A longitudinal DNA methylation atlas and its link to brain structure and mental health.
The 7 matches · 2 of them tie a paragraph to a whole file without given lines: weak matches, whose lines are not tinted
- [1] § Materials and methods › Clustering analysis of DNAm data › Step 1: Consensus WGCNA modules ↔ Methylation_Running/(Reply1-1-1)Clustering_direct_WGCNA.R, lines 2 to 57 · score 0.71 · soft thresholding, scale free topology, CpGs, WGCNA, gene, matrices · Report a mismatch
- [2] § Materials and methods › Clustering analysis of DNAm data › Step 2: Hierarchical clustering of longitudinal DNAm change ↔ Methylation_Running/(5)Heatmap_and_Clustering.R, lines 2 to 52 · score 0.64 · Hierarchical clustering, flashClust, Euclidean, distance, modules, matrix · Report a mismatch
- [3] § Materials and methods › Clustering analysis of DNAm data › Step 2: Hierarchical clustering of longitudinal DNAm change ↔ Methylation_Running/(Reply1-1-1)Clustering_direct_WGCNA.R, lines 59 to 103 · score 0.63 · Hierarchical clustering, flashClust, distance, WGCNA, thresholding, modules · Report a mismatch
- [4] § Materials and methods › Clustering analysis of DNAm data › Step 1: Consensus WGCNA modules ↔ Methylation_Running/(2-1)Power_age14.R, the whole file · a weak match · score 0.61 · soft thresholding, scale free topology, WGCNA, gene, matrices, methylated · Report a mismatch
- [5] § Materials and methods › Functional and tissue-specific Enrichment analyses ↔ Methylation_Running/(6-2)Tissue_specific_Enrichment_Cluster18.R, lines 1 to 76 · score 0.59 · getNearestTSS, enrichment, probe, Genomes, tissue, Gene · Report a mismatch
- [6] § Materials and methods › Robustness of the DNAm pattern ↔ Methylation_Running/(Reply1-10)FirstPC_module.R, the whole file · a weak match · score 0.59 · variance explained, principal component, module, CpG, methylation · Report a mismatch
- [7] § Materials and methods › Polygenic risk scores of psychiatric disorders ↔ Methylation_Running/PRS_mental_health/plink_code/(1)PRS_Depression.m, lines 16 to 31 · score 0.55 · PRSice, clumping, GWAS, v1, scores, depressive · Report a mismatch
Paper
Loaded from Europe PMC by your browser; OSCR does not store it: doi.org · Europe PMC
The paper is loaded when this pane is shown.
The authors' code
R · 103 lines · 3.4 KB · no license · 2 matches
- rm(list=ls())
- setwd('/Users/dichen/Documents/Methylation_Running/')
- #setwd('F:/Methylation_Running/')
- library(R.matlab)
- num <- 372582
- sub <- 506
- mat_data <- readMat("./List_ME/substract_19_14_all_CpGs.mat")
- substract_19_14_all_CpGs<-mat_data$substract.19.14.all.CpGs
- Raw<-substract_19_14_all_CpGs[,-1]
- library(WGCNA)
- allowWGCNAThreads()
- options(stringsAsFactors=FALSE)
- gsg <- goodSamplesGenes(as.matrix(Raw), verbose=3)
- if (!gsg$allOK) {
- Raw <- Raw[gsg$goodSample, gsg$goodGenes]
- }
- library(flashClust)
- #datFT <- readRDS("Removed_Outlier_cut3_Volume_Change.rds")
- powers <- c(c(1:10), seq(from=12, to=20, by=2))
- nGene <- 90000
- sft <- pickSoftThreshold(Raw, powerVector=powers, blockSize = nGene, verbose=5)
- saveRDS(sft,file="./WGCNA/Power_information_substract_19_14_all_CpGs.rds")
- ########################################
- ##############################
- sft <- readRDS('./WGCNA/Power_information_substract_19_14_all_CpGs.rds')
- pdf(file="./WGCNA/Soft-threshold_substract_19_14_all_CpGs.pdf", width=9, height=5)
- par(mfrow=c(1,2)) #Two plots
- cex1=0.8 #具体看一下图
- plot(sft$fitIndices[,1], -sign(sft$fitIndices[,3])*sft$fitIndices[,2],xlab="Soft Threshold (power)", ylab="Scale Free Topology Model Fit, signed R^2", type="n", main=paste("Scale independence"))
- text(sft$fitIndices[,1], -sign(sft$fitIndices[,3])*sft$fitIndices[,2], labels=powers, cex=cex1, col="red")
- abline(h=0.8, col="red")
- powers <- c(c(1:10), seq(from=12, to=20, by=2))
- nGene <- 90000
- plot(sft$fitIndices[,1], sft$fitIndices[,5], xlab="Soft Threshold (power)", ylab= "Mean Connectivity", type="n", main= paste("Mean connectivity"))
- text(sft$fitIndices[,1], sft$fitIndices[,5], labels=powers, cex=cex1, col="red")
- dev.off()
- #######################
- library(WGCNA)
- allowWGCNAThreads()
- options(stringsAsFactors=FALSE)
- #datFT <- readRDS("Removed_Outlier_cut3_Volume_Change.rds")
- nGene <- 40000
- bwnet <- blockwiseModules(Raw, networkType="unsigned", TOMType="unsigned", power=3,
- maxBlockSize = nGene, detectCutHeight=0.995, minModuleSize=50,
- reassignThreshold=0, deepSplit=4, mergeCutHeight=0, numericLabels=T,
- saveTOMs=T, nThreads=20, verbose=3)
- saveRDS(bwnet, file="./WGCNA/substract_19_14_all_CpGs_Power3.rds", compress=T)
- #######################
- #######################
- bwnet <- readRDS('./WGCNA/substract_19_14_all_CpGs_Power3.rds')
- Origin <- as.data.frame(bwnet$colors)
- Origin$`bwnet$colors`
- length(tabulate(Origin$`bwnet$colors`))
- write.table(Origin, file="./WGCNA/List_Of_Methylation_Change_Power3_Min50_Merge0_UnsignedTOM_substract_19_14_all_CpGs.txt", quote=F, sep="\t", col.names=F, row.names=F)
- ME <- as.data.frame(bwnet$MEs)
- write.table(ME, file="./WGCNA/ME_Methylation_Change_Power3_Min50_Merge0_UnsignedTOM_substract_19_14_all_CpGs.txt", quote=F, sep="\t", col.names=T, row.names=F)
- ##############################
- ##########################
- library(flashClust)
- r <- cor(ME, method = "pearson", use = "complete.obs")
- sampleTree <- flashClust(dist(r), method="average")
- pdf(file="./WGCNA/Plot_Hierarchical_clustering_of_Power3_No_Merge_Network_substract_19_14_all_CpGs.pdf", width=12, height=9)
- par(cex=0.4)
- par(mar=c(0,4,2,0))
- plot(sampleTree, main= "WVCNA clusters clustering", sub="", xlab="", cex.lab=0.5, cex.axis=0.5, cex.main=2)
- abline (h=1000, col="red")
- dev.off()
- library(pheatmap)
- pheatmap(r, cluster_rows = T,cluster_cols = T,clustering_method = 'average')
(Reply1-1-1)Clustering_direct_WGCNA.R at commit 166fb8a, no license · at the source
Overview
and 14 other authors
Tomáš Paus20, Luise Poustka21, Sarah Hohmann22, Nathalie Holz5, Christian Bäuchl13, Michael N Smolka13, Nilakshi Vaidya23, Henrik Walter24, Robert Whelan25, Jianfeng Feng2,3,26, Paul M Thompson27, Gunter Schumann28,29, Tianye Jia2,3,4,30,31, Sylvane Desrivières431 affiliations
- Shanghai Key Laboratory of Mental Health and Psychological Crisis Intervention, School of Psychology and Cognitive Science, East China Normal University, Shanghai, China
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, UK
- Department of Child and Adolescent Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Discipline of Psychiatry, School of Medicine and Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin, Ireland
- Institute of Cognitive and Clinical Neuroscience, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Department of Psychology, School of Social Sciences, University of Mannheim, Mannheim, Germany
- NeuroSpin, CEA, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
- Departments of Psychiatry and Psychology, University of Vermont, Burlington, VT USA
- Sir Peter Mansfield Imaging Centre School of Physics and Astronomy, University of Nottingham, Nottingham, UK
- Department of Psychiatry and Psychotherapy, University of Tübingen, and German Center for Mental Health (DZPG), Site Tübingen, Tübingen, Germany
- Department of Psychiatry and Psychotherapy, Technische Universität Dresden, Dresden, Germany
- Physikalisch-Technische Bundesanstalt (PTB), Braunschweig and Berlin, Germany
- Institut National de la Santé et de la Recherche Médicale, INSERM U1299 “Developmental trajectories & psychiatry”; Université Paris-Saclay, Université Paris Cité, Ecole Normale supérieure Paris-Saclay, CNRS; Centre Borelli, UMR9010 Gif-sur-Yvette, France
- Psychiatry Department, Lad-D-Psy, EPS Barthélémy Durand, Etampes, France
- AP-HP. Sorbonne Université, Department of Child and Adolescent Psychiatry, Pitié-Salpêtrière Hospital, Paris, France
- Institute of Medical Psychology, Ludwig-Maximilians-Universität (LMU) in Munich, Munich, Germany
- Institut des Maladies Neurodégénératives, UMR 5293, CNRS, CEA, Université de Bordeaux, 33076 Bordeaux, France
- Departments of Psychiatry and Neuroscience, Faculty of Medicine and Centre Hosptalier Universitaire Sainte-Justine, University of Montreal, Montreal, QC Canada
- Department of Child and Adolescent Psychiatry and Psychotherapy, Heidelberg University Hospital, Blumenstrasse 8, 69115 Heidelberg, Germany
- Department of Child and Adolescent Psychiatry, Psychotherapy and Psychosomatics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Centre for Population Neuroscience and Stratified Medicine (PONS), Department of Psychiatry and Psychotherapy, Charité Universitätsmedizin Berlin, Berlin, Germany
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Psychiatry and Psychotherapy, Campus Charité Mitte, Charitéplatz 1, Berlin, Germany
- School of Psychology and Global Brain Health Institute, Trinity College Dublin, Dublin, Ireland
- Department of Computer Science, University of Warwick, Coventry, UK
- Imaging Genetics Center, Stevens Neuroimaging & Informatics Institute, Keck School of Medicine of University of Southern California, Marina del Rey, CA USA
- Centre for Population Neuroscience and Stratified Medicine (PONS), Department of Psychiatry and Neuroscience, Charité Universitätsmedizin Berlin, Berlin, Germany
- Centre for Population Neuroscience and Precision Medicine (PONS), Institute for Science and Technology of Brain-inspired Intelligence (ISTBI), Fudan University, Shanghai, China
- National Institute on Drug Dependence and Beijing Key Laboratory of Drug Dependence Research, Peking University, Beijing, China
- School of Psychology, Southampton University, Southampton, UK
Abstract
Epigenetic mechanisms are thought to contribute to neurodevelopmental vulnerability for psychiatric disorders, yet longitudinal evidence linking DNA methylation (DNAm) to brain maturation and psychopathology is limited. Using epigenome-wide DNAm (372,582 CpGs) and whole-brain structural MRI data from the IMAGEN cohort (n = 506, ages 14–19), we identified 18 co-regulated DNAm clusters, ten enriched for brain-expressed genes involved in neuronal development and signalling. The clusters showed consistent longitudinal change and were reproducible in independent adult samples (PPMI, n = 513; ADNI, n = 606). Multivariate analyses revealed coordinated coupling between DNAm change and cortical-subcortical maturation, such that greater DNAm reductions in brain-related clusters associated with greater cortical thinning and subcortical volume changes in the fronto-limbic-striatal axis. Increases in depressive symptoms, and frequency of cannabis use and binge drinking were linked to DNAm changes, with mediation models supporting DNAm as a mechanistic bridge between behaviour and brain change. Two clusters (C1 and C7) were associated with depressive and negative psychotic symptoms across adolescence. Associations of these clusters with depressive symptoms replicated in the PPMI dataset. Their coupling with amygdala–striatal maturation suggests that these DNAm signatures index environmentally shaped affective–motivational neurodevelopment.
Reproduced under the paper's license (CC BY), from the paper cited above.
Repository
Its files are read in the Code ↔ Paper reader above, with 7 matches between paragraphs and lines of code.
dichen27/dnam_pattern
166fb8a3c27929ad6ad836fbeb8a7c7713b7d166, 19 June 2025Availability: 1 check, the latest on 30 September 2026: the link answers
- 30 September 2026: the link answers
141 files
- ADNI_Running/
(1)ADNI_clean_data.R , R, 241 lines - ADNI_Running/
(2)ADNI_mapping_Mantel_t , R, 204 linesest.R - ADNI_Running/
(3)ADNI_grouping.m , MATLAB, 76 lines - ADNI_Running/
(4)ADNI_demographic.m , MATLAB, 153 lines - ADNI_Running/
ADNI/ , R, 34 lines(1)ADNI_Read_data.R - ADNI_Running/
ADNI/ , MATLAB, 131 lines(1.5)ADNI_gender_self_or der.m - ADNI_Running/
ADNI/ , R, 265 lines(2)ADNI_Preprocess.R - Methylation_Running/
(1)Methylation_regress.m , MATLAB, 134 lines - Methylation_Running/
(10)Run_CCA_cluster10.R , R, 262 lines - Methylation_Running/
(10-2)MRI_age19vsage14.m , MATLAB, 135 lines - Methylation_Running/
(10-pre)Prepare_CCA_data , MATLAB, 168 lines.m - Methylation_Running/
(11)Behavior_DNAm_age19. , MATLAB, 167 linesm - Methylation_Running/
(12)Behavior_DNAm_age14. , MATLAB, 124 linesm - Methylation_Running/
(13)PRS_With_behavior.m , MATLAB, 163 lines - Methylation_Running/
(14)Demographic Characteristics.m , MATLAB, 73 lines - Methylation_Running/
(2-1)Power_age14.R , R, 59 lines, 1 match - Methylation_Running/
(2-2)Power_age19.R , R, 61 lines - Methylation_Running/
(3)WVCNA_Consensus.R , R, 66 lines - Methylation_Running/
(4)age19-age14.m , MATLAB, 182 lines - Methylation_Running/
(5)Heatmap_and_Clusterin , R, 118 lines, 1 matchg.R - Methylation_Running/
(6-1)Functional_Enrichme , R, 216 linesnt_Mantel_test_Cluster18 .R - Methylation_Running/
(6-2)Tissue_specific_Enr , R, 114 lines, 1 matchichment_Cluster18.R - Methylation_Running/
(7)data_Cluster18.R , R, 85 lines - Methylation_Running/
(8)data_Module175.R , R, 109 lines - Methylation_Running/
(9)Freesurfer_data.m , MATLAB, 85 lines - Methylation_Running/
(Reply1-1-1)Clustering_d , R, 103 lines, 2 matchesirect_WGCNA.R - Methylation_Running/
(Reply1-1-2)data_module1 , MATLAB, 164 lines90.m - Methylation_Running/
(Reply1-1-3)Heatmap_modu , R, 99 linesle190.R - Methylation_Running/
(Reply1-1-4)Heatmap_clus , R, 75 linester18_450k_850k.R - Methylation_Running/
(Reply1-10)FirstPC_modul , R, 89 lines, 1 matche.R - Methylation_Running/
(Reply1-11)Enrichment_st , R, 218 linesability.R - Methylation_Running/
(Reply1-12)Genomic_locat , R, 83 linesion_Cluster.R - Methylation_Running/
(Reply1-2)Enrichment_Mod , R, 168 linesule_0.R - Methylation_Running/
(Reply1-3)Run_CCA_methy_ , R, 242 linesMRI_Nobrain_cluster8.R - Methylation_Running/
(Reply1-4)Module175-MDD. , MATLAB, 63 linesm - Methylation_Running/
(Reply1-5)Z-test_consens , R, 39 linesusVSnoconsensus.R - Methylation_Running/
(Reply1-6)Behavior_Contr , MATLAB, 54 linesoled_PRS_age14.m - Methylation_Running/
(Reply1-7)Behavior_Contr , MATLAB, 90 linesoled_PRS_age19.m - Methylation_Running/
(Reply1-8)Regress_cluste , MATLAB, 91 linesr18_final_pattern.m - Methylation_Running/
(Reply1-9)Heatmap_cluste , R, 89 linesr18_age14_age19.R - Methylation_Running/
(Reply2-1)Run_CCA_methy_ , R, 243 linesMRI_Nobrain_allcluster18 .R - Methylation_Running/
PRS_mental_health/ , MATLAB, 62 lines, 1 matchplink_code/ (1)PRS_Depression.m - Methylation_Running/
PRS_mental_health/ , MATLAB, 52 linesplink_code/ (13)PRS_SCZ.m - PPMI_Running/
(1)PPMI_mapping_cluster1 , R, 177 lines8_Mantel_test.R - PPMI_Running/
(2)PPMI_ID_grouping.m , MATLAB, 98 lines - PPMI_Running/
(3)PPMI_Validation_depre , MATLAB, 101 linesssion.m - PPMI_Running/
(4)PPMI_Characteric.m , MATLAB, 121 lines - PPMI_Running/
PPMI/ , R, 112 linespreprocess/ (1)PPMI_Read_data.R - PPMI_Running/
PPMI/ , MATLAB, 97 linespreprocess/ (1.5)PPMI_gender_self_or der.m - PPMI_Running/
PPMI/ , R, 228 linespreprocess/ (2)PPMI_Preprocess.R - cd_function/
cd_BJ_ROI_2_ROI.m , MATLAB, 68 lines - cd_function/
cd_ESS.m , MATLAB, 5 lines - cd_function/
cd_FDR.m , MATLAB, 15 lines - cd_function/
cd_Fmri2TS.m , MATLAB, 38 lines - cd_function/
cd_GMV_total.m , MATLAB, 19 lines - cd_function/
cd_H2_p.m , MATLAB, 17 lines - cd_function/
cd_HCP_GMV_p.m , MATLAB, 21 lines - cd_function/
cd_HCP_ROI_2_ROI.m , MATLAB, 68 lines - cd_function/
cd_LD_cutoff.m , MATLAB, 25 lines - cd_function/
cd_LD_regression.m , MATLAB, 68 lines - cd_function/
cd_LD_regression_weight. , MATLAB, 75 linesm - cd_function/
cd_PPR.m , MATLAB, 29 lines - cd_function/
cd_QC_pic.m , MATLAB, 37 lines - cd_function/
cd_RMSE.m , MATLAB, 13 lines - cd_function/
cd_VDI_corr.m , MATLAB, 78 lines - cd_function/
cd_VDI_quantile.m , MATLAB, 13 lines - cd_function/
cd_VDI_regression.m , MATLAB, 88 lines - cd_function/
cd_VDI_score.m , MATLAB, 13 lines - cd_function/
cd_VDI_t.m , MATLAB, 64 lines - cd_function/
cd_VDI_t_new.m , MATLAB, 52 lines - cd_function/
cd_WBC_covariance.m , MATLAB, 109 lines - cd_function/
cd_WBC_covariance_fix.m , MATLAB, 108 lines - cd_function/
cd_WBC_covariance_improv , MATLAB, 84 linese.m - cd_function/
cd_abs_sum.m , MATLAB, 19 lines - cd_function/
cd_abs_sum_negative.m , MATLAB, 25 lines - cd_function/
cd_abs_sum_positive.m , MATLAB, 25 lines - cd_function/
cd_accuracy.m , MATLAB, 16 lines - cd_function/
cd_activation.m , MATLAB, 39 lines - cd_function/
cd_align_intersect.m , MATLAB, 14 lines - cd_function/
cd_auc_all.m , MATLAB, 85 lines - cd_function/
cd_bootstat_adjust.m , MATLAB, 17 lines - cd_function/
cd_bootstrap_95CI.m , MATLAB, 17 lines - cd_function/
cd_bootstrap_P.m , MATLAB, 30 lines - cd_function/
cd_cell_ts_fc.m , MATLAB, 37 lines - cd_function/
cd_chi2test.m , MATLAB, 60 lines - cd_function/
cd_chi2test2.m , MATLAB, 59 lines - cd_function/
cd_chi2test_improve.m , MATLAB, 71 lines - cd_function/
cd_chi2test_massive.m , MATLAB, 199 lines - cd_function/
cd_circos.m , MATLAB, 29 lines - cd_function/
cd_cluster.m , MATLAB, 173 lines - cd_function/
cd_corr_NaN.m , MATLAB, 9 lines - cd_function/
cd_cov2000_abs_P.m , MATLAB, 9 lines - cd_function/
cd_cov_station.m , MATLAB, 16 lines - cd_function/
cd_dele_nan_row.m , MATLAB, 6 lines - cd_function/
cd_effect_sample.m , MATLAB, 9 lines - cd_function/
cd_find_block.m , MATLAB, 39 lines - cd_function/
cd_find_num.m , MATLAB, 20 lines - cd_function/
cd_grouplabel.m , MATLAB, 7 lines - cd_function/
cd_img2dto3dmask.m , MATLAB, 11 lines - cd_function/
cd_index_char.m , MATLAB, 16 lines - cd_function/
cd_index_char_cell.m , MATLAB, 16 lines - cd_function/
cd_log_p.m , MATLAB, 21 lines - cd_function/
cd_map_circos.m , MATLAB, 16 lines - cd_function/
cd_map_tval.m , MATLAB, 18 lines - cd_function/
cd_matrix_2_site.m , MATLAB, 20 lines - cd_function/
cd_mni2num.m , MATLAB, 60 lines - cd_function/
cd_mse.m , MATLAB, 7 lines - cd_function/
cd_nan.m , MATLAB, 11 lines - cd_function/
cd_num2table.m , MATLAB, 6 lines - cd_function/
cd_partialcorr.m , MATLAB, 39 lines - cd_function/
cd_partialcorr_NaN.m , MATLAB, 39 lines - cd_function/
cd_permutation3D.m , MATLAB, 109 lines - cd_function/
cd_permute.m , MATLAB, 10 lines - cd_function/
cd_plot.m , MATLAB, 19 lines - cd_function/
cd_plot_all.m , MATLAB, 48 lines - cd_function/
cd_plot_fit.m , MATLAB, 17 lines - cd_function/
cd_plot_regress.m , MATLAB, 28 lines - cd_function/
cd_r2d.m , MATLAB, 12 lines - cd_function/
cd_r2d_full.m , MATLAB, 14 lines - cd_function/
cd_r2t.m , MATLAB, 13 lines - cd_function/
cd_r_PRS.m , MATLAB, 21 lines - cd_function/
cd_regress_residual.m , MATLAB, 15 lines - cd_function/
cd_regression.m , MATLAB, 26 lines - cd_function/
cd_result2nii.m , MATLAB, 50 lines - cd_function/
cd_roc.m , MATLAB, 46 lines - cd_function/
cd_sample_matrix.m , MATLAB, 16 lines - cd_function/
cd_save_R.m , MATLAB, 10 lines - cd_function/
cd_save_csv.m , MATLAB, 7 lines - cd_function/
cd_sensitivity_specifici , MATLAB, 35 linesty.m - cd_function/
cd_site_inverse.m , MATLAB, 25 lines - cd_function/
cd_svm_select_function.m , MATLAB, 52 lines - cd_function/
cd_t2d.m , MATLAB, 32 lines - cd_function/
cd_table2double.m , MATLAB, 11 lines - cd_function/
cd_try_auc.m , MATLAB, 33 lines - cd_function/
cd_ttest2.m , MATLAB, 74 lines - cd_function/
cd_voxel2ROI.m , MATLAB, 60 lines - cd_function/
cd_zscore.m , MATLAB, 17 lines - cd_function/
function_source/ , MATLAB, 29 linesgong_fmri_ts.m - cd_function/
function_source/ , MATLAB, 20 linesregress_wei_improve.m - cd_function/
function_source/ , MATLAB, 18 linesttest2_cov_improve.m - README.md, Text, 24 lines
Code availability
Clustering analyses were conducted using the R package “WGCNA” (version 1.72-5). Functional enrichment analyses were performed with the R package “missMethyl” (version 1.34.0). Tissue-specific enrichment was assessed using the R package “TissueEnrich” (version 1.20.0). T1-weighted MRI images were processed with FreeSurfer (version 6.0; http://
Reproduced under the paper's license (CC BY), from the paper cited above.
Tracing map
Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.
What the map holds:
- 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
- 140 scripts, each with its path and the digest of its content;
- 7 matches between paragraphs of the paper and lines of the code (method lexical-v1);
- neither the text of the paper nor the code itself.
Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.
Data
No dataset and no data link were found in the paper.
Data availability
The IMAGEN data is available from a dedicated database at https://
Reproduced under the paper's license (CC BY), from the paper cited above.
Versions
The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.
Version 1, 30 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 34 authors, 2 keywords, 13 MeSH terms, 5 funders, 80 references.
Cite
This paper
Chen, D., Yu, X., Cheng, W., Wang, L., Xiang, S., Zhang, W., Banaschewski, T., Bokde, A. L. W., Flor, H., Grigis, A., Garavan, H., Gowland, P., Heinz, A., Brühl, R., Martinot, J.-L., Paillère Martinot, M.-L., Artiges, E., Nees, F., Orfanos, D. P., . . . Desrivières, S. (2026). A longitudinal DNA methylation atlas and its link to brain structure and mental health. Molecular psychiatry, 31(8), 4535-4549. https://
BibTeX
@article{chen2026longitu
author = {Chen, Di and Yu, Xinyang and Cheng, Wei and Wang, Linbo and Xiang, Shitong and Zhang, Wei and Banaschewski, Tobias and Bokde, Arun L W and Flor, Herta and Grigis, Antoine and Garavan, Hugh and Gowland, Penny and Heinz, Andreas and Brühl, Rüdiger and Martinot, Jean-Luc and Paillère Martinot, Marie-Laure and Artiges, Eric and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Lemaître, Hervé and Paus, Tomáš and Poustka, Luise and Hohmann, Sarah and Holz, Nathalie and Bäuchl, Christian and Smolka, Michael N and Vaidya, Nilakshi and Walter, Henrik and Whelan, Robert and Feng, Jianfeng and Thompson, Paul M and Schumann, Gunter and Jia, Tianye and Desrivières, Sylvane},
title = {{A longitudinal DNA methylation atlas and its link to brain structure and mental health}},
journal = {Molecular psychiatry},
year = {2026},
month = mar,
volume = {31},
number = {8},
pages = {4535--4549},
publisher = {Springer Nature},
issn = {1359-4184},
doi = {10.1038/
url = {https://
pmid = {41917495},
pmcid = {PMC13364678}
}
RIS
TY - JOUR
AU - Chen, Di
AU - Yu, Xinyang
AU - Cheng, Wei
AU - Wang, Linbo
AU - Xiang, Shitong
AU - Zhang, Wei
AU - Banaschewski, Tobias
AU - Bokde, Arun L W
AU - Flor, Herta
AU - Grigis, Antoine
AU - Garavan, Hugh
AU - Gowland, Penny
AU - Heinz, Andreas
AU - Brühl, Rüdiger
AU - Martinot, Jean-Luc
AU - Paillère Martinot, Marie-Laure
AU - Artiges, Eric
AU - Nees, Frauke
AU - Orfanos, Dimitri Papadopoulos
AU - Lemaître, Hervé
AU - Paus, Tomáš
AU - Poustka, Luise
AU - Hohmann, Sarah
AU - Holz, Nathalie
AU - Bäuchl, Christian
AU - Smolka, Michael N
AU - Vaidya, Nilakshi
AU - Walter, Henrik
AU - Whelan, Robert
AU - Feng, Jianfeng
AU - Thompson, Paul M
AU - Schumann, Gunter
AU - Jia, Tianye
AU - Desrivières, Sylvane
TI - A longitudinal DNA methylation atlas and its link to brain structure and mental health
T2 - Molecular psychiatry
J2 - Mol Psychiatry
PY - 2026
DA - 2026/
VL - 31
IS - 8
SP - 4535
EP - 4549
SN - 1359-4184
PB - Springer Nature
DO - 10.1038/
UR - https://
LA - en
ER -
CSL-JSON
{
"id": "10.1038/
"type": "article-journal",
"title": "A longitudinal DNA methylation atlas and its link to brain structure and mental health",
"container-title": "Molecular psychiatry",
"author": [
{
"family": "Chen",
"given": "Di"
},
{
"family": "Yu",
"given": "Xinyang"
},
{
"family": "Cheng",
"given": "Wei"
},
{
"family": "Wang",
"given": "Linbo"
},
{
"family": "Xiang",
"given": "Shitong"
},
{
"family": "Zhang",
"given": "Wei"
},
{
"family": "Banaschewski",
"given": "Tobias"
},
{
"family": "Bokde",
"given": "Arun L W"
},
{
"family": "Flor",
"given": "Herta"
},
{
"family": "Grigis",
"given": "Antoine"
},
{
"family": "Garavan",
"given": "Hugh"
},
{
"family": "Gowland",
"given": "Penny"
},
{
"family": "Heinz",
"given": "Andreas"
},
{
"family": "Brühl",
"given": "Rüdiger"
},
{
"family": "Martinot",
"given": "Jean-Luc"
},
{
"family": "Paillère Martinot",
"given": "Marie-Laure"
},
{
"family": "Artiges",
"given": "Eric"
},
{
"family": "Nees",
"given": "Frauke"
},
{
"family": "Orfanos",
"given": "Dimitri Papadopoulos"
},
{
"family": "Lemaître",
"given": "Hervé"
},
{
"family": "Paus",
"given": "Tomáš"
},
{
"family": "Poustka",
"given": "Luise"
},
{
"family": "Hohmann",
"given": "Sarah"
},
{
"family": "Holz",
"given": "Nathalie"
},
{
"family": "Bäuchl",
"given": "Christian"
},
{
"family": "Smolka",
"given": "Michael N"
},
{
"family": "Vaidya",
"given": "Nilakshi"
},
{
"family": "Walter",
"given": "Henrik"
},
{
"family": "Whelan",
"given": "Robert"
},
{
"family": "Feng",
"given": "Jianfeng"
},
{
"family": "Thompson",
"given": "Paul M"
},
{
"family": "Schumann",
"given": "Gunter"
},
{
"family": "Jia",
"given": "Tianye"
},
{
"family": "Desrivières",
"given": "Sylvane"
}
],
"container-title-short":
"volume": "31",
"issue": "8",
"page": "4535-4549",
"DOI": "10.1038/
"PMID": "41917495",
"PMCID": "PMC13364678",
"ISSN": "1359-4184",
"publisher": "Springer Nature",
"URL": "https://
"language": "en",
"issued": {
"date-parts": [
[
2026,
3,
31
]
]
}
}
The tracing map gets a citation of its own once an author has validated it and it has a DOI.
Similar papers
The papers with a page that share the most with this one: the tools found in their code, their categories, datasets, cited references and authors, the rarest counting most.
- [1] doi:10.1038/s41467-025-67398-w [code]
- Neurocognitive characterization of behaviour and mental illness through time-varying brain network analysis.Journal: Nature communicationsIn common: Statistics and Machine Learning Toolbox, 5 references, 20 authors
- [2] doi:10.1038/s41467-025-61471-0 [code]
- Genetic risk-dependent brain markers of resilience to childhood Trauma.Journal: Nature communicationsIn common: ggplot2, depression, genetics / omics, 2 references, 20 authors
- [3] doi:10.1038/s41398-026-04010-9 [code]
- Bullying victimization and brain development: a longitudinal structural magnetic resonance imaging study from adolescence to early adulthood.Journal: Translational psychiatryIn common: psych, ggplot2, structural MRI / diffusion, 5 references, 19 authors
- [4] doi:10.21203/rs.3.rs-6864753/v1 [code]
- Lifespan investigation of brain volumetric changes associated with substance use disordersJournal: Research Square (preprint)In common: Statistics and Machine Learning Toolbox, 2 references, 20 authors
- [5] doi:10.1038/s41467-024-50305-0 [code]
- Investigating grey matter volumetric trajectories through the lifespan at the individual level.Journal: Nature communicationsIn common: ggplot2, structural MRI / diffusion, 5 references, 19 authors
- [6] doi:10.1126/sciadv.aed0772 [code]
- Deep learning reveals a neurocomputational mechanism predicting depression risk in adolescents.Journal: Science advancesIn common: ggplot2, depression, 3 references, 19 authors
- [7] doi:10.1126/sciadv.adr8164 [code]
- Adolescent maturation of cortical excitation-inhibition ratio based on individualized biophysical network modeling.Journal: Science advancesIn common: 1 reference, 20 authors
- [8] doi:10.1038/s44220-024-00354-7 [code]
- Relationships of eating behaviors with psychopathology, brain maturation and genetic risk for obesity in an adolescent cohort study.Journal: Nature. Mental healthIn common: psych, ggplot2, Statistics and Machine Learning Toolbox, genetics / omics, 4 references, 18 authors
- [9] doi:10.1038/s41467-025-62812-9 [code]
- Mapping the coupling between tract reachability and cortical geometry of the human brain.Journal: Nature communicationsIn common: Tools for NIfTI and ANALYZE image (MATLAB), Parallel Computing Toolbox, Image Processing Toolbox, 2 other tools, structural MRI / diffusion, 1 reference, 18 authors
- [10] doi:10.1038/s41467-024-52366-7 [code]
- Regional patterns of human cortex development correlate with underlying neurobiology.Journal: Nature communicationsIn common: structural MRI / diffusion, 4 references, 18 authors
Contribute
The authors of this paper can claim it, correct its record and validate its tracing map, and the maintainers of its code (its owner, or a public member of its organization) correct what it says of their repository; anyone signed in can ask for its removal. Every request goes to OSCR's own machine, which answers it; your account page follows them.
Sign in with ORCID to claim this paper as one of its authors, correct its record or validate its tracing map: when the paper's metadata lists your ORCID iD, you are recognized at once. Maintainers of its code: sign in with GitHub, then claim the repository on your account page.
Claim this paper
Correct its record
Say what each link of this record is, remove the ones that are not the paper's, add the ones that are missing. The correction becomes a new version of the record, in its Versions section.
Validate its tracing map
You validate the map as this page shows it: 1 repository of the authors' code, each at its verified commit and with its license, 140 scripts, and 7 matches between paragraphs and code (see the Code and Map sections). It then receives a DOI on Zenodo, with you (your ORCID iD) and OSCR as its creators; the code itself is not deposited.
The map's fingerprint: sha256:ef1eb386ab9e9b0d…
Add the badge to the code's README
If you are an author or a maintainer of this paper's code, you can add this badge. It says what OSCR knows of the paper (its code, its validated tracing map) and links the code to this page. Paste one of these snippets under the README's title. Keep the two marks around it, so that the badge can be replaced in place and is never added twice. OSCR changes nothing in your repository.
Markdown
<!-- oscr-badge:start -->
[](https://openscicode.org/badge/doi/10.1038/s41380-026-03554-y)
<!-- oscr-badge:end -->reStructuredText
.. oscr-badge:start
.. image:: https://openscicode.org/badge/doi/10.1038/s41380-026-03554-y.svg
:target: https://openscicode.org/badge/doi/10.1038/s41380-026-03554-y
:alt: OSCR
.. oscr-badge:endHTML
<!-- oscr-badge:start -->
<a href="https://openscicode.org/badge/doi/10.1038/s41380-026-03554-y"><img src="https://openscicode.org/badge/doi/10.1038/s41380-026-03554-y.svg" alt="OSCR"></a>
<!-- oscr-badge:end -->On GitHub, open the README, choose Edit (the pencil), paste the snippet under the title, then "Commit changes".
If you choose to, you can have the badge kept up to date for you, with oscr badge --write from the command line or with the GitHub Action in your repository's workflows. Every other form and option (a card, AsciiDoc, LaTeX, shields.io) is on the badge page.
Request its removal
To ask OSCR to remove this record, the copies of its authors' scripts or its tracing map, use the removal request page: signed in, you say who you are, what to remove and why, then review and confirm the request. Published rules decide every request (how).
Discussion, reproductions, activity
Discussion: code errors and mismatches between the code and the paper about this paper and its code, from readers and its authors, beside the paper and its tracing map.
Report a mismatch between the code and the paper · Report a code error (signed in)
Reproductions: reports from readers who ran the authors' code and did not get the paper's result, what they ran, with which environment, commit and data.
Report a reproduction failure (signed in)
Versions of its code: the releases of its code tied to a version of this paper (the preprint, the accepted manuscript, the version of record…), each with the tracing map versioned with it.
Activity: what happens around this paper: new versions of its record, its map's validation, discussions and reproductions. It opens with sign-in.
