• Reference Citation Analysis
  • v
  • v
  • Find an Article
Find an Article PDF (5081128)   Today's Articles (1155)
For: Liu Q, Hu Z, Jiang R, Zhou M. DeepCDR: a hybrid graph convolutional network for predicting cancer drug response. Bioinformatics 2021;36:i911-i918. [PMID: 33381841 DOI: 10.1093/bioinformatics/btaa822] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]  Open
Number Cited by Other Article(s)
1
Dai W, Chen G, Peng W, Chen C, Fu X, Liu L, Liu L, Yu N. Domain alignment method based on masked variational autoencoder for predicting patient anticancer drug response. Methods 2025;238:61-73. [PMID: 40090506 DOI: 10.1016/j.ymeth.2025.03.012] [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: 08/19/2024] [Revised: 02/03/2025] [Accepted: 03/14/2025] [Indexed: 03/18/2025]  Open
2
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]
3
He Y, Li S, Lan H, Long W, Zhai S, Li M, Wen Z. A Transfer Learning Framework for Predicting and Interpreting Drug Responses via Single-Cell RNA-Seq Data. Int J Mol Sci 2025;26:4365. [PMID: 40362602 PMCID: PMC12072357 DOI: 10.3390/ijms26094365] [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: 04/14/2025] [Revised: 04/29/2025] [Accepted: 05/02/2025] [Indexed: 05/15/2025]  Open
4
Shi H, Xu T, Li X, Gao Q, Xiong Z, Xia J, Yue Z. DRExplainer: Quantifiable interpretability in drug response prediction with directed graph convolutional network. Artif Intell Med 2025;163:103101. [PMID: 40056540 DOI: 10.1016/j.artmed.2025.103101] [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: 07/14/2024] [Revised: 01/08/2025] [Accepted: 02/23/2025] [Indexed: 03/10/2025]
5
Salimi A, Lee JY. Hybrid intelligence for environmental pollution: biodegradability assessment of organic compounds through multimodal integration of graph attention networks and QSAR models. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2025;27:981-991. [PMID: 40052292 DOI: 10.1039/d4em00594e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2025]
6
Codicè F, Pancotti C, Rollo C, Moreau Y, Fariselli P, Raimondi D. The specification game: rethinking the evaluation of drug response prediction for precision oncology. J Cheminform 2025;17:33. [PMID: 40087708 PMCID: PMC11907791 DOI: 10.1186/s13321-025-00972-y] [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: 10/28/2024] [Accepted: 02/13/2025] [Indexed: 03/17/2025]  Open
7
Narykov O, Zhu Y, Brettin T, Evrard YA, Partin A, Xia F, Shukla M, Vasanthakumari P, Doroshow JH, Stevens RL. Data imbalance in drug response prediction: multi-objective optimization approach in deep learning setting. Brief Bioinform 2025;26:bbaf134. [PMID: 40178282 PMCID: PMC11966611 DOI: 10.1093/bib/bbaf134] [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: 09/19/2024] [Revised: 02/07/2025] [Accepted: 02/18/2025] [Indexed: 04/05/2025]  Open
8
Yin J, Zhang H, Sun X, You N, Mou M, Lu M, Pan Z, Li F, Li H, Zeng S, Zhu F. Decoding Drug Response With Structurized Gridding Map-Based Cell Representation. IEEE J Biomed Health Inform 2025;29:1702-1713. [PMID: 38090819 DOI: 10.1109/jbhi.2023.3342280] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2025]
9
Peng W, Chen C, Dai W, Yu N, Wang J. Predicting Clinical Anticancer Drug Response of Patients by Using Domain Alignment and Prototypical Learning. IEEE J Biomed Health Inform 2025;29:1534-1545. [PMID: 39292588 DOI: 10.1109/jbhi.2024.3462811] [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: 09/20/2024]
10
Prasanna S, Kumar A, Rao D, Simoes EJ, Rao P. A scalable tool for analyzing genomic variants of humans using knowledge graphs and graph machine learning. Front Big Data 2025;7:1466391. [PMID: 39906190 PMCID: PMC11790625 DOI: 10.3389/fdata.2024.1466391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Accepted: 12/12/2024] [Indexed: 02/06/2025]  Open
11
Wang C, Kumar GA, Rajapakse JC. Drug discovery and mechanism prediction with explainable graph neural networks. Sci Rep 2025;15:179. [PMID: 39747341 PMCID: PMC11696803 DOI: 10.1038/s41598-024-83090-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Accepted: 12/11/2024] [Indexed: 01/04/2025]  Open
12
Xiao M, Zheng Q, Popa P, Mi X, Hu J, Zou F, Zou B. Drug molecular representations for drug response predictions: a comprehensive investigation via machine learning methods. Sci Rep 2025;15:20. [PMID: 39748003 PMCID: PMC11696021 DOI: 10.1038/s41598-024-84711-7] [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: 08/23/2024] [Accepted: 12/26/2024] [Indexed: 01/04/2025]  Open
13
Gu Y, Zheng S, Zhang B, Kang H, Jiang R, Li J. Deep multiple instance learning on heterogeneous graph for drug-disease association prediction. Comput Biol Med 2025;184:109403. [PMID: 39577348 DOI: 10.1016/j.compbiomed.2024.109403] [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: 01/09/2024] [Revised: 11/05/2024] [Accepted: 11/08/2024] [Indexed: 11/24/2024]
14
Dong Y, Zhang Y, Qian Y, Zhao Y, Yang Z, Feng X. ASGCL: Adaptive Sparse Mapping-based graph contrastive learning network for cancer drug response prediction. PLoS Comput Biol 2025;21:e1012748. [PMID: 39883719 PMCID: PMC11781687 DOI: 10.1371/journal.pcbi.1012748] [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: 03/21/2024] [Accepted: 12/23/2024] [Indexed: 02/01/2025]  Open
15
Sederman C, Yang CH, Cortes-Sanchez E, Di Sera T, Huang X, Scherer SD, Zhao L, Chu Z, White ER, Atkinson A, Wagstaff J, Varley KE, Lewis MT, Qiao Y, Welm BE, Welm AL, Marth GT. A precision oncology-focused deep learning framework for personalized selection of cancer therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.12.628190. [PMID: 39763776 PMCID: PMC11702554 DOI: 10.1101/2024.12.12.628190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2025]
16
Jiang Z, Li P. DeepDR: a deep learning library for drug response prediction. Bioinformatics 2024;40:btae688. [PMID: 39558584 PMCID: PMC11629690 DOI: 10.1093/bioinformatics/btae688] [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: 09/09/2024] [Revised: 10/29/2024] [Accepted: 11/13/2024] [Indexed: 11/20/2024]  Open
17
Yang K, Cheng J, Cao S, Pan X, Shen HB, Yuan Y. Predicting transcriptional changes induced by molecules with MiTCP. Brief Bioinform 2024;26:bbaf006. [PMID: 39847444 PMCID: PMC11756340 DOI: 10.1093/bib/bbaf006] [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: 08/26/2024] [Revised: 12/05/2024] [Accepted: 01/21/2025] [Indexed: 01/24/2025]  Open
18
Karampuri A, Jakkula BK, Perugu S. ResisenseNet hybrid neural network model for predicting drug sensitivity and repurposing in breast Cancer. Sci Rep 2024;14:23949. [PMID: 39397003 PMCID: PMC11471817 DOI: 10.1038/s41598-024-71076-0] [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: 06/04/2024] [Accepted: 08/23/2024] [Indexed: 10/15/2024]  Open
19
Xia X, Zhu C, Zhong F, Liu L. TransCDR: a deep learning model for enhancing the generalizability of drug activity prediction through transfer learning and multimodal data fusion. BMC Biol 2024;22:227. [PMID: 39385185 PMCID: PMC11462810 DOI: 10.1186/s12915-024-02023-8] [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: 02/20/2024] [Accepted: 09/30/2024] [Indexed: 10/11/2024]  Open
20
Hu X, Zhang P, Zhang J, Deng L. DeepFusionCDR: Employing Multi-Omics Integration and Molecule-Specific Transformers for Enhanced Prediction of Cancer Drug Responses. IEEE J Biomed Health Inform 2024;28:6248-6258. [PMID: 38935469 DOI: 10.1109/jbhi.2024.3417014] [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: 06/29/2024]
21
Saranya KR, Vimina ER. DRN-CDR: A cancer drug response prediction model using multi-omics and drug features. Comput Biol Chem 2024;112:108175. [PMID: 39191166 DOI: 10.1016/j.compbiolchem.2024.108175] [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: 02/20/2024] [Revised: 08/09/2024] [Accepted: 08/14/2024] [Indexed: 08/29/2024]
22
Gu Y, Xu Z, Yang C. Empowering Graph Neural Network-Based Computational Drug Repositioning with Large Language Model-Inferred Knowledge Representation. Interdiscip Sci 2024:10.1007/s12539-024-00654-7. [PMID: 39325266 DOI: 10.1007/s12539-024-00654-7] [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: 05/30/2024] [Revised: 08/15/2024] [Accepted: 08/19/2024] [Indexed: 09/27/2024]
23
Gutierrez JJG, Lau E, Dharmapalan S, Parker M, Chen Y, Álvarez MA, Wang D. Multi-output prediction of dose-response curves enables drug repositioning and biomarker discovery. NPJ Precis Oncol 2024;8:209. [PMID: 39304771 DOI: 10.1038/s41698-024-00691-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 08/28/2024] [Indexed: 09/22/2024]  Open
24
Connell W, Garcia K, Goodarzi H, Keiser MJ. Learning chemical sensitivity reveals mechanisms of cellular response. Commun Biol 2024;7:1149. [PMID: 39278951 PMCID: PMC11402971 DOI: 10.1038/s42003-024-06865-4] [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: 12/11/2023] [Accepted: 09/06/2024] [Indexed: 09/18/2024]  Open
25
Xu M, Zhu Z, Zhao Y, He K, Huang Q, Zhao Y. RedCDR: Dual Relation Distillation for Cancer Drug Response Prediction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024;21:1468-1479. [PMID: 38776197 DOI: 10.1109/tcbb.2024.3404262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2024]
26
Huang Z, Fan Z, Shen S, Wu M, Deng L. MolMVC: Enhancing molecular representations for drug-related tasks through multi-view contrastive learning. Bioinformatics 2024;40:ii190-ii197. [PMID: 39230706 PMCID: PMC11373324 DOI: 10.1093/bioinformatics/btae386] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]  Open
27
Hao M, Gong J, Zeng X, Liu C, Guo Y, Cheng X, Wang T, Ma J, Zhang X, Song L. Large-scale foundation model on single-cell transcriptomics. Nat Methods 2024;21:1481-1491. [PMID: 38844628 DOI: 10.1038/s41592-024-02305-7] [Citation(s) in RCA: 66] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 05/10/2024] [Indexed: 08/10/2024]
28
Mohammadzadeh-Vardin T, Ghareyazi A, Gharizadeh A, Abbasi K, Rabiee HR. DeepDRA: Drug repurposing using multi-omics data integration with autoencoders. PLoS One 2024;19:e0307649. [PMID: 39058696 PMCID: PMC11280260 DOI: 10.1371/journal.pone.0307649] [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: 05/13/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024]  Open
29
Lenhof K, Eckhart L, Rolli LM, Lenhof HP. Trust me if you can: a survey on reliability and interpretability of machine learning approaches for drug sensitivity prediction in cancer. Brief Bioinform 2024;25:bbae379. [PMID: 39101498 PMCID: PMC11299037 DOI: 10.1093/bib/bbae379] [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: 03/07/2024] [Revised: 07/08/2024] [Accepted: 07/19/2024] [Indexed: 08/06/2024]  Open
30
Shukla N, Shamim U, Agarwal P, Pandey R, Narayan J. From bench to bedside: potential of translational research in COVID-19 and beyond. Brief Funct Genomics 2024;23:349-362. [PMID: 37986554 DOI: 10.1093/bfgp/elad051] [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: 09/07/2023] [Revised: 10/25/2023] [Accepted: 11/02/2023] [Indexed: 11/22/2023]  Open
31
Wall P, Ideker T. Representing mutations for predicting cancer drug response. Bioinformatics 2024;40:i160-i168. [PMID: 38940147 PMCID: PMC11256944 DOI: 10.1093/bioinformatics/btae209] [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] [Indexed: 06/29/2024]  Open
32
Abinas V, Abhinav U, Haneem EM, Vishnusankar A, Nazeer KAA. Integration of autoencoder and graph convolutional network for predicting breast cancer drug response. J Bioinform Comput Biol 2024;22:2450013. [PMID: 39051144 DOI: 10.1142/s0219720024500136] [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]
33
Campana PA, Prasse P, Lienhard M, Thedinga K, Herwig R, Scheffer T. Cancer drug sensitivity estimation using modular deep Graph Neural Networks. NAR Genom Bioinform 2024;6:lqae043. [PMID: 38680251 PMCID: PMC11055499 DOI: 10.1093/nargab/lqae043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 03/01/2024] [Accepted: 04/17/2024] [Indexed: 05/01/2024]  Open
34
Dey V, Ning X. Improving Anticancer Drug Selection and Prioritization via Neural Learning to Rank. J Chem Inf Model 2024;64:4071-4088. [PMID: 38740382 PMCID: PMC11134508 DOI: 10.1021/acs.jcim.3c01060] [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: 07/12/2023] [Revised: 03/27/2024] [Accepted: 04/16/2024] [Indexed: 05/16/2024]
35
Kim Y, Han Y, Hopper C, Lee J, Joo JI, Gong JR, Lee CK, Jang SH, Kang J, Kim T, Cho KH. A gray box framework that optimizes a white box logical model using a black box optimizer for simulating cellular responses to perturbations. CELL REPORTS METHODS 2024;4:100773. [PMID: 38744288 PMCID: PMC11133856 DOI: 10.1016/j.crmeth.2024.100773] [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: 05/13/2023] [Revised: 03/19/2024] [Accepted: 04/19/2024] [Indexed: 05/16/2024]
36
Lawrence PJ, Burns B, Ning X. Enhancing drug and cell line representations via contrastive learning for improved anti-cancer drug prioritization. NPJ Precis Oncol 2024;8:106. [PMID: 38762647 PMCID: PMC11102516 DOI: 10.1038/s41698-024-00589-8] [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: 10/30/2023] [Accepted: 03/22/2024] [Indexed: 05/20/2024]  Open
37
Yao R, Shen Z, Xu X, Ling G, Xiang R, Song T, Zhai F, Zhai Y. Knowledge mapping of graph neural networks for drug discovery: a bibliometric and visualized analysis. Front Pharmacol 2024;15:1393415. [PMID: 38799167 PMCID: PMC11116974 DOI: 10.3389/fphar.2024.1393415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 04/12/2024] [Indexed: 05/29/2024]  Open
38
Ovchinnikova K, Born J, Chouvardas P, Rapsomaniki M, Kruithof-de Julio M. Overcoming limitations in current measures of drug response may enable AI-driven precision oncology. NPJ Precis Oncol 2024;8:95. [PMID: 38658785 PMCID: PMC11043358 DOI: 10.1038/s41698-024-00583-0] [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: 08/16/2023] [Accepted: 03/22/2024] [Indexed: 04/26/2024]  Open
39
Hsu YC, Chiu YC, Lu TP, Hsiao TH, Chen Y. Predicting drug response through tumor deconvolution by cancer cell lines. PATTERNS (NEW YORK, N.Y.) 2024;5:100949. [PMID: 38645769 PMCID: PMC11026976 DOI: 10.1016/j.patter.2024.100949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 02/07/2024] [Accepted: 02/12/2024] [Indexed: 04/23/2024]
40
Abbasi M, Carvalho FG, Ribeiro B, Arrais JP. Predicting drug activity against cancer through genomic profiles and SMILES. Artif Intell Med 2024;150:102820. [PMID: 38553160 DOI: 10.1016/j.artmed.2024.102820] [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: 12/05/2022] [Revised: 01/09/2024] [Accepted: 02/21/2024] [Indexed: 04/02/2024]
41
Chen Y, Zhang L. Hi-GeoMVP: a hierarchical geometry-enhanced deep learning model for drug response prediction. Bioinformatics 2024;40:btae204. [PMID: 38614131 PMCID: PMC11060866 DOI: 10.1093/bioinformatics/btae204] [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: 08/03/2023] [Revised: 02/11/2024] [Accepted: 04/11/2024] [Indexed: 04/15/2024]  Open
42
Wang H, Lin K, Zhang Q, Shi J, Song X, Wu J, Zhao C, He K. HyperTMO: a trusted multi-omics integration framework based on hypergraph convolutional network for patient classification. Bioinformatics 2024;40:btae159. [PMID: 38530977 PMCID: PMC11212491 DOI: 10.1093/bioinformatics/btae159] [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: 04/06/2023] [Revised: 02/02/2024] [Accepted: 03/24/2024] [Indexed: 03/28/2024]  Open
43
Nguyen T, Campbell A, Kumar A, Amponsah E, Fiterau M, Shahriyari L. Optimal fusion of genotype and drug embeddings in predicting cancer drug response. Brief Bioinform 2024;25:bbae227. [PMID: 38754407 PMCID: PMC11097979 DOI: 10.1093/bib/bbae227] [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: 10/29/2023] [Revised: 04/14/2024] [Accepted: 04/25/2024] [Indexed: 05/18/2024]  Open
44
Hajim WI, Zainudin S, Mohd Daud K, Alheeti K. Optimized models and deep learning methods for drug response prediction in cancer treatments: a review. PeerJ Comput Sci 2024;10:e1903. [PMID: 38660174 PMCID: PMC11042005 DOI: 10.7717/peerj-cs.1903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 01/31/2024] [Indexed: 04/26/2024]
45
Lao C, Zheng P, Chen H, Liu Q, An F, Li Z. DeepAEG: a model for predicting cancer drug response based on data enhancement and edge-collaborative update strategies. BMC Bioinformatics 2024;25:105. [PMID: 38461284 PMCID: PMC10925015 DOI: 10.1186/s12859-024-05723-8] [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: 12/25/2023] [Accepted: 02/27/2024] [Indexed: 03/11/2024]  Open
46
Zhao X, Singhal A, Park S, Kong J, Bachelder R, Ideker T. Cancer Mutations Converge on a Collection of Protein Assemblies to Predict Resistance to Replication Stress. Cancer Discov 2024;14:508-523. [PMID: 38236062 PMCID: PMC10905674 DOI: 10.1158/2159-8290.cd-23-0641] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 10/25/2023] [Accepted: 12/21/2023] [Indexed: 01/19/2024]
47
Lin CX, Guan Y, Li HD. Artificial intelligence approaches for molecular representation in drug response prediction. Curr Opin Struct Biol 2024;84:102747. [PMID: 38091924 DOI: 10.1016/j.sbi.2023.102747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/26/2023] [Accepted: 11/26/2023] [Indexed: 02/09/2024]
48
Liu H, Peng W, Dai W, Lin J, Fu X, Liu L, Liu L, Yu N. Improving anti-cancer drug response prediction using multi-task learning on graph convolutional networks. Methods 2024;222:41-50. [PMID: 38157919 DOI: 10.1016/j.ymeth.2023.11.018] [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: 07/21/2023] [Revised: 09/19/2023] [Accepted: 11/19/2023] [Indexed: 01/03/2024]  Open
49
Vasanthakumari P, Zhu Y, Brettin T, Partin A, Shukla M, Xia F, Narykov O, Weil MR, Stevens RL. A Comprehensive Investigation of Active Learning Strategies for Conducting Anti-Cancer Drug Screening. Cancers (Basel) 2024;16:530. [PMID: 38339281 PMCID: PMC10854925 DOI: 10.3390/cancers16030530] [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: 11/28/2023] [Revised: 01/12/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024]  Open
50
Kim J, Park SH, Lee H. PANCDR: precise medicine prediction using an adversarial network for cancer drug response. Brief Bioinform 2024;25:bbae088. [PMID: 38487849 PMCID: PMC10940842 DOI: 10.1093/bib/bbae088] [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: 07/17/2023] [Revised: 01/09/2024] [Accepted: 02/16/2024] [Indexed: 03/18/2024]  Open
PrevPage 1 of 3 123Next
© 2004-2025 Baishideng Publishing Group Inc. All rights reserved. 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA