{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,5]],"date-time":"2026-04-05T12:00:15Z","timestamp":1775390415651,"version":"3.50.1"},"reference-count":109,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2026,8,1]],"date-time":"2026-08-01T00:00:00Z","timestamp":1785542400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,8,1]],"date-time":"2026-08-01T00:00:00Z","timestamp":1785542400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,8,1]],"date-time":"2026-08-01T00:00:00Z","timestamp":1785542400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2026,8,1]],"date-time":"2026-08-01T00:00:00Z","timestamp":1785542400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,8,1]],"date-time":"2026-08-01T00:00:00Z","timestamp":1785542400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2026,8,1]],"date-time":"2026-08-01T00:00:00Z","timestamp":1785542400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,8,1]],"date-time":"2026-08-01T00:00:00Z","timestamp":1785542400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/100009392","name":"Prince Sattam bin Abdulaziz University","doi-asserted-by":"publisher","award":["PSAU\/2025\/01\/39110"],"award-info":[{"award-number":["PSAU\/2025\/01\/39110"]}],"id":[{"id":"10.13039\/100009392","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Computational Biology and Chemistry"],"published-print":{"date-parts":[[2026,8]]},"DOI":"10.1016\/j.compbiolchem.2026.108973","type":"journal-article","created":{"date-parts":[[2026,2,21]],"date-time":"2026-02-21T00:27:37Z","timestamp":1771633657000},"page":"108973","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"special_numbering":"C","title":["Next-generation computational strategies for neurodegenerative biomarkers: Multi-omics integration, AI, and molecular modeling"],"prefix":"10.1016","volume":"123","author":[{"given":"Pravej","family":"Alam","sequence":"first","affiliation":[]},{"given":"Gulam Mustafa","family":"Hasan","sequence":"additional","affiliation":[]},{"given":"Taj","family":"Mohammad","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3663-4940","authenticated-orcid":false,"given":"Md. Imtaiyaz","family":"Hassan","sequence":"additional","affiliation":[]}],"member":"78","reference":[{"key":"10.1016\/j.compbiolchem.2026.108973_bib1","doi-asserted-by":"crossref","unstructured":"\u2014\u2014\u2014. 2023. Artificial intelligence in multi-omics data integration: Advancing precision medicine, biomarker discovery and genomic-driven disease interventions. Int J Sci Res Arch 8 (1):1012-1030.","DOI":"10.30574\/ijsra.2023.8.1.0189"},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.108973_bib2","first-page":"1","article-title":"A multidisciplinary analysis of quantum inspired neural architectures for high efficiency signal processing in bioinformatics applications","volume":"1","author":"Abdullayev","year":"2025","journal-title":"Int. J. Mod. Sci. Discov."},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.108973_bib3","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1080\/03602532.2022.2029475","article-title":"Mass spectrometry based protein biomarkers and drug target discovery and clinical diagnosis in age-related progressing neurodegenerative diseases","volume":"54","author":"Agrawal","year":"2022","journal-title":"Drug Metab. Rev."},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.108973_bib4","doi-asserted-by":"crossref","first-page":"iyad031","DOI":"10.1093\/genetics\/iyad031","article-title":"The gene ontology knowledgebase in 2023","volume":"224","author":"Aleksander","year":"2023","journal-title":"Genetics"},{"issue":"10","key":"10.1016\/j.compbiolchem.2026.108973_bib5","first-page":"71","article-title":"AI in neurodegenerative disease research: early detection, cognitive decline prediction, and brain imaging biomarker identification","volume":"6","author":"Ali","year":"2022","journal-title":"Int. J. Eng. Technol. Res Manag"},{"issue":"02","key":"10.1016\/j.compbiolchem.2026.108973_bib6","first-page":"98","article-title":"Neurodegenerative diseases: insights into early diagnosis and therapeutic approaches","volume":"1","author":"Ali","year":"2024","journal-title":"Trends Life Sci. Biotechnol."},{"key":"10.1016\/j.compbiolchem.2026.108973_bib7","article-title":"Impact of Gln94Glu mutation on the structure and function of protection of telomere 1, a cause of cutaneous familial melanoma","author":"Amir","year":"2019","journal-title":"J. Biomol. Struct. Dyn."},{"issue":"6","key":"10.1016\/j.compbiolchem.2026.108973_bib8","doi-asserted-by":"crossref","DOI":"10.15252\/msb.20178124","article-title":"Multi-Omics Factor Analysis\u2014a framework for unsupervised integration of multi-omics data sets","volume":"14","author":"Argelaguet","year":"2018","journal-title":"Mol. Syst. Biol."},{"issue":"8","key":"10.1016\/j.compbiolchem.2026.108973_bib9","doi-asserted-by":"crossref","first-page":"1279","DOI":"10.3390\/cells11081279","article-title":"Mass spectrometry for neurobiomarker discovery: the relevance of post-translational modifications","volume":"11","author":"Azevedo","year":"2022","journal-title":"Cells"},{"issue":"s1","key":"10.1016\/j.compbiolchem.2026.108973_bib10","doi-asserted-by":"crossref","first-page":"S161","DOI":"10.3233\/JAD-179939","article-title":"Religious orders study and rush memory and aging project","volume":"64","author":"Bennett","year":"2018","journal-title":"J. Alzheimer\u2019S. Dis."},{"issue":"6","key":"10.1016\/j.compbiolchem.2026.108973_bib11","article-title":"A review on neurodegenerative disorder--alzheimer's disease","volume":"13","author":"Bhavani","year":"2020","journal-title":"Drug Invent. Today"},{"issue":"7726","key":"10.1016\/j.compbiolchem.2026.108973_bib12","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1038\/s41586-018-0579-z","article-title":"The UK Biobank resource with deep phenotyping and genomic data","volume":"562","author":"Bycroft","year":"2018","journal-title":"Nature"},{"issue":"11","key":"10.1016\/j.compbiolchem.2026.108973_bib13","doi-asserted-by":"crossref","first-page":"6016","DOI":"10.3390\/ijms22116016","article-title":"Protein aggregation landscape in neurodegenerative diseases: clinical relevance and future applications","volume":"22","author":"Candelise","year":"2021","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.compbiolchem.2026.108973_bib14","doi-asserted-by":"crossref","DOI":"10.3389\/fnagi.2025.1591796","article-title":"Advancements in multi-omics research to addressing challenges in Alzheimer's disease: a systems biology approach utilizing molecular biomarkers and innovative strategies","volume":"17","author":"Cardillo","year":"2025","journal-title":"Front. Aging Neurosci."},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.108973_bib15","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1038\/s41531-024-00853-5","article-title":"Multiomics approach identifies dysregulated lipidomic and proteomic networks in Parkinson\u2019s disease patients mutated in TMEM175","volume":"11","author":"Carrillo","year":"2025","journal-title":"npj Park. 's. Dis."},{"key":"10.1016\/j.compbiolchem.2026.108973_bib16","series-title":"Neurodegenerative Diseases: Multifactorial Degenerative Processes, Biomarkers and Therapeutic Approaches","first-page":"26","article-title":"Protein aggregation in neurodegenerative diseases","author":"Chaudhary","year":"2022"},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.108973_bib17","doi-asserted-by":"crossref","first-page":"349","DOI":"10.3233\/JAD-200110","article-title":"Proteomic profiling of plasma and brain tissue from Alzheimer\u2019s disease patients reveals candidate network of plasma biomarkers","volume":"76","author":"Chen","year":"2020","journal-title":"J. Alzheimer\u2019S. Dis."},{"key":"10.1016\/j.compbiolchem.2026.108973_bib18","doi-asserted-by":"crossref","DOI":"10.1016\/j.bbrc.2025.152166","article-title":"Structure-guided discovery of tau-phosphorylating kinase DYRK1A inhibitors for therapeutic targeting of neuroinflammatory diseases: insights from microsecond MD simulation and MMPBSA analyses","author":"Choudhury","year":"2025","journal-title":"Biochem. Biophys. Res. Commun."},{"issue":"5","key":"10.1016\/j.compbiolchem.2026.108973_bib19","doi-asserted-by":"crossref","first-page":"1572","DOI":"10.3390\/s24051572","article-title":"Machine learning and digital biomarkers can detect early stages of neurodegenerative diseases","volume":"24","author":"Chudzik","year":"2024","journal-title":"Sensors"},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.108973_bib20","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1186\/s13195-021-00814-7","article-title":"An integrative multi-omics approach reveals new central nervous system pathway alterations in Alzheimer\u2019s disease","volume":"13","author":"Clark","year":"2021","journal-title":"Alzheimer's. Res. Ther."},{"key":"10.1016\/j.compbiolchem.2026.108973_bib21","unstructured":"Collins, S. 2018. The Identification and Development of Small Molecule Inhibitors of Amyloid \u03b2 Aggregation."},{"key":"10.1016\/j.compbiolchem.2026.108973_bib22","doi-asserted-by":"crossref","DOI":"10.3389\/fcell.2022.884748","article-title":"Single-cell and single-nuclei RNA sequencing as powerful tools to decipher cellular heterogeneity and dysregulation in neurodegenerative diseases","volume":"10","author":"Cuevas-Diaz Duran","year":"2022","journal-title":"Front. Cell Dev. Biol."},{"issue":"2","key":"10.1016\/j.compbiolchem.2026.108973_bib23","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1093\/bfgp\/elac017","article-title":"Multiomics technologies: role in disease biomarker discoveries and therapeutics","volume":"22","author":"Dar","year":"2023","journal-title":"Brief. Funct. Genom."},{"issue":"6","key":"10.1016\/j.compbiolchem.2026.108973_bib24","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbac442","article-title":"Intersection of network medicine and machine learning towards investigating the key biomarkers and pathways underlying amyotrophic lateral sclerosis: a systematic review","volume":"23","author":"Das","year":"2022","journal-title":"Brief. Bioinforma."},{"issue":"11","key":"10.1016\/j.compbiolchem.2026.108973_bib25","doi-asserted-by":"crossref","first-page":"2403","DOI":"10.4103\/1673-5374.371364","article-title":"Combination of novel RNA sequencing and sophisticated network modeling to reveal a common denominator in amyotrophic lateral sclerosis?","volume":"18","author":"Dash","year":"2023","journal-title":"Neural Regen. Res."},{"issue":"2","key":"10.1016\/j.compbiolchem.2026.108973_bib26","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1007\/s00401-019-01994-1","article-title":"The role of ABCA7 in Alzheimer\u2019s disease: evidence from genomics, transcriptomics and methylomics","volume":"138","author":"De Roeck","year":"2019","journal-title":"Acta Neuropathol."},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.108973_bib27","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1146\/annurev-biodatasci-102523-103640","article-title":"Spatially resolved single-cell omics: methods, challenges, and future perspectives","volume":"7","author":"Dezem","year":"2024","journal-title":"Annu. Rev. Biomed. Data Sci."},{"issue":"D1","key":"10.1016\/j.compbiolchem.2026.108973_bib28","doi-asserted-by":"crossref","first-page":"D649","DOI":"10.1093\/nar\/gkx1132","article-title":"The reactome pathway knowledgebase","volume":"46","author":"Fabregat","year":"2018","journal-title":"Nucleic Acids Res."},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.108973_bib29","doi-asserted-by":"crossref","first-page":"649","DOI":"10.1186\/s12967-023-04516-6","article-title":"Integrating single-nucleus sequence profiling to reveal the transcriptional dynamics of Alzheimer\u2019s disease, Parkinson\u2019s disease, and multiple sclerosis","volume":"21","author":"Fan","year":"2023","journal-title":"J. Transl. Med."},{"issue":"2","key":"10.1016\/j.compbiolchem.2026.108973_bib30","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2020.108263","article-title":"Single-cell transcriptomics of Parkinson\u2019s disease human in vitro models reveals dopamine neuron-specific stress responses","volume":"33","author":"Fernandes","year":"2020","journal-title":"Cell Rep."},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.108973_bib31","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1186\/s13024-016-0085-4","article-title":"Frontotemporal dementia: insights into the biological underpinnings of disease through gene co-expression network analysis","volume":"11","author":"Ferrari","year":"2016","journal-title":"Mol. Neurodegener."},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.108973_bib32","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1186\/s12974-022-02580-1","article-title":"Pathogenesis, therapeutic strategies and biomarker development based on \u201comics\u201d analysis related to microglia in Alzheimer\u2019s disease","volume":"19","author":"Gao","year":"2022","journal-title":"J. Neuroinflamm."},{"issue":"9","key":"10.1016\/j.compbiolchem.2026.108973_bib33","doi-asserted-by":"crossref","first-page":"770","DOI":"10.1016\/j.biopsych.2022.11.002","article-title":"Prioritization of drug targets for neurodegenerative diseases by integrating genetic and proteomic data from brain and blood","volume":"93","author":"Ge","year":"2023","journal-title":"Biol. Psychiatry"},{"issue":"2","key":"10.1016\/j.compbiolchem.2026.108973_bib34","doi-asserted-by":"crossref","DOI":"10.1063\/5.0180691","article-title":"Advanced computational approaches to understand protein aggregation","volume":"5","author":"Ghosh","year":"2024","journal-title":"Biophys. Rev."},{"issue":"12","key":"10.1016\/j.compbiolchem.2026.108973_bib35","doi-asserted-by":"crossref","DOI":"10.1136\/bmjopen-2021-053674","article-title":"Biomarker discovery studies for patient stratification using machine learning analysis of omics data: a scoping review","volume":"11","author":"Glaab","year":"2021","journal-title":"BMJ Open"},{"issue":"4","key":"10.1016\/j.compbiolchem.2026.108973_bib36","doi-asserted-by":"crossref","first-page":"bbaf350","DOI":"10.1093\/bib\/bbaf350","article-title":"The integration of genome-wide and transcriptome-wide association studies in neurodegenerative diseases: opportunities, challenges, and current methodological innovations","volume":"26","author":"Gu","year":"2025","journal-title":"Brief. Bioinforma."},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.108973_bib37","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1038\/s41580-024-00768-2","article-title":"Profiling cell identity and tissue architecture with single-cell and spatial transcriptomics","volume":"26","author":"Gulati","year":"2025","journal-title":"Nat. Rev. Mol. Cell Biol."},{"issue":"6","key":"10.1016\/j.compbiolchem.2026.108973_bib38","doi-asserted-by":"crossref","first-page":"2916","DOI":"10.1021\/acs.jcim.1c00217","article-title":"Misfolding and self-assembly dynamics of microtubule-binding repeats of the Alzheimer-related protein tau","volume":"61","author":"He","year":"2021","journal-title":"J. Chem. Inf. Model."},{"key":"10.1016\/j.compbiolchem.2026.108973_bib39","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.neuint.2019.02.020","article-title":"Virtual screening identification of novel chemical inhibitors for aberrant interactions between pathogenic mutant SOD1 and tubulin","volume":"126","author":"Hirayama","year":"2019","journal-title":"Neurochem. Int."},{"issue":"4","key":"10.1016\/j.compbiolchem.2026.108973_bib40","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1517\/14728222.2016.1135132","article-title":"Accelerating medicines partnership: Alzheimer\u2019s disease (AMP-AD) knowledge portal aids Alzheimer\u2019s drug discovery through open data sharing","volume":"20","author":"Hodes","year":"2016","journal-title":"Expert Opin. Ther. Targets"},{"issue":"12","key":"10.1016\/j.compbiolchem.2026.108973_bib41","doi-asserted-by":"crossref","first-page":"29179","DOI":"10.3390\/ijms161226148","article-title":"Bioinformatics mining and modeling methods for the identification of disease mechanisms in neurodegenerative disorders","volume":"16","author":"Hofmann-Apitius","year":"2015","journal-title":"Int. J. Mol. Sci."},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.108973_bib42","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1186\/s12859-020-03950-3","article-title":"SNF-NN: computational method to predict drug-disease interactions using similarity network fusion and neural networks","volume":"22","author":"Jarada","year":"2021","journal-title":"BMC Bioinforma."},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.108973_bib43","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: kyoto encyclopedia of genes and genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res."},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.108973_bib44","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbab454","article-title":"A roadmap for multi-omics data integration using deep learning","volume":"23","author":"Kang","year":"2022","journal-title":"Brief. Bioinforma."},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.108973_bib45","article-title":"Structure-guided screening identified bioactive phytoconstituents Hernandonine and Anolobine as potential inhibitors of dual specificity protein kinase CLK1","volume":"15","author":"Khan","year":"2025","journal-title":"Sci. Rep."},{"key":"10.1016\/j.compbiolchem.2026.108973_bib46","doi-asserted-by":"crossref","DOI":"10.1016\/j.arr.2023.101924","article-title":"Nature's toolbox against tau aggregation: an updated review of current research","volume":"87","author":"Khan","year":"2023","journal-title":"Ageing Res. Rev."},{"issue":"6","key":"10.1016\/j.compbiolchem.2026.108973_bib47","doi-asserted-by":"crossref","first-page":"701","DOI":"10.3390\/bioengineering10060701","article-title":"Personalized explanations for early diagnosis of alzheimer\u2019s disease using explainable graph neural networks with population graphs","volume":"10","author":"Kim","year":"2023","journal-title":"Bioengineering"},{"issue":"21","key":"10.1016\/j.compbiolchem.2026.108973_bib48","doi-asserted-by":"crossref","first-page":"11406","DOI":"10.3390\/ijms252111406","article-title":"Integrative metabolome and proteome analysis of cerebrospinal fluid in Parkinson\u2019s disease","volume":"25","author":"Kim","year":"2024","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.compbiolchem.2026.108973_bib49","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1146\/annurev.arplant.043008.092114","article-title":"Quantitative genomics: analyzing intraspecific variation using global gene expression polymorphisms or eQTLs","volume":"60","author":"Kliebenstein","year":"2009","journal-title":"Annu. Rev. Plant Biol."},{"issue":"3","key":"10.1016\/j.compbiolchem.2026.108973_bib50","doi-asserted-by":"crossref","first-page":"423","DOI":"10.3390\/genes12030423","article-title":"Transcript variants of genes involved in neurodegeneration are differentially regulated by the APOE and MAPT haplotypes","volume":"12","author":"Koks","year":"2021","journal-title":"Genes"},{"issue":"2","key":"10.1016\/j.compbiolchem.2026.108973_bib51","doi-asserted-by":"crossref","first-page":"331","DOI":"10.4103\/1673-5374.343898","article-title":"A perspective on causality assessment in epigenetic research on neurodegenerative disorders","volume":"18","author":"Koulousakis","year":"2023","journal-title":"Neural Regen. Res."},{"issue":"6693","key":"10.1016\/j.compbiolchem.2026.108973_bib52","doi-asserted-by":"crossref","DOI":"10.1126\/science.adl2528","article-title":"Generalized biomolecular modeling and design with RoseTTAFold All-Atom","volume":"384","author":"Krishna","year":"2024","journal-title":"Science"},{"issue":"2","key":"10.1016\/j.compbiolchem.2026.108973_bib53","doi-asserted-by":"crossref","first-page":"1813","DOI":"10.3934\/mbe.2021094","article-title":"Data-driven biomarker analysis using computational omics approaches to assess neurodegenerative disease progression","volume":"18","author":"Krokidis","year":"2021","journal-title":"Math. Biosci. Eng."},{"issue":"9","key":"10.1016\/j.compbiolchem.2026.108973_bib54","doi-asserted-by":"crossref","first-page":"4820","DOI":"10.3390\/ijms22094820","article-title":"Omics data and their integrative analysis to support stratified medicine in neurodegenerative diseases","volume":"22","author":"La Cognata","year":"2021","journal-title":"Int. J. Mol. Sci."},{"issue":"2","key":"10.1016\/j.compbiolchem.2026.108973_bib55","doi-asserted-by":"crossref","first-page":"135","DOI":"10.3390\/genes16020135","article-title":"Genomic and transcriptomic approaches advance the diagnosis and prognosis of neurodegenerative diseases","volume":"16","author":"Liu","year":"2025","journal-title":"Genes"},{"key":"10.1016\/j.compbiolchem.2026.108973_bib56","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1016\/j.jbi.2018.07.004","article-title":"An unsupervised machine learning method for discovering patient clusters based on genetic signatures","volume":"85","author":"Lopez","year":"2018","journal-title":"J. Biomed. Inform."},{"issue":"12","key":"10.1016\/j.compbiolchem.2026.108973_bib57","doi-asserted-by":"crossref","first-page":"1460","DOI":"10.1002\/acn3.644","article-title":"The Parkinson's progression markers initiative (PPMI)\u2013establishing a PD biomarker cohort","volume":"5","author":"Marek","year":"2018","journal-title":"Ann. Clin. Transl. Neurol."},{"key":"10.1016\/j.compbiolchem.2026.108973_bib58","unstructured":"Maria, G. 2021. RNA metabolism and DNA damage in neurodegeneration: a new pathological relationship in Amyotrophic Lateral Sclerosis patients."},{"issue":"D1","key":"10.1016\/j.compbiolchem.2026.108973_bib59","doi-asserted-by":"crossref","first-page":"D613","DOI":"10.1093\/nar\/gkaa1024","article-title":"WikiPathways: connecting communities","volume":"49","author":"Martens","year":"2021","journal-title":"Nucleic Acids Res."},{"issue":"3","key":"10.1016\/j.compbiolchem.2026.108973_bib60","doi-asserted-by":"crossref","DOI":"10.3390\/metabo13030369","article-title":"Metabolomic footprint of disrupted energetics and amino acid metabolism in neurodegenerative diseases: perspectives for early diagnosis and monitoring of therapy","volume":"13","author":"Maszka","year":"2023","journal-title":"Metabolites"},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.108973_bib61","doi-asserted-by":"crossref","first-page":"6252","DOI":"10.1038\/s41467-020-19957-6","article-title":"Increasing the reproducibility of fluid biomarker studies in neurodegenerative studies","volume":"11","author":"Mattsson-Carlgren","year":"2020","journal-title":"Nat. Commun."},{"issue":"10","key":"10.1016\/j.compbiolchem.2026.108973_bib62","doi-asserted-by":"crossref","first-page":"4288","DOI":"10.1093\/nar\/gks042","article-title":"Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation","volume":"40","author":"McCarthy","year":"2012","journal-title":"Nucleic Acids Res."},{"issue":"11","key":"10.1016\/j.compbiolchem.2026.108973_bib63","doi-asserted-by":"crossref","first-page":"643","DOI":"10.1038\/s41582-022-00714-w","article-title":"Gene\u2013environment interactions in Alzheimer disease: the emerging role of epigenetics","volume":"18","author":"Migliore","year":"2022","journal-title":"Nat. Rev. Neurol."},{"key":"10.1016\/j.compbiolchem.2026.108973_bib64","article-title":"Advancements in neurodegenerative disease diagnosis and prediction: a machine learning approach","author":"Modi","year":"2023","journal-title":"Pap. Read. Int. Health Inform. Conf."},{"issue":"4","key":"10.1016\/j.compbiolchem.2026.108973_bib65","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbaa279","article-title":"InstaDock: a single-click graphical user interface for molecular docking-based virtual high-throughput screening","volume":"22","author":"Mohammad","year":"2021","journal-title":"Brief. Bioinforma."},{"key":"10.1016\/j.compbiolchem.2026.108973_bib66","doi-asserted-by":"crossref","DOI":"10.3389\/fonc.2022.881246","article-title":"Differential gene expression and weighted correlation network dynamics in high-throughput datasets of prostate cancer","volume":"12","author":"Mohammad","year":"2022","journal-title":"Front. Oncol."},{"issue":"19","key":"10.1016\/j.compbiolchem.2026.108973_bib67","doi-asserted-by":"crossref","first-page":"14910","DOI":"10.3390\/ijms241914910","article-title":"Analysis of potential biomarkers in frontal temporal dementia: a bioinformatics approach","volume":"24","author":"Momin","year":"2023","journal-title":"Int. J. Mol. Sci."},{"issue":"4","key":"10.1016\/j.compbiolchem.2026.108973_bib68","doi-asserted-by":"crossref","first-page":"869","DOI":"10.1016\/j.nic.2005.09.008","article-title":"The Alzheimer's disease neuroimaging initiative","volume":"15","author":"Mueller","year":"2005","journal-title":"Neuroimaging Clin."},{"issue":"2","key":"10.1016\/j.compbiolchem.2026.108973_bib69","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1039\/D0MO00176G","article-title":"Metabolomics: small molecules that matter more","volume":"17","author":"Muthubharathi","year":"2021","journal-title":"Mol. Omics"},{"issue":"20","key":"10.1016\/j.compbiolchem.2026.108973_bib70","doi-asserted-by":"crossref","first-page":"1755","DOI":"10.2174\/1568026618666181025114157","article-title":"Advancements in docking and molecular dynamics simulations towards ligand-receptor interactions and structure-function relationships","volume":"18","author":"Naqvi","year":"2018","journal-title":"Curr. Top. Med. Chem."},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.108973_bib71","doi-asserted-by":"crossref","first-page":"124","DOI":"10.69980\/ajpr.v28i1.71","article-title":"AI-driven drug discovery: transforming neurological and neurodegenerative disease treatment through bioinformatics and genomic research","volume":"28","author":"Nuka","year":"2025","journal-title":"Am. J. Psychiatr. Rehabil."},{"key":"10.1016\/j.compbiolchem.2026.108973_bib72","doi-asserted-by":"crossref","DOI":"10.47852\/bonviewMEDIN42022335","article-title":"Bioinformatics applications in chronic diseases: a comprehensive review of genomic, transcriptomics, proteomic, metabolomics, and machine learning approaches","author":"Ogunjobi","year":"2024","journal-title":"Medinformatics"},{"issue":"03","key":"10.1016\/j.compbiolchem.2026.108973_bib73","first-page":"31","article-title":"Revolutionizing early diagnosis: the role of artificial intelligence in neurodegenerative disorders","volume":"16","author":"Pal","year":"2025","journal-title":"J. Adv. Sci. Res."},{"issue":"2","key":"10.1016\/j.compbiolchem.2026.108973_bib74","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1016\/j.bioana.2024.05.005","article-title":"A comprehensive study on epigenetic biomarkers in early detection and prognosis of Alzheimer's disease","volume":"1","author":"Parikh","year":"2024","journal-title":"Biomed. Anal."},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.108973_bib75","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1007\/s11011-021-00800-w","article-title":"Neurodegenerative disorders of alzheimer, parkinsonism, amyotrophic lateral sclerosis and multiple sclerosis: an early diagnostic approach for precision treatment","volume":"37","author":"Pathak","year":"2022","journal-title":"Metab. Brain Dis."},{"issue":"7","key":"10.1016\/j.compbiolchem.2026.108973_bib76","doi-asserted-by":"crossref","first-page":"286","DOI":"10.3390\/metabo10070286","article-title":"Find the needle in the haystack, then find it again: replication and validation in the \u2018omics era","volume":"10","author":"Perng","year":"2020","journal-title":"Metabolites"},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.108973_bib77","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1186\/s13073-021-00878-y","article-title":"Emerging genetic complexity and rare genetic variants in neurodegenerative brain diseases","volume":"13","author":"Perrone","year":"2021","journal-title":"Genome Med."},{"issue":"6","key":"10.1016\/j.compbiolchem.2026.108973_bib78","doi-asserted-by":"crossref","first-page":"346","DOI":"10.1038\/s41582-023-00809-y","article-title":"Single-cell and spatial transcriptomics: deciphering brain complexity in health and disease","volume":"19","author":"Piwecka","year":"2023","journal-title":"Nat. Rev. Neurol."},{"key":"10.1016\/j.compbiolchem.2026.108973_bib79","first-page":"101","article-title":"Protein\u2013protein interactions in neurodegenerative diseases","volume":"II","author":"Poluri","year":"2023"},{"issue":"10","key":"10.1016\/j.compbiolchem.2026.108973_bib80","doi-asserted-by":"crossref","first-page":"dmm049492","DOI":"10.1242\/dmm.049492","article-title":"Integrated multi-omics analysis of Huntington disease identifies pathways that modulate protein aggregation","volume":"15","author":"Pradhan","year":"2022","journal-title":"Dis. Models Mech."},{"issue":"4","key":"10.1016\/j.compbiolchem.2026.108973_bib81","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0152342","article-title":"Identification of differentially expressed genes through integrated study of Alzheimer\u2019s disease affected brain regions","volume":"11","author":"Puthiyedth","year":"2016","journal-title":"PloS One"},{"key":"10.1016\/j.compbiolchem.2026.108973_bib82","unstructured":"Raftopoulou, P., and E.G. Petrakis. 2008. iCluster: a self-organizing overlay network for P2P information retrieval. Paper read at European Conference on Information Retrieval."},{"issue":"10","key":"10.1016\/j.compbiolchem.2026.108973_bib83","doi-asserted-by":"crossref","first-page":"747","DOI":"10.3390\/brainsci10100747","article-title":"Comprehensive analysis of RNA-seq gene expression profiling of brain transcriptomes reveals novel genes, regulators, and pathways in autism spectrum disorder","volume":"10","author":"Rahman","year":"2020","journal-title":"Brain Sci."},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.108973_bib84","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1016\/j.jagp.2019.06.007","article-title":"Postmortem cortical transcriptomics of Lewy body dementia reveal mitochondrial dysfunction and lack of neuroinflammation","volume":"28","author":"Rajkumar","year":"2020","journal-title":"Am. J. Geriatr. Psychiatry"},{"key":"10.1016\/j.compbiolchem.2026.108973_bib85","doi-asserted-by":"crossref","DOI":"10.1016\/j.prp.2025.155942","article-title":"Discovering potential therapeutic targets in glioblastoma multiforme using a multi-omics approach","volume":"269","author":"Saeed","year":"2025","journal-title":"Pathol. Res. Pract."},{"issue":"18","key":"10.1016\/j.compbiolchem.2026.108973_bib86","doi-asserted-by":"crossref","first-page":"2318","DOI":"10.3390\/cells12182318","article-title":"Biochemical and molecular pathways in neurodegenerative diseases: an integrated view","volume":"12","author":"Sanghai","year":"2023","journal-title":"Cells"},{"key":"10.1016\/j.compbiolchem.2026.108973_bib87","doi-asserted-by":"crossref","first-page":"532","DOI":"10.3389\/fbioe.2020.00532","article-title":"On the conformational dynamics of \u03b2-amyloid forming peptides: a computational perspective","volume":"8","author":"Saravanan","year":"2020","journal-title":"Front. Bioeng. Biotechnol."},{"issue":"4","key":"10.1016\/j.compbiolchem.2026.108973_bib88","doi-asserted-by":"crossref","first-page":"232","DOI":"10.3390\/brainsci10040232","article-title":"Do post-translational modifications influence protein aggregation in neurodegenerative diseases: a systematic review","volume":"10","author":"Schaffert","year":"2020","journal-title":"Brain Sci."},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.108973_bib89","doi-asserted-by":"crossref","first-page":"2524","DOI":"10.1038\/s41467-019-10513-5","article-title":"Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins","volume":"10","author":"Shao","year":"2019","journal-title":"Nat. Commun."},{"issue":"5","key":"10.1016\/j.compbiolchem.2026.108973_bib90","doi-asserted-by":"crossref","DOI":"10.1002\/alz.70012","article-title":"Comparative mapping of single-cell transcriptomic landscapes in neurodegenerative diseases","volume":"21","author":"Shwab","year":"2025","journal-title":"Alzheimer's. Dement."},{"issue":"11","key":"10.1016\/j.compbiolchem.2026.108973_bib91","doi-asserted-by":"crossref","first-page":"1777","DOI":"10.2174\/0113892010298545241108062449","article-title":"Advances in molecular docking techniques for targeting protein misfolding in neurodegenerative diseases","volume":"26","author":"Singh","year":"2025","journal-title":"Curr. Pharm. Biotechnol."},{"issue":"17","key":"10.1016\/j.compbiolchem.2026.108973_bib92","doi-asserted-by":"crossref","first-page":"3055","DOI":"10.1093\/bioinformatics\/bty1054","article-title":"DIABLO: an integrative approach for identifying key molecular drivers from multi-omics assays","volume":"35","author":"Singh","year":"2019","journal-title":"Bioinformatics"},{"key":"10.1016\/j.compbiolchem.2026.108973_bib93","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1016\/j.pbiomolbio.2018.12.003","article-title":"Molecular binding response of naringin and naringenin to H46R mutant SOD1 protein in combating protein aggregation using density functional theory and discrete molecular dynamics","volume":"145","author":"Srinivasan","year":"2019","journal-title":"Prog. Biophys. Mol. Biol."},{"key":"10.1016\/j.compbiolchem.2026.108973_bib94","series-title":"Integrative Omics","first-page":"157","article-title":"Integrative omics approaches for identification of biomarkers","author":"Srivastava","year":"2024"},{"issue":"3","key":"10.1016\/j.compbiolchem.2026.108973_bib95","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1021\/acschemneuro.2c00672","article-title":"Identification of LRRK2 inhibitors through computational drug repurposing","volume":"14","author":"Tan","year":"2023","journal-title":"ACS Chem. Neurosci."},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.108973_bib96","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1186\/s40708-024-00222-1","article-title":"Interpreting artificial intelligence models: a systematic review on the application of LIME and SHAP in Alzheimer\u2019s disease detection","volume":"11","author":"Vimbi","year":"2024","journal-title":"Brain Inform."},{"issue":"3","key":"10.1016\/j.compbiolchem.2026.108973_bib97","doi-asserted-by":"crossref","first-page":"389","DOI":"10.3390\/microarrays4030389","article-title":"Microarray meta-analysis and cross-platform normalization: integrative genomics for robust biomarker discovery","volume":"4","author":"Walsh","year":"2015","journal-title":"Microarrays"},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.108973_bib98","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1186\/s13024-020-00384-6","article-title":"Integrated analysis of ultra-deep proteomes in cortex, cerebrospinal fluid and serum reveals a mitochondrial signature in Alzheimer\u2019s disease","volume":"15","author":"Wang","year":"2020","journal-title":"Mol. Neurodegener."},{"issue":"9","key":"10.1016\/j.compbiolchem.2026.108973_bib99","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1007\/s12031-023-02152-9","article-title":"Transcriptomics meta-analysis reveals phagosome and innate immune system dysfunction as potential mechanisms in the cortex of Alzheimer\u2019s disease mouse strains","volume":"73","author":"Widjaya","year":"2023","journal-title":"J. Mol. Neurosci."},{"issue":"4","key":"10.1016\/j.compbiolchem.2026.108973_bib100","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1016\/j.cell.2022.12.032","article-title":"Hallmarks of neurodegenerative diseases","volume":"186","author":"Wilson","year":"2023","journal-title":"Cell"},{"key":"10.1016\/j.compbiolchem.2026.108973_bib101","article-title":"AI-driven multi-omics integration for multi-scale predictive modeling of genotype-environment-phenotype relationships","author":"Wu","year":"2025","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"10.1016\/j.compbiolchem.2026.108973_bib102","doi-asserted-by":"crossref","DOI":"10.3389\/fnagi.2025.1536142","article-title":"Deciphering novel mitochondrial signatures: multi-omics analysis uncovers cross-disease markers and oligodendrocyte pathways in Alzheimer\u2019s disease and glioblastoma","volume":"17","author":"Xu","year":"2025","journal-title":"Front. Aging Neurosci."},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.108973_bib103","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1038\/s41392-023-01381-z","article-title":"AlphaFold2 and its applications in the fields of biology and medicine","volume":"8","author":"Yang","year":"2023","journal-title":"Signal Transduct. Target. Ther."},{"issue":"6","key":"10.1016\/j.compbiolchem.2026.108973_bib104","doi-asserted-by":"crossref","DOI":"10.26855\/acc.2023.12.009","article-title":"Construction and analysis of disease networks based on multi-omics data","volume":"5","author":"Yin","year":"2024","journal-title":"Adv. Comput. Commun."},{"issue":"2","key":"10.1016\/j.compbiolchem.2026.108973_bib105","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1038\/s41583-023-00779-6","article-title":"Data-driven modelling of neurodegenerative disease progression: thinking outside the black box","volume":"25","author":"Young","year":"2024","journal-title":"Nat. Rev. Neurosci."},{"issue":"3","key":"10.1016\/j.compbiolchem.2026.108973_bib106","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1007\/s13205-023-03514-1","article-title":"Computational insight into in silico analysis and molecular dynamics simulation of the dimer interface residues of ALS-linked hSOD1 forms in apo\/holo states: a combined experimental and bioinformatic perspective","volume":"13","author":"Zaji","year":"2023","journal-title":"3 Biotech"},{"key":"10.1016\/j.compbiolchem.2026.108973_bib107","series-title":"Nanocarriers in neurodegenerative disorders","first-page":"29","article-title":"Neurodegenerative disorders: available therapies and their limitations","author":"Zaky","year":"2024"},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.108973_bib108","article-title":"Combined multi-omics and brain pathology reveal novel biomarkers for alzheimer\u2019s disease","volume":"15","author":"Zhao","year":"2025","journal-title":"Sci. Rep."},{"key":"10.1016\/j.compbiolchem.2026.108973_bib109","doi-asserted-by":"crossref","DOI":"10.3389\/fgene.2022.984338","article-title":"Network approaches for omics studies of neurodegenerative diseases","volume":"13","author":"Zhao","year":"2022","journal-title":"Front. Genet."}],"updated-by":[{"DOI":"10.1016\/j.compbiolchem.2026.109004","type":"erratum","label":"Erratum","source":"publisher","updated":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T00:00:00Z","timestamp":1773619200000}}],"container-title":["Computational Biology and Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1476927126000988?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1476927126000988?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,4,5]],"date-time":"2026-04-05T11:10:53Z","timestamp":1775387453000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1476927126000988"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8]]},"references-count":109,"alternative-id":["S1476927126000988"],"URL":"https:\/\/doi.org\/10.1016\/j.compbiolchem.2026.108973","relation":{},"ISSN":["1476-9271"],"issn-type":[{"value":"1476-9271","type":"print"}],"subject":[],"published":{"date-parts":[[2026,8]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Next-generation computational strategies for neurodegenerative biomarkers: Multi-omics integration, AI, and molecular modeling","name":"articletitle","label":"Article Title"},{"value":"Computational Biology and Chemistry","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.compbiolchem.2026.108973","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 Elsevier Ltd. All rights are reserved, including those for text and data mining, AI training, and similar technologies.","name":"copyright","label":"Copyright"}],"article-number":"108973"}}