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For: Bouhaddou M, Memon D, Meyer B, White KM, Rezelj VV, Correa Marrero M, Polacco BJ, Melnyk JE, Ulferts S, Kaake RM, Batra J, Richards AL, Stevenson E, Gordon DE, Rojc A, Obernier K, Fabius JM, Soucheray M, Miorin L, Moreno E, Koh C, Tran QD, Hardy A, Robinot R, Vallet T, Nilsson-Payant BE, Hernandez-Armenta C, Dunham A, Weigang S, Knerr J, Modak M, Quintero D, Zhou Y, Dugourd A, Valdeolivas A, Patil T, Li Q, Hüttenhain R, Cakir M, Muralidharan M, Kim M, Jang G, Tutuncuoglu B, Hiatt J, Guo JZ, Xu J, Bouhaddou S, Mathy CJP, Gaulton A, Manners EJ, Félix E, Shi Y, Goff M, Lim JK, McBride T, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, De Wit E, Leach AR, Kortemme T, Shoichet B, Ott M, Saez-Rodriguez J, tenOever BR, Mullins RD, Fischer ER, Kochs G, Grosse R, García-Sastre A, Vignuzzi M, Johnson JR, Shokat KM, Swaney DL, Beltrao P, Krogan NJ. The Global Phosphorylation Landscape of SARS-CoV-2 Infection. Cell 2020;182:685-712.e19. [PMID: 32645325 PMCID: PMC7321036 DOI: 10.1016/j.cell.2020.06.034] [Citation(s) in RCA: 774] [Impact Index Per Article: 154.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/09/2020] [Accepted: 06/23/2020] [Indexed: 02/07/2023]
Number Cited by Other Article(s)
1
Jia X, Chen J, Li C, Li J, Su M, Yang K, Zhang Y, Li Z. Glycogen synthase kinase 3 promotes the proliferation of porcine epidemic diarrhoea virus by phosphorylating the nucleocapsid protein. Virulence 2025;16:2506504. [PMID: 40391683 PMCID: PMC12101597 DOI: 10.1080/21505594.2025.2506504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2025] [Revised: 04/10/2025] [Accepted: 04/27/2025] [Indexed: 05/22/2025]  Open
2
Perfilova KV, Matyuta IO, Minyaev ME, Boyko KM, Cooley RB, Sluchanko NN. High-resolution structure reveals enhanced 14-3-3 binding by a mutant SARS-CoV-2 nucleoprotein variant with improved replicative fitness. Biochem Biophys Res Commun 2025;767:151915. [PMID: 40318379 DOI: 10.1016/j.bbrc.2025.151915] [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: 04/21/2025] [Accepted: 04/27/2025] [Indexed: 05/07/2025]
3
Aw DZH, Zhang DX, Vignuzzi M. Strategies and efforts in circumventing the emergence of antiviral resistance against conventional antivirals. NPJ ANTIMICROBIALS AND RESISTANCE 2025;3:54. [PMID: 40490516 DOI: 10.1038/s44259-025-00125-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2024] [Accepted: 05/21/2025] [Indexed: 06/11/2025]
4
Peng W, Wei X, Wu Y, Shi C, Liu X, Wu J, Yang H, Rong N, Zhao B, Zhang G, Zhang W, Liu J, Liu J, Yang J. Dynamic Molecular Changes in Brain, Lung, and Heart of Hamsters Infected With SARS-CoV-2: Insights From a Severe and Recovery Phase Model. J Med Virol 2025;97:e70410. [PMID: 40432336 DOI: 10.1002/jmv.70410] [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: 01/07/2025] [Revised: 04/13/2025] [Accepted: 05/08/2025] [Indexed: 05/29/2025]
5
Eltayeb A, Adilović M, Golzardi M, Hromić-Jahjefendić A, Rubio-Casillas A, Uversky VN, Redwan EM. Intrinsic factors behind long COVID: exploring the role of nucleocapsid protein in thrombosis. PeerJ 2025;13:e19429. [PMID: 40416618 PMCID: PMC12101441 DOI: 10.7717/peerj.19429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2024] [Accepted: 04/15/2025] [Indexed: 05/27/2025]  Open
6
Xu C, Yu F, Xue M, Huang Z, Jiang N, Li Y, Meng Y, Liu W, Zheng Y, Fan Y, Zhou Y. Proteogenomic analysis of Cyprinid herpesvirus 2 using high-resolution mass spectrometry. J Virol 2025;99:e0196024. [PMID: 40172206 PMCID: PMC12090726 DOI: 10.1128/jvi.01960-24] [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: 11/06/2024] [Accepted: 02/10/2025] [Indexed: 04/04/2025]  Open
7
Pipart J, Holstein T, Martens L, Muth T. MultiStageSearch: An Iterative Workflow for Unbiased Taxonomic Analysis of Pathogens Using Proteogenomics. J Proteome Res 2025. [PMID: 40384001 DOI: 10.1021/acs.jproteome.4c00901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2025]
8
Walter Z, Li M, Molho M, Berish L, Isopi A, O'Mara M, Dittmar M, Nwaezeapu C, Richards A, McCullagh M, Krogan NJ, Cherry S, Johnson JR, Ramage H. An integrated proteomics approach identifies phosphorylation sites on viral and host proteins that regulate West Nile virus infection. Cell Rep 2025;44:115728. [PMID: 40381193 DOI: 10.1016/j.celrep.2025.115728] [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: 05/02/2024] [Revised: 03/22/2025] [Accepted: 04/30/2025] [Indexed: 05/20/2025]  Open
9
Loonen S, van Steenis L, Bauer M, Šoštarić N. Phosphorylation Changes SARS-CoV-2 Nucleocapsid Protein's Structural Dynamics and Its Interaction With RNA. Proteins 2025. [PMID: 40375582 DOI: 10.1002/prot.26842] [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: 11/05/2024] [Revised: 05/01/2025] [Accepted: 05/07/2025] [Indexed: 05/18/2025]
10
Krüger N, Laufer SA, Pillaiyar T. An overview of progress in human metapneumovirus (hMPV) research: Structure, function, and therapeutic opportunities. Drug Discov Today 2025;30:104364. [PMID: 40286981 DOI: 10.1016/j.drudis.2025.104364] [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: 02/27/2025] [Revised: 04/09/2025] [Accepted: 04/22/2025] [Indexed: 04/29/2025]
11
Li Y, Wang B, Zheng Y, Kang H, He A, Zhao L, Guo N, Liu H, Mardinoglu A, Mamun M, Gao Y, Chen X. The multifaceted role of post-translational modifications of LSD1 in cellular processes and disease pathogenesis. Genes Dis 2025;12:101307. [PMID: 40028036 PMCID: PMC11870172 DOI: 10.1016/j.gendis.2024.101307] [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: 10/02/2023] [Revised: 01/31/2024] [Accepted: 03/13/2024] [Indexed: 03/05/2025]  Open
12
Wang Z, Cao G, Collier MP, Qiu X, Broadway-Stringer S, Šaman D, Ng JZY, Sen N, Azad AJ, Hooper C, Zimmermann J, McDonough MA, Brem J, Rabe P, Song H, Alderson TR, Schofield CJ, Bolla JR, Djinovic-Carugo K, Fürst DO, Warscheid B, Degiacomi MT, Allison TM, Hochberg GKA, Robinson CV, Gehmlich K, Benesch JLP. Filamin C dimerisation is regulated by HSPB7. Nat Commun 2025;16:4090. [PMID: 40312381 PMCID: PMC12046049 DOI: 10.1038/s41467-025-58889-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: 01/11/2024] [Accepted: 04/02/2025] [Indexed: 05/03/2025]  Open
13
Keskitalo S, Seppänen MRJ, Del Sol A, Varjosalo M. From rare to more common: The emerging role of omics in improving understanding and treatment of severe inflammatory and hyperinflammatory conditions. J Allergy Clin Immunol 2025;155:1435-1450. [PMID: 39978687 DOI: 10.1016/j.jaci.2025.02.011] [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: 10/07/2024] [Revised: 01/31/2025] [Accepted: 02/11/2025] [Indexed: 02/22/2025]
14
Petrillo M, Querci M, Brogna C, Ponti J, Cristoni S, Markov PV, Valsesia A, Leoni G, Benedetti A, Wiss T, Van den Eede G. Evidence of SARS-CoV-2 bacteriophage potential in human gut microbiota. F1000Res 2025;11:292. [PMID: 40444030 PMCID: PMC12120431 DOI: 10.12688/f1000research.109236.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/17/2025] [Indexed: 06/02/2025]  Open
15
Petrillo M, Querci M, Brogna C, Ponti J, Cristoni S, Markov PV, Valsesia A, Leoni G, Benedetti A, Wiss T, Van den Eede G. Evidence of SARS-CoV-2 bacteriophage potential in human gut microbiota. F1000Res 2025;11:292. [PMID: 40444030 PMCID: PMC12120431 DOI: 10.12688/f1000research.109236.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/17/2025] [Indexed: 06/11/2025]  Open
16
Janevska M, Naessens E, Verhasselt B. Impact of SARS-CoV-2 Wuhan and Omicron Variant Proteins on Type I Interferon Response. Viruses 2025;17:569. [PMID: 40285011 PMCID: PMC12031613 DOI: 10.3390/v17040569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2025] [Revised: 04/08/2025] [Accepted: 04/09/2025] [Indexed: 04/29/2025]  Open
17
Zhao C, Hao M, Bian T, Zhao X, Chi X, Chen Z, Fu G, Zhu Z, Fang T, Yu C, Li J, Chen W. Screening of Neutralizing Antibodies Targeting Gc Protein of RVFV. Viruses 2025;17:559. [PMID: 40285002 PMCID: PMC12031069 DOI: 10.3390/v17040559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2025] [Revised: 04/06/2025] [Accepted: 04/07/2025] [Indexed: 04/29/2025]  Open
18
Hagbi-Levi S, Abraham M, Gamaev L, Mishaelian I, Hay O, Zorde-Khevalevsky E, Wald O, Wald H, Olam D, Weiss L, Peled A. Identification of Dinaciclib and Ganetespib as anti-inflammatory drugs using a novel HTP screening assay that targets IFNγ-dependent PD-L1. Front Immunol 2025;16:1502094. [PMID: 40264756 PMCID: PMC12011776 DOI: 10.3389/fimmu.2025.1502094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2024] [Accepted: 03/19/2025] [Indexed: 04/24/2025]  Open
19
Chen H, Charles PD, Gu Q, Liberatori S, Robertson DL, Palmarini M, Wilson SJ, Mohammed S, Castello A. Omics Analyses Uncover Host Networks Defining Virus-Permissive and -Hostile Cellular States. Mol Cell Proteomics 2025;24:100966. [PMID: 40204275 DOI: 10.1016/j.mcpro.2025.100966] [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: 11/15/2024] [Revised: 03/24/2025] [Accepted: 04/04/2025] [Indexed: 04/11/2025]  Open
20
Liu J, Guo L, Zhong J, Wu Y, Wang X, Tang X, Min K, Yang Y, Peng W, Wang Q, Ding T, Gu X, Zhang H, Liu Y, Huang C, Cao B, Wang J, Ren L, Yang J. Proteomic Analysis of 442 Clinical Plasma Samples From Individuals With Symptom Records Revealed Subtypes of Convalescent Patients Who Had COVID-19. J Med Virol 2025;97:e70203. [PMID: 40207927 PMCID: PMC11984345 DOI: 10.1002/jmv.70203] [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: 09/30/2024] [Revised: 01/11/2025] [Accepted: 01/21/2025] [Indexed: 04/11/2025]
21
Singh M, Shanmukha S, Eldesouki RE, Harraz MM. FDA-approved drug repurposing screen identifies inhibitors of SARS-CoV-2 pseudovirus entry. Front Pharmacol 2025;16:1537912. [PMID: 40166473 PMCID: PMC11955658 DOI: 10.3389/fphar.2025.1537912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2024] [Accepted: 02/17/2025] [Indexed: 04/02/2025]  Open
22
Abou Mansour M, El Rassi C, Sleem B, Borghol R, Arabi M. Thromboembolic Events in the Era of COVID-19: A Detailed Narrative Review. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2025;2025:3804576. [PMID: 40226433 PMCID: PMC11986918 DOI: 10.1155/cjid/3804576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Accepted: 02/14/2025] [Indexed: 04/15/2025]
23
Krogsaeter EK, McKetney J, Valiente-Banuet L, Marquez A, Willis A, Cakir Z, Stevenson E, Jang GM, Rao A, Li E, Zhou A, Attili A, Chang TS, Kampmann M, Huang Y, Krogan NJ, Swaney DL. Lysosomal proteomics reveals mechanisms of neuronal apoE4-associated lysosomal dysfunction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2023.10.02.560519. [PMID: 37873080 PMCID: PMC10592882 DOI: 10.1101/2023.10.02.560519] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
24
Vallejo-Arróliga M, Villalobos-Agüero RA, Zamora-Sanabria R, Karkashian-Córdoba J. Molecular analysis of 4/91-like variants of avian infectious bronchitis virus (IBV) obtained after the introduction of a 4/91 live-attenuated vaccine in Costa Rica during 2017. Virusdisease 2025;36:81-92. [PMID: 40290772 PMCID: PMC12021757 DOI: 10.1007/s13337-025-00910-4] [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: 10/12/2024] [Accepted: 01/18/2025] [Indexed: 04/30/2025]  Open
25
Schreiber A, Ludwig S. Host-targeted antivirals against SARS-CoV-2 in clinical development - Prospect or disappointment? Antiviral Res 2025;235:106101. [PMID: 39923941 DOI: 10.1016/j.antiviral.2025.106101] [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: 12/29/2024] [Revised: 02/05/2025] [Accepted: 02/06/2025] [Indexed: 02/11/2025]
26
San Felipe CJ, Batra J, Muralidharan M, Malpotra S, Anand D, Bauer R, Verba KA, Swaney DL, Krogan NJ, Grabe M, Fraser JS. Coupled equilibria of dimerization and lipid binding modulate SARS Cov 2 Orf9b interactions and interferon response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.16.638509. [PMID: 40027672 PMCID: PMC11870501 DOI: 10.1101/2025.02.16.638509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2025]
27
Wang J, Xiao M, Hu Z, Lin Y, Li K, Chen P, Lu C, Dong Z, Pan M. Bombyx mori nucleopolyhedrovirus LEF-2 disrupts the cell cycle in the G2/M phase by triggering a host cell DNA damage response. INSECT MOLECULAR BIOLOGY 2025;34:81-93. [PMID: 39150688 DOI: 10.1111/imb.12951] [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: 05/07/2024] [Accepted: 07/25/2024] [Indexed: 08/17/2024]
28
Xu D, Guo M, Xu X, Luo G, Liu Y, Bush SJ, Wang C, Xu T, Zeng W, Liao C, Wang Q, Zhao W, Zhao W, Liu Y, Li S, Zhao S, Jiu Y, Sauvonnet N, Lu W, Sansonetti PJ, Ye K. Shigella infection is facilitated by interaction of human enteric α-defensin 5 with colonic epithelial receptor P2Y11. Nat Microbiol 2025;10:509-526. [PMID: 39901059 DOI: 10.1038/s41564-024-01901-9] [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: 02/28/2024] [Accepted: 12/02/2024] [Indexed: 02/05/2025]
29
Zeng Q, Chen Z, Huang Y, Fu Q, Chen Z, Wu H. SRPK1 facilitates IBDV replication by phosphorylating VP1 at S48. Int J Biol Macromol 2025;291:139002. [PMID: 39716705 DOI: 10.1016/j.ijbiomac.2024.139002] [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: 08/11/2024] [Revised: 12/15/2024] [Accepted: 12/17/2024] [Indexed: 12/25/2024]
30
Zodda E, Pons M, DeMoya-Valenzuela N, Calvo-González C, Benítez-Rodríguez C, López-Ayllón BD, Hibot A, Zuin A, Crosas B, Cascante M, Montoya M, Pujol MD, Rubio-Martínez J, Thomson TM. Induction of the Inflammasome by the SARS-CoV-2 Accessory Protein ORF9b, Abrogated by Small-Molecule ORF9b Homodimerization Inhibitors. J Med Virol 2025;97:e70145. [PMID: 39902616 DOI: 10.1002/jmv.70145] [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: 06/11/2024] [Revised: 10/07/2024] [Accepted: 11/07/2024] [Indexed: 02/05/2025]
31
Kokot T, Zimmermann JP, Chand Y, Krier F, Reimann L, Scheinost L, Höfflin N, Esch A, Höhfeld J, Warscheid B, Köhn M. Identification of phosphatases that dephosphorylate the co-chaperone BAG3. Life Sci Alliance 2025;8:e202402734. [PMID: 39562141 PMCID: PMC11576475 DOI: 10.26508/lsa.202402734] [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: 03/25/2024] [Revised: 11/06/2024] [Accepted: 11/07/2024] [Indexed: 11/21/2024]  Open
32
Ruhoff VT, Leijnse N, Doostmohammadi A, Bendix PM. Filopodia: integrating cellular functions with theoretical models. Trends Cell Biol 2025;35:129-140. [PMID: 38969554 DOI: 10.1016/j.tcb.2024.05.005] [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: 02/29/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 07/07/2024]
33
Hickey TE, Mudunuri U, Hempel HA, Kemp TJ, Roche NV, Talsania K, Sellers BA, Cherry JM, Pinto LA. Proteomic and serologic assessments of responses to mRNA-1273 and BNT162b2 vaccines in human recipient sera. Front Immunol 2025;15:1502458. [PMID: 39931577 PMCID: PMC11808009 DOI: 10.3389/fimmu.2024.1502458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2024] [Accepted: 11/25/2024] [Indexed: 02/13/2025]  Open
34
Liu Y, Rao S, Hoskins I, Geng M, Zhao Q, Chacko J, Ghatpande V, Qi K, Persyn L, Wang J, Zheng D, Zhong Y, Park D, Cenik ES, Agarwal V, Ozadam H, Cenik C. Translation efficiency covariation across cell types is a conserved organizing principle of mammalian transcriptomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.08.11.607360. [PMID: 39149359 PMCID: PMC11326257 DOI: 10.1101/2024.08.11.607360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
35
Sekine R, Takeda K, Suenaga T, Tsuno S, Kaiya T, Kiso M, Yamayoshi S, Takaku Y, Ohno S, Yamaguchi Y, Nishizawa S, Sumitomo K, Ikuta K, Kanda T, Kawaoka Y, Nishimura H, Kuge S. G-quadruplex-forming small RNA inhibits coronavirus and influenza A virus replication. Commun Biol 2025;8:27. [PMID: 39815031 PMCID: PMC11735773 DOI: 10.1038/s42003-024-07351-7] [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: 02/27/2024] [Accepted: 12/03/2024] [Indexed: 01/18/2025]  Open
36
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] [Grants] [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]
37
Xu F, Shang D, Zhu C, Du G, Shi J, Dong X, Li X, Liang X. In Situ MXene-Controlled Synthesis of Polycrystalline TiO2 for Highly Efficient Enrichment of Phosphopeptides. ACS APPLIED MATERIALS & INTERFACES 2025;17:260-268. [PMID: 39714392 DOI: 10.1021/acsami.4c14113] [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: 12/24/2024]
38
dos Santos F, Vindel-Alfageme J, Ciordia S, Castro V, Orera I, Garaigorta U, Gastaminza P, Corrales F. Dynamic Cellular Proteome Remodeling during SARS-CoV-2 Infection. Identification of Plasma Protein Readouts. J Proteome Res 2025;24:171-188. [PMID: 39593238 PMCID: PMC11705369 DOI: 10.1021/acs.jproteome.4c00566] [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: 07/03/2024] [Revised: 11/06/2024] [Accepted: 11/19/2024] [Indexed: 11/28/2024]
39
Liu M, Peng W, Ji X. Repurposing of CDK Inhibitors as Host Targeting Antivirals: A Mini- Review. Mini Rev Med Chem 2025;25:178-189. [PMID: 39185650 DOI: 10.2174/0113895575311618240820103549] [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] [Revised: 04/30/2024] [Accepted: 07/09/2024] [Indexed: 08/27/2024]
40
Song Z, Jiang M, Wang M, Zou J, Chen Z, Zheng F, Wang Q. MAPK pathways regulated apoptosis and pyroptosis in respiratory epithelial cells of a primitive vertebrate model during bacterial infection. Int J Biol Macromol 2025;286:138587. [PMID: 39662566 DOI: 10.1016/j.ijbiomac.2024.138587] [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: 07/03/2024] [Revised: 12/07/2024] [Accepted: 12/07/2024] [Indexed: 12/13/2024]
41
Lai H, Zhu T, Xie S, Luo X, Hong F, Luo D, Dao F, Lin H, Shu K, Lv H. Empirical Comparison and Analysis of Artificial Intelligence-Based Methods for Identifying Phosphorylation Sites of SARS-CoV-2 Infection. Int J Mol Sci 2024;25:13674. [PMID: 39769436 PMCID: PMC11678915 DOI: 10.3390/ijms252413674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2024] [Revised: 12/18/2024] [Accepted: 12/19/2024] [Indexed: 01/11/2025]  Open
42
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. ARXIV 2024:arXiv:2402.05016v4. [PMID: 39010877 PMCID: PMC11247916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
43
Thakur N, Chakraborty P, Tufariello JM, Basler CF. SARS-CoV-2 Nsp14 binds Tollip and activates pro-inflammatory pathways while downregulating interferon-α and interferon-γ receptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.12.628214. [PMID: 39713296 PMCID: PMC11661139 DOI: 10.1101/2024.12.12.628214] [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]
44
Huuskonen S, Liu X, Pöhner I, Redchuk T, Salokas K, Lundberg R, Maljanen S, Belik M, Reinholm A, Kolehmainen P, Tuhkala A, Tripathi G, Laine P, Belanov S, Auvinen P, Vartiainen M, Keskitalo S, Österlund P, Laine L, Poso A, Julkunen I, Kakkola L, Varjosalo M. The comprehensive SARS-CoV-2 'hijackome' knowledge base. Cell Discov 2024;10:125. [PMID: 39653747 PMCID: PMC11628605 DOI: 10.1038/s41421-024-00748-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: 04/30/2024] [Accepted: 10/29/2024] [Indexed: 12/12/2024]  Open
45
Zhou Z, Jin Z, Tian Y, Huangfu C, Fan Z, Liu D. CDK14 is regulated by IGF2BP2 and involved in osteogenic differentiation via Wnt/β-catenin signaling pathway in vitro. Life Sci 2024;358:123148. [PMID: 39447733 DOI: 10.1016/j.lfs.2024.123148] [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: 06/18/2024] [Revised: 10/07/2024] [Accepted: 10/14/2024] [Indexed: 10/26/2024]
46
Aboulache BL, Hoitsma NM, Luger K. Phosphorylation regulates the chromatin remodeler SMARCAD1 in nucleosome binding, ATP hydrolysis, and histone exchange. J Biol Chem 2024;300:107893. [PMID: 39424143 PMCID: PMC11742319 DOI: 10.1016/j.jbc.2024.107893] [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: 07/12/2024] [Revised: 09/13/2024] [Accepted: 10/03/2024] [Indexed: 10/21/2024]  Open
47
Sui L, Wang W, Guo X, Zhao Y, Tian T, Zhang J, Wang H, Xu Y, Chi H, Xie H, Xu W, Liu N, Zhao L, Song G, Wang Z, Zhang K, Che L, Zhao Y, Wang G, Liu Q. Multi-protomics analysis identified host cellular pathways perturbed by tick-borne encephalitis virus infection. Nat Commun 2024;15:10435. [PMID: 39616195 PMCID: PMC11608235 DOI: 10.1038/s41467-024-54628-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 11/15/2024] [Indexed: 05/17/2025]  Open
48
Sui L, Guo X, Wang W, Xu Y, Zhao Y, Liu Q. Multi-proteomics and interactome dataset of tick-borne encephalitis virus infected host cells. Sci Data 2024;11:1280. [PMID: 39587125 PMCID: PMC11589117 DOI: 10.1038/s41597-024-04036-y] [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: 05/23/2024] [Accepted: 10/23/2024] [Indexed: 11/27/2024]  Open
49
Yu J, Ge S, Li J, Zhang Y, Xu J, Wang Y, Liu S, Yu X, Wang Z. Interaction between coronaviruses and the autophagic response. Front Cell Infect Microbiol 2024;14:1457617. [PMID: 39650836 PMCID: PMC11621220 DOI: 10.3389/fcimb.2024.1457617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Accepted: 10/18/2024] [Indexed: 12/11/2024]  Open
50
Bonet-Aleta J, Maehara T, Craig BA, Bernardes GJL. Small Molecule RNA Degraders. Angew Chem Int Ed Engl 2024;63:e202412925. [PMID: 39162084 DOI: 10.1002/anie.202412925] [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: 07/09/2024] [Revised: 08/19/2024] [Accepted: 08/20/2024] [Indexed: 08/21/2024]
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