Every paper, by date: page 139

44,644 papers with a page: 24,189 with their authors' code, 4,955 with code on request, 15,495 with data only. The most recent first, 224 a page. Page 139 of 200: 8 January 2024 to 1 January 2024.

Monday, 8 January 2024 (30 papers, 10 on this page)

[30913] doi:10.1038/s41598-023-51127-8 [paper, data]

Development and immunological evaluation of an mRNA-based vaccine targeting Naegleria fowleri for the treatment of primary amoebic meningoencephalitis.

Journal: Scientific reports

Status: data only, 1 dataset cited

[30914] doi:10.1073/pnas.2308812120 [paper, repository]

Accurate estimation of biological age and its application in disease prediction using a multimodal image Transformer system.

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

Authors' code: PKU-BDBA/BioAge (Apache-2.0)

Status: code verified, 11 files readable, 3 matches

[30915] doi:10.1073/pnas.2312913120 [paper, data]

Hormonal basis of sex differences in anesthetic sensitivity.

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

Status: data only, 1 dataset cited

[30916] doi:10.1080/01621459.2023.2278201 [paper, repository]

Bayesian Lesion Estimation with a Structured Spike-and-Slab Prior.

Journal: Journal of the American Statistical Association

Authors' code: annamenacher/BLESS (MIT)

Status: code verified, 25 files readable, 32 matches

[30917] doi:10.1371/journal.pcbi.1011760 [paper, repository]

Mapping the dynamics of visual feature coding: Insights into perception and integration.

Journal: PLoS computational biology

Authors' code: Tijl/features-eeg (no license)

Status: code verified, 27 files readable, 4 matches

[30918] doi:10.3389/fneur.2023.1280047 [paper, data]

A nomogram for the prediction of short-term mortality in patients with aneurysmal subarachnoid hemorrhage requiring mechanical ventilation: a post-hoc analysis.

Journal: Frontiers in neurology

Status: data only, 1 dataset cited

[30919] doi:10.3389/fnins.2023.1302470 [paper, data]

Characterization of a loss-of-function NSF attachment protein beta mutation in monozygotic triplets affected with epilepsy and autism using cortical neurons from proband-derived and CRISPR-corrected induced pluripotent stem cell lines.

Journal: Frontiers in neuroscience

Status: data only, 3 datasets cited

[30920] doi:10.3389/fnint.2023.1299087 [paper, repository]

Brain structure and function: a multidisciplinary pipeline to study hominoid brain evolution.

Journal: Frontiers in integrative neuroscience

Authors' code: rmcelreath/EBC_brain_vocal_modeling (no license), rmcelreath/rethinking (no license)

Status: code verified, 71 files readable, 1 match

[30921] doi:10.3389/frai.2023.1334613 [paper, repository]

Explaining graph convolutional network predictions for clinicians-An explainable AI approach to Alzheimer's disease classification.

Journal: Frontiers in artificial intelligence

Authors' code: suletekkesinoglu/GCN_XAI_ADNI (no license)

Status: code verified, 1 file readable

[30922] doi:10.3390/ijms25020783 [paper, data]

Therapeutic Effects of Aβ-Specific Regulatory T Cells in Alzheimer's Disease: A Study in 5xFAD Mice.

Journal: International journal of molecular sciences

Status: data only, 8 datasets cited

Saturday, 6 January 2024 (12 papers)

[30923] doi:10.1002/alz.13610 [paper, data]

Genetic risk score for Alzheimer's disease predicts brain volume differences in mid and late life in UK biobank participants.

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

Status: data only, 1 dataset cited

[30924] doi:10.1002/alz.13676 [paper, repository]

A blood-based multi-pathway biomarker assay for early detection and staging of Alzheimer's disease across ethnic groups.

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

Authors' code: yjiangah/Biomarker_study (no license)

Status: code verified, 5 files readable, 2 matches

[30925] doi:10.1016/j.biopha.2023.116096 [paper, repository]

Drug repurposing for neurodegenerative diseases using Zebrafish behavioral profiles.

Journal: Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie

Authors' code: brown-ccv/Automated-Analysis-of-Zebrafish (no license)

Status: code verified, 9 files readable, 3 matches

[30926] doi:10.1016/j.celrep.2023.113662 [paper, repository]

TDP-43 chronic deficiency leads to dysregulation of transposable elements and gene expression by affecting R-loop and 5hmC crosstalk.

Journal: Cell reports

Authors' code: YaoLabEmory/shTDP43 (no license)

Status: code verified, 11 files readable

[30927] doi:10.1016/j.dcn.2024.101341 [paper, repository]

White matter and literacy: A dynamic system in flux.

Journal: Developmental cognitive neuroscience

Authors' code: earoy/longitudinal_wm (no license)

Status: code verified, 10 files readable, 5 matches

[30928] doi:10.1016/j.ebiom.2023.104958 [paper, data]

Metabolite profiles of medulloblastoma for rapid and non-invasive detection of molecular disease groups.

Journal: EBioMedicine

Status: data only, 1 dataset cited

[30929] doi:10.1016/j.heliyon.2024.e24050 [paper, data]

Icariin prevents methylmercury-induced experimental neurotoxicity: Evidence from cerebrospinal fluid, blood plasma, brain samples, and in-silico investigations.

Journal: Heliyon

Status: data only, 3 datasets cited

[30930] doi:10.1016/j.isci.2024.108816 [paper]

Paying attention to natural scenes in area V1.

Journal: iScience

Status: code on request

[30931] doi:10.1038/s41597-023-02888-4 [paper, repository]

An RNA-seq atlas of mouse brain areas during fasting and diet-induced obesity.

Journal: Scientific data

Authors' code: perslab/wgcna-toolbox (no license), Zenodo 10116113 (MIT), pvtodorov/dmb (MIT)

Status: code verified, 29 files readable, 6 matches

[30932] doi:10.1038/s41598-024-51357-4 [paper, data]

Circulating microRNAs from plasma as preclinical biomarkers of epileptogenesis and epilepsy.

Journal: Scientific reports

Status: data only, 1 dataset cited

[30933] doi:10.1111/jnc.16032 [paper, data]

Brain energy metabolism: A roadmap for future research.

Journal: Journal of neurochemistry

Status: data only, 3 datasets cited

[30934] doi:10.3390/cells13020114 [paper, data]

Synaptopodin Regulates Denervation-Induced Plasticity at Hippocampal Mossy Fiber Synapses.

Journal: Cells

Status: data only, 1 dataset cited

Friday, 5 January 2024 (38 papers)

[30935] doi:10.1007/s12035-023-03755-4 [paper]

Single-Cell Transcriptome Reveals Cell Type-Specific Molecular Pathology in a 2VO Cerebral Ischemic Mouse Model.

Journal: Molecular neurobiology

Status: data only

[30936] doi:10.1007/s12264-023-01159-x [paper]

Dynamic Changes of the Infralimbic Cortex and Its Regulation of the Prelimbic Cortex in Rats with Chronic Inflammatory Pain.

Journal: Neuroscience bulletin

Status: code on request

[30937] doi:10.1016/j.crmeth.2023.100681 [paper, repository]

A modular and adaptable analysis pipeline to compare slow cerebral rhythms across heterogeneous datasets.

Journal: Cell reports methods

Authors' code: Zenodo 10210141 (BSD-3-Clause), Zenodo 10198748 (GPL-3.0), gin.g-node.org/inm-6/cobrawap_publication_code (BSD-3-Clause), Zenodo 17197618 (GPL-3.0), Zenodo 17048329 (GPL-3.0), Zenodo 15005123 (GPL-3.0), Zenodo 13134351 (GPL-3.0), Zenodo 13268635 (GPL-3.0), Zenodo 13268634 (GPL-3.0)

Status: code verified, 562 files readable, 16 matches

[30938] doi:10.1016/j.ebiom.2023.104953 [paper, data]

Intron retention as a productive mechanism in human MAPT: RNA species generated by retention of intron 3.

Journal: EBioMedicine

Status: data only, 2 datasets cited

[30939] doi:10.1016/j.isci.2024.108807 [paper]

Glioblastoma extracellular vesicles modulate immune PD-L1 expression in accessory macrophages upon radiotherapy.

Journal: iScience

Status: code on request

[30940] doi:10.1038/s41467-023-44367-9 [paper, repository]

MENDER: fast and scalable tissue structure identification in spatial omics data.

Journal: Nature communications

Authors' code: mender-tutorial.readthedocs.io (no license), stagate.readthedocs.io (no license), tencentailabhealthcare/sotip (no license), zhengli09.github.io/bass-analysis (no license), jianhuupenn/spagcn (MIT), hongleir/SpaceFlow (MIT), zhengli09/bass-analysis (no license), Zenodo 4075515 (other-open), yuanzhiyuan/MENDER (MIT), Zenodo 10216989 (CC-BY-4.0), dgoodwin208/exseqprocessing (MIT)

Status: code verified, 1,257 files readable, 4 matches

[30941] doi:10.1038/s41467-023-44591-3 [paper, repository]

Radiomic tractometry reveals tract-specific imaging biomarkers in white matter.

Journal: Nature communications

Authors' code: mic-dkfz/radtract (Apache), Zenodo 10255076 (CC-BY-4.0)

Status: code verified, 17 files readable, 8 matches

[30942] doi:10.1038/s41593-023-01513-2 [paper, repository]

Women's neuroplasticity during gestation, childbirth and postpartum.

Journal: Nature neuroscience

Authors' code: neuromaternal/peripartum_neuroplasticity (no license)

Status: code verified, 6 files readable, 8 matches

[30943] doi:10.1038/s41593-023-01520-3 [paper, repository]

Latent neural population dynamics underlying breathing, opioid-induced respiratory depression and gasping.

Journal: Nature neuroscience

Authors' code: lindermanlab/ssm (MIT)

Status: code verified, 67 files readable, 2 matches

[30944] doi:10.1038/s41597-023-02892-8 [paper, repository]

Changes in oscillatory patterns of microstate sequence in patients with first-episode psychosis.

Journal: Scientific data

Authors' code: zddzxxsmile/Chaos-game-representation-of-EEG-microstate (GPL-3.0), figshare 23803467 (CC-BY-4.0)

Status: code verified, 8 files readable, 3 matches

[30945] doi:10.1038/s41598-023-49656-3 [paper, repository]

Comprehensive allostatic load risk index is associated with increased frontal and left parietal white matter hyperintensities in mid-life cognitively healthy adults.

Journal: Scientific reports

Authors' code: fil.ion.ucl.ac.uk/spm (no license)

Status: code verified

[30946] doi:10.1038/s41598-024-51259-5 [paper, data]

Selenoprotein P expression in glioblastoma as a regulator of ferroptosis sensitivity: preservation of GPX4 via the cycling-selenium storage.

Journal: Scientific reports

Status: data only, 1 dataset cited

[30947] doi:10.1038/s41746-023-00983-9 [paper]

An interpretable model based on graph learning for diagnosis of Parkinson's disease with voice-related EEG.

Journal: NPJ digital medicine

Status: code on request

[30948] doi:10.1038/s42003-023-05725-x [paper, repository]

Differential methylation analysis in neuropathologically confirmed dementia with Lewy bodies.

Journal: Communications biology

Authors' code: pireho/EWAS-Lewy_body_dementia (no license), Zenodo 10365334 (CC-BY-4.0)

Status: code verified, 2 files readable

[30949] doi:10.1073/pnas.2304406120 [paper, repository]

Impossibility theorems for feature attribution.

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

Authors' code: google-research/interpretability-theory (Apache-2.0)

Status: code verified, 10 files readable, 2 matches

[30950] doi:10.1073/pnas.2306682120 [paper, data]

Decreasing the intrinsically disordered protein α-synuclein levels by targeting its structured mRNA with a ribonuclease-targeting chimera.

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

Status: data only, 2 datasets cited

[30951] doi:10.1111/psyp.14503 [paper, repository]

Multiple mechanisms of visual prediction as revealed by the timecourse of scene-object facilitation.

Journal: Psychophysiology

Authors' code: npinto/v1s-0.0.4_scene (other)

Status: code verified, 11 files readable, 2 matches

[30952] doi:10.1117/1.jmi.11.1.014005 [paper, data]

Robust fiber orientation distribution function estimation using deep constrained spherical deconvolution for diffusion-weighted magnetic resonance imaging.

Journal: Journal of medical imaging (Bellingham, Wash.)

Status: code on request, 2 datasets cited

[30953] doi:10.1136/gutjnl-2023-330365 [paper, repository]

Prebiotic diet changes neural correlates of food decision-making in overweight adults: a randomised controlled within-subject cross-over trial.

Journal: Gut

Authors' code: gitlab.gwdg.de/gut_brain_study/food-wanting/task-fmri-behavior-analysis (no license), gitlab.gwdg.de/gut_brain_study/food-wanting/fmri-analysis (no license), identifiers.org/neurovault.collection:14111 (no license)

Status: code verified, 56 files readable, 3 matches

[30954] doi:10.1162/imag_a_00054 [paper, repository]

Event-induced modulation of aperiodic background EEG: Attention-dependent and age-related shifts in E:I balance, and their consequences for behavior.

Journal: Imaging neuroscience (Cambridge, Mass.)

Authors' code: OSF dfbwa (no license)

Status: code verified, 1 file readable

[30955] doi:10.1162/imag_a_00055 [paper, repository]

Robust frequency-dependent diffusional kurtosis computation using an efficient direction scheme, axisymmetric modelling, and spatial regularization.

Journal: Imaging neuroscience (Cambridge, Mass.)

Authors' code: cfmm/matlab/matmri (MIT), RafaelNH/Radial_Tensor_Kurtosis (no license), Zenodo 4495477 (CC-BY-4.0)

Status: code verified, 100 files readable, 4 matches

[30956] doi:10.1162/imag_a_00057 [paper, repository]

Denoising task-correlated head motion from motor-task fMRI data with multi-echo ICA.

Journal: Imaging neuroscience (Cambridge, Mass.)

Authors' code: BrightLab-ANVIL/PreProc_BRAIN (no license), BrightLab-ANVIL/Reddy_MotorMEICA (MIT), Zenodo 5541689 (LGPL-2.1), Zenodo 7926293 (LGPL-2.1), me-ica/tedana (LGPL-2.1)

Status: code verified, 215 files readable, 17 matches

[30957] doi:10.1242/bio.060087 [paper, repository]

The influence of carbon dioxide on cerebral metabolism and oxygen consumption: combining multimodal monitoring with dynamic systems modelling.

Journal: Biology open

Authors' code: bcmd/co2 (CC-BY-4.0)

Status: empty repository, 2 files readable

[30958] doi:10.1371/journal.pcbi.1011785 [paper, data]

sc2MeNetDrug: A computational tool to uncover inter-cell signaling targets and identify relevant drugs based on single cell RNA-seq data.

Journal: PLoS computational biology

Status: data only, 3 datasets cited

[30959] doi:10.1371/journal.pone.0295346 [paper, data]

Integrated bioinformatics analysis and experimental validation identified CDCA families as prognostic biomarkers and sensitive indicators for rapamycin treatment of glioma.

Journal: PloS one

Status: data only, 1 dataset cited

[30960] doi:10.1371/journal.pone.0295411 [paper, repository]

Fat tails and the need to disclose distribution parameters of qEEG databases.

Journal: PloS one

Authors' code: supp:PMC10769036/pone.0295411.s004.r (no license)

Status: code verified, 1 file readable

[30961] doi:10.21203/rs.3.rs-3818580/v1 [paper, repository]

Post-COVID cognitive deficits at one year are global and associated with elevated brain injury markers and grey matter volume reduction: national prospective study

Journal: Research Square (preprint)

Authors' code: OSF fgyhb (no license)

Status: empty repository

[30962] doi:10.26508/lsa.202302258 [paper, data]

<i>USP27X</i> variants underlying X-linked intellectual disability disrupt protein function via distinct mechanisms.

Journal: Life science alliance

Status: data only, 3 datasets cited

[30963] doi:10.3389/fnana.2023.1330384 [paper, repository]

Age-related changes in the primary auditory cortex of newborn, adults and aging bottlenose dolphins (<i>Tursiops truncatus</i>) are located in the upper cortical layers.

Journal: Frontiers in neuroanatomy

Authors' code: cran.r-project.org/pac (no license)

Status: dead link

[30964] doi:10.3389/fnbot.2023.1289406 [paper, data]

Intelligent digital tools for screening of brain connectivity and dementia risk estimation in people affected by mild cognitive impairment: the AI-Mind clinical study protocol.

Journal: Frontiers in neurorobotics

Status: data only, 1 dataset cited

[30965] doi:10.3389/fnbot.2023.1294211 [paper, data]

Vehicle re-identification method based on multi-attribute dense linking network combined with distance control module.

Journal: Frontiers in neurorobotics

Status: data only, 2 datasets cited

[30966] doi:10.3389/fphys.2023.1287342 [paper, repository]

Deep transfer learning for automated single-lead EEG sleep staging with channel and population mismatches.

Journal: Frontiers in physiology

Authors' code: akaraspt/tinysleepnet (Apache-2.0)

Status: code verified, 16 files readable

[30967] doi:10.3390/diagnostics14020128 [paper, data]

An Interpretable Approach with Explainable AI for Heart Stroke Prediction.

Journal: Diagnostics (Basel, Switzerland)

Status: data only, 1 dataset cited

[30968] doi:10.3390/ijms25020707 [paper, data]

Gene Expression Profiling of Post Mortem Midbrain of Parkinson's Disease Patients and Healthy Controls.

Journal: International journal of molecular sciences

Status: data only, 1 dataset cited

[30969] doi:10.7554/elife.86547 [paper, repository]

Criticality supports cross-frequency cortical-thalamic information transfer during conscious states.

Journal: eLife

Authors' code: figshare 24777081 (CC-BY-4.0)

Status: code verified, 5 files readable, 7 matches

[30970] doi:10.7554/elife.87271 [paper, repository]

Acute stress reduces effortful prosocial behaviour.

Journal: eLife

Authors' code: OSF 4bqf7 (no license)

Status: code verified, 1 file readable, 6 matches

[30971] doi:10.7554/elife.87965 [paper, repository]

Inhibitory CCK+ basket synapse defects in mouse models of dystroglycanopathy.

Journal: eLife

Authors' code: jnjahncke/mini_analysis (MIT)

Status: empty repository, 2 files readable

[30972] doi:10.7554/elife.90133 [paper, data]

Homeodomain proteins hierarchically specify neuronal diversity and synaptic connectivity.

Journal: eLife

Status: data only, 1 dataset cited

Thursday, 4 January 2024 (32 papers)

[30973] doi:10.1007/s00401-023-02658-x [paper, repository]

Cortical matrix remodeling as a hallmark of relapsing-remitting neuroinflammation in MR elastography and quantitative MRI.

Journal: Acta neuropathologica

Authors' code: ChariteExpMri/antx2 (LGPL-2.1)

Status: code verified, 2,000 files readable, 2 matches

[30974] doi:10.1007/s00401-023-02667-w [paper, repository]

p-tau Ser356 is associated with Alzheimer's disease pathology and is lowered in brain slice cultures using the NUAK inhibitor WZ4003.

Journal: Acta neuropathologica

Authors' code: Spires-Jones-Lab (no license)

Status: code verified

[30975] doi:10.1016/j.isci.2024.108787 [paper]

Perceptual reorganization from prior knowledge emerges late in childhood.

Journal: iScience

Status: code on request

[30976] doi:10.1016/j.isci.2024.108793 [paper, data]

Innate sensitivity to face-to-face biological motion.

Journal: iScience

Status: data only, 1 dataset cited

[30977] doi:10.1016/j.isci.2024.108795 [paper]

Maintaining Toll signaling in <i>Drosophila</i> brain is required to sustain autophagy for dopamine neuron survival.

Journal: iScience

Status: code on request

[30978] doi:10.1016/j.isci.2024.108796 [paper, repository]

Post-interaction neuroplasticity of inter-brain networks underlies the development of social relationship.

Journal: iScience

Authors' code: doi:10.17632/xd9zr7hh3z.1 (no license), support.razer.com/console/razer-hydra (no license)

Status: code verified

[30979] doi:10.1016/j.isci.2024.108800 [paper]

Behavioral, metabolic, and lipidomic characterization of the 5xFADxTg30 mouse model of Alzheimer's disease.

Journal: iScience

Status: code on request

[30980] doi:10.1016/j.neurot.2023.e00308 [paper, repository]

Neurostimulation treatments for epilepsy: Deep brain stimulation, responsive neurostimulation and vagus nerve stimulation.

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

Authors' code: neuroquery.org (no license), neurosynth.org (no license)

Status: code verified

[30981] doi:10.1038/s41467-023-44354-0 [paper, repository]

Petascale pipeline for precise alignment of images from serial section electron microscopy.

Journal: Nature communications

Authors' code: AllenInstitute/BigFeta (BSD-2-Clause), seung-lab/corgie (Apache-2.0), seung-lab/metroem (Apache-2.0)

Status: code verified, 154 files readable, 4 matches

[30982] doi:10.1038/s41467-023-44569-1 [paper, repository]

Mapping expectancy-based appetitive placebo effects onto the brain in women.

Journal: Nature communications

Authors' code: OSF 2fnmj (no license)

Status: code verified, 7 files readable, 2 matches

[30983] doi:10.1038/s41531-023-00619-5 [paper, repository]

Proxy-analysis of the genetics of cognitive decline in Parkinson's disease through polygenic scores.

Journal: NPJ Parkinson's disease

Authors' code: johannfaouzi/genetics_cognitive_decline_PD (BSD-3-Clause)

Status: code verified, 10 files readable, 3 matches

[30984] doi:10.1038/s41592-023-02128-y [paper, repository]

RNA structure profiling at single-cell resolution reveals new determinants of cell identity.

Journal: Nature methods

Authors' code: noahpieta/scSports (MIT)

Status: code verified, 292 files readable, 12 matches

[30985] doi:10.1038/s41593-023-01511-4 [paper, repository]

A neural mechanism for conserved value computations integrating information and rewards.

Journal: Nature neuroscience

Authors' code: ethan-bromberg-martin/a-neural-mechanism-for-conserved-value-computations-integrating-information-and-rewards (no license)

Status: empty repository, 1 file readable

[30986] doi:10.1038/s41598-023-51137-6 [paper, repository]

Transcriptome analysis in a humanized mouse model of familial dysautonomia reveals tissue-specific gene expression disruption in the peripheral nervous system.

Journal: Scientific reports

Authors' code: igraph/igraph (GPL-2.0)

Status: code verified, 1,874 files readable, 1 match

[30987] doi:10.1085/jgp.202313365 [paper, data]

Asymmetric contribution of a selectivity filter gate in triggering inactivation of CaV1.3 channels.

Journal: The Journal of general physiology

Status: data only, 1 dataset cited

[30988] doi:10.1088/1741-2552/ad1610 [paper, repository]

Neural regulation of slow waves and phasic contractions in the distal stomach: a mathematical model.

Journal: Journal of neural engineering

Authors' code: figshare 23624622 (CC-BY-4.0)

Status: code verified, 23 files readable, 9 matches

[30989] doi:10.1088/1741-2552/ad1611 [paper]

Selective chronic recording in small nerve fascicles of sciatic nerve with carbon nanotube yarns in rats.

Journal: Journal of neural engineering

Status: code on request

[30990] doi:10.1101/2024.01.04.573933 [paper, data]

The neurodevelopmental trajectory of beta band oscillations: an OPM-MEG study

Journal: bioRxiv (preprint)

Status: data only, 2 datasets cited

[30991] doi:10.1172/jci.insight.175159 [paper]

Sarm1 knockout prevents type 1 diabetic bone disease in females independent of neuropathy.

Journal: JCI insight

Status: code on request

[30992] doi:10.1186/s12974-023-02987-4 [paper, repository]

Identification of female-enriched and disease-associated microglia (FDAMic) contributes to sexual dimorphism in late-onset Alzheimer's disease.

Journal: Journal of neuroinflammation

Authors' code: KimChow-Lab/FDAMic (no license)

Status: code verified, 14 files readable, 19 matches

[30993] doi:10.1186/s12974-023-03002-6 [paper, repository]

Commonly disrupted pathways in brain and kidney in a pig model of systemic endotoxemia.

Journal: Journal of neuroinflammation

Authors' code: fryerlab/LPS_pigs (no license)

Status: code verified, 25 files readable, 17 matches

[30994] doi:10.1186/s12974-023-03003-5 [paper, data]

Peripheral blood amyloid-β involved in the pathogenesis of Alzheimer's disease via impacting on peripheral innate immune cells.

Journal: Journal of neuroinflammation

Status: data only, 1 dataset cited

[30995] doi:10.1186/s12974-023-03004-4 [paper, data]

Doxycycline for transgene control disrupts gut microbiome diversity without compromising acute neuroinflammatory response.

Journal: Journal of neuroinflammation

Status: data only, 1 dataset cited

[30996] doi:10.1186/s13148-023-01621-7 [paper, data]

Malignant peripheral nerve sheath tumor (MPNST) and MPNST-like entities are defined by a specific DNA methylation profile in pediatric and juvenile population.

Journal: Clinical epigenetics

Status: data only, 1 dataset cited

[30997] doi:10.1364/boe.510333 [paper, repository]

Dynamic light scattering and laser speckle contrast imaging of the brain: theory of the spatial and temporal statistics of speckle pattern evolution.

Journal: Biomedical optics express

Authors' code: BUNPC/SpeckleDynamicsModelFitting (no license)

Status: code verified, 6 files readable

[30998] doi:10.1371/journal.pcbi.1011768 [paper, repository]

Quantifying the distribution of feature values over data represented in arbitrary dimensional spaces.

Journal: PLoS computational biology

Authors' code: pridalab/structure_index (GPL-3.0)

Status: code verified, 5 files readable, 1 match

[30999] doi:10.3389/fnins.2023.1228952 [paper, repository]

Evaluation of tractography-based myelin-weighted connectivity across the lifespan.

Journal: Frontiers in neuroscience

Authors' code: daducci/commit (other)

Status: code verified, 41 files readable

[31000] doi:10.3389/fphar.2023.1288994 [paper, repository]

P2X4 signalling contributes to hyperactivity but not pain sensitization comorbidity in a mouse model of attention deficit/hyperactivity disorder.

Journal: Frontiers in pharmacology

Authors' code: Zenodo 14882323 (CC-BY-4.0), sandrassb/macroglia_cell-morphology-analysis (CC-BY-4.0), Zenodo 14872354 (CC-BY-4.0), Zenodo 14871925 (CC-BY-4.0), Zenodo 14922374 (CC-BY-4.0)

Status: code verified, 2 files readable

[31001] doi:10.3389/fpsyt.2023.1303430 [paper, repository]

Unraveling shared susceptibility loci and Mendelian genetic associations linking educational attainment with multiple neuropsychiatric disorders.

Journal: Frontiers in psychiatry

Authors' code: zhenin/HDL (no license), bulik/ldsc (GPL-3.0), chr1swallace/coloc (no license), mrcieu/TwoSampleMR (other)

Status: code verified, 181 files readable, 4 matches

[31002] doi:10.3390/e26010049 [paper, repository]

Transfer Learning in Multiple Hypothesis Testing.

Journal: Entropy (Basel, Switzerland)

Authors' code: colab.research.google.com/drive/1tdm1fsvkm1gi55riuxolbzcecm3feong (no license)

Status: code verified

[31003] doi:10.3390/genes15010071 [paper, data]

Cerebrospinal Fluid C1-Esterase Inhibitor and Tie-1 Levels Affect Cognitive Performance: Evidence from Proteome-Wide Mendelian Randomization.

Journal: Genes

Status: data only, 1 dataset cited

[31004] doi:10.7554/elife.85442 [paper, repository]

Cell type-specific connectome predicts distributed working memory activity in the mouse brain.

Journal: eLife

Authors' code: XY-DIng/mouse_dist_wm (GPL-3.0)

Status: code verified, 16 files readable, 6 matches

Wednesday, 3 January 2024 (32 papers)

[31005] doi:10.1002/mds.29702 [paper, repository]

Longitudinal Associations of Magnetic Susceptibility with Clinical Severity in Parkinson's Disease.

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

Authors' code: gecthomas/QSM_PD_longitudinal (no license)

Status: code verified, 5 files readable, 1 match

[31006] doi:10.1007/s00401-023-02666-x [paper, data]

Disruption of MAM integrity in mutant FUS oligodendroglial progenitors from hiPSCs.

Journal: Acta neuropathologica

Status: data only, 1 dataset cited

[31007] doi:10.1016/j.csbj.2023.12.038 [paper, repository]

AIMER: A SNP-independent software for identifying imprinting-like allelic methylated regions from DNA methylome.

Journal: Computational and structural biotechnology journal

Authors' code: ZhaoLab-TMU/AIMER (MIT), gitee.com/zhaolab_tmu/aimer (MIT)

Status: code verified, 8 files readable, 2 matches

[31008] doi:10.1016/j.dcn.2023.101338 [paper, repository]

Building towards an adolescent neural urbanome: Expanding environmental measures using linked external data (LED) in the ABCD study.

Journal: Developmental cognitive neuroscience

Authors' code: OSF nmdtg (no license)

Status: code verified, 6 files readable, 9 matches

[31009] doi:10.1038/s41398-023-02722-w [paper]

Aberrant resting-state co-activation network dynamics in major depressive disorder.

Journal: Translational psychiatry

Status: code on request

[31010] doi:10.1038/s41421-023-00628-x [paper, data]

TMEM63B channel is the osmosensor required for thirst drive of interoceptive neurons.

Journal: Cell discovery

Status: data only, 1 dataset cited

[31011] doi:10.1038/s41422-023-00867-3 [paper, repository]

Mapping of individual sensory nerve axons from digits to spinal cord with the transparent embedding solvent system.

Journal: Cell research

Authors' code: Albertd1ng/TESOS_stitcher (no license)

Status: code verified, 43 files readable

[31012] doi:10.1038/s41467-023-44295-8 [paper, repository]

Awake ripples enhance emotional memory encoding in the human brain.

Journal: Nature communications

Authors' code: Zenodo 10082278 (CC-BY-4.0)

Status: code verified, 12 files readable, 2 matches

[31013] doi:10.1038/s41467-023-44363-z [paper, repository]

Multimodal measures of spontaneous brain activity reveal both common and divergent patterns of cortical functional organization.

Journal: Nature communications

Authors' code: allensdk.readthedocs.io (no license), hadivafaii/Ca-fMRI (no license), premgopalan/svinet (GPL-3.0), AllenInstitute/mouse_connectivity_models (BSD-2-Clause), santofortunato.net/resources (no license), juhuntenburg/mouse_gradients (no license), bioimagesuiteweb.github.io/webapp (no license), CoBrALab/RABIES (other), YaleMRRC/calPrep (no license)

Status: code verified, 270 files readable, 7 matches

[31014] doi:10.1038/s41467-023-44374-w [paper, repository]

Elevated CSF GAP-43 is associated with accelerated tau accumulation and spread in Alzheimer's disease.

Journal: Nature communications

Authors' code: nfranzme/published (no license)

Status: code verified, 2 files readable

[31015] doi:10.1038/s41531-023-00602-0 [paper, repository]

Resting-state EEG measures cognitive impairment in Parkinson's disease.

Journal: NPJ Parkinson's disease

Authors' code: MDFahimAnjum (no license), narayanan.lab.uiowa.edu (no license)

Status: code verified

[31016] doi:10.1038/s41531-023-00620-y [paper, data]

Transcriptomic profiling of early synucleinopathy in rats induced with preformed fibrils.

Journal: NPJ Parkinson's disease

Status: data only, 1 dataset cited

[31017] doi:10.1038/s41586-023-06888-7 [paper, data]

Na&lt;sub&gt;v&lt;/sub&gt;1.7 as a chondrocyte regulator and therapeutic target for osteoarthritis.

Journal: Nature

Status: data only, 1 dataset cited

[31018] doi:10.1038/s41593-023-01510-5 [paper, repository]

The logic of recurrent circuits in the primary visual cortex.

Journal: Nature neuroscience

Authors' code: willyh101/live2p (MIT), gregoryhandy/Logic_of_Recurrent_Circuits (BSD-2-Clause), willyh101/100spikesAnalysis (no license)

Status: code verified, 567 files readable, 1 match

[31019] doi:10.1038/s41593-023-01514-1 [paper, repository]

Inferring neural activity before plasticity as a foundation for learning beyond backpropagation.

Journal: Nature neuroscience

Authors' code: zalandoresearch/fashion-mnist (MIT), YuhangSong/Prospective-Configuration (AGPL-3.0), opensource.org/licenses/gpl-3.0 (no license)

Status: code verified, 47 files readable, 5 matches

[31020] doi:10.1038/s41598-023-49801-y [paper, data]

ITGB4 upregulation is associated with progression of lower grade glioma.

Journal: Scientific reports

Status: data only, 1 dataset cited

[31021] doi:10.1038/s41598-023-50609-z [paper, repository]

EEG epilepsy seizure prediction: the post-processing stage as a chronology.

Journal: Scientific reports

Authors' code: JoanaFBatista/EEG-Epilepsy-Seizure-Prediction-The-Post-processing-Stage-as-a-Chronology (CC0-1.0)

Status: code verified, 16 files readable, 1 match

[31022] doi:10.1038/s44271-023-00053-6 [paper, repository]

Auditory-motor synchronization and perception suggest partially distinct time scales in speech and music.

Journal: Communications psychology

Authors' code: Zenodo 6142988 (other-open), OSF 9qthr (no license), fassaneo/speechsynchrony (no license)

Status: code verified, 22 files readable

[31023] doi:10.1093/braincomms/fcad355 [paper, repository]

Differential microRNA editing may drive target pathway switching in human temporal lobe epilepsy.

Journal: Brain communications

Authors' code: khodosevichlab/Epilepsy19 (MIT), Javizuma/ADAR_analysis (no license), NgocTNguyen/mirna-differential-editing-analysis (no license)

Status: code verified, 45 files readable, 2 matches

[31024] doi:10.1126/sciadv.adi1788 [paper, repository]

Septins provide microenvironment sensing and cortical actomyosin partitioning in motile amoeboid T lymphocytes.

Journal: Science advances

Authors' code: Zenodo 10035419 (CC-BY-NC-4.0)

Status: code verified, 1 file readable

[31025] doi:10.1126/sciadv.adi6470 [paper, repository]

Predictive neural computations in the cerebellum contribute to motor planning and faster behavioral responses in larval zebrafish.

Journal: Science advances

Authors' code: Zenodo 8396667 (CC-BY-4.0)

Status: code verified

[31026] doi:10.1126/sciadv.adi7624 [paper, data]

Sequential maturation of stimulus-specific adaptation in the mouse lemniscal auditory system.

Journal: Science advances

Status: data only, 1 dataset cited

[31027] doi:10.1126/sciadv.adj6102 [paper, repository]

Computational model links normalization to chemoarchitecture in the human visual system.

Journal: Science advances

Authors' code: VU-Cog-Sci/prfpy (GPL-3.0), VU-Cog-Sci/prfpytools (MIT), Zenodo 10201022 (CC-BY-4.0)

Status: code verified, 57 files readable

[31028] doi:10.1186/s10020-023-00765-9 [paper]

Key roles of autophagosome/endosome maturation mediated by Syntaxin17 in methamphetamine-induced neuronal damage in mice.

Journal: Molecular medicine (Cambridge, Mass.)

Status: data only

[31029] doi:10.1186/s12984-023-01300-x [paper, data]

Effects of anodal tDCS on resting state eeg power and motor function in acute stroke: a randomized controlled trial.

Journal: Journal of neuroengineering and rehabilitation

Status: data only, 1 dataset cited

[31030] doi:10.1364/boe.507517 [paper, repository]

Numerical study of a convective cooling strategy for increasing safe power levels in two-photon brain imaging.

Journal: Biomedical optics express

Authors' code: adi-roy/2pPointScanHeating (no license)

Status: code verified, 18 files readable, 3 matches

[31031] doi:10.3389/fnhum.2023.1159821 [paper, repository]

Modelling phenomenological differences in aetiologically distinct visual hallucinations using deep neural networks.

Journal: Frontiers in human neuroscience

Authors' code: ksk-S/ModellingHallucinations (MIT)

Status: code verified, 26 files readable

[31032] doi:10.3389/fnimg.2023.1320989 [paper, data]

Asymmetries and hemispheric interaction in the auditory system of elderly people.

Journal: Frontiers in neuroimaging

Status: data only, 1 dataset cited

[31033] doi:10.3389/fninf.2023.1275903 [paper, repository]

NeuroDecodeR: a package for neural decoding in R.

Journal: Frontiers in neuroinformatics

Authors' code: emeyers/NeuroDecodeR (no license)

Status: code verified, 44 files readable, 12 matches

[31034] doi:10.3389/fnmol.2023.1303718 [paper, data]

A maternal high-fat diet during pregnancy and lactation induced depression-like behavior in offspring and myelin-related changes in the rat prefrontal cortex.

Journal: Frontiers in molecular neuroscience

Status: data only, 2 datasets cited

[31035] doi:10.3389/fphys.2023.1271254 [paper, repository]

Feasibility of high-resolution perfusion imaging using arterial spin labeling MRI at 3 Tesla.

Journal: Frontiers in physiology

Authors' code: physimals/oxasl (Apache-2.0)

Status: code verified, 63 files readable, 5 matches

[31036] doi:10.3390/biom14010066 [paper, data]

Proteomic Signaling of Dual-Specificity Phosphatase 4 (DUSP4) in Alzheimer's Disease.

Journal: Biomolecules

Status: code on request, 1 dataset cited

Tuesday, 2 January 2024 (47 papers)

[31037] doi:10.1001/jamanetworkopen.2023.51839 [paper, repository]

Intranasal Naloxone Repeat Dosing Strategies and Fentanyl Overdose: A Simulation-Based Randomized Clinical Trial.

Journal: JAMA network open

Authors' code: FDA/Mechanistic-PK-PD-Model-to-Rescue-Opioid-Overdose (no license)

Status: code verified, 40 files readable, 3 matches

[31038] doi:10.1016/j.conctc.2024.101254 [paper, repository]

Characteristics and use of patient-reported outcomes of clinical trials for high-risk neurological medical devices that received FDA premarket approval from 2001 to 2022.

Journal: Contemporary clinical trials communications

Authors' code: accessdata.fda.gov/scripts/cdrh (no license)

Status: code verified

[31039] doi:10.1016/j.crmeth.2023.100673 [paper]

A fluorescent splice-switching mouse model enables high-throughput, sensitive quantification of antisense oligonucleotide delivery and activity.

Journal: Cell reports methods

Status: code on request

[31040] doi:10.1038/s41467-023-44121-1 [paper, repository]

Histone lactylation couples cellular metabolism with developmental gene regulatory networks.

Journal: Nature communications

Authors' code: broadinstitute/picard (MIT)

Status: code verified, 757 files readable, 4 matches

[31041] doi:10.1038/s41467-023-44216-9 [paper, repository]

Towards a transferable fermionic neural wavefunction for molecules.

Journal: Nature communications

Authors' code: mdsunivie/deeperwin (MIT), figshare 23585358 (MIT), Zenodo 10081846 (MIT)

Status: code verified, 313 files readable, 20 matches

[31042] doi:10.1038/s41467-023-44286-9 [paper, repository]

The psychological, computational, and neural foundations of indebtedness.

Journal: Nature communications

Authors' code: xiaoxuepsy/Indebtedness (MIT), Zenodo 8328235 (other-open), Zenodo 7015135 (other-open), cosanlab/nltools (MIT), xiaoxuepsy/indebtedness_gao2021 (MIT)

Status: code verified, 319 files readable, 9 matches

[31043] doi:10.1038/s41467-023-44301-z [paper]

Non-canonical interplay between glutamatergic NMDA and dopamine receptors shapes synaptogenesis.

Journal: Nature communications

Status: code on request

[31044] doi:10.1038/s41467-023-44352-2 [paper, repository]

Gene regulation and speciation in a migratory divide between songbirds.

Journal: Nature communications

Authors' code: tsackton/brood-parasite-genomics (no license), kdelmore/swth_rnaseq (no license)

Status: code verified, 42 files readable, 9 matches

[31045] doi:10.1038/s41467-023-44358-w [paper, repository]

Dopamine release in human associative striatum during reversal learning.

Journal: Nature communications

Authors' code: Zenodo 10100769 (CC-BY-4.0), grillfilip/dopamine-release-in-human-associative-striatum-during-reversal-learning (no license)

Status: code verified, 11 files readable, 4 matches

[31046] doi:10.1038/s41467-023-44377-7 [paper, repository]

Structural heterogeneity of the ion and lipid channel TMEM16F.

Journal: Nature communications

Authors' code: ninailieva/SMFS_clustering (no license), arin83/U1067 (no license), galvanetto/Fodis (apache)

Status: code verified, 83 files readable, 2 matches

[31047] doi:10.1038/s41467-023-44516-0 [paper, repository]

Spontaneous emergence of rudimentary music detectors in deep neural networks.

Journal: Nature communications

Authors' code: snormanhaignere/natsound165-neuron2015 (no license), Zenodo 10081609 (CC-BY-4.0), kgspiano/music (CC-BY-4.0)

Status: code verified, 186 files readable, 7 matches

[31048] doi:10.1038/s41467-023-44632-x [paper, repository]

Prefrontal signals precede striatal signals for biased credit assignment in motivational learning biases.

Journal: Nature communications

Authors' code: tuhauser/TAfT (no license), johalgermissen/Algermissen2024NatComms (MIT), denoudenlab/Algermissen2024NatComms (MIT), Zenodo 10352241 (CC-BY-4.0)

Status: code verified, 638 files readable, 37 matches

[31049] doi:10.1038/s41514-023-00129-x [paper, repository]

An ensemble learning model for continuous cognition assessment based on resting-state EEG.

Journal: npj aging

Authors' code: Sun199510/adaboost_matlab (no license)

Status: code verified, 2 files readable

[31050] doi:10.1038/s41531-023-00607-9 [paper]

Linking acetylated α-Tubulin redistribution to α-Synuclein pathology in brain of Parkinson's disease patients.

Journal: NPJ Parkinson's disease

Status: code on request

[31051] doi:10.1038/s41587-023-02024-y [paper, repository]

Detection of mosaic and population-level structural variants with Sniffles2.

Journal: Nature biotechnology

Authors' code: fritzsedlazeck/Sniffles (MIT), smolkmo/Sniffles2-Supplement (MIT), Zenodo 8121996 (MIT), Zenodo 8122060 (MIT)

Status: code verified, 50 files readable, 16 matches

[31052] doi:10.1038/s41587-023-02031-z [paper, data]

Combined small-molecule treatment accelerates maturation of human pluripotent stem cell-derived neurons.

Journal: Nature biotechnology

Status: data only, 1 dataset cited

[31053] doi:10.1038/s41593-023-01515-0 [paper, repository]

Synaptic-like transmission between neural axons and arteriolar smooth muscle cells drives cerebral neurovascular coupling.

Journal: Nature neuroscience

Authors' code: JialabEleven/new_vessel_diameter_detection (no license), JialabEleven/calcium_spark_adjustment (no license)

Status: code verified, 2 files readable

[31054] doi:10.1038/s41598-023-45249-2 [paper]

HSV1 microRNAs in glioblastoma development: an in silico study.

Journal: Scientific reports

Status: data only

[31055] doi:10.1038/s41598-023-49355-z [paper, repository]

CW_ICA: an efficient dimensionality determination method for independent component analysis.

Journal: Scientific reports

Authors' code: yzy0080/CW_ICA (no license)

Status: code verified, 4 files readable, 3 matches

[31056] doi:10.1038/s41598-023-49375-9 [paper, repository]

Domain-general and language-specific contributions to speech production in a second language: an fMRI study using functional localizers.

Journal: Scientific reports

Authors' code: OSF s85hk (no license)

Status: code verified, 2 files readable, 4 matches

[31057] doi:10.1038/s41598-023-49538-8 [paper, repository]

Individual differences in the neural architecture in semantic processing.

Journal: Scientific reports

Authors' code: humanconnectome.org/study/hcp-young-adult (no license)

Status: code verified

[31058] doi:10.1038/s41598-023-50526-1 [paper]

Subregion and sex differences in ethanol activation of cholinergic and glutamatergic cells in the mesopontine tegmentum.

Journal: Scientific reports

Status: code on request

[31059] doi:10.1038/s41598-023-50631-1 [paper, repository]

Histogram-based features track Alzheimer's progression in brain MRI.

Journal: Scientific reports

Authors' code: kaggle.com/tourist55/alzheimers-dataset-4-class-of-images (no license)

Status: dead link

[31060] doi:10.1038/s41598-023-50683-3 [paper, repository]

Exploring the costs of phenotypic plasticity for evolvable digital organisms.

Journal: Scientific reports

Authors' code: karinemiras/revolve2 (no license)

Status: code verified, 150 files readable, 2 matches

[31061] doi:10.1038/s41598-023-50736-7 [paper, repository]

A robust deep learning detector for sleep spindles and K-complexes: towards population norms.

Journal: Scientific reports

Authors' code: nicolasigor/Sleep-EEG-Event-Detector (MIT)

Status: code verified, 71 files readable, 9 matches

[31062] doi:10.1038/s41598-023-50939-y [paper, data]

BAF45D-binding to HOX genes was differentially targeted in H9-derived spinal cord neural stem cells.

Journal: Scientific reports

Status: data only, 1 dataset cited

[31063] doi:10.1038/s42003-023-05689-y [paper, repository]

Human Purkinje cells outperform mouse Purkinje cells in dendritic complexity and computational capacity.

Journal: Communications biology

Authors' code: modeldb:9848 (no license), modeldb:267694 (no license), Zenodo 10213964 (CC-BY-4.0)

Status: code verified, 58 files readable, 4 matches

[31064] doi:10.1038/s42003-023-05690-5 [paper, repository]

scMD facilitates cell type deconvolution using single-cell DNA methylation references.

Journal: Communications biology

Authors' code: codeocean:2549317 (no license), randel/scmd (no license), randel/EnsDeconv (other), aet21/EpiSCORE (no license), SalasLab/HiBED (no license), Zenodo 10223092 (CC-BY-4.0)

Status: code verified, 68 files readable, 9 matches

[31065] doi:10.1038/s42003-023-05699-w [paper, repository]

Activation of M1 cholinergic receptors in mouse somatosensory cortex enhances information processing and detection behaviour.

Journal: Communications biology

Authors' code: MishraWricha/Cholinergic-M1-receptors-in-sensory-procesing (no license), Zenodo 10360563 (CC-BY-4.0)

Status: code verified, 4 files readable, 2 matches

[31066] doi:10.1038/s42003-023-05728-8 [paper, repository]

Synchronized LFP rhythmicity in the social brain reflects the context of social encounters.

Journal: Communications biology

Authors' code: Zenodo 10232644 (CC-BY-4.0)

Status: code verified, 761 files readable, 9 matches

[31067] doi:10.1038/s44318-023-00016-x [paper, data]

Pan-cancer ion transport signature reveals functional regulators of glioblastoma aggression.

Journal: The EMBO journal

Status: data only, 2 datasets cited

[31068] doi:10.1038/s44318-023-00018-9 [paper, data]

Disease-associated polyalanine expansion mutations impair UBA6-dependent ubiquitination.

Journal: The EMBO journal

Status: data only, 1 dataset cited

[31069] doi:10.1038/s44321-023-00014-w [paper, data]

Methotrimeprazine is a neuroprotective antiviral in JEV infection via adaptive ER stress and autophagy.

Journal: EMBO molecular medicine

Status: data only, 1 dataset cited

[31070] doi:10.1159/000535871 [paper, data]

Posterior Circulation Mechanical Thrombectomy through Primitive Trigeminal Artery: A Case Report.

Journal: Case reports in neurology

Status: data only, 1 dataset cited

[31071] doi:10.1172/jci171235 [paper, data]

Spliceosome malfunction causes neurodevelopmental disorders with overlapping features.

Journal: The Journal of clinical investigation

Status: data only, 1 dataset cited

[31072] doi:10.1186/s11689-023-09514-9 [paper]

Degraded inferior colliculus responses to complex sounds in prenatally exposed VPA rats.

Journal: Journal of neurodevelopmental disorders

Status: code on request

[31073] doi:10.1186/s12864-023-09863-8 [paper, repository]

Identification of eQTLs using different sets of single nucleotide polymorphisms associated with carcass and body composition traits in pigs.

Journal: BMC genomics

Authors' code: bioinformatics-ptp/zanardi (no license)

Status: code verified, 16 files readable, 1 match

[31074] doi:10.1186/s12868-023-00841-0 [paper, repository]

Graph neural network and machine learning analysis of functional neuroimaging for understanding schizophrenia.

Journal: BMC neuroscience

Authors' code: drive.google.com/drive/folders (no license)

Status: code verified

[31075] doi:10.1186/s12920-023-01775-6 [paper, data]

Bioinformatic identification and experiment validation reveal 6 hub genes, promising diagnostic and therapeutic targets for Alzheimer's disease.

Journal: BMC medical genomics

Status: data only, 1 dataset cited

[31076] doi:10.1242/dev.202095 [paper, data]

TFAP2 paralogs regulate midfacial development in part through a conserved ALX genetic pathway.

Journal: Development (Cambridge, England)

Status: data only, 1 dataset cited

[31077] doi:10.1371/journal.pcbi.1011008 [paper, repository]

The spinal cord facilitates cerebellar upper limb motor learning and control; inputs from neuromusculoskeletal simulation.

Journal: PLoS computational biology

Authors' code: Zenodo 7701436 (no license)

Status: code verified

[31078] doi:10.1371/journal.pone.0296328 [paper, repository]

The landscape of SETBP1 gene expression and transcription factor activity across human tissues.

Journal: PloS one

Authors' code: lasseignelab/230323_JW_DiseaseNetworks (MIT), Zenodo 8225613 (other-open), Zenodo 8225317 (other-open), lasseignelab/230227_JW_Setbp1Manuscript (MIT)

Status: code verified, 89 files readable, 8 matches

[31079] doi:10.1371/journal.pone.0296360 [paper, repository]

An improved F98 glioblastoma rat model to evaluate novel treatment strategies incorporating the standard of care.

Journal: PloS one

Authors' code: VelislavaZoteva/PlosOne (other)

Status: empty repository, 1 file readable

[31080] doi:10.2967/jnumed.123.265931 [paper, repository]

MRI or ¹⁸F-FDG PET for Brain Age Gap Estimation: Links to Cognition, Pathology, and Alzheimer Disease Progression.

Journal: Journal of nuclear medicine : official publication, Society of Nuclear Medicine

Authors' code: juaml.github.io/julearn (no license)

Status: code verified

[31081] doi:10.3390/bioengineering11010049 [paper, data]

Blood Urea Nitrogen-to-Albumin Ratio May Predict Mortality in Patients with Traumatic Brain Injury from the MIMIC Database: A Retrospective Study.

Journal: Bioengineering (Basel, Switzerland)

Status: data only, 2 datasets cited

[31082] doi:10.7554/elife.92523 [paper, data]

RNA fusion in human retinal development.

Journal: eLife

Status: data only, 1 dataset cited

[31083] doi:10.7717/peerj-cs.1754 [paper, repository]

Brain tumor segmentation using U-Net in conjunction with EfficientNet.

Journal: PeerJ. Computer science

Authors' code: supp:PMC10773611/peerj-cs-10-1754-s001.py (no license)

Status: code verified, 1 file readable, 1 match

Monday, 1 January 2024 (161 papers, 53 on this page)

[31084] doi:10.1002/brb3.3348 [paper]

Predicting suicidality in late-life depression by 3D convolutional neural network and cross-sample entropy analysis of resting-state fMRI.

Journal: Brain and behavior

Status: code on request

[31085] doi:10.1002/brb3.3358 [paper, data]

Identification and validation of cortisol-related hub biomarkers and the related pathogenesis of biomarkers in Ischemic Stroke.

Journal: Brain and behavior

Status: data only, 1 dataset cited

[31086] doi:10.1002/brb3.3395 [paper, repository]

Functional neural networks stratify Parkinson's disease patients across the spectrum of cognitive impairment.

Journal: Brain and behavior

Authors' code: thomasyeolab/cbig (MIT)

Status: code verified, 2,000 files readable, 3 matches

[31087] doi:10.1002/dad2.12526 [paper]

Personalized modeling of Alzheimer's disease progression estimates neurodegeneration severity from EEG recordings.

Journal: Alzheimer's & dementia (Amsterdam, Netherlands)

Status: code on request

[31088] doi:10.1002/hbm.26549 [paper, data]

Common and distinct BOLD correlates of Simon and flanker conflicts which can(not) be reduced to time-on-task effects.

Journal: Human brain mapping

Status: code on request, 1 dataset cited

[31089] doi:10.1002/hbm.26554 [paper, repository]

Graph alignment exploiting the spatial organization improves the similarity of brain networks.

Journal: Human brain mapping

Authors' code: geomstats/geomstats (MIT)

Status: code verified, 602 files readable, 6 matches

[31090] doi:10.1002/hbm.26558 [paper, repository]

Brain structure ages-A new biomarker for multi-disease classification.

Journal: Human brain mapping

Authors' code: ha-ha-ha-han/UKBiobank_deep_pretrain (MIT), benniatli/BrainAgePredictionResNet (no license)

Status: code verified, 19 files readable

[31091] doi:10.1002/hbm.26571 [paper, repository]

Neural sensitivity to translational self- and object-motion velocities.

Journal: Human brain mapping

Authors' code: neuropower/neurodesign (MIT)

Status: code verified, 19 files readable

[31092] doi:10.1002/hbm.26581 [paper, repository]

Identifying subgroups of eating behavior traits unrelated to obesity using functional connectivity and feature representation learning.

Journal: Human brain mapping

Authors' code: neuroanatomyandconnectivity/pipelines (MIT), by9433/funp (no license), MICA-MNI/BrainSpace (BSD-3-Clause), MICA-MNI/ENIGMA (BSD-3-Clause), gudtls17/EatBehav.RepresentLearning (no license), ftp.gwdg.de/pub/misc (no license), neuroanatomyandconnectivity/tree (no license)

Status: code verified, 590 files readable, 10 matches

[31093] doi:10.1002/jev2.12397 [paper]

Recommendations for reproducibility of cerebrospinal fluid extracellular vesicle studies.

Journal: Journal of extracellular vesicles

Status: data only

[31094] doi:10.1002/jev2.12403 [paper, repository]

Dysregulation of extracellular vesicle protein cargo in female myalgic encephalomyelitis/chronic fatigue syndrome cases and sedentary controls in response to maximal exercise.

Journal: Journal of extracellular vesicles

Authors' code: cran.r-project.org/web/packages (no license)

Status: code verified

[31095] doi:10.1007/978-1-0716-3854-5_11 [paper, repository]

Lumen Pressure Modulation in Chicken Embryos.

Journal: Methods in molecular biology (Clifton, N.J.)

Authors' code: susie-m/lumen_pressure_reading (BSD-3-Clause)

Status: code verified, 3 files readable

[31096] doi:10.1016/j.cell.2023.12.018 [paper, repository]

Coordinating brain-distributed network activities in memory resistant to extinction.

Journal: Cell

Authors' code: Zenodo 10351412 (CC-BY-4.0), Zenodo 10351398 (CC-BY-4.0)

Status: code verified, 8 files readable, 4 matches

[31097] doi:10.1016/j.xpro.2023.102795 [paper, repository]

Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers.

Journal: STAR protocols

Authors' code: hippenmeyerlab/undrift (LGPL-3.0), Zenodo 10183022 (CC-BY-4.0), hippenmeyerlab (no license)

Status: code verified, 10 files readable, 1 match

[31098] doi:10.1037/xge0001476 [paper, repository]

Demands on perceptual and mnemonic fidelity are a key determinant of age-related cognitive decline throughout the lifespan.

Journal: Journal of experimental psychology. General

Authors' code: OSF 24vqk (no license), konklab.fas.harvard.edu (no license)

Status: code verified, 2 files readable, 2 matches

[31099] doi:10.1042/bsr20230502 [paper, data]

Uncovering the essential roles of glutamate carboxypeptidase 2 orthologs in Caenorhabditis elegans.

Journal: Bioscience reports

Status: data only, 1 dataset cited

[31100] doi:10.1080/10253890.2024.2312467 [paper, data]

Chronic adolescent stress alters GR-FKBP5 interactions in the hippocampus of adult female rats.

Journal: Stress (Amsterdam, Netherlands)

Status: data only, 1 dataset cited

[31101] doi:10.1080/19490976.2023.2298697 [paper]

Microbiome function and neurodevelopment in Black infants: vitamin B&lt;sub&gt;12&lt;/sub&gt; emerges as a key factor.

Journal: Gut microbes

Status: data only

[31102] doi:10.1080/19490976.2024.2319844 [paper, data]

Regulation of colonic neuropeptide Y expression by the gut microbiome in patients with ulcerative colitis and its association with anxiety- and depression-like behavior in mice.

Journal: Gut microbes

Status: data only, 1 dataset cited

[31103] doi:10.1080/19490976.2024.2323752 [paper]

A modified Mediterranean-style diet enhances brain function via specific gut-microbiome-brain mechanisms.

Journal: Gut microbes

Status: data only

[31104] doi:10.1080/19490976.2024.2359729 [paper, data]

Hydrogen peroxide in breast milk is crucial for gut microbiota formation and myelin development in neonatal mice.

Journal: Gut microbes

Status: data only, 1 dataset cited

[31105] doi:10.1080/19490976.2024.2363011 [paper]

A novel Mediterranean diet-inspired supplement ameliorates cognitive, microbial, and metabolic deficits in a mouse model of low-grade inflammation.

Journal: Gut microbes

Status: data only

[31106] doi:10.1080/19490976.2024.2363015 [paper, data]

Gut microbiota depletion delays somatic peripheral nerve development and impairs neuromuscular junction maturation.

Journal: Gut microbes

Status: data only, 2 datasets cited

[31107] doi:10.1080/19490976.2024.2385524 [paper, repository]

Supplier-origin gut microbiomes affect host body weight and select autism-related behaviors.

Journal: Gut microbes

Authors' code: ahof1704/VocalMat (Apache-2.0), ericsson-lab/btbr_2024 (no license)

Status: code verified, 65 files readable, 7 matches

[31108] doi:10.1080/24740527.2024.2425596 [paper, data]

Neuroethical issues in adopting brain imaging for personalized chronic pain management: Attitudes of people with lived experience of chronic pain.

Journal: Canadian journal of pain = Revue canadienne de la douleur

Status: data only, 1 dataset cited

[31109] doi:10.1093/bib/bbad526 [paper]

Computational insights into the cross-talk between medin and Aβ: implications for age-related vascular risk factors in Alzheimer's disease.

Journal: Briefings in bioinformatics

Status: code on request

[31110] doi:10.1093/bib/bbae038 [paper, repository]

Modeling genotype-protein interaction and correlation for Alzheimer's disease: a multi-omics imaging genetics study.

Journal: Briefings in bioinformatics

Authors' code: dulei323/MT-GPIC (no license)

Status: dead link

[31111] doi:10.1093/bib/bbae051 [paper, repository]

STW-MD: a novel spatio-temporal weighting and multi-step decision tree method for considering spatial heterogeneity in brain gene expression data.

Journal: Briefings in bioinformatics

Authors' code: tsnm1/STW-MD (no license)

Status: code verified, 4 files readable, 5 matches

[31112] doi:10.1093/bib/bbae088 [paper, repository]

PANCDR: precise medicine prediction using an adversarial network for cancer drug response.

Journal: Briefings in bioinformatics

Authors' code: DMCB-GIST/PANCDR (no license)

Status: code verified, 11 files readable, 1 match

[31113] doi:10.1093/bioinformatics/btae269 [paper, repository]

MEG-PPIS: a fast protein-protein interaction site prediction method based on multi-scale graph information and equivariant graph neural network.

Journal: Bioinformatics (Oxford, England)

Authors' code: dhz234/MEG-PPIS (no license)

Status: code verified, 5 files readable, 4 matches

[31114] doi:10.1093/brain/awad362 [paper]

Transdiagnostic inflexible learning dynamics explain deficits in depression and schizophrenia.

Journal: Brain : a journal of neurology

Status: code on request

[31115] doi:10.1093/cercor/bhad427 [paper, repository]

Functional and anatomical connectivity predict brain stimulation's mnemonic effects.

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

Authors' code: memory.psych.upenn.edu/electrophysiological_data (no license)

Status: code verified

[31116] doi:10.1093/cercor/bhad431 [paper, repository]

Deficits in neuronal architecture but not over-inhibition are main determinants of reduced neuronal network activity in a mouse model of overexpression of Dyrk1A.

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

Authors' code: lmanubens/ee_ca1 (MIT)

Status: code verified, 38 files readable, 6 matches

[31117] doi:10.1093/cercor/bhad447 [paper, repository]

Dissociable contributions of the hippocampus and orbitofrontal cortex to representing task space in a social context.

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

Authors' code: JJliao13/Social_Navigation (MIT)

Status: code verified, 3 files readable

[31118] doi:10.1093/cercor/bhad479 [paper, data]

Novel inductively coupled ear-bars (ICEs) to enhance restored fMRI signal from susceptibility compensation in rats.

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

Status: data only, 1 dataset cited

[31119] doi:10.1093/cercor/bhad482 [paper, repository]

Test-retest reliability of spectral parameterization by 1/f characterization using SpecParam.

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

Authors' code: MindSpaceLab/Aperiodic_Test_Retest (no license)

Status: code verified, 1 file readable

[31120] doi:10.1093/cercor/bhad485 [paper, repository]

Parallel cognitive maps for multiple knowledge structures in the hippocampal formation.

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

Authors' code: doi:10.5061/dryad.nk08s (no license)

Status: code verified

[31121] doi:10.1093/cercor/bhad506 [paper, data]

Measures of resting-state brain network segregation and integration vary in relation to data quantity: implications for within and between subject comparisons of functional brain network organization.

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

Status: data only, 1 dataset cited

[31122] doi:10.1093/cercor/bhad515 [paper]

Neuroplasticity of the left dorsolateral prefrontal cortex in patients with treatment-resistant depression as indexed with paired associative stimulation: a TMS-EEG study.

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

Status: code on request

[31123] doi:10.1093/cercor/bhad519 [paper, repository]

Representation of event and object concepts in ventral anterior temporal lobe and angular gyrus.

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

Authors' code: OSF mn8ft (no license)

Status: code verified, 20 files readable, 4 matches

[31124] doi:10.1093/cercor/bhad537 [paper, data]

Basis of executive functions in fine-grained architecture of cortical and subcortical human brain networks.

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

Status: data only, 1 dataset cited

[31125] doi:10.1093/cercor/bhad542 [paper, repository]

Dynamic multilayer functional connectivity detects preclinical and clinical Alzheimer's disease.

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

Authors' code: softmatterlab/braph-2-matlab (other)

Status: code verified, 588 files readable, 4 matches

[31126] doi:10.1093/cercor/bhae002 [paper, data]

Neural correlates of object identity and reward outcome in the sensory cortical-hippocampal hierarchy: coding of motivational information in perirhinal cortex.

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

Status: data only, 1 dataset cited

[31127] doi:10.1093/cercor/bhae029 [paper, repository]

Mapping individual aspects of bilingual experience to adaptations in brain structure.

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

Authors' code: OSF ab8u3 (no license)

Status: code verified, 7 files readable, 1 match

[31128] doi:10.1093/chemse/bjae030 [paper, repository]

Olfactory receptor neurons are sensitive to stimulus onset asynchrony: implications for odor source discrimination.

Journal: Chemical senses

Authors' code: grg2rsr/sssort (GPL-3.0), grg2rsr/rgs_ephaptic (GPL-3.0)

Status: code verified, 25 files readable, 6 matches

[31129] doi:10.1093/ehjimp/qyae064 [paper]

Predicting elevated natriuretic peptide in chest radiography: emerging utilization gap for artificial intelligence.

Journal: European heart journal. Imaging methods and practice

Status: code on request

[31130] doi:10.1093/gbe/evad239 [paper, data]

Astrocytes Drive Divergent Metabolic Gene Expression in Humans and Chimpanzees.

Journal: Genome biology and evolution

Status: data only, 1 dataset cited

[31131] doi:10.1093/gigascience/giad097 [paper, repository]

EAGS: efficient and adaptive Gaussian smoothing applied to high-resolved spatial transcriptomics.

Journal: GigaScience

Authors' code: STOmics/EAGS (MIT)

Status: code verified, 11 files readable, 5 matches

[31132] doi:10.1093/gigascience/giae009 [paper, repository]

On the variability of dynamic functional connectivity assessment methods.

Journal: GigaScience

Authors' code: Zenodo 10161176 (MIT), neurodatascience/dFC (MIT)

Status: code verified, 119 files readable, 15 matches

[31133] doi:10.1093/gigascience/giae042 [paper, repository]

spatiAlign: an unsupervised contrastive learning model for data integration of spatially resolved transcriptomics.

Journal: GigaScience

Authors' code: STOmics/Spatialign (MIT), spatialign-tutorials.readthedocs.io (no license)

Status: code verified, 13 files readable, 5 matches

[31134] doi:10.1093/gigascience/giae049 [paper, repository]

CAT: a computational anatomy toolbox for the analysis of structural MRI data.

Journal: GigaScience

Authors' code: ChristianGaser/tfce (GPL-2.0)

Status: code verified, 57 files readable, 2 matches

[31135] doi:10.1093/gigascience/giae057 [paper, repository]

Deep learning links localized digital pathology phenotypes with transcriptional subtype and patient outcome in glioblastoma.

Journal: GigaScience

Authors' code: tovaroe/GBMatch_CNN (GPL-3.0), Zenodo 8358673 (CC0-1.0)

Status: code verified, 18 files readable, 5 matches

[31136] doi:10.1093/gigascience/giae100 [paper, repository]

A dataset profiling the multiomic landscape of the prefrontal cortex in amyotrophic lateral sclerosis.

Journal: GigaScience

Authors' code: imsb-uke/MAXOMOD_Pipeline (MIT)

Status: code verified, 118 files readable, 7 matches

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