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Personalized functional topography-based multisite brain age prediction modeling reveals divergent neurodevelopment in major depression.

Code ↔ Paper

2 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 2 matches
  1. [1] § Materials and Methods › Examining the Associations between Gene Expression and BAG-Related Functional Topography. ↔ 4.gene/s1_brainspan.m, lines 28–98 · score 0.57 · neurodevelopmental processes, axon, synapse, dendrite, BrainSpan, genes
  2. [2] § Materials and Methods › Calculating Individualized Functional Network Topography. ↔ 1.Predict_brain_age/s1.NMF/src/backNMF_u.m, lines 1–70 · score 0.55 · fMRI, spatial maps, NMF, matrix, age

Paper

Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC

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The authors' code

MATLAB · 98 lines · 4.5 KB · no license · 1 match

  1. load('D:\study\sub2\brain_age\brain_span\age_cortical_am_hip.mat','age_new_day')
  2. load('D:\study\sub2\brain_age\brain_span\column_pos_cortical_am_hip.mat','column_pos')
  3. data = readmatrix('D:\study\sub2\brain_age\brain_span\expression_matrix_my.csv');
  4. data_new=data(:,column_pos);
  5. filename = 'D:\study\sub2\brain_age\brain_span\columns_metadata.csv';
  6. opts = detectImportOptions(filename);
  7. opts.SelectedVariableNames = opts.VariableNames(7);
  8. strData = readmatrix(filename, opts, 'OutputType', 'string');
  9. brain_new=strData(column_pos);
  10. rowsToDelete = all(data_new == 0, 2);
  11. data_new(rowsToDelete, :) = [];
  12. filename = 'D:\study\sub2\brain_age\brain_span\rows_metadata.csv';
  13. opts = detectImportOptions(filename);
  14. opts.SelectedVariableNames = opts.VariableNames(4); % 选择第一列
  15. strData = readmatrix(filename, opts, 'OutputType', 'string');
  16. gene_new=strData;
  17. gene_new(rowsToDelete)=[];
  18. %%
  19. condi='sub1'
  20. domi_pos=find(brain_new=='OFC'|brain_new=='ITC'|brain_new=='STC');
  21. domi_notpos=find(~(brain_new=='OFC'|brain_new=='ITC'|brain_new=='STC'));
  22. %condi='sub2'
  23. %domi_pos=find(brain_new=='M1C'|brain_new=='V1C'|brain_new=='VFC'|brain_new=='HIP'|brain_new=='AMY'|brain_new=='DFC');
  24. %domi_notpos=find(~(brain_new=='M1C'|brain_new=='V1C'|brain_new=='VFC'|brain_new=='HIP'|brain_new=='AMY'|brain_new=='DFC'));
  25. %%
  26. load('D:\study\sub2\brain_age\brain_span\neurodev_proc.mat');
  27. field = fieldnames(neurodev_proc); % four neurodevelopment processes
  28. for i = 1:length(field)
  29. i
  30. proc = field{i};
  31. gene_proc = getfield(neurodev_proc, proc);
  32. [isMember, indexInB] = ismember(gene_new, gene_proc);
  33. genepos1 = find(isMember);
  34. gene_remain_pos=find(isMember==0);
  35. gene_domi1=data_new(genepos1,domi_pos);
  36. gene_nodomi1=data_new(genepos1,domi_notpos);
  37. Data = zscore( [ gene_domi1'; gene_nodomi1' ] );%region(domi/nodomi)*gene(developmental process gene)
  38. [ ~, PC ] = pca( Data, 'Centered', false );
  39. if corr( PC( :, 1 ), mean( Data, 2 ) ) < 0
  40. PC = -PC;
  41. end
  42. PC = PC(:,1);%region*1
  43. PC_normalized = (PC- min(PC)) ./ (max(PC) - min(PC));
  44. % for trajactory
  45. domAge = log2(age_new_day(domi_pos));%是domi 脑区的那些年龄
  46. notdomAge = log2(age_new_day(domi_notpos));%不是domi 脑区的那些年龄
  47. domPC_minmax = PC_normalized(1:size(gene_domi1,2));% Data = zscore( [ gene_domi1'; gene_nodomi1' ] );%region*gene
  48. notdomPC_minmax = PC_normalized((size(gene_domi1,2)+1):end);
  49. dataTable = table(domAge, domPC_minmax, 'VariableNames', {'age', 'y'});
  50. filename = strcat('D:\study\sub2\brain_age\brain_span\',proc,'_',condi,'_domi_cortical.xlsx');
  51. writetable(dataTable, filename);
  52. dataTable = table(notdomAge, notdomPC_minmax, 'VariableNames', {'age', 'y'});
  53. filename = strcat('D:\study\sub2\brain_age\brain_span\',proc,'_',condi,'_nodomi_cortical.xlsx');
  54. writetable(dataTable, filename);
  55. % for significant analyze
  56. domPC = PC(1:length(domAge));
  57. notdomPC = PC((length(domAge)+1):end);
  58. Index_dom_6_14 = find(domAge >= log2(4281) & domAge <= log2(14866));
  59. Index_notdom_6_14 = find(notdomAge >=log2(4281) & notdomAge <=log2(14866));%here
  60. domPC_6_14 = mean(domPC(Index_dom_6_14));
  61. notdomPC_6_14 = mean(notdomPC(Index_notdom_6_14));
  62. diff_PC(i) = domPC_6_14 - notdomPC_6_14;
  63. nperm = 1000; % permutation number
  64. for j = 1 : nperm
  65. j
  66. myresample = randsample(length(gene_remain_pos),length(genepos1));
  67. myresample=gene_remain_pos(myresample);
  68. domGene_perm = data_new(myresample,domi_pos);
  69. notdomGene_perm = data_new(myresample,domi_notpos);
  70. Dataperm = zscore( [ domGene_perm'; notdomGene_perm' ] );
  71. [ ~, PCperm ] = pca( Dataperm, 'Centered', false );
  72. if corr( PCperm( :, 1 ), mean( Dataperm, 2 ) ) < 0
  73. PCperm = -PCperm;
  74. end
  75. domPCperm = PCperm(1:length(domAge));
  76. notdomPCperm = PCperm((length(domAge) + 1):end);
  77. domPCperm_6_14 = mean(domPCperm(Index_dom_6_14));
  78. notdomPCperm_6_14 = mean(notdomPCperm(Index_notdom_6_14));
  79. diff_PCperm(j,i) = domPCperm_6_14 - notdomPCperm_6_14;
  80. end
  81. if diff_PC(i) > 0
  82. p_perm(i) = length(find(diff_PCperm(:,i) > diff_PC(i))) / nperm;
  83. else
  84. p_perm(i) = length(find(diff_PCperm(:,i) < diff_PC(i))) / nperm;
  85. end
  86. end
  87. Myelin=diff_PCperm(:,1);
  88. Axon=diff_PCperm(:,2);
  89. Dendrite=diff_PCperm(:,3);
  90. Synapse=diff_PCperm(:,6);
  91. %save('D:\study\sub2\draw\permut_all.mat','Myelin','Axon','Dendrite','Synapse')
  92. % save('D:\study\sub2\draw\permut_sub1_cortical.mat','Myelin','Axon','Dendrite','Synapse')
  93. save('D:\study\sub2\draw\permut_sub1.mat','Myelin','Axon','Dendrite','Synapse')

s1_brainspan.m at commit ce1c5e7, no license · at the source

Overview

Authors: Chenxuan Pang1,2,3, Xiaoyi Sun1,2,3,4, Jianlong Zhao1,2,3, Xinyuan Liang1,2,3, Lianglong Sun1,2,3, Qixiang Lin1,2,3, Jinrong Sun5,6,7, Xiaowen Lu5,6,8, Qiangli Dong5,6,9, Liang Zhang5,6,10, Xiaoqin Wang11,12, Dongtao Wei11,12, Yuan Chen13, Bangshan Liu5,6, Chu-Chung Huang14, Yanting Zheng15, Yankun Wu16, Taolin Chen17,18,19, Yuqi Cheng20, Xiufeng Xu21
and 13 other authorsQiyong Gong17,18,19, Tianmei Si16, Shijun Qiu15, Ching-Po Lin22,23,24, Jingliang Cheng13, Yanqing Tang25, Fei Wang25, Jiang Qiu11,12, Peng Xie26,27, Lingjiang Li5,6, Yong He1,2,3,28, DIDA-MDD Working Group, Mingrui Xia1,2,3
28 affiliations
  1. State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875, China
  2. Beijing Key Laboratory of Brain Imaging and Connectomics, Beijing Normal University, Beijing 100875, China
  3. International Data Group/McGovern Institute for Brain Research, Beijing Normal University, Beijing 100875, China
  4. School of Systems Science, Beijing Normal University, Beijing 100875, China
  5. Department of Psychiatry and National Clinical Research Center for Mental Disorders, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410013, China
  6. Mental Health Institute of Central South University, China National Technology Institute on Mental Disorders, Hunan Technology Institute of Psychiatry, Hunan Key Laboratory of Psychiatry and Mental Health, Hunan Medical Center for Mental Health, National Technology Institute on Mental Disorders, Hunan Technology Institute of Psychiatry, Changsha, Hunan 410083, China
  7. Affiliated WuTaiShan Hospital of Medical College of Yangzhou University, Yangzhou Mental Health Centre, Yangzhou, Jiangsu 225003, China
  8. Affiliated Wuhan Mental Health Center, Huazhong University of Science and Technology, Wuhan, Hubei 430012, China
  9. Department of Psychiatry, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, China
  10. Mental Health Education and Counseling Center, Shanghai University of Medicine and Health Sciences, Shanghai 201318, China
  11. Key Laboratory of Cognition and Personality (Southwest University), Ministry of Education, Chongqing 400715, China
  12. Department of Psychology, Southwest University, Chongqing 400715, China
  13. Department of Magnetic Resonance Imaging, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
  14. Key Laboratory of Brain Functional Genomics (Ministry of Education), Affiliated Mental Health Center (East China Normal University), School of Psychology and Cognitive Science, East China Normal University, Shanghai 200062, China
  15. Department of Radiology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China
  16. Peking University Sixth Hospital, Peking University Institute of Mental Health, National Health Commission Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Peking University, Beijing 100191, China
  17. Department of Radiology, Huaxi MR Research Center, Institute of Radiology and Medical Imaging, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
  18. Psychoradiology Key Laboratory of Sichuan Province, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
  19. Xiamen Key Lab of Psychoradiology and Neuromodulation, Department of Radiology, West China Xiamen Hospital of Sichuan University, Xiamen, Fujian 361022, China
  20. Affiliated Mental Health Center and Hangzhou Seventh People’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310013, China
  21. Department of Psychiatry, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, China
  22. Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China
  23. Institute of Neuroscience, National Yang Ming Chiao Tung University, Taipei 112304, China
  24. Department of Education and Research, Taipei City Hospital, Taipei 103212, China
  25. Department of Psychiatry, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, China
  26. Chongqing Key Laboratory of Neurobiology, Chongqing 400016, China
  27. Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
  28. Chinese Institute for Brain Research, Beijing 102206, China
Dates: received 22 July 2025; accepted 10 February 2026; published online 11 March 2026; in print 17 March 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1073/pnas.2519586123 · PMID 41811439 · PMCID PMC12994210 · OpenAlex W7135039044
Open access: hybrid, a free copy (OpenAlex)
Status: code verified
Categories: genetics / omics (modality), structural MRI / diffusion (modality), human (organism), depression (population), developmental (subfield)
Methods: Spectral & time-frequency, Connectivity, Statistics, Smoothing, state filtering, decompositions, Machine learning, fMRI & imaging, Physiology & signal measures
Keywords: major depressive disorder, brain age, lifespan trajectory, connectome, transcriptome
MeSH: Brain*, Major Depressive Disorder*, Adult, Aging, Case-Control Studies, Female, Humans, Magnetic Resonance Imaging, Male, Middle Aged, Neurodevelopment (* major topic)
Topic: Functional Brain Connectivity Studies (Cognitive Neuroscience, Neuroscience), according to OpenAlex
Funding: MOST | National Natural Science Foundation of China (NSFC) (82021004, 824B2051, 82402368, T24B2012, 82071998); Beijing Natural Science Foundation (JQ23033); STI 2030-Major Profects (2021ZD0211500, 2022ZD0200500)
Citations: cited by 1 paper (Europe PMC); 81 references in the paper

Abstract

The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.

Repository

Its files are read in the Code ↔ Paper reader above, with 2 matches between paragraphs and lines of code.

ALICE1029/topography_MDD

License: none: the authors keep all their rights
State: the link answers, verified on 30 September 2026
Evidence: files inventoried
Commit: ce1c5e766d572851c68b3b0552e93e90da73c40e, 11 May 2026
Languages: MATLAB (55), Python (4), R (1)
Size: 65 files, 60 scripts
Software Heritage: not archived
Found in: the text, “Materials and Methods”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: Tools for NIfTI and ANALYZE image (MATLAB) (16 files), Statistics and Machine Learning Toolbox (12 files), SciPy (4 files), SPM (4 files), Image Processing Toolbox (3 files), BrainSMASH (2 files), GIfTI library for MATLAB (2 files), NumPy (2 files), pandas (2 files), scikit-learn (2 files), cowplot (1 file), ggpubr (1 file), patchwork (1 file), rstatix (1 file), statsmodels (1 file)
Availability: 1 check, the latest on 30 September 2026: the link answers
  • 30 September 2026: the link answers
61 files

The paper's code and data availability statement is in the Data section.

Tracing map

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  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 60 scripts, each with its path and the digest of its content;
  • 2 matches between paragraphs of the paper and lines of the code (method lexical-v1);
  • neither the text of the paper nor the code itself.

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Data

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Code and data availability statement

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Read it in the paper: doi.org/10.1073/pnas.2519586123.

Versions

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Version 1, 30 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 33 authors, 5 keywords, 11 MeSH terms, 3 funders, 74 references.

Cite

This paper

Pang, C., Sun, X., Zhao, J., Liang, X., Sun, L., Lin, Q., Sun, J., Lu, X., Dong, Q., Zhang, L., Wang, X., Wei, D., Chen, Y., Liu, B., Huang, C.-C., Zheng, Y., Wu, Y., Chen, T., Cheng, Y., . . . Xia, M. (2026). Personalized functional topography-based multisite brain age prediction modeling reveals divergent neurodevelopment in major depression. Proceedings of the National Academy of Sciences of the United States of America, 123(11), e2519586123. https://doi.org/10.1073/pnas.2519586123

BibTeX

@article{pang2026personalized,
author = {Pang, Chenxuan and Sun, Xiaoyi and Zhao, Jianlong and Liang, Xinyuan and Sun, Lianglong and Lin, Qixiang and Sun, Jinrong and Lu, Xiaowen and Dong, Qiangli and Zhang, Liang and Wang, Xiaoqin and Wei, Dongtao and Chen, Yuan and Liu, Bangshan and Huang, Chu-Chung and Zheng, Yanting and Wu, Yankun and Chen, Taolin and Cheng, Yuqi and Xu, Xiufeng and Gong, Qiyong and Si, Tianmei and Qiu, Shijun and Lin, Ching-Po and Cheng, Jingliang and Tang, Yanqing and Wang, Fei and Qiu, Jiang and Xie, Peng and Li, Lingjiang and He, Yong and {DIDA-MDD Working Group} and Xia, Mingrui},
title = {{Personalized functional topography-based multisite brain age prediction modeling reveals divergent neurodevelopment in major depression}},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
year = {2026},
month = mar,
volume = {123},
number = {11},
pages = {e2519586123},
publisher = {National Academy of Sciences},
issn = {0027-8424},
doi = {10.1073/pnas.2519586123},
url = {https://doi.org/10.1073/pnas.2519586123},
pmid = {41811439},
pmcid = {PMC12994210}
}

RIS

TY - JOUR
AU - Pang, Chenxuan
AU - Sun, Xiaoyi
AU - Zhao, Jianlong
AU - Liang, Xinyuan
AU - Sun, Lianglong
AU - Lin, Qixiang
AU - Sun, Jinrong
AU - Lu, Xiaowen
AU - Dong, Qiangli
AU - Zhang, Liang
AU - Wang, Xiaoqin
AU - Wei, Dongtao
AU - Chen, Yuan
AU - Liu, Bangshan
AU - Huang, Chu-Chung
AU - Zheng, Yanting
AU - Wu, Yankun
AU - Chen, Taolin
AU - Cheng, Yuqi
AU - Xu, Xiufeng
AU - Gong, Qiyong
AU - Si, Tianmei
AU - Qiu, Shijun
AU - Lin, Ching-Po
AU - Cheng, Jingliang
AU - Tang, Yanqing
AU - Wang, Fei
AU - Qiu, Jiang
AU - Xie, Peng
AU - Li, Lingjiang
AU - He, Yong
AU - DIDA-MDD Working Group
AU - Xia, Mingrui
TI - Personalized functional topography-based multisite brain age prediction modeling reveals divergent neurodevelopment in major depression
T2 - Proceedings of the National Academy of Sciences of the United States of America
J2 - Proc Natl Acad Sci U S A
PY - 2026
DA - 2026/03/11
VL - 123
IS - 11
SP - e2519586123
SN - 0027-8424
PB - National Academy of Sciences
DO - 10.1073/pnas.2519586123
UR - https://doi.org/10.1073/pnas.2519586123
LA - en
ER -

CSL-JSON

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