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For: Cheng F, Kovács IA, Barabási AL. Network-based prediction of drug combinations. Nat Commun 2019;10:1197. [PMID: 30867426 PMCID: PMC6416394 DOI: 10.1038/s41467-019-09186-x] [Citation(s) in RCA: 412] [Impact Index Per Article: 68.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 02/20/2019] [Indexed: 12/12/2022]  Open
Number Cited by Other Article(s)
1
Anderson A, Kinahan MW, Gonzalez AH, Udekwu K, Hernandez-Vargas EA. Invariant set theory for predicting potential failure of antibiotic cycling. Infect Dis Model 2025;10:897-908. [PMID: 40297503 PMCID: PMC12036053 DOI: 10.1016/j.idm.2025.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2024] [Revised: 01/22/2025] [Accepted: 04/01/2025] [Indexed: 04/30/2025]  Open
2
Lyu Z, Yang J, Xu Z, Wang W, Cheng W, Tsui KL, Zhang Q. Predicting the risk of ischemic stroke in patients with atrial fibrillation using heterogeneous drug-protein-disease network-based deep learning. APL Bioeng 2025;9:026104. [PMID: 40191603 PMCID: PMC11970939 DOI: 10.1063/5.0242570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2024] [Accepted: 02/11/2025] [Indexed: 04/09/2025]  Open
3
Wu J, Lai J, Zhao X, Wang Z, Zhang Y, Wang L, Su Y, He Y, Li S, Jiang Y, Han J. DeepCCDS: Interpretable Deep Learning Framework for Predicting Cancer Cell Drug Sensitivity through Characterizing Cancer Driver Signals. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025:e2416958. [PMID: 40397390 DOI: 10.1002/advs.202416958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2024] [Revised: 04/18/2025] [Indexed: 05/22/2025]
4
Park H, Miyano S. Network-based multi-class classifier to identify optimized gene networks for acute leukemia cell line classification. PLoS One 2025;20:e0321549. [PMID: 40338916 PMCID: PMC12061184 DOI: 10.1371/journal.pone.0321549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2024] [Accepted: 03/07/2025] [Indexed: 05/10/2025]  Open
5
Wu J, Guo D. Understanding dosage effects of traditional Chinese medicine using network analysis. Front Pharmacol 2025;16:1534129. [PMID: 40406490 PMCID: PMC12095143 DOI: 10.3389/fphar.2025.1534129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2024] [Accepted: 04/25/2025] [Indexed: 05/26/2025]  Open
6
Karasu N, Kuzucu M, Mat OC, Gul M, Yay A, Dundar M. Protective effect of deinoxanthin in sorafenib-induced nephrotoxicity in rats with the hepatocellular carcinoma model. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2025;398:5969-5988. [PMID: 39625488 DOI: 10.1007/s00210-024-03633-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2024] [Accepted: 11/13/2024] [Indexed: 04/11/2025]
7
Wang M, Chen X, Liu M, Luo H, Zhang S, Guo J, Wang J, Zhou L, Zhang N, Li H, Wang C, Li L, Wang Z, Wang H, Guo Z, Li Y, Wang Y. Decoding herbal combination models through systematic strategies: insights from target information and traditional Chinese medicine clinical theory. Brief Bioinform 2025;26:bbaf229. [PMID: 40407387 PMCID: PMC12100621 DOI: 10.1093/bib/bbaf229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2025] [Revised: 04/12/2025] [Accepted: 04/28/2025] [Indexed: 05/26/2025]  Open
8
Ren Z, Zeng X, Lao Y, You Z, Shang Y, Zou Q, Lin C. Predicting rare drug-drug interaction events with dual-granular structure-adaptive and pair variational representation. Nat Commun 2025;16:3997. [PMID: 40301328 PMCID: PMC12041321 DOI: 10.1038/s41467-025-59431-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Accepted: 04/16/2025] [Indexed: 05/01/2025]  Open
9
Pourmousa M, Jain S, Barnaeva E, Jin W, Hochuli J, Itkin Z, Maxfield T, Melo-Filho C, Thieme A, Wilson K, Klumpp-Thomas C, Michael S, Southall N, Jaakkola T, Muratov EN, Barzilay R, Tropsha A, Ferrer M, Zakharov AV. AI-driven discovery of synergistic drug combinations against pancreatic cancer. Nat Commun 2025;16:4020. [PMID: 40301300 PMCID: PMC12041571 DOI: 10.1038/s41467-025-56818-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 01/31/2025] [Indexed: 05/01/2025]  Open
10
Lucchini S, Nicholson JG, Zhang X, Househam J, Lim YM, Mossner M, Millner TO, Brandner S, Graham T, Marino S. A novel model of glioblastoma recurrence to identify therapeutic vulnerabilities. EMBO Mol Med 2025:10.1038/s44321-025-00237-z. [PMID: 40295888 DOI: 10.1038/s44321-025-00237-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 03/21/2025] [Accepted: 03/25/2025] [Indexed: 04/30/2025]  Open
11
Hui W, Lei KM, Liu Y, Huang X, Zhong Y, Chen X, Wei M, Yan J, Shen R, Mak PI, Martins RP, Yi S, Wang P, Jia Y. Identification and Drug Screening of Single Cells from Human Tumors on Semiconductor Chip for Cancer Precision Medicine. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025:e2503131. [PMID: 40271835 DOI: 10.1002/advs.202503131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2025] [Revised: 04/02/2025] [Indexed: 04/25/2025]
12
Nussinov R, Yavuz BR, Jang H. Tumors and their microenvironments: Learning from pediatric brain pathologies. Biochim Biophys Acta Rev Cancer 2025;1880:189328. [PMID: 40254040 DOI: 10.1016/j.bbcan.2025.189328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2024] [Revised: 04/15/2025] [Accepted: 04/16/2025] [Indexed: 04/22/2025]
13
Lim HI, Kim GY, Choi YJ, Lee K, Ko SG. Uncovering the anti-cancer mechanism of cucurbitacin D against colorectal cancer through network pharmacology and molecular docking. Discov Oncol 2025;16:551. [PMID: 40244518 PMCID: PMC12006582 DOI: 10.1007/s12672-025-02056-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2024] [Accepted: 11/01/2024] [Indexed: 04/18/2025]  Open
14
Zhang S, Wang X, Li F, Peng S. CPDP: Contrastive Protein-Drug Pre-Training for Novel Drug Discovery. Int J Mol Sci 2025;26:3761. [PMID: 40332398 PMCID: PMC12028240 DOI: 10.3390/ijms26083761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2025] [Revised: 04/01/2025] [Accepted: 04/10/2025] [Indexed: 05/08/2025]  Open
15
Yue C, Chen B, Pan F, Wang Z, Yu H, Liu G, Li W, Wang R, Tang Y. TCnet: A Novel Strategy to Predict Target Combination of Alzheimer's Disease via Network-Based Methods. J Chem Inf Model 2025;65:3866-3878. [PMID: 40172120 DOI: 10.1021/acs.jcim.5c00172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2025]
16
Wang J, Niu Q, Yu Y, Liu J, Zhang S, Zong W, Tian S, Wang Z, Li B. Modular-Based Synergetic Mechanisms of Jasminoidin and Ursodeoxycholic Acid in Cerebral Ischemia Therapy. Biomedicines 2025;13:938. [PMID: 40299522 PMCID: PMC12025273 DOI: 10.3390/biomedicines13040938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2025] [Revised: 04/03/2025] [Accepted: 04/07/2025] [Indexed: 04/30/2025]  Open
17
Tan D, Chen Y, Ilboudo Y, Liang KYH, Butler-Laporte G, Richards JB. Caution when using network partners for target identification in drug discovery. HGG ADVANCES 2025;6:100409. [PMID: 39861949 PMCID: PMC11850190 DOI: 10.1016/j.xhgg.2025.100409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Revised: 01/21/2025] [Accepted: 01/21/2025] [Indexed: 01/27/2025]  Open
18
Ren Y, Pieper AA, Cheng F. Utilization of precision medicine digital twins for drug discovery in Alzheimer's disease. Neurotherapeutics 2025;22:e00553. [PMID: 39965994 PMCID: PMC12047495 DOI: 10.1016/j.neurot.2025.e00553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2024] [Revised: 01/11/2025] [Accepted: 02/06/2025] [Indexed: 02/20/2025]  Open
19
Liu L, Ma J, Chen W, Zhang J, Zuo W, Wang M, Li J. UVB-induced HaCat cell damage and Myricaria Paniculata's molecular effects. Sci Rep 2025;15:10909. [PMID: 40157969 PMCID: PMC11954898 DOI: 10.1038/s41598-025-93633-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2024] [Accepted: 03/07/2025] [Indexed: 04/01/2025]  Open
20
Yuan Y, Yu L, Bi C, Huang L, Su B, Nie J, Dou Z, Yang S, Li Y. A new paradigm for drug discovery in the treatment of complex diseases: drug discovery and optimization. Chin Med 2025;20:40. [PMID: 40122800 PMCID: PMC11931805 DOI: 10.1186/s13020-025-01075-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2024] [Accepted: 02/10/2025] [Indexed: 03/25/2025]  Open
21
Tanoli Z, Fernández-Torras A, Özcan UO, Kushnir A, Nader KM, Gadiya Y, Fiorenza L, Ianevski A, Vähä-Koskela M, Miihkinen M, Seemab U, Leinonen H, Seashore-Ludlow B, Tampere M, Kalman A, Ballante F, Benfenati E, Saunders G, Potdar S, Gómez García I, García-Serna R, Talarico C, Beccari AR, Schaal W, Polo A, Costantini S, Cabri E, Jacobs M, Saarela J, Budillon A, Spjuth O, Östling P, Xhaard H, Quintana J, Mestres J, Gribbon P, Ussi AE, Lo DC, de Kort M, Wennerberg K, Fratelli M, Carreras-Puigvert J, Aittokallio T. Computational drug repurposing: approaches, evaluation of in silico resources and case studies. Nat Rev Drug Discov 2025:10.1038/s41573-025-01164-x. [PMID: 40102635 DOI: 10.1038/s41573-025-01164-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2025] [Indexed: 03/20/2025]
22
Adebayo G, Ayanda OI, Rottmann M, Ajibaye OS, Oduselu G, Mulindwa J, Ajani OO, Aina O, Mäser P, Adebiyi E. The Importance of Murine Models in Determining In Vivo Pharmacokinetics, Safety, and Efficacy in Antimalarial Drug Discovery. Pharmaceuticals (Basel) 2025;18:424. [PMID: 40143200 PMCID: PMC11944934 DOI: 10.3390/ph18030424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2025] [Revised: 03/10/2025] [Accepted: 03/13/2025] [Indexed: 03/28/2025]  Open
23
Choopanian P, Andressoo JO, Mirzaie M. A fast approach for structural and evolutionary analysis based on energetic profile protein comparison. Nat Commun 2025;16:2231. [PMID: 40044697 PMCID: PMC11882786 DOI: 10.1038/s41467-025-57374-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 02/14/2025] [Indexed: 03/09/2025]  Open
24
Li Y, Shen Y, Cai Y, Zhang Y, Gao J, Huang L, Si W, Zhou K, Gao S, Luo Q. Integrating transcriptomic data with a novel drug efficacy prediction model for TCM active compound discovery. Sci Rep 2025;15:7688. [PMID: 40044718 PMCID: PMC11882833 DOI: 10.1038/s41598-024-82498-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Accepted: 12/03/2024] [Indexed: 03/09/2025]  Open
25
Zhang F, Zhao X, Wei J, Wu L. PathSynergy: a deep learning model for predicting drug synergy in liver cancer. Brief Bioinform 2025;26:bbaf192. [PMID: 40273429 PMCID: PMC12021016 DOI: 10.1093/bib/bbaf192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2024] [Revised: 03/13/2025] [Accepted: 04/01/2025] [Indexed: 04/26/2025]  Open
26
Chowdhury S, Rajaganapathy S, Sun L, Wang L, Yang P, Cerhan JR, Zong N. SensitiveCancerGPT: Leveraging Generative Large Language Model on Structured Omics Data to Optimize Drug Sensitivity Prediction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.27.640661. [PMID: 40060567 PMCID: PMC11888479 DOI: 10.1101/2025.02.27.640661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/15/2025]
27
Wang B, Zhang T, Liu Q, Sutcharitchan C, Zhou Z, Zhang D, Li S. Elucidating the role of artificial intelligence in drug development from the perspective of drug-target interactions. J Pharm Anal 2025;15:101144. [PMID: 40099205 PMCID: PMC11910364 DOI: 10.1016/j.jpha.2024.101144] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 10/29/2024] [Accepted: 11/08/2024] [Indexed: 03/19/2025]  Open
28
Iijima H, Ambrosio F. Network Medicine as a Tool to Enhance Regenerative Rehabilitation Practice. Am J Phys Med Rehabil 2025;104:271-279. [PMID: 39948738 DOI: 10.1097/phm.0000000000002665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2025]
29
Wang X, Zhu H, Liu Q, Liu Q. Fusing Micro- and Macro-Scale Information to Predict Anticancer Synergistic Drug Combinations. IEEE J Biomed Health Inform 2025;29:2297-2309. [PMID: 40030241 DOI: 10.1109/jbhi.2024.3500789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2025]
30
Yang J, Wang M, Dönitz J, Chapuy B, Beißbarth T. Advancing personalized cancer therapy: Onko_DrugCombScreen-a novel Shiny app for precision drug combination screening. NAR Genom Bioinform 2025;7:lqaf004. [PMID: 39897104 PMCID: PMC11783568 DOI: 10.1093/nargab/lqaf004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 12/24/2024] [Accepted: 01/13/2025] [Indexed: 02/04/2025]  Open
31
Puniani S, Gupta P, Singh N, Nagpal D, Sheikh AM. Targeting disease: Computational approaches for drug target identification. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2025;103:163-184. [PMID: 40175040 DOI: 10.1016/bs.apha.2025.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2025]
32
Li S, Zhang L, Zhang W, Chen H, Hong M, Xia J, Zhang W, Luan X, Zheng G, Lu D. Identifying traditional Chinese medicine combinations for breast cancer treatment based on transcriptional regulation and chemical structure. Chin Med 2025;20:23. [PMID: 39953557 PMCID: PMC11829537 DOI: 10.1186/s13020-025-01074-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2024] [Accepted: 01/24/2025] [Indexed: 02/17/2025]  Open
33
Pržulj N, Malod-Dognin N. Simplicity within biological complexity. BIOINFORMATICS ADVANCES 2025;5:vbae164. [PMID: 39927291 PMCID: PMC11805345 DOI: 10.1093/bioadv/vbae164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 10/01/2024] [Accepted: 10/23/2024] [Indexed: 02/11/2025]
34
Wang Y, Liao B, Shan X, Ye H, Wen Y, Guo H, Xiao F, Zhu H. Revealing rutaecarpine's promise: A pathway to parkinson's disease relief through PPAR modulation. Int Immunopharmacol 2025;147:114076. [PMID: 39809102 DOI: 10.1016/j.intimp.2025.114076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2024] [Revised: 01/04/2025] [Accepted: 01/08/2025] [Indexed: 01/16/2025]
35
Dong X, Liu H, Tong T, Wu L, Wang J, You T, Wei Y, Yi X, Yang H, Hu J, Wang H, Wang X, Li MJ. Personalized prediction of anticancer potential of non-oncology drugs through learning from genome derived molecular pathways. NPJ Precis Oncol 2025;9:36. [PMID: 39905223 PMCID: PMC11794852 DOI: 10.1038/s41698-025-00813-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/19/2025] [Indexed: 02/06/2025]  Open
36
Wang G, Feng H, Cao C. BiRNN-DDI: A Drug-Drug Interaction Event Type Prediction Model Based on Bidirectional Recurrent Neural Network and Graph2Seq Representation. J Comput Biol 2025;32:198-211. [PMID: 39049806 DOI: 10.1089/cmb.2024.0476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]  Open
37
J SG, P D, P E. Enhancing drug discovery in schizophrenia: a deep learning approach for accurate drug-target interaction prediction - DrugSchizoNet. Comput Methods Biomech Biomed Engin 2025;28:170-187. [PMID: 38375638 DOI: 10.1080/10255842.2023.2282951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/05/2023] [Accepted: 10/17/2023] [Indexed: 02/21/2024]
38
Soni Sharmila K, Revathi S T, Sree PK. DDINet: Drug-drug interaction prediction network based on multi-molecular fingerprint features and multi-head attention centered weighted autoencoder. J Bioinform Comput Biol 2025;23:2550003. [PMID: 40169368 DOI: 10.1142/s0219720025500039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2025]
39
Zong W, Tian S, Niu Q, Li X, Wang P, Tong L, Zhang S, Zheng D, Zhang Y, Xiong W, Cai Q, Zeng Z, Wang J, Xu H, Zhang H, Li B. Comparable clinical advantages identification of three formulae on rheumatic disease using a modular-based network proximity approach. JOURNAL OF ETHNOPHARMACOLOGY 2025;337:118764. [PMID: 39218127 DOI: 10.1016/j.jep.2024.118764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 08/09/2024] [Accepted: 08/28/2024] [Indexed: 09/04/2024]
40
Zhang W, Deng S, Zhang XE, Huang C, Liu Q, Jiang G. Network-Based Identification of Key Toxic Compounds in Airborne Chemical Exposome. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2025;59:1712-1723. [PMID: 39808486 DOI: 10.1021/acs.est.4c09711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2025]
41
Poustforoosh A. Optimizing kinase and PARP inhibitor combinations through machine learning and in silico approaches for targeted brain cancer therapy. Mol Divers 2025:10.1007/s11030-025-11114-9. [PMID: 39841319 DOI: 10.1007/s11030-025-11114-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2024] [Accepted: 01/08/2025] [Indexed: 01/23/2025]
42
Halu A, Chelvanambi S, Decano JL, Matamalas JT, Whelan M, Asano T, Kalicharran N, Singh SA, Loscalzo J, Aikawa M. Integrating pharmacogenomics and cheminformatics with diverse disease phenotypes for cell type-guided drug discovery. Genome Med 2025;17:7. [PMID: 39833831 PMCID: PMC11744892 DOI: 10.1186/s13073-025-01431-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 01/08/2025] [Indexed: 01/22/2025]  Open
43
Li F, Mou M, Li X, Xu W, Yin J, Zhang Y, Zhu F. DrugMAP 2.0: molecular atlas and pharma-information of all drugs. Nucleic Acids Res 2025;53:D1372-D1382. [PMID: 39271119 PMCID: PMC11701670 DOI: 10.1093/nar/gkae791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2024] [Revised: 08/23/2024] [Accepted: 08/31/2024] [Indexed: 09/15/2024]  Open
44
Cao Y, Wang Y, Li Y, Liu S, Wang L, Zhou L, Zhu T. Angelic acid triggers ferroptosis in colorectal cancer cells via targeting and impairing NRF2 protein stability. J Nat Med 2025;79:82-94. [PMID: 39433724 DOI: 10.1007/s11418-024-01849-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2024] [Accepted: 09/26/2024] [Indexed: 10/23/2024]
45
Shi Y, Guan S, Liu X, Zhai H, Zhang Y, Liu J, Yang W, Wang Z. Genetic Commonalities Between Metabolic Syndrome and Rheumatic Diseases Through Disease Interactome Modules. J Cell Mol Med 2025;29:e70329. [PMID: 39789419 PMCID: PMC11717667 DOI: 10.1111/jcmm.70329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 11/21/2024] [Accepted: 12/18/2024] [Indexed: 01/12/2025]  Open
46
Tong Y, Li X, Wan J, Zhou Q, Jiang C, Li N, Jin Z, Gu J, Li F, Li J. Integrating Ultra-High-Performance Liquid Chromatography and Orbitrap High-Resolution Mass Spectrometry, Feature-Based Molecular Networking, and Network Medicine to Unlock Harvesting Strategies for Endangered Sinocalycanthus Chinensis. J Sep Sci 2025;48:e70072. [PMID: 39760617 DOI: 10.1002/jssc.70072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2024] [Revised: 12/23/2024] [Accepted: 12/25/2024] [Indexed: 01/07/2025]
47
Zhang L, Sheng Y, Yang J, Hu Z, Peng B. Predicting the toxic side effects of drug interactions using chemical structures and protein sequences. Sci Rep 2024;14:31503. [PMID: 39733005 PMCID: PMC11682051 DOI: 10.1038/s41598-024-82981-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2024] [Accepted: 12/10/2024] [Indexed: 12/30/2024]  Open
48
Xu Q, Liu X, Jiang X, Kim Y. Simulate Scientific Reasoning with Multiple Large Language Models: An Application to Alzheimer's Disease Combinatorial Therapy. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.12.10.24318800. [PMID: 39711724 PMCID: PMC11661384 DOI: 10.1101/2024.12.10.24318800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/24/2024]
49
Rajan S, Schwarz E. Network-based artificial intelligence approaches for advancing personalized psychiatry. Am J Med Genet B Neuropsychiatr Genet 2024;195:e32997. [PMID: 39031613 DOI: 10.1002/ajmg.b.32997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 05/24/2024] [Accepted: 06/06/2024] [Indexed: 07/22/2024]
50
Javanmard Z, Pourhajibagher M, Bahador A. Advancing Anti-Biofilm Strategies: Innovations to Combat Biofilm-Related Challenges and Enhance Efficacy. J Basic Microbiol 2024;64:e2400271. [PMID: 39392011 DOI: 10.1002/jobm.202400271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 08/20/2024] [Accepted: 09/11/2024] [Indexed: 10/12/2024]
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