α-Lipoic acid mitigates age-related macular degeneration via ferroptosis: integrative multi-omics and network pharmacology by Yaqiong Zhang, Yaqiong Zhang, Yuanyuan Chen, Chenglin Sun, Fang Li, Yin Shen, Yin Shen

“…Molecular docking and molecular dynamics simulations were performed to assess the binding affinity and stability between ALA and its predicted targets. …”
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Exploring the efficacy of Benincasa hispida extract on obesity linked inflammatory bowel disease by integrating computational analysis and experimental validations by Santosh B. Patil, Manisha B. Kuvalekar, Deepak A. Yaraguppi, D. S. N. B. K. Prasanth, Sangameshwar G. Halkavatagi, Gururaj B. Tennalli, Mukhatar Ahmed Javali, T. M. Yunus Khan

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Integrated Transcriptomic and Targeted Metabolomic Analyses Elucidate the Molecular Mechanism Underlying Dihydromyricetin Synthesis in <i>Nekemias grossedentata</i> by Fuwen Wu, Zhi Feng, Zhi Yao, Peiling Zhang, Yiqiang Wang, Meng Li

“…The strong specific binding of NgF3′5′H3 to dihydromyricetin precursor metabolites catalyzed their conversion into DHM, resulting in higher DHM contents in bud tips than in other tissues or plants. …”
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Integrative analysis based on ATAC-seq and RNA-seq reveals a novel oncogene PRPF3 in hepatocellular carcinoma by Yi Bai, Xiyue Deng, Dapeng Chen, Shuangqing Han, Zijie Lin, Zhongmin Li, Wen Tong, Jinming Li, Tianze Wang, Xiangyu Liu, Zirong Liu, Zilin Cui, Yamin Zhang

“…Conversely, downregulated DARs were associated with the TGF-β, cAMP, and p53 signaling pathways and the CTCF family. Integration of the datasets revealed a positive correlation between specific DARs and DEGs. …”
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Integrative Multi‐Omics Approaches Reveal Selectivity Profiles and Molecular Mechanisms of FIIN‐2, a Covalent FGFR Inhibitor by Ying Fu, Dandan Zhu, Xiaojuan Chen, Lingzhi Qu, Ming Guo, Shuhong Zhang, Guangyu Xu, Zhuchu Chen, Maoyu Li, Yongheng Chen

“…Notably, adenosine monophosphate‐activated protein kinase α1 (AMPKα1) is identified as a novel target of FIIN‐2, with Cys185 identified as its covalent binding site. These findings reveal that FIIN‐2 can induce autophagy by directly binding to and activating AMPKα1, influencing its anti‐tumor activity in HCC cells. …”
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Integrative pan-cancer analysis reveals a common architecture of dysregulated transcriptional networks characterized by loss of enhancer methylation. by Jørgen Ankill, Zhi Zhao, Xavier Tekpli, Elin H Kure, Vessela N Kristensen, Anthony Mathelier, Thomas Fleischer

“…Taken together, our integrative pan-cancer analysis reveals a common architecture where hallmark cancer-driving functions are affected by the loss of enhancer methylation and may be epigenetically regulated.…”
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Development of an Integrated Computational Pipeline for PARP‐1 Inhibitor Screening Using Hybrid Virtual Screening and Molecular Dynamics Simulations by Guan Wang, Jingjing Guo, Feng Xu, Mingjuan Ji

“…In this study, we developed a virtual screening workflow that synergistically integrates the capabilities of TransFoxMol, KarmaDock, and AutoDock Vina. …”
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Multifunctional molecular hybrid for targeted colorectal cancer cells: Integrating doxorubicin, AS1411 aptamer, and T9/U4 ASO. by Kanpitcha Jiramitmongkon, Pichayanoot Rotkrua, Paisan Khanchaitit, Jiraporn Arunpanichlert, Boonchoy Soontornworajit

“…To improve efficacy, a multifunctional drug delivery platform has been developed, integrating bioactive materials, anticancer agents, and targeted recognition ligands into a single molecule. …”
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Integrating network pharmacology and in vivo model to reveal the cardiovascular protective effects of kaempferol-3-O-rutinoside on heart failure by Guo Lu-Qin, Zhou Lan, Li Sheng-Nan, Bai Juan, Shi Ling-Li, Hua Fang, Zhou Peng

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Chromatin retained MUSHER lncRNA integrates ABA and DOG1 signalling pathways to enhance Arabidopsis seeds dormancy by Sebastian Przemyslaw Sacharowski, Michal Krzyszton, Lien Brzezniak, Karol Jerzy Rogowski, Miguel Montez, Katarzyna Rosol, Magdalena Wrona, Ruslan Yatusevich, Veena Halale Manjunath, Lukasz Szewc, Artur Jarmolowski, Szymon Swiezewski

“…Abstract Many plant lncRNAs regulate gene expression by binding to chromatin, but how they are retained at the target loci is unclear. …”
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Serum S100A12 in the clinical diagnosis of sepsis-induced myocardial dysfunction: an integrated bioinformatics and clinical data analysis by Fang Wu, Helin Hong, Ye Tian, Xiaoyan Wang

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Machine learning-based integration identifies plasma cells-related gene signature ST6GAL1 in idiopathic pulmonary fibrosis by Fanjie Lin, Ken Lin, Donglei Li, Weiguo Kong, Jiayu Zhuang, Wei He, Xinguang Wei, Tianchi Xiao, Hao Zu, Zili Zhang, Wenju Lu

“…In addition, a machine learning-based integrative procedure for constructing a concordance plasma cells-related gene signature (PCRGS) was developed. …”
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The Cell Envelope Integrity Protein Homologue D0Y85_RS06240 of Stenotrophomonas Confers Multiantibiotic Resistance by Chuanqing Zhong, Xiaoqiang Deng, Aihua Jiang, Yayu Liu, Yuanyuan Liu, Jiafang Fu, Guangxiang Cao

“…The potential role of cell envelope integrity proteins in mediating antibiotic resistance is not well understood. …”
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Integrating network pharmacology and experimental validation to reveal the anti-growth mechanism of panaxadiol against glioblastoma via calcium signaling by Guobin Qiu, Zhiyong Wu, Dunhui Yang, Luqiu Zhou

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Integrated multiple machine learning and Mendelian randomization reveal LTF gene as a prognostic biomarker for nonspecific orbital inflammation by Zixuan Wu, Jinfeng Xu, Yuan Gao, Kang Tan, Xiaolei Yao, Qinghua Peng

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Integrated pharmacoanalysis, bioinformatics analysis, and experimental validation to identify the ingredients and mechanisms of Xiao-Luo-Wan in uterine fibroids treatment by Yonghui Yu, Haojun Zhang, Fang Yang, Hong Liu

“…The predicted targets were further identified by RT–PCR and western blotting.Results There were 16 chemical components identified in XLW drug-containing serum, with 53 target genes predicated in the treatment of UFs. The molecular binding of core targets, including TRIM9, NF-κB and p38MAPK, was relatively stable to components, especially buergerinin B, cedrol and ent-15B-16-epoxy- kauan-17-ol. …”
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Integrative bioinformatics frameworks for abdominal aortic aneurysm using GWAS meta-analysis, biological network construction, and structural modeling by Pakorn Sagulkoo, Hathaichanok Chuntakaruk, Apichat Suratanee, Kitiporn Plaimas, Nuttinee Teerakulkittipong

“…Drug repurposing and molecular docking suggested abciximab and paclitaxel as potential therapeutic agents targeting CD40, while ivermectin emerged as a strong candidate for LRP1 binding. In conclusion, our integrative bioinformatics frameworks links genomics and transcriptomics with network biology and structural modeling, providing valuable insights into the molecular mechanisms of AAA and potential therapeutic strategies.…”
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Unraveling Cordia myxa’s anti-malarial potential: integrative insights from network pharmacology, molecular modeling, and machine learning by Yufei Miao, Wenkang Liu, Sarah Mohammed Saeed Alsallameh, Norah A. Albekairi, Ziyad Tariq Muhseen, Christopher J. Butch

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Molecular Dynamics Simulation and Pharmacoinformatic Integrated Analysis of Bioactive Phytochemicals from Azadirachta indica (Neem) to Treat Diabetes Mellitus by Asif Abdullah, Partha Biswas, Md. Sahabuddin, Afiya Mubasharah, Dhrubo Ahmed Khan, Akram Hossain, Tanima Roy, Nishat Md. R. Rafi, Dipta Dey, Md. Nazmul Hasan, Shabana Bibi, Mahmoud Moustafa, Ali Shati, Hesham Hassan, Ruchika Garg

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Multi-Target Anti-Aging Mechanisms of Multani Mitti (Fuller’s Earth): Integrating Enzyme Inhibition and Molecular Docking for Cosmeceuticals by Muhammad Javid Iqbal, Pía Loren, Viviana Burgos, Luis A. Salazar

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