

Authors' code: google/neuroglancer (Apache-2.0), jabae/Cmito (MIT), Zenodo 5539913 (other-open), seung-lab/kimimaro (GPL-3.0)

Status: code verified, 962 files readable

[19318] doi:10.1002/exp.20240349 [paper, data]

Engineered Exosome-Based Senolytic Therapy Alleviates Stroke by Targeting p21<sup>+</sup>CD86<sup>+</sup> Microglia.

Journal: Exploration (Beijing, China)

Status: data only, 1 dataset cited

[19319] doi:10.1007/s12031-025-02316-9 [paper, repository]

Discovery of Novel Protein-Coding and Long Non-coding Transcripts in Distinct Regions of the Human Brain.

Journal: Journal of molecular neuroscience : MN

Authors' code: janitz-lab/novel-isoform-discovery (no license)

Status: empty repository

[19320] doi:10.1016/j.celrep.2025.115389 [paper]

Fast face-selective responses in prefrontal face patches of the macaque.

Journal: Cell reports

Status: code on request

[19321] doi:10.1016/j.dcn.2025.101543 [paper, repository]

Assessing neurocognitive maturation in early adolescence based on baby and adult functional brain landscapes.

Journal: Developmental cognitive neuroscience

Authors' code: okardan/Anchored_rsFC_maturation (no license), nda.nih.gov/study.html (no license)

Status: code verified, 10 files readable, 3 matches

[19322] doi:10.1016/j.stemcr.2025.102425 [paper, repository]

Robust generation of photoreceptor-dominant retinal organoids from porcine induced pluripotent stem cells.

Journal: Stem cell reports

Authors' code: stewart-lab/scRNAseq_library (MIT), stewart-lab/scRNAseq_downstream (MIT)

Status: code verified, 76 files readable, 5 matches

[19323] doi:10.1016/j.xpro.2025.103682 [paper, repository]

Protocol for semi-automatic EEG preprocessing incorporating independent component analysis and principal component analysis.

Journal: STAR protocols

Authors' code: guangouyang/EEG_preprocessing_protocol (no license), Zenodo 14816760 (CC-BY-4.0)

Status: code verified, 18 files readable, 10 matches

[19324] doi:10.1038/s41467-025-57052-w [paper, repository]

A prenatal window for enhancing spatial resolution of cortical barrel maps.

Journal: Nature communications

Authors' code: ackman678/CalciumDX (GPL-2.0), ackman678/wholeBrainDX (GPL-2.0)

Status: code verified, 273 files readable, 2 matches

[19325] doi:10.1038/s41467-025-57286-8 [paper, repository]

Cryptic mitochondrial DNA mutations coincide with mid-late life and are pathophysiologically informative in single cells across tissues and species.

Journal: Nature communications

Authors' code: SystemsAndSignalsGroup/Mito-Ageing (MIT), Zenodo 14698854 (MIT)

Status: code verified, 30 files readable, 8 matches

[19326] doi:10.1038/s41467-025-57426-0 [paper, repository]

Towards a holistic framework for multimodal LLM in 3D brain CT radiology report generation.

Journal: Nature communications

Authors' code: huggingface.co/charliebear/braingpt (MIT), Zenodo 14852686 (MIT), charlierabea/forte (MIT)

Status: code verified, 628 files readable, 2 matches

[19327] doi:10.1038/s41591-025-03574-1 [paper, repository]

Microglial mechanisms drive amyloid-β clearance in immunized patients with Alzheimer's disease.

Journal: Nature medicine

Authors' code: gatelabNW/AD_Immunization (no license)

Status: code verified, 94 files readable, 38 matches

[19328] doi:10.1038/s41593-025-01871-z [paper, repository]

Microglia dysfunction, neurovascular inflammation and focal neuropathologies are linked to IL-1- and IL-6-related systemic inflammation in COVID-19.

Journal: Nature neuroscience

Authors' code: isdneuroimaging/mmqt (BSD-3-Clause), Lieszlab (no license), Cytocast/neuro_covid19 (no license)

Status: code verified, 35 files readable, 1 match

[19329] doi:10.1038/s41597-025-04511-0 [paper, data]

A neuroimaging dataset during sequential color qualia similarity judgments with and without reports.

Journal: Scientific data

Status: data only, 2 datasets cited

[19330] doi:10.1038/s41598-024-81960-4 [paper, data]

Passenger physiology in self-driving vehicles during unexpected events.

Journal: Scientific reports

Status: code on request, 1 dataset cited

[19331] doi:10.1038/s41598-025-90988-z [paper, repository]

Classifying microfossil radiolarians on fractal pre-trained vision transformers.

Journal: Scientific reports

Authors' code: masora1030/CVPR2022-Pretrained-ViT-PyTorch (MIT)

Status: code verified, 28 files readable, 2 matches

[19332] doi:10.1038/s41598-025-91344-x [paper, data]

Exploring the active ingredients and potential mechanisms of Pingchan granules in Parkinson's disease treatment through network pharmacology and transcriptomics.

Journal: Scientific reports

Status: data only, 1 dataset cited

[19333] doi:10.1038/s41598-025-92383-0 [paper, data]

Gallic acid alleviates ferroptosis by negatively regulating APOC3 and improves nerve function deficit caused by traumatic brain injury.

Journal: Scientific reports

Status: data only, 1 dataset cited

[19334] doi:10.1038/s41598-025-92490-y [paper, repository]

Neural representation of consciously seen and unseen information.

Journal: Scientific reports

Authors' code: rodriguez-p/EEGConsciouslySeenUnseen (no license)

Status: code verified, 21 files readable, 8 matches

[19335] doi:10.1038/s42003-025-07679-8 [paper, data]

Central amygdala somatostatin neurons modulate stress-induced sleep-onset insomnia.

Journal: Communications biology

Status: data only, 1 dataset cited

[19336] doi:10.1038/s42003-025-07792-8 [paper, repository]

Theoretical analysis of low-power deep synergistic sono-optogenetic excitation of neurons by co-expressing light-sensitive and mechano-sensitive ion-channels.

Journal: Communications biology

Authors' code: Zenodo 14880424 (CC-BY-4.0)

Status: code verified, 8 files readable, 4 matches

[19337] doi:10.1038/s42003-025-07805-6 [paper, repository]

Neurophysiological insights into catecholamine-dependent tDCS modulation of cognitive control.

Journal: Communications biology

Authors' code: OSF wexgu (no license)

Status: code verified, 9 files readable, 6 matches

[19338] doi:10.1038/s44321-025-00209-3 [paper, data]

AAV-mediated expression of proneural factors stimulates neurogenesis from adult Müller glia in vivo.

Journal: EMBO molecular medicine

Status: data only, 1 dataset cited

[19339] doi:10.1093/nc/niaf005 [paper, data]

Deciphering temporal scales of visual awareness: insights from flicker frequency modulation in continuous flash suppression.

Journal: Neuroscience of consciousness

Status: data only, 1 dataset cited

[19340] doi:10.1162/imag_a_00501 [paper, repository]

Implicit neural representation of multi-shell constrained spherical deconvolution for continuous modeling of diffusion MRI.

Journal: Imaging neuroscience (Cambridge, Mass.)

Authors' code: scilus/scilpy (MIT), tomhend/MSMT-CSD_INR (GPL-3.0)

Status: code verified, 612 files readable, 3 matches

[19341] doi:10.1162/imag_a_00503 [paper, repository]

Analysis of functional connectivity changes from childhood to old age: A study using HCP-D, HCP-YA, and HCP-A datasets.

Journal: Imaging neuroscience (Cambridge, Mass.)

Authors' code: StatDeptZhang/Lifespan-Changes-in-Functional-Brain-Networks (no license)

Status: code verified, 19 files readable

[19342] doi:10.1172/jci.insight.181885 [paper, data]

MSC transplantation ameliorates depression in lupus by suppressing Th1 cell-shaped synaptic stripping.

Journal: JCI insight

Status: data only, 1 dataset cited

[19343] doi:10.1172/jci.insight.185159 [paper, data]

Investigation of a mouse model of Prader-Willi Syndrome with combined disruption of Necdin and Magel2.

Journal: JCI insight

Status: data only, 1 dataset cited

[19344] doi:10.1186/s10020-025-01115-7 [paper, data]

A genome-wide association study identifies a novel East Asian-specific locus for dementia with Lewy bodies in Japanese subjects.

Journal: Molecular medicine (Cambridge, Mass.)

Status: data only, 4 datasets cited

[19345] doi:10.1186/s12967-025-06317-5 [paper, repository]

Biomarker identification for Alzheimer's disease through integration of comprehensive Mendelian randomization and proteomics data.

Journal: Journal of translational medicine

Authors' code: MRCIEU/TwoSampleMR (other)

Status: code verified, 73 files readable, 3 matches

[19346] doi:10.1186/s40001-025-02417-6 [paper, data]

Associations between sepsis occurrence, hemoglobin level and mortality in patients with non-trauma hemorrhagic brain injuries: trajectory-based analysis.

Journal: European journal of medical research

Status: data only, 1 dataset cited

[19347] doi:10.1186/s40478-025-01973-6 [paper, repository]

Refining prognostic stratification of atypical meningiomas: significance of chromosome 1p deletion and brain invasion.

Journal: Acta neuropathologica communications

Authors' code: ekg/vcflib (MIT)

Status: code verified, 157 files readable, 1 match

[19348] doi:10.1371/journal.pcbi.1012855 [paper, repository]

Suprachiasmatic nucleus-wide estimation of oscillatory temporal dynamics.

Journal: PLoS computational biology

Authors' code: OSF p7ufh (no license)

Status: code verified, 7 files readable

[19349] doi:10.1371/journal.pone.0319346 [paper, repository]

Centrality nearest-neighbor projected-distance regression (C-NPDR) feature selection for correlation-based predictors with application to resting-state fMRI study of major depressive disorder.

Journal: PloS one

Authors' code: insilico/centralityNPDR (no license)

Status: code verified, 2 files readable

[19350] doi:10.1523/eneuro.0304-24.2025 [paper, data]

Multimodal Imaging to Identify Brain Markers of Human Prosocial Behavior.

Journal: eNeuro

Status: data only, 1 dataset cited

[19351] doi:10.3389/fcell.2025.1522094 [paper, data]

A zebrafish model of <i>crim1</i> loss of function has small and misshapen lenses with dysregulated <i>clic4</i> and <i>fgf1b</i> expression.

Journal: Frontiers in cell and developmental biology

Status: data only, 1 dataset cited

[19352] doi:10.3389/fimmu.2024.1512300 [paper, data]

Microglia-derived CXCL2 induced neuronal ferroptosis via CXCR2/Jun axis in sepsis-associated encephalopathy.

Journal: Frontiers in immunology

Status: data only, 1 dataset cited

[19353] doi:10.3389/fnins.2025.1557287 [paper, data]

AM-MTEEG: multi-task EEG classification based on impulsive associative memory.

Journal: Frontiers in neuroscience

Status: data only, 1 dataset cited

[19354] doi:10.3389/frai.2025.1520330 [paper, data]

Impact on bias mitigation algorithms to variations in inferred sensitive attribute uncertainty.

Journal: Frontiers in artificial intelligence

Status: data only, 1 dataset cited

[19355] doi:10.3390/biom15030381 [paper, data]

Neurocellular Stress Response to Mojave Type A Rattlesnake Venom: Study of Molecular Mechanisms Using Human iPSC-Derived Neural Stem Cell Model.

Journal: Biomolecules

Status: data only, 1 dataset cited

[19356] doi:10.3390/diagnostics15050639 [paper, data]

Secure Hybrid Deep Learning for MRI-Based Brain Tumor Detection in Smart Medical IoT Systems.

Journal: Diagnostics (Basel, Switzerland)

Status: data only, 1 dataset cited

[19357] doi:10.3390/ijms26052347 [paper, data]

Differentially Expressed Genes in Rat Brain Regions with Different Degrees of Ischemic Damage.

Journal: International journal of molecular sciences

Status: data only, 2 datasets cited

[19358] doi:10.3390/ijms26052361 [paper, repository]

Differential Transcriptional Programs Reveal Modular Network Rearrangements Associated with Late-Onset Alzheimer's Disease.

Journal: International journal of molecular sciences

Authors' code: csb-ig/rosmap_multiomics (MIT)

Status: code verified, 17 files readable, 1 match

[19359] doi:10.3390/nu17050921 [paper]

Host Transcriptome and Microbial Variation in Relation to Visceral Hyperalgesia.

Journal: Nutrients

Status: data only

[19360] doi:10.34133/research.0633 [paper, repository]

Retinal Vascular Morphology Reflects and Predicts Cerebral Small Vessel Disease: Evidences from Eye-Brain Imaging Analysis.

Journal: Research (Washington, D.C.)

Authors' code: Winniework/Retina-CSVD (no license)

Status: dead link

[19361] doi:10.7554/elife.102151 [paper, data]

Sphingosine-1-phosphate signaling regulates the ability of Müller glia to become neurogenic, proliferating progenitor-like cells.

Journal: eLife

Status: data only, 1 dataset cited

[19362] doi:10.7554/elife.90826 [paper, repository]

The reuniens nucleus of the thalamus facilitates hippocampo-cortical dialogue during sleep.

Journal: eLife

Authors' code: diellorbasha/matlab_for_electrophysiology (gpl), azarmehri/brain-network-interactions (gpl)

Status: code verified, 2,002 files readable, 14 matches

[19363] doi:10.7554/elife.92119 [paper, repository]

Movies reveal the fine-grained organization of infant visual cortex.

Journal: eLife

Authors' code: ntblab/experiment_menu (gnu), ntblab/infant_neuropipe (gnu)

Status: code verified, 170 files readable, 5 matches

Wednesday, 5 March 2025 (47 papers)

[19364] doi:10.1007/s00401-025-02859-6 [paper, repository]

Parkinson-like wild-type superoxide dismutase 1 pathology induces nigral dopamine neuron degeneration in a novel murine model.

Journal: Acta neuropathologica

Authors' code: RichardHarwood/image_analysis_SOD1 (no license)

Status: code verified, 3 files readable

[19365] doi:10.1007/s12026-025-09609-6 [paper, repository]

A comprehensive analysis of scRNA-Seq and RNA-Seq unveils B cell immune suppression in the AAV-loaded brain.

Journal: Immunologic research

Authors' code: codeconnoisseur5/Immune-Suppression-in-the-AAV-Loaded-Brain (Apache-2.0)

Status: empty repository, 2 files readable

[19366] doi:10.1016/j.celrep.2025.115374 [paper]

Astrocyte glypican 5 regulates synapse maturation and stabilization.

Journal: Cell reports

Status: code on request

[19367] doi:10.1016/j.celrep.2025.115384 [paper, repository]

Cell-type-specific roles of FOXP1 in the excitatory neuronal lineage during early neocortical murine development.

Journal: Cell reports

Authors' code: anabrains/neocortex_genomics_Foxp1 (no license)

Status: code verified, 22 files readable, 18 matches

[19368] doi:10.1016/j.compmedimag.2025.102518 [paper, repository]

Encoding 3D information in 2D feature maps for brain CT-Angiography.

Journal: Computerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society

Authors' code: uma-lal/Learnable-3D-pooling (no license)

Status: code verified, 3 files readable, 3 matches

[19369] doi:10.1016/j.jbc.2025.108376 [paper, data]

Human tau promotes Warburg effect-like glycolytic metabolism under acute hyperglycemia conditions.

Journal: The Journal of biological chemistry

Status: data only, 1 dataset cited

[19370] doi:10.1016/j.neurot.2025.e00556 [paper, repository]

The effects of intermittent theta burst stimulation (iTBS) on resting-state brain entropy (BEN).

Journal: Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics

Authors' code: zewangnew/BENtbx (GPL-2.0), donghui1119/BEN_ITBS (no license)

Status: code verified, 5 files readable

[19371] doi:10.1016/j.xpro.2025.103637 [paper, repository]

Protocol for SUM-PAINT spatial proteomic imaging generating neuronal architecture maps in rat hippocampal neurons.

Journal: STAR protocols

Authors' code: Zenodo 10212680 (CC-BY-4.0), jungmannlab/picasso (MIT)

Status: code verified, 126 files readable, 7 matches

[19372] doi:10.1017/s0033291725000418 [paper, data]

Accelerated brain aging in patients with major depressive disorder and its neurogenetic basis: evidence from neurotransmitters and gene expression profiles.

Journal: Psychological medicine

Status: data only, 1 dataset cited

[19373] doi:10.1038/s41398-025-03294-7 [paper, data]

Association and shared biological bases between birth weight and cortical structure.

Journal: Translational psychiatry

Status: code on request, 1 dataset cited

[19374] doi:10.1038/s41467-025-57487-1 [paper, data]

Single-nuclei sequencing of skeletal muscle reveals subsynaptic-specific transcripts involved in neuromuscular junction maintenance.

Journal: Nature communications

Status: data only, 1 dataset cited

[19375] doi:10.1038/s41537-025-00587-0 [paper]

Weaker top-down cognitive control and stronger bottom-up signaling transmission as a pathogenesis of schizophrenia.

Journal: Schizophrenia (Heidelberg, Germany)

Status: code on request

[19376] doi:10.1038/s41586-025-08603-0 [paper, repository]

Sensory input, sex and function shape hypothalamic cell type development.

Journal: Nature

Authors' code: Zenodo 7113422 (other-open), autoencoded-vocal-analysis.readthedocs.io (no license), harriskap/POA-development (no license), listerlab/pfc_development (no license)

Status: code verified, 125 files readable, 19 matches

[19377] doi:10.1038/s41586-025-08672-1 [paper, repository]

A subcortical switchboard for perseverative, exploratory and disengaged states.

Journal: Nature

Authors' code: Zenodo 3631609 (LGPL-3.0), heimel/InVivoTools (GPL-2.0), mehranahmadlou/Interaction-States (no license), swc-advanced-microscopy/bakingtray (LGPL-3.0)

Status: code verified, 2,600 files readable, 13 matches

[19378] doi:10.1038/s41594-025-01498-5 [paper, data]

Tau filaments with the Alzheimer fold in human MAPT mutants V337M and R406W.

Journal: Nature structural & molecular biology

Status: data only, 1 dataset cited

[19379] doi:10.1038/s41598-025-90380-x [paper, repository]

Self-supervised learning reduces label noise in sharp wave ripple classification.

Journal: Scientific reports

Authors' code: Saber-GRAF/ts-ssl-label-noise (MIT)

Status: code verified, 14 files readable, 8 matches

[19380] doi:10.1038/s41598-025-91580-1 [paper]

Perceptual experience in somatosensory temporal discrimination is indexed by a mid-latency fronto-central ERP difference.

Journal: Scientific reports

Status: code on request

[19381] doi:10.1038/s41746-025-01531-3 [paper, repository]

Machine learning on interictal intracranial EEG predicts surgical outcome in drug resistant epilepsy.

Journal: NPJ digital medicine

Authors' code: Hmayag11/AutoEZ (MIT)

Status: code verified, 9 files readable, 3 matches

[19382] doi:10.1038/s44271-025-00193-x [paper, repository]

Person-centered analyses reveal that developmental adversity at moderate levels and neural threat/safety discrimination are associated with lower anxiety in early adulthood.

Journal: Communications psychology

Authors' code: Yale-CANDLab/Shapes_DevAdversity_LPA (no license)

Status: code verified, 5 files readable, 8 matches

[19383] doi:10.1073/pnas.2408125122 [paper, repository]

A general framework for interpretable neural learning based on local information-theoretic goal functions.

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

Authors' code: gitlab.gwdg.de/wibral/infomorphic_networks (GPL-3.0)

Status: code verified, 31 files readable

[19384] doi:10.1073/pnas.2416381122 [paper, repository]

Conformational free energy landscape of a glutamate transporter and microscopic details of its transport mechanism.

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

Authors' code: Zenodo 14885692 (CC-BY-4.0)

Status: code verified

[19385] doi:10.1073/pnas.2419801122 [paper, data]

The neural bases of the reach-grasp movement in humans: Quantitative evidence from brain lesions.

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

Status: data only, 1 dataset cited

[19386] doi:10.1088/1741-2552/adb995 [paper, repository]

Motor somatotopy impacts imagery strategy success in human intracortical brain-computer interfaces.

Journal: Journal of neural engineering

Authors' code: nicolasgk4/Motor_Somatotopy_2025 (MIT)

Status: code verified, 11 files readable, 7 matches

[19387] doi:10.1098/rsob.240242 [paper, repository]

Pigment-dispersing factor neuropeptides act as multifunctional hormones and modulators in tardigrades.

Journal: Open biology

Authors' code: doi:10.6084/m9.figshare.c.7669679 (no license)

Status: code found, still to be checked

[19388] doi:10.1098/rsos.242138 [paper, repository]

Captivity alters behaviour but not seasonal brain size change in semi-naturally housed shrews.

Journal: Royal Society open science

Authors' code: doi:10.6084/m9.figshare.c.7667237 (no license)

Status: code found, still to be checked

[19389] doi:10.1101/2025.03.04.641459 [paper, repository]

Motifs of brain cortical folding from birth to adulthood: structural asymmetry and folding-functional links

Journal: bioRxiv (preprint)

Authors' code: Yrong-Guo/Hierarchical-surface-registration (MIT)

Status: code verified, 962 files readable

[19390] doi:10.1126/sciadv.ads8169 [paper, repository]

Aging activates escape of the silent X chromosome in the female mouse hippocampus.

Journal: Science advances

Authors' code: margaretgadek/xciescapeaging- (no license), Zenodo 13750335 (CC-BY-4.0)

Status: code verified, 2 files readable, 3 matches

[19391] doi:10.1126/sciadv.adt1288 [paper, repository]

Associations between hormone therapy use and tau accumulation in brain regions vulnerable to Alzheimer's disease.

Journal: Science advances

Authors' code: Zenodo 14584971 (CC-BY-4.0)

Status: code verified, 2 files readable, 3 matches

[19392] doi:10.1126/sciadv.adt5619 [paper, repository]

Linking birth experience and perinatal depression symptoms to neuroanatomical changes in hippocampus and amygdala.

Journal: Science advances

Authors' code: neuromaternal/Birth_experience_PD_Hpc_Amyg (no license)

Status: code verified, 5 files readable, 6 matches

[19393] doi:10.1162/netn_a_00424 [paper, repository]

Neural network embedding of functional microconnectome.

Journal: Network neuroscience (Cambridge, Mass.)

Authors' code: mutualinfo/mutual_info (Apache-2.0), ShimonoMLab/NNECode (no license)

Status: code verified, 11 files readable, 4 matches

[19394] doi:10.1162/netn_a_00428 [paper, repository]

Combined topological and spatial constraints are required to capture the structure of neural connectomes.

Journal: Network neuroscience (Cambridge, Mass.)

Authors' code: Zenodo 13376416 (CC-BY-4.0)

Status: code verified

[19395] doi:10.1162/netn_a_00429 [paper, repository]

A connectome manipulation framework for the systematic and reproducible study of structure-function relationships through simulations.

Journal: Network neuroscience (Cambridge, Mass.)

Authors' code: BlueBrain/connectome-manipulator (Apache-2.0), BlueBrain/sscx-connectome-manipulations (Apache-2.0), alleninstitute/sonata (BSD-3-Clause), BlueBrain/parquet-converters (Apache-2.0), Zenodo 8075202 (other-open), bluebrain/neurodamus (Apache-2.0)

Status: code verified, 550 files readable, 27 matches

[19396] doi:10.1186/s12974-025-03381-y [paper, repository]

Bystander neuronal progenitors in forebrain organoids promote protective antiviral responses.

Journal: Journal of neuroinflammation

Authors' code: Zenodo 14907845 (no license)

Status: dead link

[19397] doi:10.1186/s12974-025-03387-6 [paper, data]

The protective PLCγ2-P522R variant mitigates Alzheimer's disease-associated pathologies by enhancing beneficial microglial functions.

Journal: Journal of neuroinflammation

Status: data only, 3 datasets cited

[19398] doi:10.1523/jneurosci.1699-24.2024 [paper, repository]

Network Mechanisms Underlying the Regional Diversity of Variance and Time Scales of the Brain's Spontaneous Activity Fluctuations.

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

Authors' code: NeuralSystemsAndSignals/humanStructureFunction (no license), adrianponce/BrainScales (no license)

Status: code verified, 58 files readable, 11 matches

[19399] doi:10.2196/65190 [paper]

Machine Learning-Based Prediction of Delirium and Risk Factor Identification in Intensive Care Unit Patients With Burns: Retrospective Observational Study.

Journal: JMIR formative research

Status: code on request

[19400] doi:10.3389/fnhum.2025.1542774 [paper, repository]

Cognitive load recognition in simulated flight missions: an EEG study.

Journal: Frontiers in human neuroscience

Authors' code: vlawhern/arl-eegmodels (CC0-1.0), chenxiachan/EEGNeX (MIT), iis-eth-zurich/eeg-tcnet (Apache-2.0)

Status: code verified, 14 files readable, 3 matches

[19401] doi:10.3389/fnins.2025.1512799 [paper, data]

Emotion recognition based on multimodal physiological electrical signals.

Journal: Frontiers in neuroscience

Status: data only, 1 dataset cited

[19402] doi:10.3389/frmbi.2025.1454909 [paper, data]

Probiotic supplementation prevents stress-impaired spatial learning and enhances the effects of environmental enrichment.

Journal: Frontiers in microbiomes

Status: data only, 1 dataset cited

[19403] doi:10.3390/brainsci15030276 [paper, repository]

Could Traumatic Brain Injury Be a Risk Factor for Bruxism and Temporomandibular Disorders? A Scoping Review.

Journal: Brain sciences

Authors' code: OSF n83fa (no license)

Status: empty repository

[19404] doi:10.3390/brainsci15030277 [paper]

Evaluating Cognitive Function and Brain Activity Patterns via Blood Oxygen Level-Dependent Transformer in N-Back Working Memory Tasks.

Journal: Brain sciences

Status: code on request

[19405] doi:10.3390/diagnostics15050624 [paper, data]

Learning Architecture for Brain Tumor Classification Based on Deep Convolutional Neural Network: Classic and ResNet50.

Journal: Diagnostics (Basel, Switzerland)

Status: data only, 2 datasets cited

[19406] doi:10.3390/ijms26052304 [paper, data]

Unraveling the Roles of UBE3A in Neurodevelopment and Neurodegeneration.

Journal: International journal of molecular sciences

Status: data only, 2 datasets cited

[19407] doi:10.3758/s13415-025-01281-5 [paper, repository]

The impact of impulsivity and compulsivity on error processing in different motivational contexts.

Journal: Cognitive, affective & behavioral neuroscience

Authors' code: adrianfischer.de/teaching.html (no license)

Status: code verified

[19408] doi:10.7554/elife.103260 [paper, repository]

Dopamine activity encodes the changing valence of the same stimulus in conditioned taste aversion paradigms.

Journal: eLife

Authors' code: maxineloh/loh-elife-2024 (GPL-3.0)

Status: code verified, 19 files readable

[19409] doi:10.7554/elife.91765 [paper, repository]

Post-ejaculatory inhibition of female sexual drive via heterogeneous neuronal ensembles in the medial preoptic area.

Journal: eLife

Authors' code: stuberlab/Ishii-MPOA-Ejaculation-2023 (MIT)

Status: code verified, 14 files readable, 8 matches

[19410] doi:10.7554/elife.98485 [paper, repository]

A deep learning framework for automated and generalized synaptic event analysis.

Journal: eLife

Authors' code: delvendahl/miniML (MIT)

Status: code verified, 45 files readable, 9 matches

Tuesday, 4 March 2025 (31 papers)

[19411] doi:10.1002/mrm.30436 [paper, repository]

3D MERMAID: 3D Multi-shot enhanced recovery motion artifact insensitive diffusion for submillimeter, multi-shell, and SNR-efficient diffusion imaging.

Journal: Magnetic resonance in medicine

Authors' code: TardifLab/3D-MERMAID (no license)

Status: code verified, 27 files readable, 14 matches

[19412] doi:10.1002/pchj.70002 [paper, data]

Affective Modulation of Preparatory Cognitive Activity.

Journal: PsyCh journal

Status: data only, 1 dataset cited

[19413] doi:10.1007/s00018-025-05629-5 [paper, data]

NEIL3 influences adult neurogenesis and behavioral pattern separation via WNT signaling.

Journal: Cellular and molecular life sciences : CMLS

Status: data only, 1 dataset cited

[19414] doi:10.1007/s10334-025-01237-3 [paper, data]

Fast whole brain relaxometry with Magnetic Resonance Spin TomogrAphy in Time-domain (MR-STAT) at 3 T: a retrospective cohort study.

Journal: Magma (New York, N.Y.)

Status: data only, 1 dataset cited

[19415] doi:10.1007/s11357-025-01582-0 [paper]

Attention-dependent coupling with forebrain and brainstem neuromodulatory nuclei differs across the lifespan.

Journal: GeroScience

Status: code on request

[19416] doi:10.1007/s11571-025-10230-4 [paper, data]

Shared neural dynamics of facial expression processing.

Journal: Cognitive neurodynamics

Status: data only, 1 dataset cited

[19417] doi:10.1007/s12035-025-04803-x [paper, repository]

Sex-Specific Effects of Early-Life Stress Exposure on Memory Performance and the Medial Prefrontal Cortex Transcriptomic Pattern in Adolescent Mice.

Journal: Molecular neurobiology

Authors' code: bernardo-heberle/dcnl_rna_seq_els_vs_ct (no license)

Status: code verified, 6 files readable

[19418] doi:10.1016/j.cub.2025.02.014 [paper, repository]

Altered proportions of retinal cell types and distinct visual codes in rodents occupying divergent ecological niches.

Journal: Current biology : CB

Authors' code: Zenodo 8067826 (other-open), shekharlab/RetinaEvolution (no license)

Status: code verified, 60 files readable, 5 matches

[19419] doi:10.1016/j.isci.2025.112156 [paper, repository]

Evidence of self-care tooling and phylogenetic modeling reveal parrot tool use is not rare.

Journal: iScience

Authors' code: Zenodo 12732282 (GPL-3.0), ScottClaessens/phyloParrot (GPL-3.0)

Status: code verified, 15 files readable, 13 matches

[19420] doi:10.1016/j.isci.2025.112159 [paper, data]

Echolocation and dietary adaptations mediate brain-endocast covariation in bats.

Journal: iScience

Status: code on request, 1 dataset cited

[19421] doi:10.1016/j.ynirp.2025.100247 [paper]

Domain-specific brain regions are associated with cognitive impairment in progressive supranuclear palsy.

Journal: Neuroimage. Reports

Status: code on request

[19422] doi:10.1021/acschemneuro.4c00789 [paper, data]

Monoamine Oxidase Inhibitors Present in Tobacco Modulate Dopamine Balance Via the Dopamine Transporter.

Journal: ACS chemical neuroscience

Status: data only, 2 datasets cited

[19423] doi:10.1038/s41467-025-57041-z [paper, repository]

Processing of pain and itch information by modality-specific neurons within the anterior cingulate cortex in mice.

Journal: Nature communications

Authors' code: daharoni/Miniscope_DAQ_Software (MIT), JinghaoLu/MIN1PIPE (GPL-3.0), zivlab/CellReg (GPL-2.0), yoplaitlid/pain_itch (GPL-3.0), sourceforge.net/weka (no license), chuljkwak/pain_itch_freezing (no license), Zenodo 14435325 (CC-BY-4.0)

Status: code verified, 231 files readable, 7 matches

[19424] doi:10.1038/s41467-025-57043-x [paper, repository]

Temporal Contrastive Learning through implicit non-equilibrium memory.

Journal: Nature communications

Authors' code: falkma/ContrastiveMemory-Exp (MIT), atstrupp/ContrastiveMemory-SynapseAnalysis (no license)

Status: code verified, 11 files readable, 1 match

[19425] doi:10.1038/s41467-025-57445-x [paper, data]

Functional optic tract rewiring via subtype- and target-specific axonal regeneration and presynaptic activity enhancement.

Journal: Nature communications

Status: code on request, 1 dataset cited

[19426] doi:10.1038/s44303-025-00071-5 [paper]

MRI detects blood-brain barrier alterations in a rat model of Alzheimer's disease and lung infection.

Journal: Npj imaging

Status: code on request

[19427] doi:10.1093/braincomms/fcaf099 [paper, repository]

Uncovering atrophy progression pattern and mechanisms in individuals at risk of Alzheimer's disease.

Journal: Brain communications

Authors' code: villeneuvelab/vlpp (MIT), christina.science/papers/atrophy-progression-fhad (no license)

Status: code verified, 48 files readable, 9 matches

[19428] doi:10.1093/nsr/nwaf086 [paper, repository]

Canine EEG helps human: cross-species and cross-modality epileptic seizure detection via multi-space alignment.

Journal: National science review

Authors' code: wzwvv/TASA (no license), wzwvv/CST (no license)

Status: code verified, 23 files readable

[19429] doi:10.1111/jcpp.14143 [paper, repository]

Different sensory dimensions in infancy are associated with separable etiological influences and with autistic traits in toddlerhood.

Journal: Journal of child psychology and psychiatry, and allied disciplines

Authors' code: brainhabit/BT-ITSP (no license)

Status: code verified, 6 files readable, 5 matches

[19430] doi:10.1159/000545074 [paper, data]

Androgen Aggravates Chorioamnionitis-Induced White Matter Brain Injury and Neurobehavioral Impairments in Males.

Journal: Developmental neuroscience

Status: data only, 2 datasets cited

[19431] doi:10.1172/jci.insight.188962 [paper, data]

Vitamin A treatment restores vision failures arising from Leber's hereditary optic neuropathy-linked mtDNA mutation.

Journal: JCI insight

Status: data only, 1 dataset cited

[19432] doi:10.1186/s12974-025-03383-w [paper, repository]

Decoding dengue's neurological assault: insights from single-cell CNS analysis in an immunocompromised mouse model.

Journal: Journal of neuroinflammation

Authors' code: OpenGene/fastp (MIT), satijalab/seurat (other)

Status: code verified, 204 files readable, 3 matches

[19433] doi:10.1186/s12974-025-03384-9 [paper, data]

Active Cryptococcus neoformans glucuronoxylomannan production prevents elimination of cryptococcal CNS infection in vivo.

Journal: Journal of neuroinflammation

Status: data only, 4 datasets cited

[19434] doi:10.1523/eneuro.0384-24.2025 [paper, repository]

Facial Paralysis Algorithm: A Tool to Infer Facial Paralysis in Awake Mice.

Journal: eNeuro

Authors' code: FaPA305/FaPA-Facial-Paralysis-Algorithm-a-tool-applied-in-mice (no license)

Status: code verified, 1 file readable

[19435] doi:10.3389/fneur.2025.1523468 [paper]

Gene mutations linked to drug-resistant epilepsy in astrocytoma.

Journal: Frontiers in neurology

Status: data only

[19436] doi:10.3389/fnins.2024.1505017 [paper, repository]

Accelerated algorithms for source orientation detection and spatiotemporal LCMV beamforming in EEG source localization.

Journal: Frontiers in neuroscience

Authors' code: Avayekta/ALCMV-AORI (no license)

Status: code verified, 1 file readable

[19437] doi:10.3389/fnmol.2025.1469467 [paper, repository]

Bioenergetic-related gene expression in the hippocampus predicts internalizing vs. externalizing behavior in an animal model of temperament.

Journal: Frontiers in molecular neuroscience

Authors' code: hagenaue/NIDA_bLRvsbHR_F2Cross_HC_RNASeq (MIT)

Status: code verified, 68 files readable, 23 matches

[19438] doi:10.3389/froh.2025.1463458 [paper, data]

Comparison of light gradient boosting and logistic regression for interactomic hub genes in <i>Porphyromonas gingivalis</i> and <i>Fusobacterium nucleatum</i>-induced periodontitis with Alzheimer's disease.

Journal: Frontiers in oral health

Status: data only, 1 dataset cited

[19439] doi:10.3390/bioengineering12030258 [paper, repository]

Intensity-Based Assessment of Hippocampal Segmentation Algorithms Using Paired Precontrast and Postcontrast MRI.

Journal: Bioengineering (Basel, Switzerland)

Authors' code: radiplab/hippo-seg-analysis (MIT)

Status: code verified, 5 files readable, 9 matches

[19440] doi:10.7554/elife.100570 [paper, data]

Deuterium metabolic imaging phenotypes mouse glioblastoma heterogeneity through glucose turnover kinetics.

Journal: eLife

Status: data only, 1 dataset cited

[19441] doi: [paper, data]

Transcranial direct current stimulation and lesions hierarchically reorganize brain network dynamics with biological annotations

Journal: Fundamental research

Status: data only, 1 dataset cited

Monday, 3 March 2025 (35 papers)

[19442] doi:10.1001/jamanetworkopen.2025.1310 [paper, repository]

Generalizability of Treatment Outcome Prediction Across Antidepressant Treatment Trials in Depression.

Journal: JAMA network open

Authors' code: peterzhukovsky/MDD_response_prediction (no license)

Status: code verified, 20 files readable

[19443] doi:10.1002/path.6406 [paper, data]

Multiomic spatial atlas shows deleted in malignant brain tumors 1 (DMBT1) glycoprotein is lost in colonic dysplasia.

Journal: The Journal of pathology

Status: code on request, 1 dataset cited

[19444] doi:10.1016/j.dcn.2025.101532 [paper, repository]

Developmental timing of adversity and neural network organization: An fNIRS study of the impact of refugee displacement.

Journal: Developmental cognitive neuroscience

Authors' code: OSF 9wkmf (no license)

Status: code found, still to be checked

[19445] doi:10.1016/j.ebiom.2025.105606 [paper, repository]

Influences of electrode density on intracranial seizure localisation: a single-blinded randomised crossover study.

Journal: EBioMedicine

Authors' code: Kleen-Lab/OPSCEA (other), Kleen-Lab/OPSCEAhilo (Apache-2.0)

Status: code verified, 24 files readable, 2 matches

[19446] doi:10.1016/j.isci.2025.112136 [paper, repository]

Spine loss in depression impairs dendritic signal integration in human cortical microcircuit models.

Journal: iScience

Authors' code: BlueBrain/BluePyOpt (GPL-3.0)

Status: code verified, 189 files readable

[19447] doi:10.1016/j.isci.2025.112145 [paper, repository]

Enhanced human sensorimotor integration via self-modulation of the somatosensory activity.

Journal: iScience

Authors' code: Junichi-Ushiba-Laboratory/enhanced-human-sensorimotor-integration-via-self-modulation-of-the-somatosensory-activity (no license)

Status: code verified, 8 files readable, 1 match

[19448] doi:10.1021/acsomega.4c07078 [paper, repository]

Deep Learning for Odor Prediction on Aroma-Chemical Blends.

Journal: ACS omega

Authors' code: BioMachineLearning/openpom (MIT), odor-pair/odor-pair (MIT), pyrfume/pyrfume-data (MIT)

Status: code verified, 168 files readable, 9 matches

[19449] doi:10.1038/s41418-025-01470-2 [paper, data]

KDM3A controls postnatal hippocampal neurogenesis via dual regulation of the Wnt/β-catenin signaling pathway.

Journal: Cell death and differentiation

Status: data only, 1 dataset cited

[19450] doi:10.1038/s41467-025-56779-w [paper]

Cortical processing of discrete prosodic patterns in continuous speech.

Journal: Nature communications

Status: code on request

[19451] doi:10.1038/s41592-025-02608-3 [paper, repository]

Cell2fate infers RNA velocity modules to improve cell fate prediction.

Journal: Nature methods

Authors' code: BayraktarLab/cell2fate (Apache-2.0), Zenodo 13883214 (CC-BY-4.0), AlexanderAivazidis/cell2fate_notebooks (no license), AlexanderAivazidis/fate_benchmarking (no license)

Status: code verified, 99 files readable, 13 matches

[19452] doi:10.1038/s41598-025-89261-0 [paper, repository]

EEG connectivity and BDNF correlates of fast motor learning in laparoscopic surgery.

Journal: Scientific reports

Authors' code: Zenodo 12810004 (no license)

Status: dead link

[19453] doi:10.1038/s41598-025-92030-8 [paper, data]

Single-nucleus RNA sequencing uncovers metabolic dysregulation in the prefrontal cortex of major depressive disorder patients.

Journal: Scientific reports

Status: code on request, 1 dataset cited

[19454] doi:10.1038/s42003-025-07566-2 [paper]

Maternal immune activation followed by peripubertal stress combinedly produce reactive microglia and confine cerebellar cognition.

Journal: Communications biology

Status: code on request

[19455] doi:10.1038/s44318-025-00400-9 [paper]

PLK1 inhibition delays mitotic entry revealing changes to the phosphoproteome of mammalian cells early in division.

Journal: The EMBO journal

Status: data only

[19456] doi:10.1073/pnas.2402117122 [paper, data]

Inhibition of amyloid beta oligomer accumulation by NU-9: A unifying mechanism for the treatment of neurodegenerative diseases.

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

Status: data only, 1 dataset cited

[19457] doi:10.1073/pnas.2416433122 [paper, repository]

Brain aging shows nonlinear transitions, suggesting a midlife "critical window" for metabolic intervention.

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

Authors' code: lcneuro.org/analytic/networkstability (no license), lcneuro/pub_pagb (no license)

Status: code verified, 21 files readable, 7 matches

[19458] doi:10.1093/braincomms/fcaf096 [paper, repository]

Influence of apolipoprotein E genotype on the proteomic profile in cerebral microdialysis after human severe traumatic brain injury: a prospective observational study.

Journal: Brain communications

Authors' code: carolinelindblad/apoE_TBI_20240804_CL (no license)

Status: code verified, 1 file readable, 2 matches

[19459] doi:10.1093/pnasnexus/pgaf057 [paper, repository]

Analytical methods for cytoplasmic streaming in elongated cells.

Journal: PNAS nexus

Authors' code: Zenodo 14861849 (CC-BY-4.0), stevenhtet/cytoplasmicstreaminglubrication (no license)

Status: code verified, 72 files readable, 10 matches

[19460] doi:10.1093/pnasnexus/pgaf072 [paper, repository]

Quantitative mapping of key glucose metabolic rates in the human brain using dynamic deuterium magnetic resonance spectroscopic imaging.

Journal: PNAS nexus

Authors' code: Zenodo 14983911 (MIT), cmrrchenlab/dynamicdmrsi (MIT)

Status: code verified, 7 files readable

[19461] doi:10.1101/gad.352272.124 [paper, data]

Hao-Fountain syndrome protein USP7 controls neuronal differentiation via BCOR-ncPRC1.1.

Journal: Genes & development

Status: data only, 1 dataset cited

[19462] doi:10.1162/imag_a_00488 [paper, repository]

Individual variation in the functional lateralization of human ventral temporal cortex: Local competition and long-range coupling.

Journal: Imaging neuroscience (Cambridge, Mass.)

Authors' code: rmldj.github.io/hcp-utils (no license), viscog-cmu/blauch_imaging_neuro_2025 (no license)

Status: code verified, 33 files readable, 20 matches

[19463] doi:10.1162/imag_a_00495 [paper, repository]

Combining video telemetry and wearable MEG for naturalistic imaging.

Journal: Imaging neuroscience (Cambridge, Mass.)

Authors' code: georgeoneill/study-videomeg (no license), CMU-Perceptual-Computing-Lab/openpose (BSD-2-Clause)

Status: code verified, 200 files readable, 1 match

[19464] doi:10.1162/netn_a_00417 [paper, data]

Thalamocortical interactions reflecting the intensity of flicker light-induced visual hallucinatory phenomena.

Journal: Network neuroscience (Cambridge, Mass.)

Status: data only, 1 dataset cited

[19465] doi:10.1162/netn_a_00418 [paper, repository]

Localization of the epileptogenic network from scalp EEG using a patient-specific whole-brain model.

Journal: Network neuroscience (Cambridge, Mass.)

Authors' code: ymmx2/eCOALIA (GPL-3.0)

Status: code verified, 18 files readable, 2 matches

[19466] doi:10.1162/netn_a_00425 [paper, repository]

The control costs of human brain dynamics.

Journal: Network neuroscience (Cambridge, Mass.)

Authors' code: NeuroenergeticsLab/control_costs (no license)

Status: code verified, 15 files readable, 1 match

[19467] doi:10.1162/netn_a_00432 [paper]

Dynamic brain states underlying advanced concentrative absorption meditation: A 7-T fMRI-intensive case study.

Journal: Network neuroscience (Cambridge, Mass.)

Status: code on request

[19468] doi:10.1172/jci188942 [paper, repository]

Multimodal single-cell analyses reveal molecular markers of neuronal senescence in human drug-resistant epilepsy.

Journal: The Journal of clinical investigation

Authors' code: FlameHuang/ZJU_DRE_Patch_seq_analysis (no license), Saintgene-Xu-lab/Colocalization-analysis (GPL-3.0)

Status: code verified, 19 files readable, 2 matches

[19469] doi:10.1186/s12987-025-00634-z [paper, repository]

Applying machine learning to high-dimensional proteomics datasets for the identification of Alzheimer's disease biomarkers.

Journal: Fluids and barriers of the CNS

Authors' code: ToffeIO/AD-Biomarkers-Project (no license)

Status: code verified, 3 files readable, 7 matches

[19470] doi:10.1186/s12991-025-00551-3 [paper, repository]

Genetic overlap between schizophrenia and constipation: insights from a genome-wide association study in a European population.

Journal: Annals of general psychiatry

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

Status: code verified, 77 files readable, 1 match

[19471] doi:10.1186/s13041-024-01159-6 [paper, data]

Quercetin carbon quantum dots: dual-target therapy for intracerebral hemorrhage in mice.

Journal: Molecular brain

Status: data only, 1 dataset cited

[19472] doi:10.1186/s13195-025-01703-z [paper, data]

Synaptic protein CSF levels relate to memory scores in individuals without dementia.

Journal: Alzheimer's research & therapy

Status: data only, 3 datasets cited

[19473] doi:10.21037/tlcr-24-800 [paper, data]

<i>ANKRD11</i> as a potential biomarker for brain metastasis from lung adenocarcinoma via cerebrospinal fluid liquid biopsy.

Journal: Translational lung cancer research

Status: data only, 1 dataset cited

[19474] doi:10.31744/einstein_journal/2025rw0753 [paper, data]

Tranexamic acid in the management of traumatic brain injury: a systematic review and meta-analysis with trial sequential analysis.

Journal: Einstein (Sao Paulo, Brazil)

Status: data only, 1 dataset cited

[19475] doi:10.3389/fphar.2025.1496061 [paper, data]

SysNatMed: rational natural medicine discovery by systems genetics.

Journal: Frontiers in pharmacology

Status: data only, 1 dataset cited

[19476] doi:10.7554/elife.99920 [paper, repository]

Reevaluating the neural noise in dyslexia using biomarkers from electroencephalography and high-resolution magnetic resonance spectroscopy.

Journal: eLife

Authors' code: OSF 4e7ps (no license)

Status: code verified

Sunday, 2 March 2025 (3 papers)

[19477] doi:10.1016/j.xpro.2025.103652 [paper, repository]

Computational protocol for modeling and analyzing synaptic dynamics using SRPlasticity.

Journal: STAR protocols

Authors' code: nauralcodinglab/srplasticity (GPL-3.0), Zenodo 14775430 (GPL-3.0), jgbeninger/srplasticitystarprotocol2025 (GPL-3.0)

Status: code verified, 57 files readable, 38 matches

[19478] doi:10.1038/s41467-025-57414-4 [paper, repository]

Disruption of tryptophan metabolism by high-fat diet-triggered maternal immune activation promotes social behavioral deficits in male mice.

Journal: Nature communications

Authors' code: gitee.com/neokie/code-for-nc (no license)

Status: empty repository, 1 file readable

[19479] doi:10.1038/s41531-025-00877-5 [paper, repository]

Epigenetic insights into neuropsychiatric and cognitive symptoms in Parkinson's disease: A DNA co-methylation network analysis.

Journal: NPJ Parkinson's disease

Authors' code: NathanSkene/EWCE (no license), JoshHarveyGit/PD_TraitNetworkAnalysis (no license)

Status: code verified, 138 files readable, 9 matches

Saturday, 1 March 2025 (93 papers, 9 on this page)

[19480] doi:10.1002/alz.14493 [paper]

Altered triple network model connectivity is associated with cognitive function and depressive symptoms in older adults.

Journal: Alzheimer's & dementia : the journal of the Alzheimer's Association

Status: code on request

[19481] doi:10.1002/alz.14496 [paper, repository]

Blood DNA methylation signature for incident dementia: Evidence from longitudinal cohorts.

Journal: Alzheimer's & dementia : the journal of the Alzheimer's Association

Authors' code: TransBioInfoLab/blood-dnam-and-incident-dementia (no license), miami-ad.org (no license)

Status: code verified, 26 files readable, 12 matches

[19482] doi:10.1002/alz.70024 [paper, repository]

Multi-omics delineate growth factor network underlying exercise effects in an Alzheimer's mouse model.

Journal: Alzheimer's & dementia : the journal of the Alzheimer's Association

Authors' code: r3fang/SnapATAC (GPL-3.0)

Status: code verified, 33 files readable, 7 matches

[19483] doi:10.1002/alz.70025 [paper, repository]

Systematic review and meta-analysis of bulk RNAseq studies in human Alzheimer's disease brain tissue.

Journal: Alzheimer's & dementia : the journal of the Alzheimer's Association

Authors' code: UK-SBCoA-EbbertLab/AD_bulk_RNAseq_review (MIT)

Status: code verified, 57 files readable, 10 matches

[19484] doi:10.1002/alz.70041 [paper, repository]

Mediterranean vs. Western diet effects on the primate cerebral cortical pre-synaptic proteome: Relationships with the transcriptome and multi-system phenotypes.

Journal: Alzheimer's & dementia : the journal of the Alzheimer's Association

Authors' code: elo-nsrb/Brain-study-NHP-2024 (no license)

Status: code verified, 7 files readable, 2 matches

[19485] doi:10.1002/alz.70060 [paper, data]

Metabolic stress and age drive inflammation and cognitive decline in mice and humans.

Journal: Alzheimer's & dementia : the journal of the Alzheimer's Association

Status: data only, 2 datasets cited

[19486] doi:10.1002/alz.70073 [paper, repository]

Heterogeneous brain abnormalities in subjective cognitive decline converge on a common network and their transcriptional signature.

Journal: Alzheimer's & dementia : the journal of the Alzheimer's Association

Authors' code: juryxy/JuSpace (no license), OSF vadru (no license)

Status: code verified, 23 files readable

[19487] doi:10.1002/alz.70087 [paper, repository]

Pathways underlying selective neuronal vulnerability in Alzheimer's disease: Contrasting the vulnerable locus coeruleus to the resilient substantia nigra.

Journal: Alzheimer's & dementia : the journal of the Alzheimer's Association

Authors' code: Zenodo 14057599 (MIT)

Status: code verified, 6 files readable, 2 matches

[19488] doi:10.1002/brb3.70311 [paper, data]

KEAP1-NRF2/HO-1 Pathway Promotes Ferroptosis and Neuronal Injury in Schizophrenia.

Journal: Brain and behavior

Status: data only, 1 dataset cited

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