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1
Aggarwal N, Janjua D, Chaudhary A, Joshi U, Tripathi T, Chandra Keshavam C, Yadav J, Chhokar A, Chandra Bharti A. Insights into expression and localization of HPV16 LCR-associated transcription factors and association with LCR activity in HNSCC. MOLECULAR THERAPY. ONCOLOGY 2025;33:200926. [PMID: 39886356 PMCID: PMC11780949 DOI: 10.1016/j.omton.2024.200926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 10/29/2024] [Accepted: 12/18/2024] [Indexed: 02/01/2025]
2
Dey L, Chakraborty S. Supervised learning approaches for predicting Ebola-Human Protein-Protein interactions. Gene 2025;942:149228. [PMID: 39828063 DOI: 10.1016/j.gene.2025.149228] [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: 10/17/2024] [Revised: 12/04/2024] [Accepted: 01/07/2025] [Indexed: 01/22/2025]
3
Mattern S, Hollfoth V, Bag E, Ali A, Riemenschneider P, Jarboui MA, Boldt K, Sulyok M, Dickemann A, Luibrand J, Fusco S, Franz-Wachtel M, Singer K, Goeppert B, Schilling O, Malek N, Fend F, Macek B, Ueffing M, Singer S. An AI-assisted morphoproteomic approach is a supportive tool in esophagitis-related precision medicine. EMBO Mol Med 2025:10.1038/s44321-025-00194-7. [PMID: 39901020 DOI: 10.1038/s44321-025-00194-7] [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: 11/03/2023] [Revised: 01/14/2025] [Accepted: 01/14/2025] [Indexed: 02/05/2025]  Open
4
Saha D, Talukdar D, Mukherjee P, Mitra D, Mukherjee R, Guha S, Bhattacharjee A, Naskar R, Kumar Sahu S, Alam N, Das G, Murmu N. Green synthesis of gold nano-particles using Madhuca indica flower extract and their anticancer activity on head and neck cancer: Characterization and mechanistic study. Eur J Pharm Biopharm 2025;207:114625. [PMID: 39756711 DOI: 10.1016/j.ejpb.2025.114625] [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: 12/12/2024] [Accepted: 01/02/2025] [Indexed: 01/07/2025]
5
Sun X, Chen X, Ni Y, Li X, Song J, Wang J, Xu S, Shu W, Chen M. Latexin (LXN) enhances tumor immune surveillance in mice by inhibiting Treg cells through the macrophage exosome pathway. Int J Biol Macromol 2025;289:138822. [PMID: 39694381 DOI: 10.1016/j.ijbiomac.2024.138822] [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: 09/10/2024] [Revised: 12/12/2024] [Accepted: 12/14/2024] [Indexed: 12/20/2024]
6
Balaraman AK, Moglad E, Afzal M, Babu MA, Goyal K, Roopashree R, Kaur I, Kumar S, Kumar MR, Chauhan AS, Hemalatha S, Gupta G, Ali H. Liquid biopsies and exosomal ncRNA: Transforming pancreatic cancer diagnostics and therapeutics. Clin Chim Acta 2025;567:120105. [PMID: 39706249 DOI: 10.1016/j.cca.2024.120105] [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: 11/16/2024] [Revised: 12/17/2024] [Accepted: 12/17/2024] [Indexed: 12/23/2024]
7
S D, D S, P VK, K S. Enhancing pancreatic cancer classification through dynamic weighted ensemble: a game theory approach. Comput Methods Biomech Biomed Engin 2025;28:145-169. [PMID: 37982236 DOI: 10.1080/10255842.2023.2281277] [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: 08/10/2023] [Revised: 10/27/2023] [Accepted: 11/02/2023] [Indexed: 11/21/2023]
8
Yadav J, Tripathi T, Chaudhary A, Janjua D, Joshi U, Aggarwal N, Chhokar A, Keshavam CC, Senrung A, Bharti AC. Influence of head and neck cancer exosomes on macrophage polarization. Cytokine 2025;186:156831. [PMID: 39700664 DOI: 10.1016/j.cyto.2024.156831] [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: 09/14/2024] [Revised: 12/05/2024] [Accepted: 12/08/2024] [Indexed: 12/21/2024]
9
Sun L, Yin Z, Lu L. ISLRWR: A network diffusion algorithm for drug-target interactions prediction. PLoS One 2025;20:e0302281. [PMID: 39883675 PMCID: PMC11781719 DOI: 10.1371/journal.pone.0302281] [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: 12/15/2023] [Accepted: 04/01/2024] [Indexed: 02/01/2025]  Open
10
Zhang B, Quan L, Zhang Z, Cao L, Chen Q, Peng L, Wang J, Jiang Y, Nie L, Li G, Wu T, Lyu Q. MVCL-DTI: Predicting Drug-Target Interactions Using a Multiview Contrastive Learning Model on a Heterogeneous Graph. J Chem Inf Model 2025;65:1009-1026. [PMID: 39812134 DOI: 10.1021/acs.jcim.4c02073] [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: 01/16/2025]
11
Kiouri DP, Batsis GC, Chasapis CT. Structure-Based Approaches for Protein-Protein Interaction Prediction Using Machine Learning and Deep Learning. Biomolecules 2025;15:141. [PMID: 39858535 PMCID: PMC11763140 DOI: 10.3390/biom15010141] [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: 12/12/2024] [Revised: 01/11/2025] [Accepted: 01/14/2025] [Indexed: 01/27/2025]  Open
12
Zueva E, Burbage M. Pogo transposons provide tools to restrict cancer growth. Mol Oncol 2025. [PMID: 39814373 DOI: 10.1002/1878-0261.13801] [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: 12/11/2024] [Accepted: 12/19/2024] [Indexed: 01/18/2025]  Open
13
Yang G, Liu Y, Wen S, Chen W, Zhu X, Wang Y. DTI-MHAPR: optimized drug-target interaction prediction via PCA-enhanced features and heterogeneous graph attention networks. BMC Bioinformatics 2025;26:11. [PMID: 39800678 PMCID: PMC11726937 DOI: 10.1186/s12859-024-06021-z] [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: 08/01/2024] [Accepted: 12/20/2024] [Indexed: 01/16/2025]  Open
14
Rawal O, Turhan B, Peradejordi IF, Chandrasekar S, Kalayci S, Gnjatic S, Johnson J, Bouhaddou M, Gümüş ZH. PhosNetVis: A web-based tool for fast kinase-substrate enrichment analysis and interactive 2D/3D network visualizations of phosphoproteomics data. PATTERNS (NEW YORK, N.Y.) 2025;6:101148. [PMID: 39896259 PMCID: PMC11783894 DOI: 10.1016/j.patter.2024.101148] [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: 06/20/2024] [Revised: 11/12/2024] [Accepted: 12/11/2024] [Indexed: 02/04/2025]
15
Chen X, Zeng Q, Yin L, Yan B, Wu C, Feng J, Wu Y, He J, Ding W, Zhong J, Shen Y, Zu X. Enhancing immunotherapy efficacy in colorectal cancer: targeting the FGR-AKT-SP1-DKK1 axis with DCC-2036 (Rebastinib). Cell Death Dis 2025;16:8. [PMID: 39788945 PMCID: PMC11718245 DOI: 10.1038/s41419-024-07263-8] [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: 07/09/2024] [Revised: 11/17/2024] [Accepted: 11/26/2024] [Indexed: 01/12/2025]
16
Farahani RM. Neural differentiation in perspective: mitochondria as early programmers. Front Neurosci 2025;18:1529855. [PMID: 39844856 PMCID: PMC11751005 DOI: 10.3389/fnins.2024.1529855] [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: 11/17/2024] [Accepted: 12/23/2024] [Indexed: 01/24/2025]  Open
17
Xu Y, Zhang Y, Song K, Liu J, Zhao R, Zhang X, Pei L, Li M, Chen Z, Zhang C, Wang P, Li F. ScDrugAct: a comprehensive database to dissect tumor microenvironment cell heterogeneity contributing to drug action and resistance across human cancers. Nucleic Acids Res 2025;53:D1536-D1546. [PMID: 39526387 PMCID: PMC11701732 DOI: 10.1093/nar/gkae994] [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: 08/13/2024] [Revised: 09/27/2024] [Accepted: 10/15/2024] [Indexed: 11/16/2024]  Open
18
Zou H, Li S, Guo J, Wen L, Lv C, Leng F, Chen Z, Zeng M, Xu J, Li Y, Li X. Pan-cancer analysis reveals age-associated genetic alterations in protein domains. Am J Hum Genet 2025;112:44-58. [PMID: 39708814 PMCID: PMC11739924 DOI: 10.1016/j.ajhg.2024.11.011] [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: 07/02/2024] [Revised: 11/26/2024] [Accepted: 11/26/2024] [Indexed: 12/23/2024]  Open
19
Xie Y, Wang X, Wang P, Bi X. A pseudo-label supervised graph fusion attention network for drug–target interaction prediction. EXPERT SYSTEMS WITH APPLICATIONS 2025;259:125264. [DOI: 10.1016/j.eswa.2024.125264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2025]
20
Wright SN, Colton S, Schaffer LV, Pillich RT, Churas C, Pratt D, Ideker T. State of the interactomes: an evaluation of molecular networks for generating biological insights. Mol Syst Biol 2025;21:1-29. [PMID: 39653848 PMCID: PMC11697402 DOI: 10.1038/s44320-024-00077-y] [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: 09/18/2024] [Revised: 11/07/2024]