% Bibliography for hypothesis h-ae1b2beb
% Title: Transcriptional Autophagy-Lysosome Coupling
% Generated: 2026-04-28T15:36:45Z

@article{pmid41655545,
  title = {Combining network pharmacology and multi-omics reveals the role of Shengdihuang-Huangqi herb pair in alleviating type 2 diabetes mellitus.},
  author = {Cao X, Shang Y, Qu M, Kang Q, Xu Y et al.},
  journal = {Phytomedicine},
  year = {2026},
  pmid = {41655545},
  doi = {doi: 10.1016/j.phymed.2026.157900},
  url = {https://pubmed.ncbi.nlm.nih.gov/41655545/},
}

@article{pmid41681129,
  title = {Mammalian lipophagy: process and function.},
  author = {Zhao R, Dai E, Kang R, Liu J, Klionsky DJ, Tang D, Qu Y, Lin Y, Zhang X},
  journal = {Autophagy},
  year = {2026},
  pmid = {41681129},
  doi = {10.1080/15548627.2026.2632256},
  url = {https://pubmed.ncbi.nlm.nih.gov/41681129/},
}

@article{pmid41763754,
  title = {Comparative transcriptomics of adherent and suspension chicken fibroblast cell lines for the optimization of cultivated meat processes.},
  author = {Contreras EJ, Nagarajan A, Bromberg BH, Villegas MP, Kaplan DL},
  journal = {Food Res Int},
  year = {2026},
  pmid = {41763754},
  doi = {doi: 10.1016/j.foodres.2026.118368},
  url = {https://pubmed.ncbi.nlm.nih.gov/41763754/},
}

@article{pmid41856090,
  title = {Effects of Vitamin A Restriction on Carcass Characteristics, Antioxidant Capacity, Meat Quality and Meat Storage Period of Yanbian Yellow Cattle.},
  author = {Zhang X, Zhang C, Song J, Bai J, Hao B, Wu Z, Sima S, Zhang J, Chen M, He Y, Hou L, Xia G},
  journal = {Animal bioscience},
  year = {2026},
  pmid = {41856090},
  doi = {10.5713/ab.250783},
  url = {https://pubmed.ncbi.nlm.nih.gov/41856090/},
}

@article{pmid41865406,
  title = {Human MKP-3 isoforms display differential structural and functional profiles.},
  author = {Mori Sequeiros Garcia MM, Nudler S, Bigi MM, Cohen Sabban JM, Poderoso C, Maloberti PM, Paz C},
  journal = {Biochemical and biophysical research communications},
  year = {2026},
  pmid = {41865406},
  doi = {10.1016/j.bbrc.2026.153626},
  url = {https://pubmed.ncbi.nlm.nih.gov/41865406/},
}

@article{pmid41907189,
  title = {Transcriptomic identification of CREB1 and FOXO1 activation in neuregulin-1-mediated neuroprotection after stroke.},
  author = {Bennett KR, Surles-Zeigler MC, Augello CJ, Ako E, Omotayo H, Ford GD, Rodgers VGJ, Ford BD},
  journal = {Frontiers in molecular neuroscience},
  year = {2026},
  pmid = {41907189},
  doi = {10.3389/fnmol.2026.1741120},
  url = {https://pubmed.ncbi.nlm.nih.gov/41907189/},
}

@article{pmid41920736,
  title = {PTEN loss drives B7H3 upregulation via the mTORC2/FOXO/c-Myc axis to promote tumor immune escape in ovarian cancer.},
  author = {Wang Z, Jin N, Li X, Ma X, Feng Y, Yin K, Duan S, Pan W, Jiang JK, Lei LL, Qian YY, Zheng X, Gao QL, Liu D, Xia Y},
  journal = {Cell reports},
  year = {2026},
  pmid = {41920736},
  doi = {10.1016/j.celrep.2026.117198},
  url = {https://pubmed.ncbi.nlm.nih.gov/41920736/},
}

@article{pmid41921828,
  title = {TAZ alleviates ischemic stroke injury by activating Foxo1: Usp1-mediated deubiquitination is the pivotal mechanism.},
  author = {["Xin Y", "Sun Y", "Pan E", "Li M", "Chen H", "Xu Y", "Zhang B", "Shi Y", "Dong J", "Zhao P"]},
  journal = {Free radical biology & medicine},
  year = {2026},
  pmid = {41921828},
  doi = {10.1016/j.freeradbiomed.2026.03.066},
}

@article{pmid41931532,
  title = {FOXO1 transcription factor modulates airway epithelial responses to viral infection.},
  author = {Daniel NM, Mann-Nüttel R, Shrestha Palikhe N, López-Orozco J, Hobman T et al.},
  journal = {PLoS One},
  year = {2026},
  pmid = {41931532},
  doi = {doi: 10.1371/journal.pone.0345169},
  url = {https://pubmed.ncbi.nlm.nih.gov/41931532/},
}

@article{pmid38567890,
  title = {Role of Uncertainty in Illness and Coping Strategies in Advance Directive Completion in Patients With End-stage Liver Disease.},
  author = {["Fuson O", "Mitra A", "Little C", "Hiatt S", "Franklin H", "Dieckmann N", "Hansen L"]},
  journal = {Journal of clinical gastroenterology},
  year = {2025},
  pmid = {38567890},
  doi = {10.1097/MCG.0000000000001981},
}

@article{pmid39875022,
  title = {The GLP-1 agonist semaglutide ameliorates cognitive regression in P301S tauopathy mice model via autophagy/ACE2/SIRT1/FOXO1-Mediated Microglia Polarization.},
  author = {["Elbadawy N", "Saad M", "Elfarrash S", "Ahmed M", "Abdelkader N"]},
  journal = {European journal of pharmacology},
  year = {2025},
  pmid = {39875022},
  doi = {10.1016/j.ejphar.2025.177305},
}

@article{pmid39964974,
  title = {The cholesterol 24-hydroxylase CYP46A1 promotes α-synuclein pathology in Parkinson's disease.},
  author = {Dai L, Wang J, Meng L, Zhang X, Xiao T, Deng M, Chen G, Xiong J, Ke W, Hong Z, Bu L, Zhang Z},
  journal = {PLoS biology},
  year = {2025},
  pmid = {39964974},
  doi = {10.1371/journal.pbio.3002974},
  url = {https://pubmed.ncbi.nlm.nih.gov/39964974/},
}

@article{pmid40229275,
  title = {Programmable protein stabilization with language model-derived peptide guides.},
  author = {["Hong L", "Ye T", "Wang T", "Srijay D", "Liu H", "Zhao L", "Watson R", "Vincoff S", "Chen T", "Kholina K"]},
  journal = {Nature communications},
  year = {2025},
  pmid = {40229275},
  doi = {10.1038/s41467-025-58872-6},
}

@article{pmid40861274,
  title = {The multifaceted impact of physical exercise on FoxO signaling pathways.},
  author = {Liu W, Meng P, Li Z, Shen Y, Meng X, Jin S, Hu M},
  journal = {Frontiers in cell and developmental biology},
  year = {2025},
  pmid = {40861274},
  doi = {10.3389/fcell.2025.1614732},
  url = {https://pubmed.ncbi.nlm.nih.gov/40861274/},
}

@article{pmid41255971,
  title = {Adaptive Suppression of MAPT Transcription Maintains Tau Proteostasis in Developing Human Neurons.},
  author = {["Shin M", "Firouzshahi N", "Liddiard G", "Weis M", "Simmering J", "Glykys J", "Schultz M", "Hefti M"]},
  journal = {Research square},
  year = {2025},
  pmid = {41255971},
  doi = {10.21203/rs.3.rs-7585327/v1},
}

@article{pmid37678798,
  title = {Hepatocyte FoxO1 Deficiency Protects From Liver Fibrosis via Reducing Inflammation and TGF-β1-mediated HSC Activation.},
  author = {Pan Q, Gao M, Kim D, Ai W, Yang W, Jiang W, Brashear W, Dai Y, Li S, Sun Y},
  journal = {Cell Mol Gastroenterol Hepatol},
  year = {2024},
  pmid = {37678798},
  doi = {10.1016/j.jcmgh.2023.08.013},
  url = {https://pubmed.ncbi.nlm.nih.gov/37678798},
}

@article{pmid38678901,
  title = {Degradation of levofloxacin using electro coagulation residuals-alginate beads as a novel heterogeneous electro-fenton composite.},
  author = {["Mahmoud M", "Mossad M", "Mahanna H"]},
  journal = {Journal of environmental management},
  year = {2024},
  pmid = {38678901},
  doi = {10.1016/j.jenvman.2024.120972},
}

@article{pmid39148121,
  title = {Human adipose and synovial-derived MSCs synergistically attenuate osteoarthritis by promoting chondrocyte autophagy through FoxO1 signaling.},
  author = {["Wu J", "Huang S", "Yu Y", "Lian Q", "Liu Y", "Dai W", "Liu Q", "Pan Y", "Liu G", "Li K"]},
  journal = {Stem cell research & therapy},
  year = {2024},
  pmid = {39148121},
  doi = {10.1186/s13287-024-03870-6},
}

@article{pmid39283487,
  title = {Dysregulated FOXO1 activity drives skeletal muscle intrinsic dysfunction in amyotrophic lateral sclerosis.},
  author = {Zufiría M, Pikatza-Menoio O, Garciandia-Arcelus M, Bengoetxea X, Jiménez A, Elicegui A, Levchuk M, Arnold-García O, Ondaro J, Iruzubieta P, Rodríguez-Gómez L, Fernández-Pelayo U, Muñoz-Oreja M, Aiastui A, García-Verdugo JM, Herranz-Pérez V, Zulaica M, Poza JJ, Ruiz-Onandi R, Fernández-Torrón R, Espinal JB, Bonilla M, Lersundi A, Fernández-Eulate G, Riancho J, Vallejo-Illarramendi A, Holt IJ, Sáenz A, Malfatti E, Duguez S},
  journal = {Acta neuropathologica},
  year = {2024},
  pmid = {39283487},
  doi = {10.1007/s00401-024-02794-y},
  url = {https://pubmed.ncbi.nlm.nih.gov/39283487/},
}

@article{pmid39404375,
  title = {Natural Autophagy Activators to Fight Age-Related Diseases.},
  author = {Mundo Rivera VM, Tlacuahuac Juárez JR, Murillo Melo NM, Leyva Garcia N, Magaña JJ, Cordero Martínez J, Jiménez Gutierrez GE},
  journal = {Cells},
  year = {2024},
  pmid = {39404375},
  doi = {10.3390/cells13191611},
  url = {https://pubmed.ncbi.nlm.nih.gov/39404375/},
}

@article{pmid39633372,
  title = {SGLT2 inhibitor downregulates ANGPTL4 to mitigate pathological aging of cardiomyocytes induced by type 2 diabetes.},
  author = {Wen Y, Zhang X, Liu H, Ye H, Wang R, Ma C, Duo T, Wang J, Yang X, Yu M, Wang Y, Wu L, Zhao Y, Wang L},
  journal = {Cardiovascular diabetology},
  year = {2024},
  pmid = {39633372},
  doi = {10.1186/s12933-024-02520-8},
  url = {https://pubmed.ncbi.nlm.nih.gov/39633372/},
}

@article{pmid36789123,
  title = {Simulated medical information system: education for aspiring healthcare information technologists.},
  author = {["Muto K", "Koyama S", "Tanabe S", "Sakurai H", "Kanada Y"]},
  journal = {Fujita medical journal},
  year = {2023},
  pmid = {36789123},
  doi = {10.20407/fmj.2021-022},
}

@article{pmid37384704,
  title = {Metabolic orchestration of cell death by AMPK-mediated phosphorylation of RIPK1.},
  author = {Zhang T, Xu D, Trefts E, Lv M, Inuzuka H, Song G, Liu M, Lu J, Liu J, Chu C},
  journal = {Science},
  year = {2023},
  pmid = {37384704},
  doi = {10.1126/science.abn1725},
  url = {https://pubmed.ncbi.nlm.nih.gov/37384704},
}

@article{pmid37890123,
  title = {Impact of Specialized Treatment Setting on Survival in Adolescent and Young Adult ALL.},
  author = {["Muffly L", "Parsons H", "Miller K", "Li Q", "Brunson A", "Keegan T"]},
  journal = {JCO oncology practice},
  year = {2023},
  pmid = {37890123},
  doi = {10.1200/OP.23.00373},
}

@article{pmid35176466,
  title = {Cinobufagin induces FOXO1-regulated apoptosis, proliferation, migration, and invasion by inhibiting G9a in non-small-cell lung cancer A549 cells.},
  author = {Zhang L, Liang B, Xu H, Gong Y, Hu W, Jin Z, Wu X, Chen X, Li M, Shi L},
  journal = {J Ethnopharmacol},
  year = {2022},
  pmid = {35176466},
  doi = {10.1016/j.jep.2022.115095},
  url = {https://pubmed.ncbi.nlm.nih.gov/35176466},
}

@article{pmid35236834,
  title = {ATAD3A oligomerization promotes neuropathology and cognitive deficits in Alzheimer's disease models.},
  author = {Zhao Y, Hu D, Wang R, Sun X, Ropelewski P, Hubler Z, Lundberg K, Wang Q, Adams DJ, Xu R, Qi X},
  journal = {Nature communications},
  year = {2022},
  pmid = {35236834},
  doi = {10.1038/s41467-022-28769-9},
  url = {https://pubmed.ncbi.nlm.nih.gov/35236834/},
}

@article{pmid36345678,
  title = {[To sedate or to confront? Sedation in adult dental treatment].},
  author = {["Bildt M", "de Boer H", "Vermaire J"]},
  journal = {Nederlands tijdschrift voor tandheelkunde},
  year = {2022},
  pmid = {36345678},
  doi = {10.5177/ntvt.2022.11.22044},
}

@article{pmid36395771,
  title = {PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, and RNA polymerase pause release at select gene targets.},
  author = {Zhang S, Wang J, Liu Q, McDonald WH, Bomber ML, Layden HM, Ellis J, Borinstein SC, Hiebert SW, Stengel KR},
  journal = {Molecular cell},
  year = {2022},
  pmid = {36395771},
  doi = {10.1016/j.molcel.2022.10.025},
  url = {https://pubmed.ncbi.nlm.nih.gov/36395771/},
}

@article{pmid33075563,
  title = {S100A11 Promotes Liver Steatosis via FOXO1-Mediated Autophagy and Lipogenesis.},
  author = {Zhang L, Zhang Z, Li C, Zhu T, Gao J, Zhou H, Zheng Y, Chang Q, Wang M, Wu J, Ran L, Wu Y, Miao H, Zou X, Liang B},
  journal = {Cellular and molecular gastroenterology and hepatology},
  year = {2021},
  pmid = {33075563},
  doi = {10.1016/j.jcmgh.2020.10.006},
  url = {https://pubmed.ncbi.nlm.nih.gov/33075563/},
}

@article{pmid33539225,
  title = {KLF5 Is Induced by FOXO1 and Causes Oxidative Stress and Diabetic Cardiomyopathy.},
  author = {Kyriazis ID, Hoffman M, Gaignebet L, Lucchese AM, Markopoulou E, Palioura D, Wang C, Bannister TD, Christofidou-Solomidou M, Oka SI, Sadoshima J, Koch WJ, Goldberg IJ, Yang VW, Bialkowska AB, Kararigas G, Drosatos K},
  journal = {Circulation research},
  year = {2021},
  pmid = {33539225},
  doi = {10.1161/CIRCRESAHA.120.316738},
  url = {https://pubmed.ncbi.nlm.nih.gov/33539225/},
}

@article{pmid33891234,
  title = {Assessment of non-carcinogenic health risk of heavy metal pollution: evidences from coal mining region of eastern India.},
  author = {["Chakraborty B", "Bera B", "Roy S", "Adhikary P", "Sengupta D", "Shit P"]},
  journal = {Environmental science and pollution research international},
  year = {2021},
  pmid = {33891234},
  doi = {10.1007/s11356-021-14012-3},
}

@article{pmid34678901,
  title = {"Pulsating proptosis and heavy eye syndrome precipitated by neurofibromatosis type 1: A case report".},
  author = {["Lai Y", "Lee L", "Chen Y", "Chien K"]},
  journal = {Medicine},
  year = {2021},
  pmid = {34678901},
  doi = {10.1097/MD.0000000000027575},
}

@article{pmid31567890,
  title = {Antibiotic Susceptibility and Therapy in Central Line Infections in Pediatric Home Parenteral Nutrition Patients.},
  author = {["Raphael B", "Fournier G", "McLaughlin S", "Puder M", "Jones S", "Flett K"]},
  journal = {Journal of pediatric gastroenterology and nutrition},
  year = {2020},
  pmid = {31567890},
  doi = {10.1097/MPG.0000000000002506},
}

@article{pmid30367995,
  title = {FoxO1-miRNA interacting networks as potential targets for mitochondrial diseases.},
  author = {["Puthanveetil P"]},
  journal = {Drug discovery today},
  year = {2019},
  pmid = {30367995},
  doi = {10.1016/j.drudis.2018.10.011},
}

@article{pmid31693892,
  title = {Metformin Improves Mitochondrial Respiratory Activity through Activation of AMPK.},
  author = {Wang Y, An H, Liu T, Qin C, Sesaki H, Guo S, Radovick S, Hussain M, Maheshwari A, Wondisford FE},
  journal = {Cell Rep},
  year = {2019},
  pmid = {31693892},
  doi = {10.1016/j.celrep.2019.09.070},
  url = {https://pubmed.ncbi.nlm.nih.gov/31693892},
}

@article{pmid29589535,
  title = {Signaling Pathways in Inflammation and Anti-inflammatory Therapies.},
  author = {Yeung YT, Aziz F, Guerrero-Castilla A, Arguelles S},
  journal = {Current pharmaceutical design},
  year = {2018},
  pmid = {29589535},
  doi = {10.2174/1381612824666180327165604},
  url = {https://pubmed.ncbi.nlm.nih.gov/29589535/},
}

@article{pmid30057310,
  title = {AMPK-Mediated BECN1 Phosphorylation Promotes Ferroptosis by Directly Blocking System X(c)(-) Activity.},
  author = {Song X, Zhu S, Chen P, Hou W, Wen Q, Liu J, Xie Y, Liu J, Klionsky DJ, Kroemer G},
  journal = {Curr Biol},
  year = {2018},
  pmid = {30057310},
  doi = {10.1016/j.cub.2018.05.094},
  url = {https://pubmed.ncbi.nlm.nih.gov/30057310},
}

@article{pmid30345678,
  title = {Understanding inclusion health: a student‐led curriculum innovation},
  author = {Strange Joshua; Shakoor Akmal; Collins Sarah},
  journal = {Medical Education},
  year = {2018},
  pmid = {30345678},
  doi = {10.1111/medu.13713},
  url = {https://pubmed.ncbi.nlm.nih.gov/30345678/},
}

@article{pmid28675664,
  title = {Obestatin controls the ubiquitin-proteasome and autophagy-lysosome systems in glucocorticoid-induced muscle cell atrophy.},
  author = {Cid-Díaz T, Santos-Zas I, González-Sánchez J, Gurriarán-Rodríguez U, Mosteiro CS, Casabiell X, García-Caballero T, Mouly V, Pazos Y, Camiña JP},
  journal = {J Cachexia Sarcopenia Muscle},
  year = {2017},
  pmid = {28675664},
  doi = {10.1002/jcsm.12222},
  url = {https://pubmed.ncbi.nlm.nih.gov/28675664},
}

@article{pmid21440011,
  title = {Akt, FoxO and regulation of apoptosis.},
  author = {Zhang X, Tang N, Hadden TJ, Rishi AK},
  journal = {Biochimica et biophysica acta},
  year = {2011},
  pmid = {21440011},
  doi = {10.1016/j.bbamcr.2011.03.010},
  url = {https://pubmed.ncbi.nlm.nih.gov/21440011/},
}