genetics / omics

Modality: 825 papers with a page, 437 of them with their authors' code.

Sunday, 27 September 2026 (1 paper)

[1] Code ↔ Paper doi:10.1002/advs.77986 [paper, repository]

DUET-seq: An Open-Source Droplet Platform for High-Fidelity Joint Chromatin and Transcriptome Profiling Reveals Temporal Regulatory Decoupling in Single Cells.

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

Authors' code: biochengd/DUET-seq (no license)

Status: code verified, 28 files readable, 34 matches

Saturday, 26 September 2026 (2 papers)

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

Beyond bacteria: a multi-omics view of the gut–brain axis in Parkinson’s disease

Journal: Frontiers in cellular and infection microbiology

Authors' code: hanhuiyeye/PD (no license), euniceokk/prisma (no license)

Status: code verified, 4 files readable, 4 matches

[3] doi: [paper, data]

Gut microbiota dysbiosis is associated with hippocampal neuronal damage and behavioral alterations in APP/PS1 mice with high-salt diet

Journal: Frontiers in microbiology

Status: data only, 1 dataset cited

Friday, 25 September 2026 (1 paper)

[4] doi:10.1002/2211-5463.70302 [paper, data]

KDAC6 alters cell morphology and motility through positive and negative modulation of F-actin distribution.

Journal: FEBS open bio

Status: data only, 10 datasets cited

Friday, 18 September 2026 (1 paper)

[5] doi:10.1126/sciadv.aef7492 [paper, data]

Real-time, cross-modal genotype mapping of free-moving <i>Drosophila</i> larvae via simultaneous mechano-electrophysiological recording.

Journal: Science advances

Status: data only, 1 dataset cited

Thursday, 17 September 2026 (1 paper)

[6] doi:10.1007/s12031-026-02598-7 [paper, data]

A Lipoylation-PDH-TCA Transcriptional Deficit in the Alzheimer's Disease Cortex - Donor-level Multi-cohort Evidence with Neuronal-composition, Disease-specificity and Matched-null Controls.

Journal: Journal of molecular neuroscience : MN

Status: data only, 1 dataset cited

Wednesday, 16 September 2026 (2 papers)

[7] Code ↔ Paper doi:10.2147/jir.s633117 [paper, repository]

Single-Nucleus Transcriptomic Mapping Reveals Correlative Microglial Changes Associated with rTMS in the Motor Cortex After Spinal Cord Injury.

Journal: Journal of inflammation research

Authors' code: 10XGenomics/cellranger (MIT)

Status: code verified, 789 files readable, 2 matches

[8] Code ↔ Paper doi:10.1002/advs.77822 [paper, repository]

Temporal Trajectories of the Tau Aggregate Interactome Reveal Stage-Specific Vulnerabilities in Alzheimer's Disease.

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

Authors' code: Zenodo 17990783 (MIT), dboeken/boeken_tau_aggregate_interactome (MIT)

Status: code verified, 19 files readable, 2 matches

Tuesday, 15 September 2026 (1 paper)

[9] Code ↔ Paper doi:10.7554/elife.108950 [paper, repository]

Comprehensive RNA velocity by modeling the cascade of gene regulation, transcription, and splicing from single-cell RNA sequencing data with TSvelo.

Journal: eLife

Authors' code: lijc0804/TSvelo (MIT), elenasabbioni/bayvel_notebooks (no license)

Status: code verified, 37 files readable, 8 matches

Monday, 14 September 2026 (3 papers)

[10] Code ↔ Paper doi:10.1038/s43587-026-01207-x [paper, repository]

A microprotein atlas of the human frontal cortex in Alzheimer's disease.

Journal: Nature aging

Authors' code: huggingface.co/spaces/brmiller/brain-microprotein-atlas-app (MIT), brendan-miller-salk/brain-microprotein-atlas (no license)

Status: code verified, 61 files readable, 29 matches

[11] doi:10.1038/s42003-026-10802-y [paper]

Transcriptome of fetal cortex of tree shrew underlying the emergence of outer subventricular zone.

Journal: Communications biology

Status: code on request

[12] doi:10.1080/19490976.2026.2726620 [paper, data]

Integrated metagenomic and metabolomic analysis identifies severity-specific inflammatory and metabolic signatures in post-stroke depression.

Journal: Gut microbes

Status: data only, 2 datasets cited

Saturday, 12 September 2026 (1 paper)

[13] doi:10.1016/j.isci.2026.117510 [paper, data]

Single-cell transcriptomic atlas of the human fetal uveal tract reveals heterogeneity in melanocyte populations.

Journal: iScience

Status: code on request, 1 dataset cited

Friday, 11 September 2026 (4 papers)

[14] doi:10.1177/11795735261488260 [paper]

Causal Effects of Gut Microbiota on Morning Chronotype, Insomnia and Sleep Duration: A Two-Sample Mendelian Randomization Study.

Journal: Journal of central nervous system disease

Status: code on request

[15] doi:10.1155/humu/4225263 [paper, data]

The Charcot-Marie-Tooth Neuropathy (CMTX3) Complex Structural Variation Causes Differential SOX3 Spatiotemporal Expression.

Journal: Human mutation

Status: data only, 1 dataset cited

[16] doi:10.1186/s12974-026-03970-5 [paper, data]

Estrogen deprivation exacerbates Alzheimer's disease pathology through neuronal CTSS signaling.

Journal: Journal of neuroinflammation

Status: data only, 1 dataset cited

[17] doi:10.1038/s43587-026-01204-0 [paper, data]

Fibronectin mediates APOE4-driven blood-brain barrier dysfunction in Alzheimer's disease.

Journal: Nature aging

Status: data only, 2 datasets cited

Thursday, 10 September 2026 (2 papers)

[18] doi:10.1111/joa.70225 [paper]

Immune proteomic associations with indices of cortical development in 5-year-old children.

Journal: Journal of anatomy

Status: code on request

[19] Code ↔ Paper doi:10.1371/journal.pone.0355902 [paper, repository]

Pericyte-derived cancer-associated fibroblasts correlate with poor survival and are enriched after chemoradiotherapy in glioblastoma.

Journal: PloS one

Authors' code: neuropromotion/CAFs-in-glioblastoma-microenvironment (no license)

Status: code verified, 12 files readable, 5 matches

Wednesday, 9 September 2026 (1 paper)

[20] doi:10.1007/s12640-026-00825-y [paper, data]

Atorvastatin Shows Limited Disease-Modifying Effects in an A53T α-Synuclein Mouse Model of Parkinson's Disease.

Journal: Neurotoxicity research

Status: data only, 1 dataset cited

Tuesday, 8 September 2026 (3 papers)

[21] Code ↔ Paper doi:10.1038/s41588-026-02737-1 [paper, repository]

Human and mouse adrenal glands are characterized by species-specific steroidogenic states and tissue turnover.

Journal: Nature genetics

Authors' code: artem-artemov/adrenal (no license), MaksimovDenis/adrenalglandscatlas (MIT), Zenodo 20258071 (CC-BY-4.0)

Status: code verified, 7 files readable, 8 matches

[22] Code ↔ Paper doi:10.1371/journal.pgen.1012126 [paper, repository]

FM-GPT: Bayesian fine mapping for phenome-wide transcriptome-wide association studies.

Journal: PLoS genetics

Authors' code: tacanida/fm-gpt (no license)

Status: code verified, 10 files readable, 2 matches

[23] doi:10.1073/pnas.2619143123 [paper, data]

Cell-type-specific circadian and light-responsive transcriptional dynamics in adult <i>Drosophila</i> neurons.

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

Status: data only, 1 dataset cited

Monday, 7 September 2026 (1 paper)

[24] doi:10.1186/s13062-026-00912-2 [paper, data]

Integrated analysis of single-cell transcriptome identifies a glial-neurovascular signaling trajectory in brain repair after ischemia.

Journal: Biology direct

Status: data only, 1 dataset cited

Friday, 4 September 2026 (1 paper)

[25] Code ↔ Paper doi:10.1038/s41592-026-03211-w [paper, repository]

Spatial isoform sequencing at single-cell resolution reveals cell-type-specific spatial isoform variability in multiple brain cell types.

Journal: Nature methods

Authors' code: dmcable/spacexr (GPL-3.0), noush-joglekar/scisorseqr (MIT), algbio/spl-IsoQuant (GPL-2.0), tilgnerlab/Spl-IsoFind (MIT), tilgnerlab/Spl-IsoFind_reproducibility (MIT)

Status: code verified, 347 files readable, 25 matches

Thursday, 3 September 2026 (4 papers)

[26] doi:10.3389/fsysb.2026.1897648 [paper, data]

Integrative genome-scale metabolic model of GABAergic neurons reveals metabolic signatures across the mild cognitive impairment - Alzheimer disease continuum.

Journal: Frontiers in systems biology

Status: data only, 1 dataset cited

[27] Code ↔ Paper doi:10.3389/fsysb.2026.1873899 [paper, repository]

A systems microbiology framework for reproducible multi-dataset omics integration with application to long COVID.

Journal: Frontiers in systems biology

Authors' code: steppenwolf0/longCOVIDMCCREFS (MIT)

Status: code verified, 35 files readable, 8 matches

[28] doi:10.1016/j.isci.2026.117343 [paper, data]

Zebrafish larvae reveal early neuropathology and host responses to nervous necrosis virus.

Journal: iScience

Status: data only, 2 datasets cited

[29] Code ↔ Paper doi:10.1073/pnas.2532946123 [paper, repository]

<i>Hex</i>-MASP for mapping the whole-tissue spatial proteome and the intrabrain distribution of monoclonal antibodies.

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

Authors' code: JunQu-Lab/MAsP (Apache-2.0)

Status: code verified, 10 files readable, 2 matches

Wednesday, 2 September 2026 (4 papers)

[30] Code ↔ Paper doi:10.1016/j.isci.2026.117412 [paper, repository]

Transcriptomic landscape of microglia in mouse models of social dysfunction and oxytocin-mediated recovery.

Journal: iScience

Authors' code: MasaTsurutani/Transcriptomic-Landscape-of-Microglia-in-Mouse-Models-of-Social-Dysfunction-and-Oxytocin-Mediated (no license)

Status: empty repository, 1 file readable

[31] Code ↔ Paper doi:10.1038/s44400-026-00125-4 [paper, repository]

Regulators of interferon-responsive microglia uncovered by Genome-wide CRISPRi screening.

Journal: NPJ dementia

Authors' code: immunogenomics/presto (no license), reetm09/mixscale (no license)

Status: code verified, 45 files readable, 5 matches

[32] Code ↔ Paper doi:10.1155/da/8792696 [paper, repository]

Connectome Gradient-Based Subtyping of Major Depressive Disorder Reveals Distinct Neurobiological and Transcriptomic Signatures.

Journal: Depression and anxiety

Authors' code: evarol/HYDRA (GPL-3.0), MICA-MNI/BrainSpace (BSD-3-Clause), Jfortin1/ComBatHarmonization (no license)

Status: code verified, 145 files readable, 2 matches

[33] Code ↔ Paper doi:10.1038/s41467-026-77302-9 [paper, repository]

Identification and validation of central amygdala FGFR1 as a therapeutic target for alcohol use disorder using single-nucleus sequencing in rats.

Journal: Nature communications

Authors' code: leohog/Fgfr1_analysis (MIT)

Status: code verified, 3 files readable, 4 matches

Tuesday, 1 September 2026 (22 papers)

[34] doi:10.3389/fnins.2026.1950353 [paper]

A neuron-distributed DEK integrates ac4C modification and neuroinflammation in pathogenesis of Parkinson disease: evidence from Mendelian randomization, multi-omics and <i>in vitro</i> validation.

Journal: Frontiers in neuroscience

Status: code on request

[35] doi:10.1111/cbdd.70396 [paper, data]

Integrated Multi-Omics and Radiogenomic Analysis Identifies S100B and ITGB5 as Complementary Candidate Biomarkers of Glioblastoma Heterogeneity.

Journal: Chemical biology & drug design

Status: code on request, 1 dataset cited

[36] doi:10.1097/md.0000000000050324 [paper, data]

Transcriptomic integration reveals immune heterogeneity in vascular dementia and identifies ELF2 as a candidate therapeutic target.

Journal: Medicine

Status: data only, 1 dataset cited

[37] Code ↔ Paper doi:10.1093/bib/bbag485 [paper, repository]

Single-cell-level perturbation-induced and condition-related signal estimation with batch effect removal using NDreamer.

Journal: Briefings in bioinformatics

Authors' code: lugia-xiao/NDreamer (GPL-3.0), lugia-xiao/NDreamer_reproducible (GPL-3.0)

Status: code verified, 46 files readable, 24 matches

[38] Code ↔ Paper doi:10.1002/alz.71823 [paper, repository]

Cellular transcriptomic signatures underpinning the heterogeneity of depression in Alzheimer's disease.

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

Authors' code: NCTrailRunner/NPS_manuscript (no license)

Status: code verified, 23 files readable, 8 matches

[39] Code ↔ Paper doi:10.1093/bib/bbag490 [paper, repository]

Systematic benchmarking and optimal strategy selection of cross-species integration methods.

Journal: Briefings in bioinformatics

Authors' code: figshare 31976259 (CC-BY-4.0)

Status: code verified, 37 files readable, 9 matches

[40] doi:10.1002/alz.71804 [paper, data]

A meta-refined human Alzheimer's disease-associated gene subset shows partial mouse-model pathway correspondence and limited cross-cohort machine-learning transportability.

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

Status: data only, 1 dataset cited

[41] Code ↔ Paper doi:10.1111/mec.70527 [paper, repository]

Epigenetic Changes Associated With a Phenotypic Transition in Namibian Cheetahs.

Journal: Molecular ecology

Authors' code: vullioud/Vullioud_et_al_2026_Molecular_Ecology_scripts (no license)

Status: code verified, 20 files readable, 12 matches

[42] Code ↔ Paper doi:10.1162/imag.a.1342 [paper, repository]

Hyperpolarized <sup>13</sup>C-bicarbonate production correlates with excitatory neuron distribution in the human brain.

Journal: Imaging neuroscience (Cambridge, Mass.)

Authors' code: Zenodo 20575695 (CC-BY-4.0), brinuthayakumar/hpmr-genetranscript_imagingneuroscience (no license)

Status: code verified, 19 files readable, 3 matches

[43] Code ↔ Paper doi:10.1002/advs.77524 [paper, repository]

MethyAnno: An Interpretable Automated Annotation Method Leveraging Multi-Scale Information and Metric Learning Framework for scDNAm Data.

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

Authors' code: BioX-NKU/MethyAnno (MIT)

Status: code verified, 22 files readable, 9 matches

[44] Code ↔ Paper doi:10.1073/pnas.2609814123 [paper, repository]

Genetic architectures of brain-related traits are shaped by strong selective constraints.

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

Authors' code: bulik/ldsc (GPL-3.0), huishengz/cns-selection (no license)

Status: code verified, 72 files readable, 10 matches

[45] doi:10.1002/brb3.71701 [paper, data]

POFUT1 Serves as an Independent Prognostic Factor and Therapeutic Target by Activating the PI3K/AKT Pathway in Glioma.

Journal: Brain and behavior

Status: data only, 1 dataset cited

[46] Code ↔ Paper doi:10.1002/alz.71714 [paper, repository]

Cross-tissue immune profiling of APOE ε4 reveals early dysregulation in Alzheimer's disease.

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

Authors' code: Art83/AD_apoe (no license)

Status: dead link

[47] doi:10.14814/phy2.71059 [paper, data]

Impact of aging on neck vasculature and brain biochemistry in female mice.

Journal: Physiological reports

Status: data only, 1 dataset cited

[48] Code ↔ Paper doi:10.1002/hbm.70635 [paper, repository]

Cerebral Cortical Structural Variation and General Cognitive Ability: Evidence From Mendelian Randomization.

Journal: Human brain mapping

Authors' code: jianyang-lab/gsmr (no license)

Status: code verified, 6 files readable, 1 match

[49] Code ↔ Paper doi:10.1093/gbe/evag222 [paper, repository]

Genomic Signatures of Selection Are Enriched in Differentially Expressed Genes in Sticklebacks Adapting to Contrasting Environments.

Journal: Genome biology and evolution

Authors' code: z0on/tag-based_RNAseq (no license)

Status: code verified, 30 files readable

[50] doi:10.1002/dev.70183 [paper]

Executive Function and Epigenetic Markers in Youth Exposed to Family and Community Violence in Childhood.

Journal: Developmental psychobiology

Status: code on request

[51] doi:10.1002/npr2.70150 [paper]

Sleep Deprivation and Neuronal Hyperexcitation Share Transcriptomic Signatures.

Journal: Neuropsychopharmacology reports

Status: data only

[52] Code ↔ Paper doi:10.1093/neuonc/noag128 [paper, repository]

Spatially-resolved single-cell imaging of melanoma brain metastases identifies localized immune patterns predictive of immune checkpoint blockade response.

Journal: Neuro-oncology

Authors' code: BodenmillerGroup/steinbock (MIT), StefanosVoglis/Voglis_et_al_2026_Neuro-Oncology (no license)

Status: code verified, 92 files readable, 18 matches

[53] Code ↔ Paper doi:10.1093/neuonc/noag119 [paper, repository]

Single-nucleus profiling of postmortem diffuse midline gliomas identifies mitochondrial biogenesis as a resistance mechanism to imipridone therapy.

Journal: Neuro-oncology

Authors' code: CancerGenomicsLab/DMG_ONC201 (MIT)

Status: code verified, 9 files readable, 2 matches

[54] Code ↔ Paper doi:10.1093/brain/awag039 [paper, repository]

Mapping the causal chain from genetic risk variants to lipid dysmetabolism in Parkinson's disease.

Journal: Brain : a journal of neurology

Authors' code: ruthbpaula/PD_multiomics (no license)

Status: code verified, 6 files readable, 11 matches

[55] doi:10.1093/brain/awag033 [paper, data]

Impairment of hippocampal gamma oscillations, mitochondria and neurovascular function in CADASIL.

Journal: Brain : a journal of neurology

Status: data only, 1 dataset cited

Monday, 31 August 2026 (8 papers)

[56] Code ↔ Paper doi:10.1002/advs.77003 [paper, repository]

SemanticST: A Scalable Multi-Contextual Graph Learning Framework for Uncovering Spatial Niches and Robust Multi-Sample Integration in Spatial Transcriptomics.

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

Authors' code: roxana9/SemanticST (MIT)

Status: code verified, 25 files readable, 9 matches

[57] Code ↔ Paper doi:10.1002/advs.77453 [paper, repository]

Tau Aggregate Imaging and Transcriptomics of Alzheimer's Disease Brain at Different Stages of Disease.

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

Authors' code: Zenodo 15635269 (MIT), dboeken/boeken_tauopathies (MIT)

Status: code verified, 11 files readable, 1 match

[58] doi:10.1016/j.ebiom.2026.106451 [paper, data]

STX1B variant-specific synaptic dysfunction is associated with network hyperexcitability in human iPSC-derived neurons.

Journal: EBioMedicine

Status: data only, 1 dataset cited

[59] Code ↔ Paper doi:10.1093/narcan/zcag021 [paper, repository]

Multi-omic cell free DNA profiles of cerebral spinal fluid from lung cancer metastasis to the brain.

Journal: NAR cancer

Authors' code: Tianqi-Kiki/nanopore_CSF_cfDNA (MIT), Zenodo 20173042 (MIT)

Status: code verified, 14 files readable, 7 matches

[60] Code ↔ Paper doi:10.1038/s44400-026-00100-z [paper, repository]

Peripheral blood microarray-based transcriptomic and epigenetic analyses identify immune, inflammation, and metabolic dysregulation in Alzheimer's disease.

Journal: NPJ dementia

Authors' code: cind/adni-mrna-dnam-analysis (no license)

Status: code verified, 17 files readable, 16 matches

[61] Code ↔ Paper doi:10.2147/jpr.s619982 [paper, repository]

Spatially Contextualized Integrative Genomics Highlights Neuronal and Glial Regulatory Programs in Low Back Pain.

Journal: Journal of pain research

Authors' code: zza070952-collab/LBP_brain_eQTL_spatial_genomics (no license)

Status: code verified, 36 files readable, 20 matches

[62] doi:10.3390/ijms27177801 [paper, data]

Expression of the Human R163C-<i>RYR1</i> Gain-of-Function Mutation Modified 2,2',3,5',6-Pentachlorobiphenyl (PCB 95) Developmental Neurotoxicity in Weanling Mice.

Journal: International journal of molecular sciences

Status: data only, 1 dataset cited

[63] Code ↔ Paper doi:10.3389/fnagi.2026.1931183 [paper, repository]

A validated workflow for paired total and small RNA sequencing from low-input submandibular gland biopsy specimens in <i>de novo</i> Parkinson's disease patients.

Journal: Frontiers in aging neuroscience

Authors' code: thelovelab/DESeq2 (no license)

Status: code verified, 52 files readable, 2 matches

Saturday, 29 August 2026 (1 paper)

[64] Code ↔ Paper doi:10.1038/s41467-026-77170-3 [paper, repository]

DNA methylation profiling identifies long-range epigenetic silencing of clustered protocadherins as a key determinant of meningioma progression.

Journal: Nature communications

Authors' code: MerkLabHIH/Meningioma_DNA_methylation_project (no license)

Status: code verified, 13 files readable, 22 matches

Thursday, 27 August 2026 (3 papers)

[65] Code ↔ Paper doi:10.1038/s41588-026-02722-8 [paper, repository]

A multiancestry polygenic risk score for Alzheimer's disease is associated with cognitive decline and neuropathological hallmarks in diverse populations.

Journal: Nature genetics

Authors' code: nkurniansyah/PRSsum_Simple (no license), nkurniansyah/Alzheimer_PRS (no license), nkurniansyah (no license), Zenodo 20818015 (CC-BY-4.0)

Status: code verified, 16 files readable, 8 matches

[66] Code ↔ Paper doi:10.1093/braincomms/fcag326 [paper, repository]

Brain multiomic profiling identifies tau-related transcriptomic dysregulation in Alzheimer's disease.

Journal: Brain communications

Authors' code: synapse.org/synapse:syn75046458 (no license)

Status: code verified

[67] doi:10.3390/ijms27177675 [paper, data]

LncRNA Gas5, a Target of the Nonsense-Mediated Decay Pathway in the Brain, Regulates Neuroinflammation and Neurodegenerative Disease Pathways in a Tauopathy Mouse Model.

Journal: International journal of molecular sciences

Status: data only, 1 dataset cited

Wednesday, 26 August 2026 (7 papers)

[68] doi:10.1007/s12035-026-06133-y [paper, data]

Systematic Review and Transcriptomic Meta-analysis of Environmental Enrichment Reveal Core Molecular Programs of Brain Plasticity.

Journal: Molecular neurobiology

Status: data only, 1 dataset cited

[69] Code ↔ Paper doi:10.1126/sciadv.aed3650 [paper, repository]

Truthful visualizations for mass spectrometry imaging enable high-spatial-resolution interactive <i>m/z</i> mapping and exploration.

Journal: Science advances

Authors' code: Zenodo 19465293 (MIT)

Status: code verified, 96 files readable, 2 matches

[70] Code ↔ Paper doi:10.1093/braincomms/fcag322 [paper, repository]

Genomic insights into stroke recovery: cross-phenotype associations.

Journal: Brain communications

Authors' code: CMAldridge/Cross-Phenotype-GWAS (no license)

Status: code verified, 9 files readable, 3 matches

[71] doi:10.1016/j.isci.2026.117332 [paper, data]

The <i>Sox2</i> regulatory region 42 produces enhancer RNAs that influence neuronal migration during cortical development.

Journal: iScience

Status: code on request, 1 dataset cited

[72] doi:10.3389/fimmu.2026.1937738 [paper, data]

Multi-regional transcriptomic analysis reveals early nociceptive and neuroinflammatory alterations in APP/PS1 mice.

Journal: Frontiers in immunology

Status: data only, 2 datasets cited

[73] doi:10.3389/fncel.2026.1908231 [paper, data]

Integrative transcriptomic- neuroimaging analysis reveals polygenic correlates of interhemispheric functional decoupling in ischemic stroke.

Journal: Frontiers in cellular neuroscience

Status: data only, 1 dataset cited

[74] doi:10.3389/fimmu.2026.1805464 [paper, data]

Chronic low-grade inflammation, genetic susceptibility, and the risk of multiple sclerosis: a prospective cohort study.

Journal: Frontiers in immunology

Status: data only, 1 dataset cited

Tuesday, 25 August 2026 (2 papers)

[75] Code ↔ Paper doi:10.1038/s41467-026-76929-y [paper, repository]

Next-generation multiplexed targeted proteomics quantifies post-translational modifications in disease and compound-protein interactions with high throughput.

Journal: Nature communications

Authors' code: thermofisherlsms/iapi (MIT), uwpr.github.io/comet (no license)

Status: code verified, 13 files readable

[76] doi:10.3389/fped.2026.1891438 [paper, data]

Identification and clinical validation of F3 as a peripheral blood biomarker for neonatal hypoxic-ischemic encephalopathy using dataset-specific bioinformatics analysis.

Journal: Frontiers in pediatrics

Status: data only, 1 dataset cited

Monday, 24 August 2026 (5 papers)

[77] Code ↔ Paper doi:10.1523/eneuro.0121-26.2026 [paper, repository]

Hippocampal Gene Expression in Zebra Finches Reveals Sex- and Subregion-Specific Topographies.

Journal: eNeuro

Authors' code: ATayl4908/ZB-DGE-analysis (no license)

Status: dead link

[78] Code ↔ Paper doi:10.1016/j.xpro.2026.104801 [paper, repository]

Protocol to characterize tumor microenvironment in a diffuse midline glioma mouse model using multi-omics approach on sequential sections.

Journal: STAR protocols

Authors' code: conda-forge/miniforge (BSD-3-Clause), Zenodo 21513336 (MIT)

Status: code verified, 14 files readable

[79] doi:10.1371/journal.pone.0355984 [paper]

An integrated systems biology and machine learning framework for identifying potential biomarkers and pathways in autism spectrum disorder.

Journal: PloS one

Status: data only

[80] Code ↔ Paper doi:10.1038/s41592-026-03194-8 [paper, repository]

Beyond benchmarking: an expert-guided consensus approach to spatially aware clustering.

Journal: Nature methods

Authors' code: SpatialHackathon/SACCELERATOR (MIT), SpatialHackathon/SpaceHack2023_study (MIT), Zenodo 15487520 (CC-BY-4.0)

Status: code verified, 129 files readable, 20 matches

[81] Code ↔ Paper doi:10.1016/j.isci.2026.117346 [paper, repository]

Spatial transcriptomics of <i>Ciona</i> adult brains reveals functional zonalization and insights into neural gland function.

Journal: iScience

Authors' code: figshare 31915545 (CC-BY-4.0), xzengComBio/Ciona_ST (no license)

Status: code verified, 12 files readable, 5 matches

Saturday, 22 August 2026 (2 papers)

[82] doi:10.1186/s13073-026-01745-4 [paper, data]

The clinical and molecular spectrum of AGO2-associated Lessel-Kreienkamp neurodevelopmental syndrome.

Journal: Genome medicine

Status: data only, 2 datasets cited

[83] doi:10.3390/cells15171512 [paper, data]

Asymmetric Functional Divergence of <i>alx4a</i> and <i>alx4b</i> in Iridophore Differentiation and Cranial Development in Nile Tilapia.

Journal: Cells

Status: data only, 1 dataset cited

Friday, 21 August 2026 (4 papers)

[84] doi:10.1371/journal.pgen.1012260 [paper, data]

Hippo signaling regulates cuticle pigmentation and dopamine metabolism in Drosophila.

Journal: PLoS genetics

Status: data only, 1 dataset cited

[85] doi:10.1186/s40478-026-02402-y [paper, data]

Overactivation of SHH signaling induces a cascade of dedifferentiation and oncogenesis in a new mouse model for choroid plexus carcinoma.

Journal: Acta neuropathologica communications

Status: data only, 5 datasets cited

[86] Code ↔ Paper doi:10.1016/j.isci.2026.117281 [paper, repository]

Spatial pattern-driven interpretable model and biological correlates in brain glioblastoma-lymphoma differentiation.

Journal: iScience

Authors' code: JLhos-fmri/SPLSM_version1.0 (GPL-3.0), JLhos-fmri/ClinicalFrequencyAnalysisToolkit (GPL-3.0), rpomponio/neuroHarmonize (MIT)

Status: code verified, 95 files readable, 2 matches

[87] doi:10.3389/fcell.2026.1876873 [paper, data]

Multi-omics integration reveals TIM-4 as a master regulatory hub of neuroinflammation and neuronal cell death.

Journal: Frontiers in cell and developmental biology

Status: data only, 1 dataset cited

Thursday, 20 August 2026 (6 papers)

[88] doi:10.1016/j.stemcr.2026.103049 [paper]

A human-specific non-coding RNA for EFHC1, an epilepsy-associated gene, regulates neural stem cell proliferation for cortical development.

Journal: Stem cell reports

Status: code on request

[89] Code ↔ Paper doi:10.1038/s41467-026-74694-6 [paper, repository]

Semi-supervised Omics Factor Analysis (SOFA) disentangles known and latent sources of variation in multi-omic data.

Journal: Nature communications

Authors' code: Zenodo 14761127 (CC-BY-4.0), tcapraz/SOFA (MIT), Zenodo 19594991 (CC-BY-4.0)

Status: code verified, 17 files readable, 3 matches

[90] Code ↔ Paper doi:10.1002/imt2.70163 [paper, repository]

Spatial multi-omics unveils sphingolipid metabolic reprogramming within the retinal pathological niche.

Journal: iMeta

Authors' code: alserglab/fgsea (MIT), pienapple1/eyeball_STSM (no license)

Status: code verified, 99 files readable, 10 matches

[91] doi:10.3389/fnins.2026.1889410 [paper, data]

Amino acid- and lipid-related metabolic remodeling in PTZ-kindled mice reveals candidate plasma signatures of chronic epilepsy.

Journal: Frontiers in neuroscience

Status: data only, 1 dataset cited

[92] doi:10.3389/fimmu.2026.1911726 [paper, data]

Identification of interleukin-11 as a comorbid risk factor for prostate cancer and Alzheimer's disease using integrated bioinformatics and machine learning.

Journal: Frontiers in immunology

Status: data only, 1 dataset cited

[93] doi:10.1038/s41467-026-76838-0 [paper, data]

The DLX/Notch axis is necessary for spatiotemporal regulation of neural cell fate.

Journal: Nature communications

Status: data only, 1 dataset cited

Wednesday, 19 August 2026 (6 papers)

[94] doi:10.1080/17590914.2026.2691563 [paper, data]

Shared Transcriptomic and Epigenomic Signatures Between Traumatic Brain Injury and Music Exposure: An Integrative Proof of Concept.

Journal: ASN neuro

Status: data only, 1 dataset cited

[95] Code ↔ Paper doi:10.1038/s41586-026-10877-x [paper, repository]

Human brain organoids record the passage of time over multiple years.

Journal: Nature

Authors' code: LSteg/EpigeneticFetalClock (no license), gemmashireby/CorticalClock (no license), tfaits/Arlotta_Lab_LongTermOrganoids (no license)

Status: code verified, 15 files readable, 21 matches

[96] Code ↔ Paper doi:10.3390/brainsci16080883 [paper, repository]

Anxiety and Depression Traits Are Moderated by a Sex-Dependent Genetic Interaction Between 5-HTTLPR and BDNF.

Journal: Brain sciences

Authors' code: LorenzoOdierna/AnxDepStudy5-HTTLPRBDNFSex (no license)

Status: empty repository

[97] Code ↔ Paper doi:10.1016/j.isci.2026.117228 [paper, repository]

Single-nucleus transcriptomics reveals cell type-specific remodeling and epilepsy-associated microglia.

Journal: iScience

Authors' code: VictoriaHo-Lab/snRNAseq-pilo (no license)

Status: code verified, 10 files readable, 11 matches

[98] Code ↔ Paper doi:10.1038/s41467-026-76675-1 [paper, repository]

Long-read proteogenomic atlas of human neuronal differentiation reveals isoform diversity informing neurodevelopmental risk mechanisms.

Journal: Nature communications

Authors' code: gandallab/Dev_Brain_IsoSeq (no license), nuoxuxu/SFARI (MIT), Zenodo 16897532 (CC-BY-4.0)

Status: code verified, 293 files readable, 40 matches

[99] Code ↔ Paper doi:10.3389/fragi.2026.1856979 [paper, repository]

A minimal three-arm oral regimen for healthspan: mechanistic alignment with transcriptomic signals from a large parental-lifespan GWAS.

Journal: Frontiers in aging

Authors' code: figshare 31951029 (CC-BY-4.0)

Status: empty repository

Tuesday, 18 August 2026 (3 papers)

[100] doi:10.1080/20008066.2026.2709174 [paper, data]

Exploring the shared genetic architecture between post-traumatic stress disorder (PTSD) and obstructive sleep apnea (OSA).

Journal: European journal of psychotraumatology

Status: data only, 1 dataset cited

[101] doi:10.7554/elife.110458 [paper, data]

TLR4 signaling drives tissue inflammation, Claudin-5 internalization, and vascular barrier breakdown in a mouse model of neonatal meningitis.

Journal: eLife

Status: data only, 1 dataset cited

[102] doi:10.3390/biology15161423 [paper]

Circulating Homocysteine and Choroid Plexus Volume Across the Alzheimer's Disease Continuum: Cross-Sectional and Progression-Related Associations.

Journal: Biology

Status: code on request

Monday, 17 August 2026 (3 papers)

[103] doi:10.3389/fphar.2026.1830927 [paper, data]

<i>Astragalus polysaccharide</i> alleviates neuropathology and cognitive deficits by modulating gut microbiota and neuroinflammation in an Alzheimer's disease model.

Journal: Frontiers in pharmacology

Status: data only, 1 dataset cited

[104] doi:10.3389/fnins.2026.1913179 [paper, data]

Decoding astrocytic tryptophan metabolism in the pathogenesis of epilepsy: evidence from artificial intelligence-driven multi-omics and clinical validation.

Journal: Frontiers in neuroscience

Status: data only, 1 dataset cited

[105] doi:10.31083/ap51694 [paper, data]

Imatinib-Induced Changes in Anxiety-Like Behaviors are Associated With Prefrontal Cortical Metabolic Remodeling in Mice.

Journal: Alpha psychiatry

Status: data only, 1 dataset cited

Sunday, 16 August 2026 (1 paper)

[106] Code ↔ Paper doi:10.1186/s12711-026-01078-1 [paper, repository]

Functional genomic dissection and prediction of body size traits in pigs.

Journal: Genetics, selection, evolution : GSE

Authors' code: susjoh/wildsim (no license)

Status: code verified, 23 files readable

Saturday, 15 August 2026 (3 papers)

[107] doi:10.1038/s44184-026-00232-3 [paper]

Integrated proteomic, transcriptomic, and epigenomic profiling identifies SRA1 as a novel therapeutic target for postpartum depression.

Journal: Npj mental health research

Status: code on request

[108] Code ↔ Paper doi:10.1038/s41467-026-76688-w [paper, repository]

Transcriptome profiling of human hypothalamic agouti-related protein and proopiomelanocortin neurons regulating energy homeostasis.

Journal: Nature communications

Authors' code: goczbalazs/PRJNA1305226_1305334 (no license)

Status: code verified, 5 files readable, 6 matches

[109] Code ↔ Paper doi:10.1038/s41467-026-76682-2 [paper, repository]

Odorant receptor coexpression and multi-expression in the dengue mosquito.

Journal: Nature communications

Authors' code: mcbridelab/Adavi_2024_snRNAseqAaegAntennae (no license)

Status: code verified, 6 files readable, 16 matches

Friday, 14 August 2026 (10 papers)

[110] Code ↔ Paper doi:10.7554/elife.93640 [paper, repository]

Sibling chimerism among microglia in marmosets.

Journal: eLife

Authors' code: broadinstitute/Drop-seq (MIT), lh3/bwa (GPL-3.0), satijalab/seurat (other), IanevskiAleksandr/sc-type (GPL-3.0), satijalab/sctransform (GPL-3.0), PMBio/peer (GPL-2.0)

Status: code verified, 2,544 files readable, 6 matches

[111] Code ↔ Paper doi:10.1371/journal.pbio.3003931 [paper, repository]

A single-cell transcriptomic atlas reveals the emergence of medusa-specific cell states in the scyphozoan Aurelia coerulea.

Journal: PLoS biology

Authors' code: technau/AureliaAtlas (no license), Zenodo 21132158 (CC-BY-4.0)

Status: code verified, 14 files readable, 16 matches

[112] Code ↔ Paper doi:10.1126/sciadv.aeg3223 [paper, repository]

The extreme diversity of retinal amacrine cells has deep evolutionary roots.

Journal: Science advances

Authors' code: shekharlab/AmacrineCells (MIT), Zenodo 20451319 (MIT)

Status: code verified, 52 files readable, 30 matches

[113] doi:10.1038/s41588-026-02709-5 [paper, data]

PLCG2 downregulation impairs synaptic function and increases Alzheimer's disease hallmarks in neuronal cultures.

Journal: Nature genetics

Status: data only, 3 datasets cited

[114] Code ↔ Paper doi:10.1186/s44477-026-00045-w [paper, repository]

Proteomic analysis of human chronic traumatic encephalopathy brain implicates proteasome and ribosome dysfunction in disease severity.

Journal: Molecular neurodegeneration advances

Authors' code: BU-Neuromics/cte-proteomics-2026 (no license)

Status: code verified, 10 files readable, 9 matches

[115] Code ↔ Paper doi:10.1016/j.isci.2026.117206 [paper, repository]

ReliST: A model-agnostic risk layer for spatial transcriptomics deconvolution.

Journal: iScience

Authors' code: tp5353/ReliST (MIT)

Status: code verified, 60 files readable, 24 matches

[116] doi:10.3390/cancers18162616 [paper, data]

Decitabine Reprograms Temozolomide-Resistant Glioblastoma Through Epigenetic Reactivation and Mesenchymal Attenuation: A Multi-Omics Study.

Journal: Cancers

Status: code on request, 1 dataset cited

[117] doi:10.3390/biom16081187 [paper, data]

Genetic Diversity and Runs of Homozygosity in Three Masu Salmon (<i>Oncorhynchus masou</i>) Populations Based on Whole-Genome Resequencing Data.

Journal: Biomolecules

Status: data only, 1 dataset cited

[118] Code ↔ Paper doi:10.3390/ijms27167275 [paper, repository]

Integrative Multi-Omics Analysis of Multiple Sclerosis Reveals Cell-Type-Specific Regulatory Landscapes and Discordant Methylation-Expression Coupling.

Journal: International journal of molecular sciences

Authors' code: alperbulbul1/MS_Omics_Data_Analysis (MIT)

Status: code verified, 104 files readable, 40 matches

[119] Code ↔ Paper doi:10.1038/s41467-026-76676-0 [paper, repository]

Determinants of functional burden pleiotropy and gene dosage responses across human traits.

Journal: Nature communications

Authors' code: martineaujeanlouis.github.io/mind-genesparallelcnv (no license), linnarsson-lab/adult-human-brain (BSD-2-Clause), SayehKazem/FunBurd (MIT), Zenodo 17038354 (MIT), funburd.readthedocs.io (no license)

Status: code verified, 114 files readable, 21 matches

Thursday, 13 August 2026 (6 papers)

[120] doi:10.64898/2026.08.12.26360241 [paper, data]

Diffusion kurtosis imaging (gen)omics unravels mechanisms of cerebral small vessel disease

Journal: medRxiv (preprint)

Status: data only, 1 dataset cited

[121] Code ↔ Paper doi:10.1002/2211-5463.70322 [paper, repository]

Identification and characterisation of calcitonin receptor isoforms expressed in glioblastoma derived glioma stem and U-87 MG cells.

Journal: FEBS open bio

Authors' code: shwetajoshi-15/discoAnt (no license)

Status: code verified, 6 files readable

[122] doi:10.3390/ijms27167238 [paper, data]

<i>RFX3</i> Pathogenic Variants as a Rare Cause of Infantile Epileptic Spasms Syndrome.

Journal: International journal of molecular sciences

Status: data only, 1 dataset cited

[123] Code ↔ Paper doi:10.3389/fgene.2026.1799530 [paper, repository]

Sex-dependent prediction of autism.

Journal: Frontiers in genetics

Authors' code: Catriona-Miller/autism_ml (no license)

Status: code verified, 4 files readable, 1 match

[124] Code ↔ Paper doi:10.3389/fnagi.2026.1839445 [paper, repository]

The molecular mechanisms of Guizhi Fuling Pills in ameliorating Alzheimer's disease-like cognitive impairment: insights from transcriptomics, metabolomics, and gut microbiome.

Journal: Frontiers in aging neuroscience

Authors' code: OpenGene/fastp (MIT), tanghaibao/GOatools (BSD-2-Clause)

Status: code verified, 204 files readable, 2 matches

[125] Code ↔ Paper doi:10.1038/s41467-026-76812-w [paper, repository]

Assessing molecular, cellular and transcriptomic bases of laminar perfusion and cytoarchitecture coupling in the human cortex.

Journal: Nature communications

Authors' code: FanhuaGuo/ASL-Bigbrain-CCSI (MIT), Zenodo 21363179 (MIT)

Status: code verified, 70 files readable, 15 matches

Wednesday, 12 August 2026 (4 papers)

[126] doi:10.64898/2026.08.11.26359568 [paper, data]

<i>TMEM106B</i> haplotypes show distinct associations with tau and TDP-43 pathologies in the aging brain

Journal: medRxiv (preprint)

Status: data only, 1 dataset cited

[127] doi:10.3389/fnins.2026.1929767 [paper, data]

Tracing fucosylation and astrocyte-associated pathogenic pattern in major depressive disorder: evidence from machine learning-based multi-omics and clinical validation.

Journal: Frontiers in neuroscience

Status: data only, 1 dataset cited

[128] doi:10.3389/fpsyt.2026.1828806 [paper, data]

Integrative multi-omics and machine learning analysis identifies candidate biomarkers associated with mitochondrial quality control in major depressive disorder.

Journal: Frontiers in psychiatry

Status: data only, 2 datasets cited

[129] Code ↔ Paper doi:10.1016/j.isci.2026.116517 [paper, repository]

Spatially resolved transcriptomics in human brain metastases identifies macrophage-tumor interactions associated with survival.

Journal: iScience

Authors' code: huayc09/SeuratExtend (GPL-3.0)

Status: code verified, 60 files readable, 4 matches

Tuesday, 11 August 2026 (2 papers)

[130] doi:10.3389/fimmu.2026.1700109 [paper]

Integrated machine learning and transcriptomics reveal immune infiltration-related orthologous transcription genes in cerebral ischemic injury.

Journal: Frontiers in immunology

Status: data only

[131] Code ↔ Paper doi:10.1038/s41467-026-76232-w [paper, repository]

Th17 effector cytokines induce shared and distinct microglial and endothelial cell responses in a mouse model for post-streptococcal encephalitis.

Journal: Nature communications

Authors' code: AgalliuLab/s-pyogenes-scRNAseq (no license)

Status: code verified, 5 files readable, 14 matches

Monday, 10 August 2026 (6 papers)

[132] doi:10.1007/s10549-026-08050-z [paper]

Association of tumor Schwann cells with epithelial-mesenchymal transition and immune-suppressive microenvironment in triple-negative breast cancer.

Journal: Breast cancer research and treatment

Status: code on request

[133] doi:10.1080/19336896.2026.2710965 [paper, data]

Epigenetic changes associated with the progression of prion disease in Syrian hamsters (&lt;i&gt;Mesocricetus auratus&lt;/i&gt;).

Journal: Prion

Status: data only, 1 dataset cited

[134] Code ↔ Paper doi:10.1016/j.isci.2026.117038 [paper, repository]

Multi-region brain transcriptomes uncover two subtypes of aging individuals with differences in Alzheimer risk and the impact of &lt;i&gt;APOEε4&lt;/i&gt;.

Journal: iScience

Authors' code: anniejlee/multi-region-transcriptomes-aging-subtypes (no license)

Status: code verified, 3 files readable, 2 matches

[135] Code ↔ Paper doi:10.3389/fnmol.2026.1909269 [paper, repository]

Convergent functional networks of intrinsic activity alterations in temporal lobe epilepsy and their molecular correlates.

Journal: Frontiers in molecular neuroscience

Authors' code: juryxy/JuSpace (no license)

Status: code verified, 21 files readable

[136] Code ↔ Paper doi:10.3389/fnmol.2026.1817096 [paper, repository]

EIF2S1-PELO co-expression architecture in human brain: pairing-family decomposition reveals constitutive transcriptional coupling and functional layer separation.

Journal: Frontiers in molecular neuroscience

Authors' code: nwharbert8-ui/eif2s1-translational-qc-hubsub (MIT), Zenodo 18626362 (MIT)

Status: code verified, 16 files readable, 20 matches

[137] Code ↔ Paper doi:10.1038/s41467-026-76522-3 [paper, repository]

Transcriptomic analysis of spinal V1 interneurons informs their multifunctional role in motor output.

Journal: Nature communications

Authors' code: Bikoff-Lab (no license), Bikoff-Lab/V1_KO_analysis (MIT)

Status: code verified, 5 files readable, 5 matches

Sunday, 9 August 2026 (1 paper)

[138] doi:10.3390/ijms27167140 [paper, data]

Astrocytic HSP90AA1 Upregulation and Altered Synaptic Signaling in Parkinson's Disease: Transcriptomic Screening and In Vivo Validation.

Journal: International journal of molecular sciences

Status: data only, 1 dataset cited

Saturday, 8 August 2026 (3 papers)

[139] Code ↔ Paper doi:10.1038/s41467-026-76506-3 [paper, repository]

Allele-specific chromatin architecture shapes imprinted domains and coordinates a distal enhancer and antisense transcription at the mouse Mest-Copg2 domain.

Journal: Nature communications

Authors' code: Whipple-Lab/capture-hic-imprinting (no license), Zenodo 21224497 (CC-BY-4.0)

Status: code verified, 46 files readable, 8 matches

[140] Code ↔ Paper doi:10.1038/s41467-026-76587-0 [paper, repository]

Uncovering the signaling networks of disseminated glioblastoma cells in vivo with INSIGHT.

Journal: Nature communications

Authors' code: cycif.org (no license), ryuhjinahn (no license), hub.docker.com/r/bumproo (no license)

Status: code verified

[141] Code ↔ Paper doi:10.1038/s41467-026-75862-4 [paper, repository]

Targeting m&lt;sup&gt;6&lt;/sup&gt;A writer METTL3 with engineered nanovesicles reduces neuroinflammation in vitro and in vivo.

Journal: Nature communications

Authors' code: Zenodo 20627531 (CC-BY-4.0), xulf1996-arch/mettl3_m6a_bulk_pipeline (no license)

Status: code verified, 24 files readable, 5 matches

Friday, 7 August 2026 (2 papers)

[142] Code ↔ Paper doi:10.21203/rs.3.rs-10380518/v1 [paper, repository]

Shared Genetic Architecture of Premenstrual Disorder and Postpartum Depression: Registry-Based and Genetic Evidence

Journal: Research Square (preprint)

Authors' code: alexploner/cfdr.pleio (GPL-3.0)

Status: code verified, 9 files readable, 1 match

[143] doi:10.1016/j.jbc.2026.113399 [paper, data]

Domain-dependent uncoupling of the co-chaperone and E3 ubiquitin ligase CHIP underlies heterogeneity in spinocerebellar ataxia 48.

Journal: The Journal of biological chemistry

Status: data only, 1 dataset cited

Thursday, 6 August 2026 (8 papers)

[144] doi:10.1111/cpr.70269 [paper, data]

Chromatin Remodeller BRD9 Orchestrates Odontoblastic Differentiation via Coordinating RUNX2-KLF4.

Journal: Cell proliferation

Status: data only, 1 dataset cited

[145] Code ↔ Paper doi:10.1038/s12276-026-01801-4 [paper, repository]

Putative glioblastoma origin-like cells in the subventricular zone: isolation and characterization.

Journal: Experimental & molecular medicine

Authors' code: hoonbiolab/yugbmoc_paper (no license)

Status: code verified, 7 files readable, 6 matches

[146] doi:10.3390/nu18152575 [paper, data]

Diminished Maternal Tryptophan Leads to Sexually Dimorphic Differences in the Placenta-Brain Axis.

Journal: Nutrients

Status: data only, 1 dataset cited

[147] Code ↔ Paper doi:10.1016/j.isci.2026.117031 [paper, repository]

Plasma metabolomic signatures of migraine in 479,760 adults.

Journal: iScience

Authors' code: sun160414/UKB_Metabolomic_Migraine (no license)

Status: code verified, 6 files readable, 9 matches

[148] doi:10.3389/fcvm.2026.1859362 [paper, data]

The association between reduced hypothalamic subregion volume and aortic aneurysm risk: a Mendelian randomization and multi-omics study with clinical MRI validation.

Journal: Frontiers in cardiovascular medicine

Status: data only, 1 dataset cited

[149] Code ↔ Paper doi:10.3389/fbinf.2026.1832826 [paper, repository]

Spatial transcriptomics reveal heterogeneous cell‒cell interactions among brain regions in cuprizone model consistent with multiple sclerosis lesions.

Journal: Frontiers in bioinformatics

Authors' code: sunduanchen/Scissor (GPL-3.0)

Status: code verified, 20 files readable, 4 matches

[150] Code ↔ Paper doi:10.3389/fneur.2026.1822479 [paper, repository]

Circulating neuron-derived cfDNA for blood-based detection of Alzheimer's and other neurodegenerative conditions.

Journal: Frontiers in neurology

Authors' code: nanoporetech/dorado (GPL-3.0), nanoporetech/modkit (GPL-3.0), Wasatch-Biolabs-Bfx/MethylSeqR (other)

Status: code verified, 925 files readable, 4 matches

[151] doi:10.3390/ncrna12040031 [paper, data]

Long-Read RNA Sequencing Reveals an Isoform Switching Pattern in Healthy Microglial Cell Lines Exposed to Radiotherapy.

Journal: Non-coding RNA

Status: data only, 1 dataset cited

Wednesday, 5 August 2026 (1 paper)

[152] doi:10.3389/fncel.2026.1901103 [paper]

Loss of epigenetic adaptation to a high-fat diet in alpha-synuclein transgenic mice.

Journal: Frontiers in cellular neuroscience

Status: data only

Tuesday, 4 August 2026 (5 papers)

[153] Code ↔ Paper doi:10.7554/elife.106081 [paper, repository]

Heritability of movie-evoked brain activity and connectivity.

Journal: eLife

Authors' code: dsclab42/Gruskin-eLife2026 (MIT)

Status: code verified, 28 files readable, 11 matches

[154] doi:10.1016/j.xpro.2026.104720 [paper, data]

Protocol using AGO-APP for isolation and sequencing of argonaute-bound miRNAs in specific neuronal subtypes of the mouse brain.

Journal: STAR protocols

Status: data only, 1 dataset cited

[155] doi:10.1016/j.cell.2026.07.023 [paper, data]

Metabolic atlas of early human cortex reveals glycolytic remodeling and pentose phosphate pathway control of cell fate transitions.

Journal: Cell

Status: code on request, 1 dataset cited

[156] doi:10.1111/bpa.70129 [paper]

Brain metastasis-associated fibroblasts shape the tumour microenvironment to enhance cancer cell invasion.

Journal: Brain pathology (Zurich, Switzerland)

Status: data only

[157] doi:10.3389/fmicb.2026.1811435 [paper, data]

Research on the role of gut microbiota metabolites in autism by multi-omics and network pharmacology.

Journal: Frontiers in microbiology

Status: data only, 1 dataset cited

Monday, 3 August 2026 (6 papers)

[158] Code ↔ Paper doi:10.1038/s41593-026-02387-w [paper, repository]

Developing mouse inhibitory neuron single-cell transcriptomes reveal distinct modes of cell-type diversification.

Journal: Nature neuroscience

Authors' code: Limlab-VIBCBD/Dev-SST-atlas (no license)

Status: code verified, 17 files readable, 23 matches

[159] Code ↔ Paper doi:10.1038/s44161-026-00844-0 [paper, repository]

Pericyte K&lt;sub&gt;ATP&lt;/sub&gt; channel hyperactivity redistributes cortical blood flow in a CADASIL mouse model.

Journal: Nature cardiovascular research

Authors' code: ntsoukias/SVD-Blood-Flow-Simulation (other), Zenodo 20722612 (CC-BY-4.0)

Status: code verified, 12 files readable, 5 matches

[160] doi:10.3390/ijms27156964 [paper, data]

Senescence Markers and Associated Transcriptomic Changes Are Expressed at Early Stages of Alzheimer's Neuropathology but Are Not Independently Related to Dementia.

Journal: International journal of molecular sciences

Status: data only, 1 dataset cited

[161] doi:10.1016/j.isci.2026.117017 [paper, data]

Across species identification of genes bridging neurological and reproductive functions in mammals.

Journal: iScience

Status: data only, 2 datasets cited

[162] Code ↔ Paper doi:10.1016/j.psj.2026.107561 [paper, repository]

Integrated Analysis of SNPs and Structural Variations via High-depth Whole-genome Sequencing Reveals the Genetic Architecture and Optimizes Genomic Prediction in Chickens.

Journal: Poultry science

Authors' code: jasmine/jasmine (MIT), HaoqiangYe/GPDLBP (MIT)

Status: code verified, 292 files readable, 3 matches

[163] doi:10.3389/fnins.2026.1785001 [paper, data]

A single-cell transcriptomic atlas of the periventricular proliferative zone in the late gestation fetal brain in the pigtail macaque.

Journal: Frontiers in neuroscience

Status: data only, 1 dataset cited

Saturday, 1 August 2026 (22 papers)

[164] Code ↔ Paper doi:10.1093/brain/awaf440 [paper, repository]

Cerebrospinal fluid-driven ependymal motile cilia defects are implicated in multiple sclerosis.

Journal: Brain : a journal of neurology

Authors' code: stratton-lab/Bigotte-2025-Cilia (GPL-3.0)

Status: code verified, 3 files readable, 3 matches

[165] Code ↔ Paper doi:10.1093/brain/awaf443 [paper, repository]

Cellular signatures underlying functional resilience in presymptomatic frontotemporal dementia.

Journal: Brain : a journal of neurology

Authors' code: kamentsvetanov/functional_resilience_ftd (GPL-3.0), mrc-cbu/riksneurotools (GPL-3.0), frantisekvasa/rotate_parcellation (MIT), BMHLab/AHBAprocessing (no license), netneurolab/hansen_genescognition (no license)

Status: code verified, 423 files readable, 6 matches

[166] doi:10.1021/acs.jproteome.5c01173 [paper, data]

Proteomic Analysis Identifies ATE1-Dependent Arginylation Dysregulation across Meningioma Grades.

Journal: Journal of proteome research

Status: data only, 1 dataset cited

[167] Code ↔ Paper doi:10.1093/bioinformatics/btag652 [paper, repository]

mmVelo: a deep generative model for estimating cell state-dependent dynamics across multiple modalities.

Journal: Bioinformatics (Oxford, England)

Authors' code: nomuhyooon/mmVelo (no license), Zenodo 20103609 (CC-BY-4.0)

Status: code verified, 170 files readable, 21 matches

[168] doi:10.1093/stcltm/szag071 [paper, data]

Temporal mapping of radiation-induced neural injury and mitigation in human cortical organoids.

Journal: Stem cells translational medicine

Status: data only, 1 dataset cited

[169] Code ↔ Paper doi:10.1093/bioinformatics/btag430 [paper, repository]

SPIDER: spatially integrated denoising via embedding regularization with single cell supervision.

Journal: Bioinformatics (Oxford, England)

Authors' code: Zenodo 20613921 (CC-BY-4.0)

Status: code verified, 11 files readable, 7 matches

[170] Code ↔ Paper doi:10.1093/bioinformatics/btag592 [paper, repository]

Network-based stratification of allele-specific expression reveals patient subgroups in Huntington's disease.

Journal: Bioinformatics (Oxford, England)

Authors' code: macsbio/HD-ASE-NBS (MIT)

Status: code verified, 40 files readable, 11 matches

[171] Code ↔ Paper doi:10.1093/bioinformatics/btag424 [paper, repository]

SlotDeconv: spatial transcriptomics deconvolution via diversity-constrained prototype learning and spatial refinement.

Journal: Bioinformatics (Oxford, England)

Authors' code: HannahNJIT/SlotDeconv (MIT)

Status: code verified, 8 files readable, 4 matches

[172] Code ↔ Paper doi:10.1093/cercor/bhag125 [paper, repository]

Heritable and experience-dependent cortical traits of reading ability.

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

Authors' code: mikaelroll/corticalreading (MIT)

Status: code verified, 5 files readable, 5 matches

[173] doi:10.1002/ctm2.70756 [paper, data]

Chronic stress-induced brain-derived small extracellular vesicles promote colorectal cancer through Treg differentiation.

Journal: Clinical and translational medicine

Status: data only, 1 dataset cited

[174] doi:10.1167/iovs.67.10.41 [paper, data]

Ascl1 Represses Müller Glial and Promotes Rod Photoreceptor Fate Through Repressing Notch Signaling in Late Retinal Progenitor Cells.

Journal: Investigative ophthalmology & visual science

Status: data only, 1 dataset cited

[175] Code ↔ Paper doi:10.3390/ijms27156925 [paper, repository]

XGBoost-SHAP Interpretable Modeling Identifies and Validates an Eight-Gene Biomarker for Hepatic Encephalopathy Risk Prediction in Cirrhosis.

Journal: International journal of molecular sciences

Authors' code: seandavi/GEOquery (MIT), ModelOriented/shapviz (GPL-2.0), alserglab/fgsea (MIT), yuanfeng-lan/HE-risk-Prediction (MIT)

Status: code verified, 159 files readable, 18 matches

[176] doi:10.1111/acel.70653 [paper, data]

Distinct Transposable Element Transcript Patterns in Microglia Across Aging and Alzheimer's Disease.

Journal: Aging cell

Status: data only, 1 dataset cited

[177] doi:10.1097/md.0000000000050109 [paper, data]

The gut-immune-brain axis in CNS tumors: Causal roles of microbiota and inflammatory proteins unveiled by Mendelian randomization and single-cell transcriptomics.

Journal: Medicine

Status: data only, 1 dataset cited

[178] doi:10.1111/cbdd.70363 [paper]

Multi-Omics Integration Reveals That SN-011 Targets JUNB to Upregulate ADGRE5 and Restore Vascular Endothelial Cell Communication in Ischemic Stroke.

Journal: Chemical biology & drug design

Status: data only

[179] doi:10.1002/ccs3.70041 [paper, data]

The suppressor of cytokine signaling 3 regulates glioma stem cell maintenance and immune microenvironment through signal transducer and activator of transcription 3 signaling.

Journal: Journal of cell communication and signaling

Status: data only, 1 dataset cited

[180] doi:10.1210/endocr/bqag087 [paper, data]

A single-nucleus multiomic study of preoptic area cells in prepubertal control vs prenatally androgenized female mice.

Journal: Endocrinology

Status: data only, 1 dataset cited

[181] Code ↔ Paper doi:10.1210/endocr/bqag084 [paper, repository]

The EDC mixture "NeuroMix" alters neuroendocrine physiology, fatty food preference, and the central reward transcriptome.

Journal: Endocrinology

Authors' code: emilyhilz/NeuroMix-2026 (no license)

Status: code verified, 3 files readable, 2 matches

[182] Code ↔ Paper doi:10.1093/gbe/evag197 [paper, repository]

Molecular Drivers of Mutualistic Association Between Anemone and Anemonefish.

Journal: Genome biology and evolution

Authors' code: sneha100895/Anemone-anemonefish-mutualism-RNA-Seq (GPL-2.0)

Status: code verified, 5 files readable, 4 matches

[183] Code ↔ Paper doi:10.1093/bioinformatics/btag578 [paper, repository]

NicheDeSig: niche-aware deconvolution and adaptive signature analysis for spatial transcriptomics.

Journal: Bioinformatics (Oxford, England)

Authors' code: Zenodo 20604815 (Apache-2.0), Davidcoach/NicheDeSig (no license), Zenodo 20685597 (Apache-2.0)

Status: code verified, 10 files readable, 1 match

[184] Code ↔ Paper doi:10.1093/bioinformatics/btag515 [paper, repository]

PRISM: Prior-enhanced Inference for Spatial Transcriptomic Cell Type Mapping.

Journal: Bioinformatics (Oxford, England)

Authors' code: lilab-ai4s/PRISM (no license), Zenodo 20529683 (CC-BY-4.0)

Status: code verified, 25 files readable, 3 matches

[185] Code ↔ Paper doi:10.1093/bioinformatics/btag540 [paper, repository]

Deciphering spatial heterogeneity by multimodal spatial transcriptomics modelling with SpatialModal.

Journal: Bioinformatics (Oxford, England)

Authors' code: xingyili/SpatialModal (no license), Zenodo 21264356 (CC-BY-4.0)

Status: code verified, 20 files readable, 6 matches

Friday, 31 July 2026 (6 papers)

[186] Code ↔ Paper doi:10.1371/journal.pone.0354882 [paper, repository]

Integrative network pharmacology, transcriptomics, and molecular docking identify candidate Centella asiatica constituents and targets in neurodegenerative diseases.

Journal: PloS one

Authors' code: Zenodo 20779507 (CC-BY-4.0)

Status: code verified, 1 file readable

[187] doi:10.1186/s12967-026-08706-w [paper, data]

Impaired NADH-linked mitochondrial respiration disrupts ventral midbrain neuronal programs in POLG disease.

Journal: Journal of translational medicine

Status: data only, 1 dataset cited

[188] doi:10.1016/j.nbas.2026.100164 [paper, data]

Single-cell transcriptomic analysis reveals age-related remodeling of brain endothelial cells.

Journal: Aging brain

Status: data only, 1 dataset cited

[189] doi:10.3389/fnins.2026.1881087 [paper, data]

Dual-graph attention autoencoder for spatial domain identification in ischemic stroke.

Journal: Frontiers in neuroscience

Status: data only, 1 dataset cited

[190] doi:10.3390/metabo16080541 [paper, data]

Spatial Metabolomics and Single-Cell Virtual Knockout Screening Reveal Solanesol Improves Parkinson's Disease-like Pathology Based on Lipid Inflammation Mechanism.

Journal: Metabolites

Status: data only, 1 dataset cited

[191] Code ↔ Paper doi:10.1038/s41467-026-75571-y [paper, repository]

Ribo-ITP enables identification of translons from limited input samples.

Journal: Nature communications

Authors' code: up114/translons (no license)

Status: code verified, 9 files readable, 7 matches

Thursday, 30 July 2026 (7 papers)

[192] Code ↔ Paper doi:10.1038/s41467-026-75700-7 [paper, repository]

Gene regulatory innovations from transposable elements in primate cerebellum development.

Journal: Nature communications

Authors' code: kaessmannlab/cerebellum_te (CC-BY-NC-SA-4.0), Zenodo 19354896 (CC-BY-4.0)

Status: code verified, 56 files readable, 18 matches

[193] Code ↔ Paper doi:10.1016/j.ebiom.2026.106408 [paper, repository]

Microcephaly-like phenotype triggered by novel reassortant and prototypic Oropouche virus strains in brain organoids.

Journal: EBioMedicine

Authors' code: iza-mcac/2025-08-Oropouche-virus-strains-brain (GPL-3.0)

Status: code verified, 6 files readable, 6 matches

[194] Code ↔ Paper doi:10.1038/s41594-026-01857-w [paper, repository]

Protein thiol alterations drive pathologic liquid-liquid phase separation in the aging brain.

Journal: Nature structural & molecular biology

Authors' code: figshare 32817593 (CC-BY-4.0)

Status: empty repository

[195] Code ↔ Paper doi:10.3390/ijms27156842 [paper, repository]

A Hierarchical Multimodal Knowledge Graph for Neural Cell-Type-Specific Regulation Integrating Single-Cell Transcriptomics and Literature Evidence.

Journal: International journal of molecular sciences

Authors' code: SiatBioInf/NeuroCellKG (MIT)

Status: code verified, 12 files readable, 16 matches

[196] doi:10.3390/brainsci16080811 [paper]

Single-Cell Analysis of Brain Arteriovenous Malformations Reveals Pro-Angiogenic Myeloid Programs.

Journal: Brain sciences

Status: code on request

[197] Code ↔ Paper doi:10.1038/s41398-026-04292-z [paper, repository]

Regional juxtacortical microstructural changes and gene expression provide insights into neurodegeneration in Alzheimer's disease.

Journal: Translational psychiatry

Authors' code: Sahuhu-Sun/Imaging-transcriptomics (no license)

Status: code verified, 5 files readable, 2 matches

[198] Code ↔ Paper doi:10.1186/s12864-026-13024-y [paper, repository]

Long-read RNA-seq maps the isoform landscape of the trigeminal ganglion in an allergic rhinitis mouse model.

Journal: BMC genomics

Authors' code: yerry77/TG-full-length (no license)

Status: code verified, 7 files readable, 5 matches

Wednesday, 29 July 2026 (7 papers)

[199] doi:10.7554/elife.108845 [paper, data]

Acute opioid responses are modulated by dynamic interactions of &lt;i&gt;Oprm1&lt;/i&gt; and &lt;i&gt;Fgf12&lt;/i&gt;.

Journal: eLife

Status: data only, 1 dataset cited

[200] Code ↔ Paper doi:10.1126/sciadv.aeh9771 [paper, repository]

Lipidomic profiling reveals age-dependent changes in plasma membrane lipids that affect neural stem cell aging.

Journal: Science advances

Authors' code: xiaoaizhao/Neural-stem-cell-NSC-aging-lipidomics (no license), Zenodo 20416165 (CC-BY-4.0)

Status: code verified, 178 files readable, 25 matches

[201] doi:10.1016/j.mocell.2026.100387 [paper, data]

USP15 mutation associated with autism spectrum disorder alters progenitor fate and neuronal maturation in human brain organoids.

Journal: Molecules and cells

Status: data only, 1 dataset cited

[202] doi:10.1186/s40035-026-00567-z [paper, data]

Transaldolase 1 contributes to pentose phosphate pathway disruption and synaptic dysfunction in Alzheimer's disease.

Journal: Translational neurodegeneration

Status: data only, 3 datasets cited

[203] doi:10.3390/ani16152325 [paper, data]

From Cellular Lysis to Microbial Explosion: Elucidating the Temporal Degradation and Spoilage Mechanisms of Frozen Mysid Shrimp as Seahorse (&lt;i&gt;Hippocampus&lt;/i&gt; spp.) Feed.

Journal: Animals : an open access journal from MDPI

Status: data only, 1 dataset cited

[204] Code ↔ Paper doi:10.3389/fnbeh.2026.1878769 [paper, repository]

&lt;i&gt;ADAMTS18&lt;/i&gt; as a candidate gene linking social stress and depression: a cross-species study in African wild dogs (&lt;i&gt;Lycaon pictus&lt;/i&gt;) and humans.

Journal: Frontiers in behavioral neuroscience

Authors' code: ncbi/sra-tools (other)

Status: code verified, 1,652 files readable, 2 matches

[205] Code ↔ Paper doi:10.1093/braincomms/fcag264 [paper, repository]

Elevated intron retention implicates neuroinflammation in brains of individuals with alcohol use disorder.

Journal: Brain communications

Authors' code: cpdong/IntronNeoantigen (no license)

Status: code verified, 5 files readable, 1 match

Tuesday, 28 July 2026 (3 papers)

[206] Code ↔ Paper doi:10.7554/elife.107531 [paper, repository]

CellCover defines marker gene panels capturing developmental progression in neocortical neural stem cell identity.

Journal: eLife

Authors' code: lanlanji/CoveringPackage (no license)

Status: code verified, 5 files readable

[207] Code ↔ Paper doi:10.1038/s41591-026-04492-6 [paper, repository]

The genetic architecture of fibromyalgia across 2.5 million individuals.

Journal: Nature medicine

Authors' code: FINNGEN/regenie-pipelines (MIT), i-kerrebijn/fibromyalgia_GWAS_meta-analysis (no license)

Status: code verified, 13 files readable, 4 matches

[208] Code ↔ Paper doi:10.1038/s41467-026-75194-3 [paper, repository]

Leucine-rich repeat kinase 2 impairs the release sites of Parkinson's disease vulnerable dopamine axons.

Journal: Nature communications

Authors' code: curtain.proteo.info (no license), Zenodo 19930567 (CC-BY-4.0), Zenodo 20244434 (CC-BY-4.0), DombeckLab/lrrk2_photometry_analysis (MIT)

Status: code verified, 19 files readable, 7 matches

Monday, 27 July 2026 (3 papers)

[209] Code ↔ Paper doi:10.1007/s11033-026-12429-y [paper, repository]

Transcriptome-wide profiling of cystic and solid vestibular schwannomas reveals candidate long non-coding RNA signatures.

Journal: Molecular biology reports

Authors' code: decodebiology/Vestibular_schwannoma_2025 (no license)

Status: code verified, 11 files readable, 5 matches

[210] Code ↔ Paper doi:10.1038/s43856-026-01510-z [paper, repository]

Mapping genetic convergence across brain structure, mental health, and cardiometabolic disease.

Journal: Communications medicine

Authors' code: BioPsyk/cleansumstats (no license), bulik/ldsc (GPL-3.0), comorment/ldsc (GPL-3.0), precimed/mix3r (no license), GenomicSEM/GenomicSEM (GPL-3.0), precimed/pleiofdr (GPL-3.0)

Status: code verified, 313 files readable, 4 matches

[211] Code ↔ Paper doi:10.3390/genes17080874 [paper, repository]

Multi-Omic Analysis of Cerebrospinal Fluid Metabolites in Autism Spectrum Disorder: Biomarker Identification, Metabolic Genetics Insights, and Network Toxicology.

Journal: Genes

Authors' code: yanglab.westlake.edu.cn/software/smr (no license)

Status: code verified

Sunday, 26 July 2026 (3 papers)

[212] doi:10.1111/bpa.70125 [paper, data]

From patient to tumor organoid: Culture protocol choice controls glioblastoma tumor architecture and identity.

Journal: Brain pathology (Zurich, Switzerland)

Status: data only, 1 dataset cited

[213] doi:10.3390/ijms27156671 [paper, data]

Inflamed Yet Immune-Evasive? A Transcriptomic Meta-Analysis Identifies Conserved Inflammatory, Developmental, and Neuronal Signatures Associated with Polyploid Giant Cancer Cells.

Journal: International journal of molecular sciences

Status: data only, 1 dataset cited

[214] Code ↔ Paper doi:10.3390/biomedicines14081677 [paper, repository]

Exploratory Genome and Transcriptome-Wide Association Analyses of Addiction-Related Phenotypes in a Twin Cohort.

Journal: Biomedicines

Authors' code: jared8844/code-for-addiction-paper (no license)

Status: code verified, 3 files readable, 5 matches

Saturday, 25 July 2026 (1 paper)

[215] doi:10.1038/s41420-026-03250-4 [paper, data]

Transcriptomic analysis reveals that neural stem cell-derived exosomes regulate the HMGB1/TLR2 signaling axis to promote astrocytic differentiation and mitochondrial biogenesis in the repair of radiation-induced blood-brain barrier damage.

Journal: Cell death discovery

Status: data only, 1 dataset cited

Friday, 24 July 2026 (3 papers)

[216] Code ↔ Paper doi:10.1007/s10519-026-10274-0 [paper, repository]

ADHD and Student Grades in Children from the ABCD Study&lt;sup&gt;®&lt;/sup&gt;: A Twin and Siblings Study.

Journal: Behavior genetics

Authors' code: lf-araujo/2023-mrdoc2-EA-ADHD (no license)

Status: empty repository

[217] Code ↔ Paper doi:10.1371/journal.pcbi.1014573 [paper, repository]

Cell-type-specific m1A dynamics are associated with microglial phenotypic transition and neuronal metabolic adaptation during spinal cord injury.

Journal: PLoS computational biology

Authors' code: Magetutor/m1A_score_manuscript (MIT)

Status: code verified, 28 files readable, 15 matches

[218] doi:10.1371/journal.pone.0352503 [paper, data]

G-protein coupled receptor, signal and signal-transduction related transcript mapping in nigral volume and pigmented neurons reveals a potential deficit of nigral feedback signals associated with Parkinson's disease.

Journal: PloS one

Status: data only, 1 dataset cited

Thursday, 23 July 2026 (6 papers)

[219] Code ↔ Paper doi:10.1172/jci.insight.207270 [paper, repository]

Progressive hypothalamic neuroinflammation in ovariectomized mice parallels aging-related transcriptomic changes in the female human hypothalamus.

Journal: JCI insight

Authors' code: jcbloom/hypo_menopauseNavarro (no license)

Status: code verified, 9 files readable, 6 matches

[220] doi:10.1186/s40035-026-00566-0 [paper, data]

Application of the Allen Human Brain Atlas in Alzheimer's disease and Parkinson's disease.

Journal: Translational neurodegeneration

Status: data only, 2 datasets cited

[221] Code ↔ Paper doi:10.1016/j.isci.2026.116906 [paper, repository]

Evaluating exon skipping in the central nervous system in Duchenne muscular dystrophy using spatial transcriptomics.

Journal: iScience

Authors' code: Qirongmao97/Xenium_DMD_brain (GPL-3.0)

Status: code verified, 12 files readable, 8 matches

[222] doi:10.1016/j.bbih.2026.101316 [paper]

Peripheral blood DNA methylation partially reports on immune cell type composition in the frontal brain.

Journal: Brain, behavior, & immunity - health

Status: data only

[223] Code ↔ Paper doi:10.1038/s41467-026-75723-0 [paper, repository]

Spatial transcriptomics reveals distinct cell type dynamics following opioid dependence in female mice with the common human μ-opioid receptor variant Oprm1 A118G.

Journal: Nature communications

Authors' code: GoogleXie/CellDynamicST (other)

Status: code verified, 36 files readable, 40 matches

[224] doi:10.3390/genes17080849 [paper]

Deciphering the Role of LNX2 as a Potential Contributor to Neurodevelopmental Disorders.

Journal: Genes

Status: data only

Wednesday, 22 July 2026 (7 papers)

[225] Code ↔ Paper doi:10.1038/s41586-026-10797-w [paper, repository]

A global molecular code for birth order and neuronal identity in Drosophila.

Journal: Nature

Authors' code: natverse/malevnc (GPL-3.0), flyconnectome/fancr (GPL-3.0), natverse/fafbseg (GPL-3.0), google/neuroglancer (Apache-2.0), FlyNeuroAtlas/DevSeqVNC (no license), Zenodo 17185431 (no license)

Status: code verified, 1,066 files readable, 2 matches

[226] doi:10.1186/s40478-026-02382-z [paper, data]

Methylation profiling and alternative classification approaches in a glioma-enriched FFPE stereotaxic biopsy cohort.

Journal: Acta neuropathologica communications

Status: data only, 1 dataset cited

[227] doi:10.1155/ijog/2045937 [paper, data]

Ubiquitin-Proteasome System-Related Prognostic Model and Immune Landscape in Glioblastoma.

Journal: International journal of genomics

Status: data only, 1 dataset cited

[228] Code ↔ Paper doi:10.3390/antiox15070908 [paper, repository]

Convergent Lower Expression of Redox-Linked Stress-Adaptation and Synaptic-Plasticity Genes in Major Depressive Disorder Across Seven Postmortem dlPFC Cohorts.

Journal: Antioxidants (Basel, Switzerland)

Authors' code: OSF 8bfrs (no license)

Status: empty repository

[229] doi:10.3390/ijms27146503 [paper, data]

Modeling Tay-Sachs Disease in Astrocyte-like Cells Reveals Significant Changes in the Transcriptomic Profile.

Journal: International journal of molecular sciences

Status: data only, 1 dataset cited

[230] Code ↔ Paper doi:10.1016/j.isci.2026.116878 [paper, repository]

Species-specific brain transcriptomic responses to clothianidin and sulfoxaflor in pollinators.

Journal: iScience

Authors' code: aswitwicka/species_insecticide_exposure (no license), Zenodo 21206760 (CC-BY-4.0)

Status: code verified, 20 files readable, 7 matches

[231] Code ↔ Paper doi:10.1016/j.bpsgos.2026.100792 [paper, repository]

&lt;i&gt;CACNA1C&lt;/i&gt; Genetic Variants Differentially Affect Neuronal Networks Through Divergent Pathways.

Journal: Biological psychiatry global open science

Authors' code: Zenodo 21992966 (CC0-1.0), ghwilkinson/mea-bursts (CC0-1.0)

Status: code verified, 6 files readable

Tuesday, 21 July 2026 (4 papers)

[232] Code ↔ Paper doi:10.1038/s41467-026-74961-6 [paper, repository]

Spatial multi-omics identifies early synaptic pruning and context-specific dopaminergic vulnerability in synucleinopathies.

Journal: Nature communications

Authors' code: fstrueb/spatial_nigra (no license)

Status: code verified, 11 files readable, 9 matches

[233] Code ↔ Paper doi:10.1038/s44321-026-00488-4 [paper, repository]

DeepPlaque: a scalable multimodal platform for Aβ pathology and cell analysis in Alzheimer's disease.

Journal: EMBO molecular medicine

Authors' code: ChengJin-git/DeepPlaque (CC-BY-NC-ND-4.0)

Status: code verified, 5 files readable, 1 match

[234] Code ↔ Paper doi:10.1016/j.isci.2026.116825 [paper, repository]

Social hierarchy shapes behavioral and transcriptional responses to chronic stress and ketamine in male mice.

Journal: iScience

Authors' code: LopezLab-KI/Behavioral_analysis_SB (no license), sgoldenlab/simba (BSD-3-Clause)

Status: code verified, 430 files readable, 4 matches

[235] Code ↔ Paper doi:10.1093/braincomms/fcag287 [paper, repository]

Plasma proteomics reveals molecular overlap between physical activity and dementia risk.

Journal: Brain communications

Authors' code: edammer/MAGMA.SPA (MIT), edammer (no license)

Status: code verified, 3 files readable

Monday, 20 July 2026 (4 papers)

[236] Code ↔ Paper doi:10.1002/trc2.70286 [paper, repository]

The proteomic and metabolomic signature of inherited chromosomally integrated HHV-6 and its role in all-cause dementia and mortality risk: The UK Biobank study.

Journal: Alzheimer's & dementia (New York, N. Y.)

Authors' code: baydounm/UKB-paper25-supplementarydata (no license)

Status: code verified, 3 files readable

[237] Code ↔ Paper doi:10.1016/j.cpblue.2026.100072 [paper, repository]

NodoMap: A single-cell and spatial transcriptomic atlas of the mouse nodose ganglion.

Journal: Cell press blue

Authors' code: sc2470/NodoMap (MIT), Zenodo 20329018 (MIT)

Status: code verified, 72 files readable, 25 matches

[238] doi:10.3390/ijms27146442 [paper, data]

Phenotype-Specific Transcriptomic Responses to Glucocorticoid Signaling in the Prefrontal Cortex and Dorsal Raphe Nucleus Following Chronic Social Stress.

Journal: International journal of molecular sciences

Status: data only, 1 dataset cited

[239] doi:10.3389/fimmu.2026.1805159 [paper, data]

Small extracellular vesicles proteome reveals persistent inflammatory and coagulopathic dysregulation in long-COVID.

Journal: Frontiers in immunology

Status: data only, 1 dataset cited

Saturday, 18 July 2026 (1 paper)

[240] doi:10.7759/cureus.112902 [paper, data]

DNA Methylation at Core N-Methyl-D-Aspartate (NMDA) Receptor Genes Reveals a Glutamatergic Signature of Aging in Post-COVID Whole Blood With Implications for Long-COVID Neuropsychiatric Sequelae.

Journal: Cureus

Status: data only, 1 dataset cited

Friday, 17 July 2026 (9 papers)

[241] Code ↔ Paper doi:10.1242/jeb.252086 [paper, repository]

Transcriptional predictors of rescue behaviour in ants.

Journal: The Journal of experimental biology

Authors' code: ljaimesnino/RescueAnts (no license)

Status: code verified, 2 files readable, 10 matches

[242] Code ↔ Paper doi:10.1038/s41467-026-75722-1 [paper, repository]

Single-nucleus analysis of the adult human olfactory epithelium uncovers shared neurogenesis programs with the brain.

Journal: Nature communications

Authors' code: well.ox.ac.uk/~wrayner/tools (no license), Zenodo 20867452 (CC-BY-4.0), Zenodo 20867451 (CC-BY-4.0), litingsong/oe_nn (no license)

Status: code verified, 30 files readable, 9 matches

[243] doi:10.3892/mmr.2026.13967 [paper, data]

Sedanolide alleviates LPS‑induced depressive‑like behaviors by modulating the C3a/C3aR signaling axis and microglial glycolysis.

Journal: Molecular medicine reports

Status: data only, 1 dataset cited

[244] doi:10.1126/sciadv.aed6825 [paper, data]

SORLA up-regulation suppresses pathological effects in aged tauopathy mouse brain.

Journal: Science advances

Status: data only, 1 dataset cited

[245] Code ↔ Paper doi:10.1038/s41467-026-75650-0 [paper, repository]

Reduced melanocortin tone modulates feeding during pregnancy in mice.

Journal: Nature communications

Authors' code: SweeneyLab-UIUC/NCOMMS-25-67317A (no license)

Status: code verified, 17 files readable, 12 matches

[246] doi:10.1016/j.xhgg.2026.100654 [paper, data]

Expanding the clinical and molecular spectrum of TUBB2B through distinct variants identified across multiple families.

Journal: HGG advances

Status: data only, 1 dataset cited

[247] doi:10.1093/nargab/lqag074 [paper, data]

Cell-type-resolved RNA-seq reveals molecular signatures of sexual experience in &lt;i&gt;Drosophila&lt;/i&gt; neuromodulatory neurons.

Journal: NAR genomics and bioinformatics

Status: data only, 1 dataset cited

[248] doi:10.3390/biology15141179 [paper, data]

Transcriptomic Evidence Identifies Two TMBIM Subgroups with Opposing Prognostic Associations in Glioma.

Journal: Biology

Status: data only, 1 dataset cited

[249] doi:10.3389/fmicb.2026.1885281 [paper]

Washed microbiota transplantation improves clinical symptoms, gut microbiota, and metabolic profiles in autism spectrum disorder in a twin cohort.

Journal: Frontiers in microbiology

Status: data only

Thursday, 16 July 2026 (6 papers)

[250] Code ↔ Paper doi:10.64898/2026.07.14.26358047 [paper, repository]

From Genes to Neurochemistry: Excitation and Inhibition Mechanisms of Sensory Differences in Autism

Journal: medRxiv (preprint)

Authors' code: HeJasonL/BATD (no license)

Status: code verified, 27 files readable, 3 matches

[251] Code ↔ Paper doi:10.1038/s41467-026-75470-2 [paper, repository]

Analysis of gene co-expression connectivity dynamics implicates aberrant neuron-oligodendroglia interactions in schizophrenia.

Journal: Nature communications

Authors' code: EugeniaRadulescu/Differentially-Connected-Genes-in (no license)

Status: dead link

[252] doi:10.1038/s41467-026-75367-0 [paper, data]

Heterogenous microglial reactivity contrasts with stable vascular transcriptional programs in mouse models of Alzheimer's, CADASIL, and Traumatic Brain Injury.

Journal: Nature communications

Status: data only, 1 dataset cited

[253] doi:10.1186/s12974-026-03964-3 [paper, data]

Circulating immune profiling reveals impaired monocyte states and trajectories driving immunosuppression in glioblastoma.

Journal: Journal of neuroinflammation

Status: data only, 3 datasets cited

[254] doi:10.1080/19490976.2026.2694805 [paper, data]

Enteric-colonized &lt;i&gt;Cronobacter&lt;/i&gt; spp. can disrupt the central nervous system without translocation across the host barriers.

Journal: Gut microbes

Status: data only, 1 dataset cited

[255] doi:10.3390/genes17070813 [paper]

Multilayer Genomic Characterization of a Shared Genetic Factor Linking Depression-Related Liability and Reduced Physical Function.

Journal: Genes

Status: code on request

Wednesday, 15 July 2026 (2 papers)

[256] doi:10.1038/s41586-026-10793-0 [paper, data]

Cell-type signatures of Alzheimer's disease shared across population groups.

Journal: Nature

Status: data only, 3 datasets cited

[257] Code ↔ Paper doi:10.3389/frmbi.2026.1834726 [paper, repository]

Shotgun metagenomic analysis reveals taxonomic and functional alterations in the gut microbiome across prodromal and symptomatic Lewy body disease.

Journal: Frontiers in microbiomes

Authors' code: xiaowei-zhao-1111/LBD_Gut_Microbiome_2026 (no license)

Status: code verified, 9 files readable, 9 matches

Tuesday, 14 July 2026 (5 papers)

[258] doi:10.1128/mbio.01294-26 [paper, data]

Single-cell analysis of Powassan virus-infected brains reveals age-dependent neuroinflammatory crosstalk and progressive Alzheimer's-like APP/Aβ accumulation.

Journal: mBio

Status: code on request, 1 dataset cited

[259] doi:10.1073/pnas.2537017123 [paper, data]

Distinct cell type-specific mechanisms underlie cognitive dysfunction during persistent integrated stress response activation.

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

Status: data only, 1 dataset cited

[260] doi:10.1002/ame2.70252 [paper, data]

Single-cell atlas of neuroglial dynamics in SNCA-A53T Parkinson's disease mouse model.

Journal: Animal models and experimental medicine

Status: data only, 1 dataset cited

[261] Code ↔ Paper doi:10.1016/j.isci.2026.116622 [paper, repository]

Multi-omics profiling reveals gut microbiome signatures associated with cognitive decline in Alzheimer's disease.

Journal: iScience

Authors' code: ngdc.cncb.ac.cn/gsa (no license), shenx08/Metagenomic-data-assembly-and-analysis (no license)

Status: code verified, 2 files readable

[262] Code ↔ Paper doi:10.3389/fnins.2026.1843319 [paper, repository]

Humanized APOE mouse brain volume increases over age irrespective of sex and APOE genotype: implications for translational validity to the human.

Journal: Frontiers in neuroscience

Authors' code: CoBrALab/minc-toolkit-extras (other), CoBrALab/optimized_antsMultivariateTemplateConstruction (other)

Status: code verified, 60 files readable, 3 matches

Monday, 13 July 2026 (6 papers)

[263] Code ↔ Paper doi:10.1016/j.celrep.2026.117670 [paper, repository]

Sustained AMPAR expression in CA3 neurons may mediate neuroprotection following FLASH-RT.

Journal: Cell reports

Authors' code: gitlab.unige.ch/lirr/nanostring_flash_mouse_brain (no license)

Status: dead link

[264] doi:10.1038/s43587-026-01154-7 [paper, data]

Spatial mapping and senolytic targeting of senescent and disease-associated microglia in aged mouse brain white matter.

Journal: Nature aging

Status: data only, 1 dataset cited

[265] doi:10.1186/s12935-026-04370-8 [paper]

Machine learning-based prognostic model and single-cell transcriptomic integration for identifying brain metastasis-associated malignant subpopulations and potential therapeutic targets in lung adenocarcinoma.

Journal: Cancer cell international

Status: data only

[266] doi:10.1186/s13020-026-01445-6 [paper, data]

Electroacupuncture enhances anti-tumor immunity in TNBC by reducing NE release and blocking α2-AR-mediated NGF/Hippo signaling.

Journal: Chinese medicine

Status: data only, 2 datasets cited

[267] doi:10.3389/ebm.2026.10948 [paper, data]

Genetic evidence for causal relationships between brain functional networks and domain-specific recovery after nondisabling ischemic stroke.

Journal: Experimental biology and medicine (Maywood, N.J.)

Status: data only, 1 dataset cited

[268] Code ↔ Paper doi:10.3389/fbinf.2026.1858866 [paper, repository]

Comparative evaluation of reference-free transcriptomic deconvolution highlights the importance of biological validation in astrocytes across Alzheimer's disease.

Journal: Frontiers in bioinformatics

Authors' code: mangaritar/Deconvolution-Astrocyte (no license)

Status: empty repository, 1 file readable

Sunday, 12 July 2026 (1 paper)

[269] doi:10.1093/braincomms/fcag268 [paper, data]

A single mild closed-head injury disrupts synaptic strength and promotes hippocampal hyperexcitability in mice.

Journal: Brain communications

Status: data only, 1 dataset cited

Saturday, 11 July 2026 (1 paper)

[270] doi:10.3390/ijms27146196 [paper, data]

Investigation of the Potential Neuroprotective Mechanisms of &lt;i&gt;Acalypha indica&lt;/i&gt; Against Alzheimer's Disease by Integrated Bioinformatics Analysis.

Journal: International journal of molecular sciences

Status: data only, 1 dataset cited

Friday, 10 July 2026 (3 papers)

[271] doi:10.1128/msystems.00149-26 [paper, data]

Effects of gut microbiota on the susceptibility of ischemic stroke in mice.

Journal: mSystems

Status: data only, 2 datasets cited

[272] doi:10.1371/journal.pone.0352693 [paper, data]

Loss of Fmr1 reorganizes the multi-elemental composition across tissues in Fragile X Syndrome mice.

Journal: PloS one

Status: data only, 1 dataset cited

[273] Code ↔ Paper doi:10.1016/j.tjpad.2026.100635 [paper, repository]

Can we identify people with Alzheimer's disease from examination of the eye? A bidirectional Mendelian randomization (MR) study.

Journal: The journal of prevention of Alzheimer's disease

Authors' code: HuKiser/Retinal_features_AD_MR (no license), bulik/ldsc (GPL-3.0)

Status: code verified, 29 files readable, 4 matches

Thursday, 9 July 2026 (7 papers)

[274] Code ↔ Paper doi:10.1002/epi4.70306 [paper, repository]

Transcriptional signatures of cortical morphometric variability in temporal lobe epilepsy.

Journal: Epilepsia open

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

Status: code verified

[275] doi:10.1371/journal.pone.0353181 [paper, data]

Dysregulated glucocorticoid-responsive immune genes in peripheral blood mononuclear cells as a shared molecular signature of autism spectrum disorder and irritable bowel syndrome.

Journal: PloS one

Status: data only, 1 dataset cited

[276] doi:10.1016/j.stemcr.2026.103012 [paper, data]

Identification of novel genes with enriched expression in human intermediate progenitors reveals a key role for CDKN3 in cortical development.

Journal: Stem cell reports

Status: code on request, 1 dataset cited

[277] Code ↔ Paper doi:10.1186/s44342-026-00076-5 [paper, repository]

Exploratory strain-associated patterns of antiviral transcriptional responses to Zika virus exposure in developing human neural tissue.

Journal: Genomics & informatics

Authors' code: abedizahra/Zika-scrnaseq-antiviral-response-code (no license)

Status: code verified, 12 files readable, 29 matches

[278] Code ↔ Paper doi:10.1002/jsp2.70200 [paper, repository]

A Porcine Model of Intervertebral Disc Injury Recapitulates Human Discogenic Pain Via Notochordal Cell Loss and Pain-Inducing Nucleus Pulposus Cell Emergence.

Journal: JOR spine

Authors' code: gkaneda/Pig-IVD-Scripts (no license)

Status: code verified, 4 files readable, 2 matches

[279] Code ↔ Paper doi:10.3389/fgene.2026.1807347 [paper, repository]

Epigenetic regulators are preferentially coordinated with protocadherin gene expression across the human brain: a genome-wide co-expression analysis.

Journal: Frontiers in genetics

Authors' code: nwharbert8-ui/epigenetic-pcdh-coordination (MIT)

Status: code verified, 12 files readable, 13 matches

[280] doi:10.3389/fneur.2026.1794851 [paper, data]

Mitochondrial protein alterations in vascular dementia: evidence from Mendelian randomization, transcriptomics, and a chronic hypoperfusion model.

Journal: Frontiers in neurology

Status: data only, 1 dataset cited

Wednesday, 8 July 2026 (9 papers)

[281] Code ↔ Paper doi:10.1038/s41386-026-02483-2 [paper, repository]

Long-term effects of adolescent risperidone treatment on the mouse cortex.

Journal: Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology

Authors' code: Hahn-BorgmannWinter/Adolescent_antipsychotics (no license)

Status: code verified, 2 files readable, 4 matches

[282] Code ↔ Paper doi:10.1186/s13073-026-01704-z [paper, repository]

Gene expression profiling enables refined parcellation of cortical layers in the heterogeneous human cerebral cortex.

Journal: Genome medicine

Authors' code: YanrongWei/GD-Ls (MIT), Zenodo 20199715 (MIT)

Status: code verified, 49 files readable, 19 matches

[283] Code ↔ Paper doi:10.1162/imag.a.1294 [paper, repository]

Toward a transcriptomic framework for ultrasound neuromodulation: A perspective on gene expression and regional brain sensitivity.

Journal: Imaging neuroscience (Cambridge, Mass.)

Authors' code: jolinefan/TUSgeneClusters (no license), jolinefan/TUSgeneClustering (no license)

Status: code verified, 19 files readable, 13 matches

[284] Code ↔ Paper doi:10.1093/braincomms/fcag257 [paper, repository]

Neuroplasticity and immune system are related to altered grey matter networks: a cohort study in sporadic Alzheimer's disease.

Journal: Brain communications

Authors' code: bettytijms/Single_Subject_Grey_Matter_Networks (MIT), sites.google.com/site/bctnet (no license)

Status: code verified, 15 files readable, 2 matches

[285] doi:10.3389/fnins.2026.1837233 [paper, data]

Integrated multi-omics and deep learning analysis reveals neurotransmitter metabolism regulatory mechanisms of Tianwang Buxin Dan.

Journal: Frontiers in neuroscience

Status: data only, 1 dataset cited

[286] doi:10.3389/fimmu.2026.1866830 [paper, data]

Heterogeneity of immune checkpoint inhibitor-related inflammatory central nervous system adverse event reporting signals in primary and metastatic brain tumors: a pharmacovigilance study with single-cell and spatial transcriptomic contextualization.

Journal: Frontiers in immunology

Status: data only, 1 dataset cited

[287] doi:10.3389/fnmol.2026.1844602 [paper, data]

Prenatal and neonatal housing conditions affect anxiety-like behavior in adulthood in rats and interact with brain-derived neurotrophic factor (BDNF) Val66Met to alter expression of BDNF and stress markers in the ventral hippocampus.

Journal: Frontiers in molecular neuroscience

Status: data only, 1 dataset cited

[288] Code ↔ Paper doi:10.1016/j.isci.2026.116355 [paper, repository]

Tera-MIND: Tera-scale mouse brain simulation via spatial mRNA-guided diffusion.

Journal: iScience

Authors' code: Zenodo 14826874 (MIT), CTPLab/Tera-MIND (MIT), musikisomorphie/tera-mind (no license)

Status: code verified, 41 files readable, 3 matches

[289] Code ↔ Paper doi:10.3390/biology15141097 [paper, repository]

Counterfactual Diffusion Modeling Enables Spatially Targeted Reprogramming of Tissue Microenvironments.

Journal: Biology

Authors' code: WenhuiDing/SPAD-CFR (MIT)

Status: code verified, 36 files readable, 14 matches

Tuesday, 7 July 2026 (5 papers)

[290] Code ↔ Paper doi:10.7554/elife.108224 [paper, repository]

Arrayed single-gene perturbations identify drivers of human anterior neural tube closure.

Journal: eLife

Authors' code: royahuang/2026_HuangAnand (MIT)

Status: code verified, 20 files readable, 8 matches

[291] Code ↔ Paper doi:10.1007/s12035-026-06041-1 [paper, repository]

Glucocorticoid Signaling in PSC-Derived Neural Systems to Elucidate Mechanisms of Stress-Induced Psychiatric Vulnerability.

Journal: Molecular neurobiology

Authors' code: eloizadalmolin/DEX_neural_models (no license)

Status: code verified, 5 files readable, 6 matches

[292] doi:10.1186/s12974-026-03951-8 [paper, data]

Forkhead box versus NF-κB hippocampal snRNA-seq profiles distinguish anti-Drebrin- and anti-GAD65-positive encephalitis.

Journal: Journal of neuroinflammation

Status: data only, 3 datasets cited

[293] doi:10.1016/j.isci.2026.116562 [paper]

Adenylyl cyclase 9: Fundamental change of regulation in vertebrates and gene sub-functionalization after teleost-specific whole-genome duplication.

Journal: iScience

Status: code on request

[294] doi:10.3390/ijms27136083 [paper, data]

Systematic Evaluation of Competing Brain Transcriptomic Representations Reveals Reciprocal Patterns Across Heterogeneous Contexts.

Journal: International journal of molecular sciences

Status: data only, 1 dataset cited

Monday, 6 July 2026 (7 papers)

[295] Code ↔ Paper doi:10.1371/journal.pcbi.1014424 [paper, repository]

Combinatorial multiomic analysis from a pedigree of Sox10Dom Hirschsprung mice identifies multiple high confidence candidate modifiers of Enteric Nervous System development.

Journal: PLoS computational biology

Authors' code: Zenodo 20671852 (CC-BY-4.0)

Status: code verified, 21 files readable, 20 matches

[296] Code ↔ Paper doi:10.1073/pnas.2511442123 [paper, repository]

Time-resolved morphological and transcriptomic characterization of early enteric neuron subtype emergence in chick.

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

Authors' code: forge.univ-lyon1.fr/melis/castellani_lab (no license)

Status: code verified

[297] doi:10.1186/s13073-026-01702-1 [paper, data]

Tandem repeat polymorphisms are associated with brain structure: results of two large population-based studies.

Journal: Genome medicine

Status: data only, 2 datasets cited

[298] Code ↔ Paper doi:10.3390/ijms27136068 [paper, repository]

Loss of Neuropeptide Y Signaling Accompanies the Neural-to-Mesenchymal Transcriptional Transition in Glioblastoma: A Multi-Scale Transcriptomic Analysis.

Journal: International journal of molecular sciences

Authors' code: itika05/NPY-GBM-transcriptomics (MIT)

Status: code verified, 14 files readable, 20 matches

[299] doi:10.3390/biom16070992 [paper, data]

Molecular Networks and Key Regulators Underlying Resilience of the Human Brain to Aging and Dementia.

Journal: Biomolecules

Status: data only, 1 dataset cited

[300] doi:10.3389/fimmu.2026.1842398 [paper, data]

A multi-omics framework integrating gut microbiota, blood metabolites, and immune cells to elucidate the pathogenesis of Alzheimer's disease.

Journal: Frontiers in immunology

Status: data only, 1 dataset cited

[301] doi:10.3389/fimmu.2026.1835359 [paper, data]

Perinatal morphine exposure induces chromatin and transcriptomic remodeling to alter immune and metabolic function.

Journal: Frontiers in immunology

Status: data only, 1 dataset cited

Sunday, 5 July 2026 (1 paper)

[302] doi:10.3390/cimb48070691 [paper, data]

Astrocyte Subtype-Specific Expression of the Sodium-Coupled Citrate Transporter &lt;i&gt;SLC13A5&lt;/i&gt; and Citrate Metabolism Genes Across Alzheimer's Disease Pseudoprogression: A Single-Nucleus RNA Sequencing Analysis of the Human Middle Temporal Gyrus.

Journal: Current issues in molecular biology

Status: code on request, 1 dataset cited

Saturday, 4 July 2026 (1 paper)

[303] Code ↔ Paper doi:10.1038/s41467-026-75193-4 [paper, repository]

Multi-ancestry gene expression models amplify transcriptome-wide association study discovery and validation.

Journal: Nature communications

Authors' code: Zenodo 14889757 (CC-BY-4.0), hakyimlab/MetaXcan (MIT), qingnanl/gsdensity_manuscript_code (no license), Zenodo 18315835 (CC-BY-4.0)

Status: code verified, 163 files readable, 11 matches

Friday, 3 July 2026 (2 papers)

[304] Code ↔ Paper doi:10.1126/sciadv.aee5076 [paper, repository]

A 3D amphioxus brain atlas illuminates the blueprint of the ancestral chordate brain and highlights unique vertebrate innovations.

Journal: Science advances

Authors' code: LCY-ICOB/amphiBrain (no license), Zenodo 19658940 (CC-BY-4.0)

Status: code verified, 1 file readable

[305] Code ↔ Paper doi:10.3389/fnins.2026.1858005 [paper, repository]

Targeted stool metabolomics suggests exploratory catecholamine- and tryptophan-linked metabolic features in autism spectrum disorder.

Journal: Frontiers in neuroscience

Authors' code: kevinliu-bmb/targeted-asd-stool-metabolomics (MIT)

Status: code verified, 3 files readable, 4 matches

Thursday, 2 July 2026 (8 papers)

[306] doi:10.1016/j.stemcr.2026.102996 [paper, data]

Neural stem cells as potential mediators of prenatal dietary stress through epigenetic mechanisms.

Journal: Stem cell reports

Status: code on request, 1 dataset cited

[307] Code ↔ Paper doi:10.1038/s41556-026-02009-4 [paper, repository]

An atlas of primate insular cortex reveals a signal-processing strategy in von Economo neurons.

Journal: Nature cell biology

Authors' code: haozhaozhe/FM_V1 (MIT), RFLiu2021/AIC_proj (no license), Zenodo 19995355 (CC-BY-4.0), Zenodo 17799559 (CC-BY-4.0)

Status: code verified, 18 files readable, 10 matches

[308] doi:10.3389/fgene.2026.1865257 [paper, data]

Disease-predominant loci across Alzheimer's disease, Parkinson's disease and Lewy body dementia: evidence from the UK Biobank prospective cohort, conditional GWAS and colocalization.

Journal: Frontiers in genetics

Status: data only, 1 dataset cited

[309] doi:10.3389/fcell.2026.1809251 [paper, data]

Pbx1 and Pbx3 cooperatively regulate intermediate progenitor genesis and corticogenesis in the mouse neocortex.

Journal: Frontiers in cell and developmental biology

Status: data only, 3 datasets cited

[310] doi:10.3389/fnins.2026.1862571 [paper, data]

Integrated bulk, single-cell, and spatial transcriptomic analyses prioritize NOTCH1 as a candidate gene associated with neurovascular and immune-related alterations in Parkinson's disease.

Journal: Frontiers in neuroscience

Status: code on request, 1 dataset cited

[311] doi:10.3389/fimmu.2026.1775662 [paper, data]

&lt;i&gt;Blomia tropicalis&lt;/i&gt; allergens induce lung DNA methylation changes in neuroimmune genes in a mouse model of airway inflammation.

Journal: Frontiers in immunology

Status: data only, 1 dataset cited

[312] doi:10.3389/fmicb.2026.1765044 [paper, data]

Integrating serum pharmacology, network pharmacology, and molecular biology analysis to reveal the mechanisms of Baihe Dihuang decoction in treating Alzheimer's disease.

Journal: Frontiers in microbiology

Status: data only, 1 dataset cited

[313] Code ↔ Paper doi:10.1016/j.isci.2026.116439 [paper, repository]

Decoding the role of transcriptomic clocks in the human prefrontal cortex.

Journal: iScience

Authors' code: martinezjaime/PFC-Transcriptomic (no license), Jacobson-CompSysBio/MENTOR-py (MIT)

Status: code verified, 68 files readable, 24 matches

Wednesday, 1 July 2026 (27 papers)

[314] Code ↔ Paper doi:10.1093/brain/awaf426 [paper, repository]

Single-nucleus multiome shows motor neuron glutamate overactivation in amyotrophic lateral sclerosis.

Journal: Brain : a journal of neurology

Authors' code: ertakeuchi/ALS_project (no license)

Status: code verified, 21 files readable, 10 matches

[315] doi:10.1093/brain/awaf432 [paper, data]

Global network and local vulnerabilities underlie brain atrophy across Parkinson's disease stages.

Journal: Brain : a journal of neurology

Status: data only, 1 dataset cited

[316] doi:10.1093/neuonc/noag080 [paper, data]

Laser interstitial thermal therapy enhances bidirectional blood-brain barrier permeability in glioblastoma.

Journal: Neuro-oncology

Status: data only, 1 dataset cited

[317] doi:10.1210/endrev/bnag008 [paper, data]

Diverse SOX3 genetic variants and their associated phenotypic spectrum in human disease.

Journal: Endocrine reviews

Status: data only, 1 dataset cited

[318] Code ↔ Paper doi:10.1093/nar/gkag454 [paper, repository]

RegRegSEA: a web server for regulatory region set enrichment analysis of epigenomic data.

Journal: Nucleic acids research

Authors' code: CCB-SB/RegRegSEA (MIT), Zenodo 19731482 (MIT)

Status: code verified, 10 files readable, 2 matches

[319] Code ↔ Paper doi:10.1002/cns.70976 [paper, repository]

Cingulate Gradient Dysfunction in End-Stage Renal Disease: Associations With Clinical Phenotypes and Exploratory Transcriptomic Signatures.

Journal: CNS neuroscience & therapeutics

Authors' code: OSF f2t9j (no license)

Status: code verified, 1 file readable

[320] doi:10.1007/s00401-026-03050-1 [paper]

Molecular changes during AT/RT progression associated with epithelial-mesenchymal transition and extracellular matrix changes.

Journal: Acta neuropathologica

Status: data only

[321] Code ↔ Paper doi:10.1073/pnas.2609132123 [paper, repository]

A human lysosomal storage disorder toolkit for decoding proteome landscapes in cortical-like and dopaminergic-like induced neurons.

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

Authors' code: sauerkrausi/neuroLSD (MIT)

Status: code verified, 22 files readable, 7 matches

[322] Code ↔ Paper doi:10.1038/s41562-026-02486-5 [paper, repository]

Genome-wide association studies of infant and toddler temperament in European and multi-ancestry populations.

Journal: Nature human behaviour

Authors' code: precimed/python_convert (GPL-3.0), PerlineDemange/GeneticNurtureNonCog (no license)

Status: code verified, 54 files readable, 3 matches

[323] Code ↔ Paper doi:10.1038/s41591-026-04485-5 [paper, repository]

Blood-based circular RNAs for early diagnosis of Alzheimer's disease.

Journal: Nature medicine

Authors' code: neurogenomicsandinformatics/rnaseq_pipeline (no license)

Status: code verified, 10 files readable, 2 matches

[324] doi:10.1186/s12883-026-05109-8 [paper, data]

A preliminary analysis of the inflammatory protein landscape in the CSF of mid- to late-stage Parkinson's disease: associations with motor severity and subtypes.

Journal: BMC neurology

Status: data only, 1 dataset cited

[325] doi:10.1186/s13073-026-01699-7 [paper, data]

De novo variants in NPTN cause a neurodevelopmental disorder with autism and neuroplastin-PMCA hypofunction.

Journal: Genome medicine

Status: data only, 1 dataset cited

[326] Code ↔ Paper doi:10.1167/iovs.67.8.9 [paper, repository]

Müller Glia-Exclusive CLRN1 Expression Drives Non-Cell-Autonomous Photoreceptor Degeneration in Usher Syndrome Type 3A.

Journal: Investigative ophthalmology & visual science

Authors' code: doyang-um/CLRN1_snRNAseq_10M (MIT)

Status: code verified, 16 files readable, 11 matches

[327] Code ↔ Paper doi:10.1111/jnc.70502 [paper, repository]

The Converging Effects of Different Categories of Antidepressants on the Brain: A Systematic Meta-Analysis of Public Transcriptional Profiling Data From the Hippocampus and Cortex.

Journal: Journal of neurochemistry

Authors' code: evageoghegan/AntidepressantMetaAnalysis (no license)

Status: code verified, 47 files readable, 22 matches

[328] Code ↔ Paper doi:10.1002/alz.71630 [paper, repository]

Genetic architecture of the limbic white matter microstructure in aging and Alzheimer's Disease.

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

Authors' code: Zenodo 13863955 (CC-BY-4.0)

Status: code verified

[329] Code ↔ Paper doi:10.1002/sim.70658 [paper, repository]

Predictor-Assisted Nonparametric Graphical Models With Multivariate Error-Prone Data.

Journal: Statistics in medicine

Authors' code: lchen723/RF_Graph (no license)

Status: dead link

[330] Code ↔ Paper doi:10.1093/bioinformatics/btag220 [paper, repository]

Riemannian metric learning for alignment of spatial multiomics.

Journal: Bioinformatics (Oxford, England)

Authors' code: raphael-group/MGW (no license), Zenodo 20074368 (CC-BY-4.0)

Status: code verified, 6 files readable, 1 match

[331] doi:10.1111/jne.70230 [paper, data]

Single-nuclei RNA sequencing reveals heterogeneity within developing GnRH3 neurons in zebrafish.

Journal: Journal of neuroendocrinology

Status: data only, 1 dataset cited

[332] doi:10.1111/acel.70616 [paper]

Transcriptomic Evidence of Mitochondrial Double-Stranded RNA Accumulation in Brain Aging and Alzheimer's Disease.

Journal: Aging cell

Status: code on request

[333] Code ↔ Paper doi:10.1111/jcmm.71280 [paper, repository]

Rapamycin Partially Reverts Cavernoma Endothelial Cell Phenotype and, When Combined With Lapatinib, Ameliorates Chronic Lesions.

Journal: Journal of cellular and molecular medicine

Authors' code: dvidmd/GSE298723_Differential_Gene_Expression_Analysis_Garcia_Colomer_et_al (no license)

Status: code verified, 12 files readable, 2 matches

[334] Code ↔ Paper doi:10.1002/hbm.70605 [paper, repository]

BrainEnrich: Revealing Biological Insights for Imaging-Derived Phenotypes Through Transcriptomic Enrichment.

Journal: Human brain mapping

Authors' code: YuLab-SMU/enrichplot (no license), zh1peng/paper_code (no license), MICA-MNI/ENIGMA (BSD-3-Clause)

Status: code verified, 386 files readable, 4 matches

[335] doi:10.1111/ene.70699 [paper, data]

A Novel RORA Hinge-Region Variant in Adult IDDECA With Cerebellar Atrophy and Marked Response to Valproate.

Journal: European journal of neurology

Status: data only, 1 dataset cited

[336] Code ↔ Paper doi:10.1111/adb.70179 [paper, repository]

Transcriptional Response to Chronic Long-Access Fentanyl Self-Administration in Rat Habenula and Amygdala.

Journal: Addiction biology

Authors' code: LieberInstitute/fentanyl_rat_hb_amy (MIT), Zenodo 17573970 (CC-BY-4.0)

Status: code verified, 27 files readable, 12 matches

[337] doi:10.1111/acel.70622 [paper, data]

High Intrinsic Aerobic Capacity Is Associated With a Distinct Epigenetic and Signaling Profile in the Aged Rat Brain.

Journal: Aging cell

Status: data only, 1 dataset cited

[338] doi:10.1002/cns.71021 [paper, data]

Multilayer Proteome and Metabolome-Based Validation Uncovers Combined Regulatory Roles and Predictive Values of 6 RNA Modifications and Cellular Senescence in Alzheimer's Disease.

Journal: CNS neuroscience & therapeutics

Status: data only, 1 dataset cited

[339] Code ↔ Paper doi:10.1093/bib/bbag411 [paper, repository]

Screening of cell-type-specific meta-programs for drug repurposing in Alzheimer's disease.

Journal: Briefings in bioinformatics

Authors' code: Zhangyx-q/AD_MPcode (no license)

Status: code verified, 9 files readable, 7 matches

[340] Code ↔ Paper doi:10.1167/iovs.67.8.61 [paper, repository]

A Shared Genetic Basis Underlying Myopia-Exotropia Comorbidity.

Journal: Investigative ophthalmology & visual science

Authors' code: chr1swallace/coloc (no license)

Status: code verified, 41 files readable, 4 matches

Tuesday, 30 June 2026 (6 papers)

[341] doi:10.1128/jvi.00656-26 [paper, data]

Neurotropism and interferon-dominated immune responses in a mouse-adapted coxsackievirus A16 infection model.

Journal: Journal of virology

Status: data only, 1 dataset cited

[342] doi:10.1038/s41598-026-56101-8 [paper, data]

Topological modeling of gene expression in the brain with Huntington's disease reveals selective disruption of co-expression network.

Journal: Scientific reports

Status: data only, 1 dataset cited

[343] Code ↔ Paper doi:10.1038/s42003-026-10402-w [paper, repository]

Temporal orchestration of transcriptional and epigenomic programming underlying maternal embryonic diapause in a cricket model.

Journal: Communications biology

Authors' code: Kataoka-K-Lab/Dnigrofasciatus_EggDiapause (no license)

Status: code verified, 36 files readable, 9 matches

[344] Code ↔ Paper doi:10.3390/ijms27135920 [paper, repository]

Metabolomic Classification of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome via Explainable Ensemble Learning and Pareto-Guided Feature Selection.

Journal: International journal of molecular sciences

Authors' code: drhilal/ME-CFS-study (no license)

Status: code verified, 1 file readable, 5 matches

[345] doi:10.3389/fphar.2026.1870571 [paper, data]

Tissue-autonomous pharmacological direction: how target expression landscapes convert balanced compounds into tissue-selective agents.

Journal: Frontiers in pharmacology

Status: data only, 3 datasets cited

[346] Code ↔ Paper doi:10.3389/fncel.2026.1713437 [paper, repository]

Single-nucleus transcriptomics identifies cell cycle and synaptic pathway dysregulation during OPC-to-glioma progression.

Journal: Frontiers in cellular neuroscience

Authors' code: dennishuang02/bbp53n_glioma_submission (no license)

Status: code verified, 6 files readable, 4 matches

Monday, 29 June 2026 (4 papers)

[347] Code ↔ Paper doi:10.1371/journal.pgen.1012170 [paper, repository]

Genome wide association study meta-analysis of neuropathologic lesions of Alzheimer's disease and related dementias in a multi-site autopsy cohort.

Journal: PLoS genetics

Authors' code: beecham-lab/ADRD-Neuropathology-Scripts (MIT)

Status: code verified, 61 files readable, 4 matches

[348] Code ↔ Paper doi:10.1186/s13059-026-04177-w [paper, repository]

Genomic sequence evolution underlying human neocortical interareal diversification.

Journal: Genome biology

Authors' code: JCVenterInstitute/NSForest (CC-BY-4.0), yal054/snATACutils (MIT), FduZhuLab/spatial_and_snMultiome (MIT), Zenodo 20581795 (MIT)

Status: code verified, 227 files readable, 27 matches

[349] Code ↔ Paper doi:10.1002/dad2.70406 [paper, repository]

Deep contrastive learning framework identifies cell-type-specific drug targets in Alzheimer's disease.

Journal: Alzheimer's & dementia (Amsterdam, Netherlands)

Authors' code: yuxin212/CLARITY (no license), ChengF-Lab/CLARITY (no license)

Status: code verified, 56 files readable

[350] Code ↔ Paper doi:10.3390/biology15131038 [paper, repository]

Genetic Basis of Divergent Growth and Muscle Development in Purebred and Crossbred Leizhou Black Goats Revealed by Whole-Genome Resequencing.

Journal: Biology

Authors' code: animal.omics.pro/code/index.php (no license)

Status: code verified

Sunday, 28 June 2026 (1 paper)

[351] doi:10.1111/imb.70052 [paper, data]

Genome-wide identification of olfactory receptor and odorant-binding protein gene families and their roles in Heliothine chemosensory evolution.

Journal: Insect molecular biology

Status: data only, 1 dataset cited

Saturday, 27 June 2026 (2 papers)

[352] doi:10.1186/s12866-026-05351-7 [paper, data]

Integrated analysis of gut microbiota, serum metabolomics, and proteomics reveals novel associations with clinical symptoms in patients with cerebral infarction.

Journal: BMC microbiology

Status: data only, 1 dataset cited

[353] doi:10.3390/cancers18132092 [paper, data]

TGFB2 as a Prognostic Biomarker Associated with Myeloid-Enriched, Multi-Checkpoint-Activated Immunosuppression in Diffuse Glioma: A Multi-Cohort Transcriptomic Study.

Journal: Cancers

Status: code on request, 1 dataset cited

Friday, 26 June 2026 (5 papers)

[354] Code ↔ Paper doi:10.1080/19490976.2026.2693397 [paper, repository]

Gut &lt;i&gt;Proteobacteria&lt;/i&gt; glycine metabolism regulates neuroplasticity, motivation, and reinstatement of cocaine self-administration in mice.

Journal: Gut microbes

Authors' code: mooredf22/quasispectral (no license)

Status: code verified, 2 files readable, 1 match

[355] doi:10.1002/advs.76340 [paper, data]

Molecular and Cellular Hallmarks of Age-Related Vestibular Hair Cell Degeneration.

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

Status: data only, 1 dataset cited

[356] Code ↔ Paper doi:10.1007/s00406-026-02302-1 [paper, repository]

Exploring the genetic correlation between inflammatory bowel disease and psychiatric disorders: insights from genome-wide association studies.

Journal: European archives of psychiatry and clinical neuroscience

Authors' code: duanxian0301/TWAS (no license)

Status: code verified, 18 files readable

[357] Code ↔ Paper doi:10.1186/s13040-026-00574-w [paper, repository]

Interpretable machine learning for Parkinson's disease diagnosis, staging, and biological mechanism exploration: a multicenter analysis.

Journal: BioData mining

Authors' code: jy2137/PD-radiomics (no license)

Status: dead link

[358] doi:10.1177/11769351261460625 [paper, data]

GFAP-Dependent Transcriptional Dynamics and Cellular Heterogeneity in Primary, Recurrent, and Grade III Gliomas.

Journal: Cancer informatics

Status: data only, 1 dataset cited

Thursday, 25 June 2026 (7 papers)

[359] Code ↔ Paper doi:10.1002/advs.76205 [paper, repository]

CHCHD10 Mitigates Alzheimer's Disease-Related Phenotypes in Association With Epigenetic Remodeling in Directly Reprogrammed Neurons.

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

Authors' code: tliu203/CHCHD10-Alleviates-Alzheimer-s-Disease-Pathogenesis-by-Modulating-Epigenetic-Landscape- (MIT)

Status: code verified, 42 files readable, 22 matches

[360] Code ↔ Paper doi:10.1016/j.stemcr.2026.102977 [paper, repository]

Integrative analysis of drug-gene signatures in human pluripotent stem cells reveals prazosin as a novel SQSTM1 regulator for ALS therapeutics.

Journal: Stem cell reports

Authors' code: maximilianh/crisporWebsite (other), usadellab/trimmomatic (GPL-3.0)

Status: code verified, 1,012 files readable, 2 matches

[361] Code ↔ Paper doi:10.1186/s12967-026-08414-5 [paper, repository]

Integrative transcriptomic analysis identifies meningeal-hippocampal immune communication in Alzheimer's disease.

Journal: Journal of translational medicine

Authors' code: yccbio/ad (no license)

Status: empty repository

[362] doi:10.1186/s13059-026-04126-7 [paper, data]

Srr2-dependent SOX2 levels govern the chromatin and transcriptional landscape of adult neural stem cell fate decisions in mouse.

Journal: Genome biology

Status: data only, 3 datasets cited

[363] doi:10.1186/s40478-026-02351-6 [paper, data]

A rare missense variant impacting NEK1 kinase function is associated with ALS.

Journal: Acta neuropathologica communications

Status: data only, 2 datasets cited

[364] doi:10.3389/fcell.2026.1816627 [paper, data]

Integrative transcriptomic and proteomic profiling reveals altered thymocyte development and microenvironment remodeling during natural thymic atrophy.

Journal: Frontiers in cell and developmental biology

Status: data only, 1 dataset cited

[365] doi:10.3390/pathophysiology33030043 [paper, data]

A Differentiated SH-SY5Y Model of Hypoxic-Ischaemic Injury Reveals Dynamic Transcriptomic Responses During Reoxygenation.

Journal: Pathophysiology : the official journal of the International Society for Pathophysiology

Status: data only, 1 dataset cited

Wednesday, 24 June 2026 (8 papers)

[366] doi:10.1136/jitc-2025-014421 [paper, data]

Spatial immune atlas of breast cancer brain metastasis reveals CD163&lt;sup&gt;+&lt;/sup&gt; macrophage reprogramming associated with immune escape.

Journal: Journal for immunotherapy of cancer

Status: data only, 2 datasets cited

[367] doi:10.1038/s41398-026-04202-3 [paper]

Single-nucleus transcriptomic atlas of sexually dimorphic molecular responses to sub-chronic variable stress in the mouse hippocampus.

Journal: Translational psychiatry

Status: code on request

[368] Code ↔ Paper doi:10.1038/s42003-026-10382-x [paper, repository]

ScQCenrich enables multi-metric quality control for single-cell RNA sequencing.

Journal: Communications biology

Authors' code: lemonlyy755/scQCenrich (other), Zenodo 20050798 (CC-BY-4.0)

Status: code verified, 62 files readable, 13 matches

[369] Code ↔ Paper doi:10.1038/s43587-026-01149-4 [paper, repository]

The blood metabolome of brain health in midlife and influences of genes, microbiome and exposome.

Journal: Nature aging

Authors' code: omics-x/BloodMetabolomics_Genes_Gut_Exposome (no license)

Status: code verified, 26 files readable, 22 matches

[370] Code ↔ Paper doi:10.1038/s41467-026-74153-2 [paper, repository]

Regional, functional and transcriptomic decoding of multidimensional brain structure alterations in obsessive-compulsive disorder.

Journal: Nature communications

Authors' code: biorender.com/bnwqaux (no license), ColeLab/ColeAnticevicNetPartition (other), richardajdear/AHBA_gradients (no license), csleo95/Multi-phenotype-morphometry (MIT), isebenius/MIND (no license), enigma.ini.usc.edu/ongoing/enigma-shape-analysis (no license), Zenodo 19770466 (MIT), codeocean:7065197 (no license)

Status: code verified, 102 files readable, 11 matches

[371] doi:10.1186/s12866-026-05296-x [paper, data]

Gut bacterial characteristics in children with autism spectrum disorder according to symptom severity: a cross-sectional study.

Journal: BMC microbiology

Status: data only, 1 dataset cited

[372] Code ↔ Paper doi:10.1186/s13059-026-04125-8 [paper, repository]

MLMarker: a machine learning framework for tissue inference and biomarker discovery.

Journal: Genome biology

Authors' code: TineClaeys/MLMarker-manuscript (no license), TineClaeys/MLMarker (Apache-2.0), TineClaeys/MLMarker-streamlit (Apache-2.0)

Status: code verified, 54 files readable, 34 matches

[373] doi:10.3389/fphys.2026.1844142 [paper, data]

CRISPR/Cas9-mediated &lt;i&gt;PHOX2B&lt;/i&gt; functional knock-out in IMR32 neuroblastoma cells impairs neuronal excitability through dysregulation of ion channels genes.

Journal: Frontiers in physiology

Status: data only, 1 dataset cited

Tuesday, 23 June 2026 (6 papers)

[374] Code ↔ Paper doi:10.1038/s41398-026-04199-9 [paper, repository]

Immune cell-specific genetic architecture of Alzheimer's disease revealed by multi-omics analysis for therapeutic target discovery and prioritization.

Journal: Translational psychiatry

Authors' code: DeepVasc-Lab/3-step_sceQTLMR (Apache-2.0)

Status: code verified, 3 files readable, 1 match

[375] Code ↔ Paper doi:10.1038/s41467-026-74171-0 [paper, repository]

Cluster replicability in single-cell and single-nucleus atlases of the mouse brain.

Journal: Nature communications

Authors' code: gillislab/mouse_brain_cluster_replicability (MIT), Zenodo 19901057 (MIT)

Status: code verified, 52 files readable, 18 matches

[376] Code ↔ Paper doi:10.1161/jaha.125.046088 [paper, repository]

Systematic Identification of Therapeutic Targets and Repurposed Drugs for Stroke: From Genome Causal Analysis to Multilevel Validation.

Journal: Journal of the American Heart Association

Authors' code: AzumitoAsneuet112358/MR-Target-in-STROKE (no license)

Status: dead link

[377] Code ↔ Paper doi:10.1016/j.cell.2026.05.047 [paper, repository]

An emergent disease-associated motor neuron state precedes cell death in ALS.

Journal: Cell

Authors' code: omgautier/Gautier_Blum_2026 (no license)

Status: code verified, 14 files readable, 40 matches

[378] doi:10.1016/j.isci.2026.116484 [paper, data]

Molecular taxonomy and spatial organization define neuronal subtypes in the mouse inferior colliculus.

Journal: iScience

Status: code on request, 1 dataset cited

[379] Code ↔ Paper doi:10.1016/j.nbscr.2026.100149 [paper, repository]

Molecular correlates of sleep deprivation in the mouse brain identified by meta-analysis of microarray data.

Journal: Neurobiology of sleep and circadian rhythms

Authors' code: FHSProject139/FSH-Project-Notebooks-and-Files (no license), ohabdalla1/Dexras1_Behavioural_Sleep (MIT)

Status: code verified, 32 files readable

Monday, 22 June 2026 (3 papers)

[380] Code ↔ Paper doi:10.1242/dev.205342 [paper, repository]

Proteomic profile of hippocampal growth cones through early postnatal development.

Journal: Development (Cambridge, England)

Authors' code: Quattrocolo-Lab/krause-et-al-2026 (MIT), gaospecial/ggVennDiagram (GPL-3.0), mbojan/alluvial (other)

Status: code verified, 71 files readable, 13 matches

[381] Code ↔ Paper doi:10.1038/s41588-026-02646-3 [paper, repository]

Co-expression-based models improve eQTL predictions for transcriptome-wide association studies and highlight new schizophrenia-associated genes.

Journal: Nature genetics

Authors' code: Zenodo 14959416 (MIT), fabiana1rossi/coTWAS (MIT), hakyimlab/MetaXcan (MIT), roussoslab/epixcan (no license)

Status: code verified, 306 files readable, 18 matches

[382] doi:10.2147/ijgm.s605071 [paper, data]

Mendelian Randomization and Single-Cell RNA Sequencing Reveal CKAP4 and PFDN5 as Tumor Cell-Specific Causal Genes for Glioblastoma.

Journal: International journal of general medicine

Status: data only, 1 dataset cited

Sunday, 21 June 2026 (2 papers)

[383] Code ↔ Paper doi:10.1038/s41398-026-04200-5 [paper, repository]

Postmortem brain single-nucleus and bulk gene expression analyses identify shared and distinct abnormalities in bipolar disorder and major depressive disorder.

Journal: Translational psychiatry

Authors' code: PsychiatKobeUniv-singlecell/Code_brain_mood_disorders (no license)

Status: code verified, 22 files readable, 7 matches

[384] Code ↔ Paper doi:10.1002/ece3.73881 [paper, repository]

Epigenetic Aging in Brain Tissue of the Self-Fertilizing Vertebrate, &lt;i&gt;Kryptolebias marmoratus&lt;/i&gt;.

Journal: Ecology and evolution

Authors' code: jubelik/Epigenetic-clock (no license), Zenodo 20491333 (CC-BY-4.0)

Status: code verified, 5 files readable, 7 matches

Saturday, 20 June 2026 (2 papers)

[385] Code ↔ Paper doi:10.1038/s41467-026-73714-9 [paper, repository]

The genetic architecture of cortical similarity networks.

Journal: Nature communications

Authors' code: jrs95/geni.plots (GPL-3.0), Zenodo 7974716 (other-open), isebenius/mind (no license)

Status: code verified, 23 files readable, 5 matches

[386] doi:10.1038/s41467-026-74712-7 [paper, data]

Trigger-day hCG effects on DNA methylation and neurodevelopment in ART offspring.

Journal: Nature communications

Status: data only, 2 datasets cited

Friday, 19 June 2026 (7 papers)

[387] doi:10.1080/17501911.2026.2691031 [paper, data]

Promoter methylation-associated brain-enriched long noncoding RNAs in glioblastoma: a multi-cohort public epigenomic re-analysis.

Journal: Epigenomics

Status: data only, 1 dataset cited

[388] Code ↔ Paper doi:10.7554/elife.106347 [paper, repository]

Esr1-dependent signaling and transcriptional maturation in the medial preoptic area of the hypothalamus shape the development of mating behavior during adolescence.

Journal: eLife

Authors' code: theislab/paga (BSD-3-Clause), stuberlab/Hashikawa-Hashikawa-eLife (MIT)

Status: code verified, 36 files readable, 9 matches

[389] Code ↔ Paper doi:10.21203/rs.3.rs-9927928/v1 [paper, repository]

Genome-wide and allele-resolved maps of the radial architecture of the mouse genome

Journal: Research Square (preprint)

Authors' code: BiCroLab/nextflow-gpseq (MIT), nf-core/rnaseq (MIT), nf-core/atacseq (MIT), elgw/chromflock (no license), BiCroLab/AllelicRadiality (no license)

Status: code verified, 248 files readable, 23 matches

[390] Code ↔ Paper doi:10.1016/j.xgen.2026.101278 [paper, repository]

Single-cell profiling of DNA methylation in autism spectrum disorder prefrontal cortex reveals distinct regulatory and aging signatures.

Journal: Cell genomics

Authors' code: chooliu/snmCTseq_Pipeline (no license)

Status: code verified, 31 files readable, 6 matches

[391] Code ↔ Paper doi:10.1038/s41467-026-73883-7 [paper, repository]

In situ graphene-seq: spatial transcriptomics and chronic electrophysiological characterization of tissue microenvironments.

Journal: Nature communications

Authors' code: LiuLab-Bioelectronics-Harvard/Graphene_seq (Apache-2.0), Zenodo 19520229 (Apache-2.0)

Status: code verified, 13 files readable, 11 matches

[392] Code ↔ Paper doi:10.1038/s44400-026-00094-8 [paper, repository]

Haplotype-resolved DNA methylation at the &lt;i&gt;APOE&lt;/i&gt; locus identifies allele-specific epigenetic signatures relevant to Alzheimer's disease risk.

Journal: NPJ dementia

Authors' code: NIH-CARD/CARDlongread_data_standardization (no license), nih-card/scmaverics (other), NIH-CARD/APOE_CpG_methylation (no license)

Status: code verified, 95 files readable, 4 matches

[393] doi:10.3389/fgene.2026.1833119 [paper]

Integrative analysis identifies Hspa5 as a key regulator of the ERS/UPR-immune axis in spinal cord injury.

Journal: Frontiers in genetics

Status: data only

Thursday, 18 June 2026 (6 papers)

[394] doi:10.1371/journal.ppat.1014314 [paper, data]

Chemo-omic pipeline enables discovery of prion synaptotoxic pathways and inhibitory drugs.

Journal: PLoS pathogens

Status: data only, 1 dataset cited

[395] Code ↔ Paper doi:10.1016/j.xgen.2026.101280 [paper, repository]

BMI-genome interactions regulate global gene expression with emphasis in brain and gut.

Journal: Cell genomics

Authors' code: rsigner/BMI_dynamic_models (MIT), Zenodo 20215573 (no license), predictdb.org/post/2021 (no license), hakyimlab/metaxcan (MIT), chandlerzuo/atSNP (no license)

Status: code verified, 161 files readable, 3 matches

[396] Code ↔ Paper doi:10.1016/j.stemcr.2026.102967 [paper, repository]

Single-cell multiomic approaches define a gradual, spatially regulated epigenetic and transcriptional transition from embryonic to adult neural stem cells.

Journal: Stem cell reports

Authors' code: immunogenomics/harmony (no license)

Status: code verified, 32 files readable, 2 matches

[397] Code ↔ Paper doi:10.1038/s41380-026-03686-1 [paper, repository]

Early oligodendrocyte dysfunction signature in Alzheimer's disease: Insights from DNA methylomics and transcriptomics.

Journal: Molecular psychiatry

Authors' code: CBettencourtLab/AD_OLGDNAm (no license)

Status: code verified, 6 files readable, 6 matches

[398] Code ↔ Paper doi:10.3390/ijms27125533 [paper, repository]

Discovery-Driven Plasma Proteomics Identifies a Multi-Protein Signature for Amyloid PET Positivity: A Machine Learning Analysis of the Bio-Hermes Cohort.

Journal: International journal of molecular sciences

Authors' code: stelioslamprou37/SML_PipelineR (MIT)

Status: code verified, 3 files readable, 1 match

[399] Code ↔ Paper doi:10.1016/j.isci.2026.116469 [paper, repository]

Neuronal differentiation of neuroblastoma cell lines for neurological disease modeling.

Journal: iScience

Authors' code: Zenodo 6401600 (MIT), Zenodo 13759327 (CC-BY-4.0), claupomm/rna-seq_snv_tumour_only (no license)

Status: code verified, 23 files readable, 4 matches

Wednesday, 17 June 2026 (5 papers)

[400] Code ↔ Paper doi:10.1371/journal.pcbi.1014422 [paper, repository]

Deciphering cell type-specific causal genetic effects on brain imaging-derived phenotypes and disorders with single-cell Mendelian randomization.

Journal: PLoS computational biology

Authors' code: sldrcyang/ExpMR (no license)

Status: code verified, 89 files readable, 9 matches

[401] Code ↔ Paper doi:10.1016/j.mcpro.2026.101604 [paper, repository]

Optimizing NGN2 Dosage Enhances the Neuronal Enrichment of iPSC-Derived Neuronal Cultures.

Journal: Molecular & cellular proteomics : MCP

Authors' code: xomicsdatascience/generation_of_iNeurons (no license)

Status: code verified, 11 files readable, 7 matches

[402] Code ↔ Paper doi:10.1038/s41586-026-10679-1 [paper, repository]

Cortical development dynamics across autism spectrum disorder mouse models.

Journal: Nature

Authors' code: modeldb:184162 (no license), git.ista.ac.at/research-sofware/mouseome (no license), Zenodo 17532669 (BSD-3-Clause), sommerc/tadpose (BSD-3-Clause)

Status: code verified, 28 files readable, 4 matches

[403] Code ↔ Paper doi:10.34133/research.1298 [paper, repository]

Multisite Chronic Pain Reveals Neuro-Immune-Metabolic Dysregulation across Rheumatoid Arthritis and Depression.

Journal: Research (Washington, D.C.)

Authors' code: qianwang-brain/Pain_RheumatoidArthritic_Depression_Fusion (no license)

Status: code verified, 7 files readable, 7 matches

[404] Code ↔ Paper doi:10.1016/j.isci.2026.116429 [paper, repository]

&lt;i&gt;HMGA2&lt;/i&gt; regulates fear and growth: Canine GWAS and functional evidence.

Journal: iScience

Authors' code: genetics-statistics/GEMMA (GPL-3.0), deweylab/RSEM (GPL-3.0), OpenGene/fastp (MIT)

Status: code verified, 505 files readable, 2 matches

Tuesday, 16 June 2026 (8 papers)

[405] Code ↔ Paper doi:10.1261/rna.080954.126 [paper, repository]

Neuronal subtype-specific ribosomal protein mRNA expression.

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

Authors' code: joagarat/RP_scRNAseq_Neurons_Code (no license)

Status: code verified, 23 files readable, 19 matches

[406] doi:10.1016/j.ebiom.2026.106330 [paper, data]

Hippocampal neuroinflammation and altered peripheral neurobiological protein profile in experimental arthritis and systemic juvenile idiopathic arthritis.

Journal: EBioMedicine

Status: data only, 1 dataset cited

[407] doi:10.1186/s12967-026-08447-w [paper, data]

Single-cell and spatial transcriptomes reveal oligodendrocyte remodeling fatty acid metabolism microenvironment of lung cancer brain metastases.

Journal: Journal of translational medicine

Status: data only, 1 dataset cited

[408] Code ↔ Paper doi:10.1186/s13073-026-01698-8 [paper, repository]

From aging to Alzheimer's disease: concordant brain DNA methylation changes in late life.

Journal: Genome medicine

Authors' code: TransBioInfoLab/AD-aging-brain-samples-analysis (MIT)

Status: code verified, 35 files readable, 13 matches

[409] Code ↔ Paper doi:10.1016/j.isci.2026.116412 [paper, repository]

KOLF2.1J iTF-Microglia: A standardized platform to study microglial transcriptional regulatory networks in CNS disease.

Journal: iScience

Authors' code: HudsonAlpha/iTF-Microglia (MIT), ENCODE-DCC/atac-seq-pipeline (MIT)

Status: code verified, 72 files readable, 27 matches

[410] doi:10.32604/or.2026.079221 [paper, data]

Single-Cell Sequencing Reveals the Heterogeneity of Glioma and Identifies IGFBP2 as A Potential Therapeutic Target.

Journal: Oncology research

Status: data only, 1 dataset cited

[411] doi:10.3389/fnins.2026.1848128 [paper, data]

Assessment of tenecteplase target-associated pathogenic mechanisms underlying depression in acute ischemic stroke patients: insights from artificial intelligence-driven multi-omics analysis and &lt;i&gt;in vitro&lt;/i&gt; validation.

Journal: Frontiers in neuroscience

Status: data only, 1 dataset cited

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

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

Journal: ACS omega

Status: code on request, 4 datasets cited

Monday, 15 June 2026 (6 papers)

[413] Code ↔ Paper doi:10.1016/j.cell.2026.05.026 [paper, repository]

The critical role of the endogenous immune compartment after CAR T cell therapy in recurrent GBM.

Journal: Cell

Authors' code: SilverbushLab/Bivalent-CAR-T-cell-therapy-in-recurrent-GBM (MIT)

Status: code verified, 71 files readable, 30 matches

[414] Code ↔ Paper doi:10.1038/s41467-026-74228-0 [paper, repository]

Spatial and network principles behind neural generation of locomotion.

Journal: Nature communications

Authors' code: albert597/TRAILMAP (MIT), BergLab/SpinalProjectome (CC0-1.0), codeocean:9317742 (no license)

Status: code verified, 78 files readable, 3 matches

[415] doi:10.1007/s00401-026-03036-z [paper, data]

Mechanisms of increased Alzheimer's disease pathology with R47H and R62H TREM2 variants.

Journal: Acta neuropathologica

Status: data only, 1 dataset cited

[416] Code ↔ Paper doi:10.1186/s12974-026-03885-1 [paper, repository]

Shared transcriptomic signatures in perilesional and contralesional cortex after ischemic stroke.

Journal: Journal of neuroinflammation

Authors' code: Zenodo 14750099 (CC-BY-4.0)

Status: code verified, 99 files readable

[417] Code ↔ Paper doi:10.3390/cells15121086 [paper, repository]

Investigating Alzheimer's Disease-Associated Genes Using Differential Splicing Frequency Analysis.

Journal: Cells

Authors' code: gaoshanT/Fastq_clean (no license)

Status: code verified, 49 files readable, 2 matches

[418] Code ↔ Paper doi:10.3389/fnins.2026.1852774 [paper, repository]

Spatial transcriptomics on an expanded dataset at the brain-electrode interface: exploration of variability and identification of novel biomarkers.

Journal: Frontiers in neuroscience

Authors' code: msureil/SpatioBiomarker (no license)

Status: code verified, 14 files readable, 4 matches

Saturday, 13 June 2026 (2 papers)

[419] Code ↔ Paper doi:10.1038/s41467-026-74320-5 [paper, repository]

Spatial architecture of autism pathogenesis reveals mosaic structural disarray during early development.

Journal: Nature communications

Authors' code: Zenodo 19229995 (CC-BY-4.0), jinyueliu0/spatial-signaling-score (no license)

Status: code verified, 20 files readable, 10 matches

[420] doi:10.1186/s12868-026-01016-3 [paper, data]

Proteomic profiling reveals structural and adhesion pathways regulated by the inverted CHRFAM7AΔ2bp variant in human neural progenitor cells.

Journal: BMC neuroscience

Status: data only, 1 dataset cited

Friday, 12 June 2026 (4 papers)

[421] Code ↔ Paper doi:10.1371/journal.pone.0351405 [paper, repository]

Unimodal vs. multimodal deep learning for non-invasive MGMT promoter methylation prediction in glioblastoma: A systematic evaluation on the BraTS 2021 dataset.

Journal: PloS one

Authors' code: kaggle.com/competitions/rsna-miccai-brain-tumor-radiogenomic-classification (no license), freddy-oulia/MGMT_Promoter_Methylation_Prediction (CC-BY-4.0)

Status: code verified, 6 files readable, 6 matches

[422] doi:10.1186/s12984-026-02048-w [paper, data]

Functional reorganization of the contralesional precentral gyrus following acute subcortical ischemic stroke and its association with gene expression profile.

Journal: Journal of neuroengineering and rehabilitation

Status: data only, 1 dataset cited

[423] doi:10.3389/fgene.2026.1818975 [paper, data]

Clock-related neuropeptides in &lt;i&gt;Acyrthosiphon pisum&lt;/i&gt;.

Journal: Frontiers in genetics

Status: data only, 1 dataset cited

[424] Code ↔ Paper doi:10.3791/71046 [paper, repository]

Spatially Resolved, Integrated Single-Cell Multiomic Profiling of the Transcriptome and Epigenomic Targets in Frozen Tissue Sections.

Journal: Journal of visualized experiments : JoVE

Authors' code: Liuy12/Mouse_Brain_Trekker_Multiome_Cuttag (no license)

Status: code verified, 2 files readable, 3 matches

Thursday, 11 June 2026 (8 papers)

[425] Code ↔ Paper doi:10.1016/j.stemcr.2026.102958 [paper, repository]

Scalable hypothalamic neuron differentiation from human pluripotent stem cells suitable for modeling metabolic disorders.

Journal: Stem cell reports

Authors' code: combine-lab/salmon (BSD-3-Clause)

Status: code verified, 95 files readable

[426] Code ↔ Paper doi:10.1038/s41398-026-04108-0 [paper, repository]

Divergent transcriptomic pathways underlie sex-biased cognitive rescue by developmental GSK3B inhibition in a mouse model of 22q11.2 deletion syndrome.

Journal: Translational psychiatry

Authors' code: PasseckerLab (no license)

Status: code verified

[427] doi:10.1007/s12017-026-08935-8 [paper]

Subgroup-Specific Associations of GRIA Genes Encoding AMPA Glutamate Receptor Subunits with Patient Survival in Medulloblastoma.

Journal: Neuromolecular medicine

Status: data only

[428] Code ↔ Paper doi:10.1016/j.isci.2026.116336 [paper, repository]

Transcriptomic signatures of synaptic loss in Alzheimer's disease.

Journal: iScience

Authors' code: Sahuhu-Sun/Imaging-transcriptomics (no license)

Status: code verified, 5 files readable, 2 matches

[429] doi:10.1016/j.isci.2026.116317 [paper]

Pathogenic mutations in clathrin heavy chain disrupt synapse architecture and learning in &lt;i&gt;Drosophila&lt;/i&gt;.

Journal: iScience

Status: code on request

[430] Code ↔ Paper doi:10.1016/j.isci.2026.116337 [paper, repository]

Multimodal atlas of single neuron metabolic electrophysiological coupling uncovers circadian rewiring.

Journal: iScience

Authors' code: SNMS-ctrl/SNMS (no license)

Status: code verified, 4 files readable

[431] Code ↔ Paper doi:10.1016/j.isci.2026.116320 [paper, repository]

Machine learning-based gait classification and genome-wide association identify a QTL for gait type in Colombian paso horses.

Journal: iScience

Authors' code: JianYang-Lab/GCTA (GPL-3.0), saigegit/SAIGE (GPL-3.0)

Status: code verified, 134 files readable, 4 matches

[432] doi:10.1016/j.apsb.2026.06.016 [paper, data]

Rhynchophylline rewires DLAT lipoylation &lt;i&gt;via&lt;/i&gt; conformational control to reverse mitochondrial bioenergetic collapse against dopaminergic neuronal injury.

Journal: Acta pharmaceutica Sinica. B

Status: data only, 2 datasets cited

Wednesday, 10 June 2026 (7 papers)

[433] Code ↔ Paper doi:10.21203/rs.3.rs-9676637/v1 [paper, repository]

A Comprehensive Benchmarking of Spatial Deconvolution and Domain Detection Methods across Diverse Tissues and Spatial Transcriptomic Technologies

Journal: Research Square (preprint)

Authors' code: Zafar-Lab/spDDB (MIT)

Status: code verified, 114 files readable, 20 matches

[434] Code ↔ Paper doi:10.1161/jaha.125.046172 [paper, repository]

Cardiovascular Disease Subtypes and Alzheimer's Disease: Phenotypic and Genetic Associations in the UK Biobank and All of Us Research Program.

Journal: Journal of the American Heart Association

Authors' code: MIILab-MTU/CVDSubtypesADCorrelation (no license)

Status: code verified, 10 files readable, 8 matches

[435] Code ↔ Paper doi:10.1126/sciadv.aeb4265 [paper, repository]

Single-nucleus profiling reveals a core disease signature and cell type-specific vulnerabilities in early Rett syndrome.

Journal: Science advances

Authors' code: Zenodo 18462624 (CC-BY-4.0), yanl54/mecp2_hippocampus_signature (no license)

Status: code verified, 18 files readable, 5 matches

[436] doi:10.1038/s41380-026-03662-9 [paper, data]

Differential DNA methylation in blood as potential mediator of the association between ambient PM&lt;sub&gt;2.5&lt;/sub&gt; and cerebrospinal fluid biomarkers of Alzheimer's disease among a cognitively normal population-based cohort.

Journal: Molecular psychiatry

Status: code on request, 1 dataset cited

[437] Code ↔ Paper doi:10.1038/s41586-026-10629-x [paper, repository]

Whole-genome duplication shaped cell-type evolution in the vertebrate brain.

Journal: Nature

Authors' code: DiracZhu1998/WGD2celltype_evolution (GPL-3.0), fmarletaz/hagfish (no license), linnarsson-lab/adult-human-brain (BSD-2-Clause), figshare 29327111 (GPL 3.0+)

Status: code verified, 209 files readable, 26 matches

[438] doi:10.1186/s13073-026-01687-x [paper, data]

Infiltrating monocyte-derived macrophages does not survive long term in stroke brain despite their dominance in the acute ischemic core and myeloid derived IGF-1 play dichotomous roles in stroke recovery.

Journal: Genome medicine

Status: data only, 1 dataset cited

[439] doi:10.3390/genes17060683 [paper]

Differential DNA Methylation of the Serotonin Receptor Signaling and Glutamatergic Synapse Pathways in Adult Twins Born Preterm.

Journal: Genes

Status: data only

Tuesday, 9 June 2026 (4 papers)

[440] Code ↔ Paper doi:10.1002/advs.75969 [paper, repository]

Accurately Deciphering Tissue Heterogeneity From Spatial Multi-Modal and Multi-Omics With STransformer.

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

Authors' code: xingyili/STransformer (no license)

Status: code verified, 18 files readable, 9 matches

[441] doi:10.1002/advs.76040 [paper, data]

Pharmacological Inhibition of FKBP51 Mitigates Early Life Adversity-Induced Social Deficits in Male Mice.

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

Status: data only, 1 dataset cited

[442] doi:10.1016/j.ebiom.2026.106325 [paper, data]

The complement C3-microglial axis in depression of Parkinson's disease: from mechanism to therapeutic intervention.

Journal: EBioMedicine

Status: data only, 1 dataset cited

[443] Code ↔ Paper doi:10.1038/s41562-026-02476-7 [paper, repository]

Genome-wide meta-analysis of quantitatively measured generalized anxiety symptoms in individuals of European ancestry.

Journal: Nature human behaviour

Authors' code: megskelton/gad-sympt-metagwas (MIT)

Status: code verified, 7 files readable, 6 matches

Monday, 8 June 2026 (4 papers)

[444] Code ↔ Paper doi:10.1038/s42003-026-10446-y [paper, repository]

Transcriptional analyses identify pericyte-centered signaling programs altered by sex and brain region in Alzheimer's Disease.

Journal: Communications biology

Authors' code: ccc-protocols.readthedocs.io (no license), Zenodo 16760785 (CC-BY-4.0)

Status: code verified

[445] doi:10.1186/s12864-026-13028-8 [paper, data]

Selective hippocampal transcriptional adaptation to long-term cannabidiol exposure in mice.

Journal: BMC genomics

Status: data only, 5 datasets cited

[446] Code ↔ Paper doi:10.1186/s12888-026-08178-8 [paper, repository]

Machine learning model to identify gut microbiome-derived metabolites as potential biomarkers of autism spectrum disorder: a pilot study.

Journal: BMC psychiatry

Authors' code: dec0der0b/IMPC (MIT)

Status: code verified, 14 files readable, 4 matches

[447] Code ↔ Paper doi:10.34133/csbj.0134 [paper, repository]

Integrated Multi-Tissue Transcriptomics Reveals Antagonistic Pleiotropy in Aging and Alzheimer's Disease.

Journal: Computational and structural biotechnology journal

Authors' code: salihoglu/Alzheimer_AP (no license)

Status: code verified, 15 files readable, 18 matches

Saturday, 6 June 2026 (5 papers)

[448] Code ↔ Paper doi:10.1038/s41467-026-74000-4 [paper, repository]

ArchVelo: archetypal velocity modeling for single-cell multi-omic trajectories.

Journal: Nature communications

Authors' code: pritykinlab/ArchVelo (BSD-3-Clause), pritykinlab/ArchVelo_notebooks (BSD-3-Clause), Zenodo 20085695 (BSD-3-Clause)

Status: code verified, 51 files readable, 14 matches

[449] Code ↔ Paper doi:10.1016/j.ebiom.2026.106324 [paper, repository]

Refined single-cell profiling captures a CCR5&lt;sup&gt;high&lt;/sup&gt; CD4&lt;sup&gt;+&lt;/sup&gt; cytotoxic T-cell precursor in multiple sclerosis.

Journal: EBioMedicine

Authors' code: YFWang-YvH/Refined-single-cell-profiling-captures-a-CCR5high-CD4-cytotoxic-T-cell-precursor-in-MS (no license)

Status: code verified, 7 files readable, 4 matches

[450] Code ↔ Paper doi:10.1038/s42003-026-10462-y [paper, repository]

SpaDC enables sequence-based integrative analysis and regulatory inference of spatial chromatin accessibility data.

Journal: Communications biology

Authors' code: mcllllllll/SpaDC (MIT), Zenodo 20300757 (CC-BY-4.0)

Status: code verified, 30 files readable, 12 matches

[451] Code ↔ Paper doi:10.1186/s10194-026-02419-7 [paper, repository]

Transcriptional correlates of structure-function coupling plasticity in trigeminal neuralgia: unveiling the synaptic and metabolic associations.

Journal: The journal of headache and pain

Authors' code: starz0275/TN_SF_Code (no license)

Status: code verified, 4 files readable, 2 matches

[452] doi:10.1186/s13195-026-02107-3 [paper, data]

FKBP51 inhibition by SAFit2 modulates tau pathology and cognitive deficits in PS19 mice.

Journal: Alzheimer's research & therapy

Status: data only, 1 dataset cited

Friday, 5 June 2026 (6 papers)

[453] doi:10.1371/journal.pone.0351146 [paper]

Differential analysis of Short chain fatty acids incubation in autistic organoids based on transcriptome sequencing.

Journal: PloS one

Status: data only

[454] Code ↔ Paper doi:10.1371/journal.pcbi.1014346 [paper, repository]

StPedf: Cell trajectory inference of spatial transcriptomics via spatial proximity embedding and spatial density-adaptive fusion.

Journal: PLoS computational biology

Authors' code: YuanZ0316/StPedf (no license)

Status: code verified, 20 files readable, 7 matches

[455] Code ↔ Paper doi:10.1038/s41420-026-03185-w [paper, repository]

An electrophysiological and proteomics roadmap for human induced glutamatergic neurons: fine-tuning of culture conditions for pathophysiological studies.

Journal: Cell death discovery

Authors' code: mathworks.com/matlabcentral/fileexchange (no license), ennionano/functional_roadmap_for_induced_glut-neurons (no license)

Status: code verified, 3 files readable, 6 matches

[456] doi:10.1038/s12276-026-01732-0 [paper, data]

Comprehensive proteogenomic characterization reveals clinically relevant molecular subtypes associated with medulloblastoma progression.

Journal: Experimental & molecular medicine

Status: data only, 1 dataset cited

[457] Code ↔ Paper doi:10.1016/j.isci.2026.116231 [paper, repository]

Endocytic turnover of endothelial cell-membrane proteins as a driver of rat blood-brain barrier specialization and dysfunction.

Journal: iScience

Authors' code: Molecular-Bionics-Labs/DP_GP_cluster_proteomics (BSD-3-Clause), PrincetonUniversity/DP_GP_cluster (BSD-3-Clause)

Status: code verified, 26 files readable, 2 matches

[458] Code ↔ Paper doi:10.1016/j.bbih.2026.101275 [paper, repository]

A protocol for the Teen Bugs study: An integrative, multi-omics approach to understanding the role of the gut microbiome and mesocorticolimbic system in adolescent mental health following early adverse caregiving.

Journal: Brain, behavior, & immunity - health

Authors' code: bablab/bablab_hoffman_metagenomics (no license)

Status: code verified, 7 files readable

Thursday, 4 June 2026 (7 papers)

[459] doi:10.1017/s0033291726104711 [paper, data]

Cell-type and spatiotemporal transcriptional signatures of white matter morphometric similarity network alterations in major depressive disorder.

Journal: Psychological medicine

Status: data only, 1 dataset cited

[460] Code ↔ Paper doi:10.1016/j.celrep.2026.117500 [paper, repository]

Spatio-molecular gene expression reflects dorsal anterior cingulate cortex structure and function in the human brain.

Journal: Cell reports

Authors' code: LieberInstitute/spatialdACC (no license), Zenodo 15830481 (CC-BY-4.0), research.libd.org/globus (no license)

Status: code verified, 2,000 files readable, 40 matches

[461] doi:10.1038/s41421-026-00897-2 [paper]

Trans-ethnic estimation and implications of genetic impact on continuous glycemic profiles.

Journal: Cell discovery

Status: code on request

[462] Code ↔ Paper doi:10.1038/s41467-026-73902-7 [paper, repository]

GWAS on short tandem repeats identifies genetic mechanisms in Alzheimer's disease.

Journal: Nature communications

Authors' code: dgmelin/ukb_ad_str_gwas (GPL-3.0), Zenodo 19484860 (GPL-3.0), Zenodo 8365671 (CC-BY-4.0), gymrek-lab/ensembletr (no license)

Status: code verified, 92 files readable, 13 matches

[463] Code ↔ Paper doi:10.1186/s12859-026-06490-4 [paper, repository]

Tissueformer: extending single-cell foundation models to predict population-level phenotypes.

Journal: BMC bioinformatics

Authors' code: ZadorLaboratory/TissueFormer (MIT), Zenodo 15595324 (GPL-3.0), zadorlaboratory/colormycells (GPL-3.0)

Status: code verified, 30 files readable, 13 matches

[464] doi:10.1016/j.isci.2026.116257 [paper, data]

Decoding neuron-specific lineage to identify diagnostic biomarkers and therapeutic targets for ischemic stroke.

Journal: iScience

Status: code on request, 1 dataset cited

[465] Code ↔ Paper doi:10.3389/fphar.2026.1830847 [paper, repository]

Sigma-1 and Sigma-2 receptors exhibit divergent genome-wide Co-expression architectures in human brain despite shared subcellular localization.

Journal: Frontiers in pharmacology

Authors' code: nwharbert8-ui/sigma-receptor-divergence (MIT), Zenodo 19024710 (MIT), nwharbert8-ui/sigma-receptor-divergence-wj (MIT)

Status: code verified, 9 files readable, 15 matches

Wednesday, 3 June 2026 (13 papers)

[466] Code ↔ Paper doi:10.1038/s41531-026-01417-5 [paper, repository]

Correlation of thalamic functional organization disturbances and genetic architecture in motor subtypes of Parkinson's disease.

Journal: NPJ Parkinson's disease

Authors' code: OSF gwzhe (no license)

Status: code verified, 1 file readable

[467] doi:10.1186/s12888-026-08189-5 [paper, data]

Deciphering the shared genetic architecture between schizophrenia and suicide attempt: a statistical genomic study.

Journal: BMC psychiatry

Status: data only, 1 dataset cited

[468] doi:10.1007/s12672-026-05341-1 [paper, data]

Single-cell data analysis of lung cancer brain metastasis reveals SEC61G serves as a potential risk indicator.

Journal: Discover oncology

Status: data only, 1 dataset cited

[469] doi:10.1371/journal.pone.0350674 [paper, data]

Transcriptomic profile of the hippocampus of rat strains with contrasting nervous system excitability.

Journal: PloS one

Status: data only, 1 dataset cited

[470] doi:10.1126/sciadv.aea3316 [paper, data]

Charting the human-specific properties of gene expression networks in the infant prefrontal cortex.

Journal: Science advances

Status: data only, 1 dataset cited

[471] Code ↔ Paper doi:10.1126/sciadv.aed5548 [paper, repository]

In situ proteomics unveils specialized domains for extrasynaptic signaling on neuronal cilia.

Journal: Science advances

Authors' code: Zenodo 18001606 (CC-BY-4.0)

Status: code verified, 1 file readable, 2 matches

[472] Code ↔ Paper doi:10.1038/s41467-026-73996-z [paper, repository]

Genetic architecture of white matter microstructure captured by unsupervised deep representation learning of fractional anisotropy maps.

Journal: Nature communications

Authors' code: ZhiGroup/UDIP-FA (MIT), Zenodo 19739801 (CC-BY-4.0)

Status: code verified, 17 files readable, 22 matches

[473] Code ↔ Paper doi:10.1038/s41593-026-02316-x [paper, repository]

Single-cell multi-omic atlas and morphogen screening informs midbrain and hindbrain organoid engineering.

Journal: Nature neuroscience

Authors' code: quadbio/atac_mapper (MIT), quadbio/posterior_multiome (MIT)

Status: code verified, 30 files readable, 15 matches

[474] doi:10.1186/s12915-026-02649-w [paper, data]

Neuronal VPS13A depletion links diacylglycerol PKC signaling and synaptic spines.

Journal: BMC biology

Status: data only, 1 dataset cited

[475] doi:10.1186/s13024-026-00946-0 [paper, data]

Insulin resistance alters cortical inhibitory neurons and microglia to exacerbate Alzheimer's knock-in mouse phenotypes.

Journal: Molecular neurodegeneration

Status: data only, 7 datasets cited

[476] Code ↔ Paper doi:10.1016/j.celrep.2026.117446 [paper, repository]

Circuit organization and transcriptomic heterogeneity of sympathetic circuits innervating cranial structures.

Journal: Cell reports

Authors' code: ncbi.nlm.nih.gov/geo/query (no license)

Status: code verified

[477] Code ↔ Paper doi:10.7717/peerj.21426 [paper, repository]

Integrated transcriptomic identification and validation reveal key autophagy-associated biomarkers in sleep deprivation.

Journal: PeerJ

Authors' code: tobejoy613/Autophagy-Genes-as-Sleep-Deprivation-Biomarkers (no license), supp:PMC13242190/peerj-14-21426-s009.r (no license), supp:PMC13242190/peerj-14-21426-s010.r (no license), supp:PMC13242190/peerj-14-21426-s011.r (no license), supp:PMC13242190/peerj-14-21426-s012.r (no license), supp:PMC13242190/peerj-14-21426-s013.r (no license), supp:PMC13242190/peerj-14-21426-s014.r (no license)

Status: code verified, 13 files readable, 11 matches

[478] doi:10.3389/fbinf.2026.1808516 [paper]

Integrative multi-cohort analysis of DNA methylation profiles for pancreatic ductal adenocarcinoma biomarker discovery and prognosis.

Journal: Frontiers in bioinformatics

Status: data only