El-Din SS, Rashed L, Medhat E, Aboulhoda BE, Badawy AD, ShamsEldeen AM et al (2020) Active form of vitamin D analogue mitigates neurodegenerative changes in Alzheimer’s disease in rats by targeting Keap1/Nrf2 and MAPK-38p/ERK signaling pathways. Steroids 156:108586

Article  Google Scholar 

Villemagne VL, Burnham S, Bourgeat P, Brown B, Ellis KA, Salvado O et al (2013) Amyloid β deposition, neurodegeneration, and cognitive decline in sporadic Alzheimer’s disease: a prospective cohort study. Lancet Neurol 12(4):357–367

Article  CAS  PubMed  Google Scholar 

Moezzi S-M-I, Mozafari N, Fazel-Hoseini S-M, Nadimi-Parashkoohi S, Abbasi H, Ashrafi H et al (2020) Apolipoprotein J in Alzheimer’s disease: shedding light on its role with cell signaling pathway perspective and possible therapeutic approaches. ACS Chem Neurosci 11(24):4060–4072

Article  CAS  PubMed  Google Scholar 

Association As (2017) 2017 Alzheimer’s disease facts and figures. Alzheimer’s Dement 13(4):325–373

Mullane K, Williams M (2019) Preclinical models of Alzheimer’s disease: relevance and translational validity. Curr Protocols Pharmacol 84(1):e57

Article  Google Scholar 

Praticò D (2008) Oxidative stress hypothesis in Alzheimer’s disease: a reappraisal. Trends Pharmacol Sci 29(12):609–615

Article  PubMed  Google Scholar 

Perl DP (2010) Neuropathology of Alzheimer’s disease. Mt Sinai J Med 77(1):32–42

Article  PubMed  PubMed Central  Google Scholar 

Villeneuve S, Wirth M, La Joie R (2015) Are AD-typical regions the convergence point of multiple pathologies? Front Aging Neurosci 7:42

Article  PubMed  PubMed Central  Google Scholar 

De Luca P, Marra P, La Mantia I, Salzano FA, Camaioni A, Di Stadio A (2022) Entorhinal Cortex and Persistent Olfactory Loss in COVID-19 Patients: A Neuroanatomical Hypothesis. Comment on Fiorentino Correlations between Persistent Olfactory and Semantic Memory Disorders after SARS-CoV-2 Infection. Brain Sci. 2022, 12, 714. Brain Sciences.12(7):850

Karimani F, Asgari Taei A, Abolghasemi-Dehaghani M-R, Safari M-S, Dargahi L (2024) Impairment of entorhinal cortex network activity in Alzheimer’s disease. Front Aging Neurosci 16:1402573

Article  PubMed  PubMed Central  Google Scholar 

Somvanshi PR, Venkatesh KV (2014) A conceptual review on systems biology in health and diseases: from biological networks to modern therapeutics. Syst Synth Biol 8(1):99–116

Article  PubMed  Google Scholar 

Aguirre M, Spence JP, Sella G, Pritchard JK (2024) Gene regulatory network structure informs the distribution of perturbation effects. bioRxiv

Coleman DJL, Keane P, Luque-Martin R, Chin PS, Blair H, Ames L et al (2023) Gene regulatory network analysis predicts cooperating transcription factor regulons required for FLT3-ITD + AML growth. Cell Rep 42(12):113568

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dehghan Z, Mirmotalebisohi SA, Mozafar M, Sameni M, Saberi F, Derakhshanfar A et al (2024) Deciphering the similarities and disparities of molecular mechanisms behind respiratory epithelium response to HCoV-229E and SARS-CoV-2 and drug repurposing, a systems biology approach. DARU J Pharm Sci 32(1):215–235

Article  CAS  Google Scholar 

Saberi F, Dehghan Z, Taheri Z, Pilehchi T, Zali H (2024) Deciphering Molecular mechanisms of Cutaneous Leishmaniasis, Pathogenesis and Drug Repurposing through systems Biology. Iran Biomed J 28(4):179

Article  PubMed  PubMed Central  Google Scholar 

Mirmotalebisohi SA, Dehghan Z, Alibakhshi A, Yarian F, Zali H (2023) Identification biomarkers and molecular mechanisms involved in lung transplant rejection, and drug repurposing: a systems biology study. J Adv Med Biomedical Res 31(149):525–535

Article  Google Scholar 

Chen K, Rajewsky N (2007) The evolution of gene regulation by transcription factors and microRNAs. Nat Rev Genet 8(2):93–103

Article  CAS  PubMed  Google Scholar 

Martinez NJ, Walhout AJ (2009) The interplay between transcription factors and microRNAs in genome-scale regulatory networks. BioEssays 31(4):435–445

Article  CAS  PubMed  PubMed Central  Google Scholar 

Urbina F, Puhl AC, Ekins S (2021) Recent advances in drug repurposing using machine learning. Curr Opin Chem Biol 65:74–84

Article  CAS  PubMed  PubMed Central  Google Scholar 

Badkas A, De Landtsheer S, Sauter T (2022) Construction and contextualization approaches for protein-protein interaction networks. Comput Struct Biotechnol J 20:3280–3290

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen C, Wang J, Pan D, Wang X, Xu Y, Yan J et al (2023) Applications of multi-omics analysis in human diseases. MedComm (2020).4(4):e315

Craig-Schapiro R, Fagan AM, Holtzman DM (2009) Biomarkers of Alzheimer’s disease. Neurobiol Dis 35(2):128–140

Article  CAS  PubMed  Google Scholar 

Wood LB, Winslow AR, Strasser SD (2015) Systems biology of neurodegenerative diseases. Integr Biol (Camb) 7(7):758–775

Article  CAS  PubMed  Google Scholar 

Onisiforou A, Christodoulou CC, Zamba-Papanicolaou E, Zanos P, Georgiou P (2024) Transcriptomic analysis reveals sex-specific patterns in the hippocampus in Alzheimer’s disease. Front Endocrinol 15:1345498

Article  Google Scholar 

Irmady K, Hale CR, Qadri R, Fak J, Simelane S, Carroll T et al (2023) Blood transcriptomic signatures associated with molecular changes in the brain and clinical outcomes in Parkinson’s disease. Nat Commun 14(1):3956

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yuen SC, Zhu H, Leung S-w (2020) A systematic bioinformatics workflow with meta-analytics identified potential pathogenic factors of Alzheimer’s disease. Front NeuroSci 14:209

Article  PubMed  PubMed Central  Google Scholar 

Christodoulou CC, Onisiforou A, Zanos P, Papanicolaou EZ (2023) Unraveling the transcriptomic signatures of Parkinson’s disease and major depression using single-cell and bulk data. Front Aging Neurosci 15:1273855

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li J, Li L, Cai S, Song K, Hu S (2024) Identification of novel risk genes for Alzheimer’s disease by integrating genetics from hippocampus. Sci Rep 14(1):27484

Article  CAS  PubMed  PubMed Central  Google Scholar 

Readhead B, Haure-Mirande J-V, Funk CC, Richards MA, Shannon P, Haroutunian V et al (2018) Multiscale analysis of independent Alzheimer’s cohorts finds disruption of molecular, genetic, and clinical networks by human herpesvirus. Neuron 99(1):64–82 e7

Article  CAS  PubMed  PubMed Central  Google Scholar 

Berchtold NC, Coleman PD, Cribbs DH, Rogers J, Gillen DL, Cotman CW (2013) Synaptic genes are extensively downregulated across multiple brain regions in normal human aging and Alzheimer’s disease. Neurobiol Aging 34(6):1653–1661

Article  CAS  PubMed  Google Scholar 

Kim E-Y, Ashlock D, Yoon SH (2019) Identification of critical connectors in the directed reaction-centric graphs of microbial metabolic networks. BMC Bioinformatics 20:1–13

Article  Google Scholar 

Yu H, Kim PM, Sprecher E, Trifonov V, Gerstein M (2007) The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol 3(4):e59

Article  PubMed  PubMed Central  Google Scholar 

Bader GD, Hogue CW (2003) An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4:1–27

Article  Google Scholar 

Latchman DS (1996) Inhibitory transcription factors. Int J Biochem Cell Biol 28(9):965–974

Article  CAS  PubMed  Google Scholar 

Wingender E, Dietze P, Karas H, Knüppel R (1996) TRANSFAC: a database on transcription factors and their DNA binding sites. Nucleic Acids Res 24(1):238–241

Article  CAS  PubMed  PubMed Central