Borhani N, Izadi I, Motahharynia A, Sheikholeslami M, Gheisari Y*. DrugTar Improves Druggability Prediction by Integrating Large Language Models and Gene Ontologies, bioRxiv. 2024
Sheikholeslami M, Mazrouei N, Gheisari Y, Fasihi A, Irajpour M, Motahharynia A*. DrugGen: Advancing Drug Discovery with Large Language Models and Reinforcement Learning Feedback. bioRxiv. 2024
Roointan A, Ghaeidamini M, Yavari P, Naimi A, Gheisari Y, Gholaminejad A*. Transcriptome meta-analysis and validation to discovery of hub genes and pathways in focal and segmental glomerulosclerosis. BMC Nephrol. 2024
Eshraghi Y, Abedi M, Gheisari Y*. Proteomics to metabolomics: A new insight into the pathogenesis of hypertensive nephropathy. Kidney Blood Press Res. 2023
Roointan A, Shafieizadegan S, Ghaeidamini M, Gheisari Y, Hudkins KL, Gholaminejad A. The Potential of Cardiac Biomarkers, NT-ProBNP and Troponin T, in Predicting the Progression of Nephropathy in Diabetic Patients: A Meta-Analysis of Prospective Cohort Studies. Diabetes Res Clin Pract. 2023
Moein S, Ahmadbeigi N, Adibi R, Kamali S, Moradzadeh K, Nematollahi P, Nardi NB, Gheisari Y*. Regenerative potential of multinucleated cells: bone marrow adiponectin-positive multinucleated cells take the lead. Stem Cell Res Ther. 2023
Kiyanpour F, Abedi M, Gheisari Y*. miR‑802‑5p is a key regulator in diabetic kidney disease. J Res Med Sci 2023
Borzou P, Ghaisari J*, Izadi I, Eshraghi Y, Gheisari Y*. A novel strategy for dynamic modeling of genome-scale interaction networks. Bioinformatics. 20231
Adibi R, Moein S, Gheisari Y*. Zoledronic acid targets chemo-resistant polyploid giant cancer cells. Sci Rep. 2023
Adibi R, Moein S, Gheisari Y*. Cisplatin-Resistant Ovarian Cancer Cells Reveal a Polyploid Phenotype with Remarkable Activation of Nuclear Processes. Adv Biomed Res. 2023
Roointan A, Gholaminejad A, Shojaie B, Hudkins KL, Gheisari Y. Candidate MicroRNA Biomarkers in Lupus Nephritis: A Meta-analysis of Profiling Studies in Kidney, Blood, and Urine Samples. Mol Diagn Ther. 2022
Gholaminejad A, Moein S, Roointan A, Mortazavi M, Nouri R, Mansourian M, Gheisari Y*. Circulating β2 and α1 microglobulins predict progression of nephropathy in diabetic patients: a meta‐analysis of prospective cohort studies. Acta Diabetol. 2022
Masoudi-Sobhanzadeh Y, Gholaminejad A, Gheisari Y, Roointan A*. Discovering driver nodes in chronic kidney disease-related networks using Trader as a newly developed algorithm. Comput Biol Med. 2022
Hojjati F, Roointan A*, Gholaminejad A, Eshraghi Y, Gheisari Y. Identification of key genes and biological regulatory mechanisms in diabetic nephropathy: Meta-analysis of gene expression datasets. Nefrologia. 2022
Motahharynia A, Moein S*, Kiyanpour F, Moradzadeh K, Yaqubi M, Gheisari Y. Olfactory receptors contribute to progression of kidney fibrosis. NPJ Syst Biol Appl. 2022
Borhani N, Ghaisari J*, Abedi M, Kamali M, Gheisari Y*. A deep learning approach to predict inter-omics interactions in multi-layer networks. BMC Bioinformatics. 2022
Abedi M, Marateb HR, Mohebian MR, Aghaee-Bakhtiari SH, Nassiri SM, Gheisari Y*. Systems biology and machine learning approaches identify drug targets in diabetic nephropathy. Sci Rep. 2021
Gholaminejad A, Gheisari Y, Jalali S, Roointan A*. Comprehensive analysis of IgA nephropathy expression profiles: identification of potential biomarkers and therapeutic agents. BMC Nephrol. 2021
Gholaminejad A, Roointan A, Gheisari Y*. Transmembrane signaling molecules play a key role in the pathogenesis of IgA nephropathy: a weighted gene co-expression network analysis study. BMC Immunol. 2021
Samadi M, Gheisari Y*. A nurturing environment for teaching molecular biology to medical students. J Educ Health Promot. 2021
Roointan A, Gheisari Y, Hudkins KL, Gholaminejad A*. Non-invasive metabolic biomarkers for early diagnosis of diabetic nephropathy: Meta-analysis of profiling metabolomics studies. Nutr Metab Cardiovasc Dis. 2021
Moein S, Nickaeen N, Roointan A, Borhani N, Heidary Z, Javanmard SH, Ghaisari J*, Gheisari Y*. Inefficiency of SIR models in forecasting COVID-19 epidemic: a case study of Isfahan. Sci Rep. 2021
Moein S, Adibi R, da Silva Meirelles L, Nardi NB, Gheisari Y*. Cancer regeneration: Polyploid cells are the key drivers of tumor progression. Biochim Biophys Acta Rev Cancer. 2020
Moein S, Moradzadeh K, Javanmard SH, Nasiri SM, Gheisari Y*. In vitro versus in vivo models of kidney fibrosis: Time‑course experimental design is crucial to avoid misinterpretations of gene expression data. J Res Med Sci 2020
Moradzadeh K, Nassiri SM, Gheisari Y*. Valproic acid restores the down-regulation of SDF-1 following kidney ischemia; experimental validation of a mathematical prediction. Res Pharm Sci. 2020
Samadi M, Tabibian F, Moradzadeh K, Nassiri SM, Gheisari Y*. Evaluating the effect of remote ischemic preconditioning on kidney ischemia–reperfusion injury. Journal of Research in Medical Sciences 2020
Kiyanpour F, Abedi M, Gheisari Y*. A systematic integrative approach reveals novel microRNAs in diabetic nephropathy. Journal of Research in Medical Sciences 2020
Nickaeen N, Ghaisari J*, Moein S, Gheisari Y*. Bifurcation Analysis of a modular model of Embryonic Kidney Development. Biosystems. 2020
Nickaeen N, Ghaisari J*, Heiner M, Moein S, Gheisari Y*. Agent-based modeling and bifurcation analysis reveal mechanisms of macrophage polarization and phenotype pattern distribution. Sci Rep. 2019
Abedi M, Fatehi R, Moradzadeh K, Gheisari Y*. Big Data to Knowledge: Common Pitfalls in Transcriptomics Data Analysis and Representation. RNA Biol. 2019
Moradzadeh K, Gheisari Y*. The analysis of a time-course transcriptome profile by systems biology approaches reveals key molecular processes in acute kidney injury. J Res Med Sci 2019
Moradzadeh K, Moein S, Nickaeen N, Gheisari Y*. Analysis of time-course microarray data: Comparison of common tools. Genomics. 2019
Rabieian R, Moein S, Khanahmad H, Mortazavi M, Gheisari Y*. Transcriptional noise in intact and TGF-beta treated human kidney cells; the importance of time-series designs. Cell Biol Int. 2018
Aghayan HR, Arjmand B, Ahmadbeigi N, Gheisari Y, Vasei M*. Draft of Iranian National Guideline for Cell Therapy Manufacturing. Arch Iran Med. 2017
Fatehi R, Khosravi S, Abedi M, Salehi R, Gheisari Y*. Heterozygosity analysis of polycystic kidney disease 1 gene microsatellite markers for linkage analysis of autosomal dominant polycystic kidney disease type 1 in the Iranian population. J Res Med Sci 2017
Rabieian R, Abedi M, Gheisari Y*. Central nodes in protein interaction networks drive critical functions in transforming growth factor beta-1 stimulated kidney cells. Cell J. 2017
Moein S, Javanmard SH, Abedi M, Izadpanahi MH, Gheisari Y*. Identification of appropriate housekeeping genes for gene expression analysis in long-term hypoxia-treated kidney cells. Adv Biomed Res. 2017
Gheisari Y, Ahmadbeigi N. Mesenchymal Stem Cells and Endothelial Cells: A Common Ancestor? Arch Iran Med. 2016
Gheisari Y, Vasei M, Shafiee A, Soleimani M, Seyedjafari E, Omidkhoda A, Langroudi L, Ahmadbeigi N*. A Three-Dimensional Scaffold-Based System for Modeling the Bone Marrow Tissue. Stem Cells Dev. 2016
Heidary Z, Ghaisari J, Moein S, Naderi M, Gheisari Y*. Stochastic Petri Net Modeling of Hypoxia Pathway Predicts a Novel Incoherent Feed-Forward Loop Controlling SDF-1 Expression in Acute Kidney Injury. IEEE Trans Nanobioscience. 2016
Abedi M, Gheisari Y*. Nodes with high centrality in protein interaction networks are responsible for driving signaling pathways in diabetic nephropathy. PeerJ. 2015
