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For: Bowler-Barnett EH, Fan J, Luo J, Magrane M, Martin MJ, Orchard S. UniProt and Mass Spectrometry-Based Proteomics-A 2-Way Working Relationship. Mol Cell Proteomics 2023;22:100591. [PMID: 37301379 PMCID: PMC10404557 DOI: 10.1016/j.mcpro.2023.100591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/20/2023] [Accepted: 06/07/2023] [Indexed: 06/12/2023]  Open
Number Cited by Other Article(s)
1
Yang X, Yang Z, Wang Y, Zeng H, Wang B. Proteomics and metabolomics elucidate the biosynthetic pathway of acid stress-induced exopolysaccharides and its impact on growth phenotypes in Lactiplantibacillus plantarum HMX2. Food Chem 2025;476:143431. [PMID: 39977986 DOI: 10.1016/j.foodchem.2025.143431] [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: 12/03/2024] [Revised: 02/07/2025] [Accepted: 02/13/2025] [Indexed: 02/22/2025]
2
Mehta S, Wagner R, Do KT, Johnson JE, Yu F, Jubenville T, Richards K, Coleman S, Popescu FE, Nesvizhskii AI, Largaespada DA, Jagtap PD, Griffin TJ. A modular, Galaxy-based immunopeptidogenomic (iPepGen) analysis pipeline for discovery, verification, and prioritization of candidate cancer neoantigen peptides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.04.07.647596. [PMID: 40291680 PMCID: PMC12026984 DOI: 10.1101/2025.04.07.647596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2025]
3
Xu F, Luo S, Huang Z, Wang J, Li T, Zhong L, Si X. The Molecular Mechanisms of Bergapten Against Abdominal Aortic Aneurysm: Evidence From Network Pharmacology, Molecular Docking/Dynamics, and Experimental Validation. J Cell Biochem 2025;126:e70029. [PMID: 40159385 DOI: 10.1002/jcb.70029] [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: 01/14/2025] [Revised: 03/02/2025] [Accepted: 03/16/2025] [Indexed: 04/02/2025]
4
Zhu F, Qin R, Ma S, Zhou Z, Tan C, Yang H, Zhang P, Xu Y, Luo Y, Chen J, Pan P. Designing a multi-epitope vaccine against Pseudomonas aeruginosa via integrating reverse vaccinology with immunoinformatics approaches. Sci Rep 2025;15:10425. [PMID: 40140433 PMCID: PMC11947098 DOI: 10.1038/s41598-025-90226-6] [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: 11/11/2024] [Accepted: 02/11/2025] [Indexed: 03/28/2025]  Open
5
Zhang Z, Rao C, Hu M, Yan W, Du Z. Highly expressed GCN1 is associated with cancer progression and poor prognosis in hepatocellular carcinoma patients. Cancer Cell Int 2025;25:107. [PMID: 40114124 PMCID: PMC11927180 DOI: 10.1186/s12935-025-03732-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: 07/21/2024] [Accepted: 03/06/2025] [Indexed: 03/22/2025]  Open
6
Hernandez R, Garcia-Rodriguez NS, Arriaga MA, Perez R, Bala AA, Leandro AC, Diego VP, Almeida M, Parsons JG, Manusov EG, Galan JA. The hepatocellular model of fatty liver disease: from current imaging diagnostics to innovative proteomics technologies. Front Med (Lausanne) 2025;12:1513598. [PMID: 40109726 PMCID: PMC11919916 DOI: 10.3389/fmed.2025.1513598] [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: 10/18/2024] [Accepted: 02/06/2025] [Indexed: 03/22/2025]  Open
7
Orchard SE. What have Data Standards ever done for us? Mol Cell Proteomics 2025:100933. [PMID: 40024375 DOI: 10.1016/j.mcpro.2025.100933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2024] [Revised: 02/21/2025] [Accepted: 02/24/2025] [Indexed: 03/04/2025]  Open
8
Wu P, Zhao L, Du Y, Lu J, He Y, Shu Q, Peng H, Wang X. Melatonin protects retinal pigment epithelium cells against ferroptosis in AMD via the PI3K/AKT/MDM2/P53 pathway. Front Pharmacol 2025;16:1543575. [PMID: 40083383 PMCID: PMC11903707 DOI: 10.3389/fphar.2025.1543575] [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: 12/11/2024] [Accepted: 01/21/2025] [Indexed: 03/16/2025]  Open
9
Huang R, Xia H, Meng T, Fan Y, Tang X, Li Y, Zhang T, Deng J, Yao B, Huang Y, Yang Y. Construction of human pluripotent stem cell-derived testicular organoids and their use as humanized testis models for evaluating the effects of semaglutide. Theranostics 2025;15:2597-2623. [PMID: 39990223 PMCID: PMC11840739 DOI: 10.7150/thno.104523] [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: 10/01/2024] [Accepted: 01/15/2025] [Indexed: 02/25/2025]  Open
10
The UniProt Consortium, Bateman A, Martin MJ, Orchard S, Magrane M, Adesina A, Ahmad S, Bowler-Barnett EH, Bye-A-Jee H, Carpentier D, Denny P, Fan J, Garmiri P, Gonzales LJDC, Hussein A, Ignatchenko A, Insana G, Ishtiaq R, Joshi V, Jyothi D, Kandasaamy S, Lock A, Luciani A, Luo J, Lussi Y, Marin JSM, Raposo P, Rice DL, Santos R, Speretta E, Stephenson J, Totoo P, Tyagi N, Urakova N, Vasudev P, Warner K, Wijerathne S, Yu CWH, Zaru R, Bridge AJ, Aimo L, Argoud-Puy G, Auchincloss AH, Axelsen KB, Bansal P, Baratin D, Batista Neto TM, Blatter MC, Bolleman JT, Boutet E, Breuza L, Gil BC, Casals-Casas C, Echioukh KC, Coudert E, Cuche B, de Castro E, Estreicher A, Famiglietti ML, Feuermann M, Gasteiger E, Gaudet P, Gehant S, Gerritsen V, Gos A, Gruaz N, Hulo C, Hyka-Nouspikel N, Jungo F, Kerhornou A, Mercier PL, Lieberherr D, Masson P, Morgat A, Paesano S, Pedruzzi I, Pilbout S, Pourcel L, Poux S, Pozzato M, Pruess M, Redaschi N, Rivoire C, Sigrist CJA, Sonesson K, Sundaram S, Sveshnikova A, Wu CH, Arighi CN, Chen C, Chen Y, Huang H, Laiho K, Lehvaslaiho M, McGarvey P, Natale DA, Ross K, Vinayaka CR, Wang Y, Zhang J. UniProt: the Universal Protein Knowledgebase in 2025. Nucleic Acids Res 2025;53:D609-D617. [PMID: 39552041 PMCID: PMC11701636 DOI: 10.1093/nar/gkae1010] [Citation(s) in RCA: 85] [Impact Index Per Article: 85.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Revised: 10/14/2024] [Accepted: 10/16/2024] [Indexed: 11/19/2024]  Open
11
Marzano V, Levi Mortera S, Putignani L. Insights on Wet and Dry Workflows for Human Gut Metaproteomics. Proteomics 2024:e202400242. [PMID: 39740098 DOI: 10.1002/pmic.202400242] [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: 07/16/2024] [Revised: 12/10/2024] [Accepted: 12/11/2024] [Indexed: 01/02/2025]
12
Chen M, Chen X, Chen Q, Chu C, Yang S, Wu C, You Y, Hung A, Yang AWH, Sun X, Zhou L, Zhao X, Li H, Liu Y. Potential candidates from a functional food Zanthoxyli Pericarpium (Sichuan pepper) for the management of hyperuricemia: high-through virtual screening, network pharmacology and dynamics simulations. Front Endocrinol (Lausanne) 2024;15:1436360. [PMID: 39722812 PMCID: PMC11668583 DOI: 10.3389/fendo.2024.1436360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 11/22/2024] [Indexed: 12/28/2024]  Open
13
Arıkan M, Atabay B. Construction of Protein Sequence Databases for Metaproteomics: A Review of the Current Tools and Databases. J Proteome Res 2024;23:5250-5262. [PMID: 39449618 DOI: 10.1021/acs.jproteome.4c00665] [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: 10/26/2024]
14
Zhu Y, Shi J, Wang Q, Zhu Y, Li M, Tian T, Shi H, Shang K, Yin Z, Zhang F. Novel dual-pathogen multi-epitope mRNA vaccine development for Brucella melitensis and Mycobacterium tuberculosis in silico approach. PLoS One 2024;19:e0309560. [PMID: 39466745 PMCID: PMC11515988 DOI: 10.1371/journal.pone.0309560] [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: 07/05/2024] [Accepted: 08/13/2024] [Indexed: 10/30/2024]  Open
15
Jiang Y, Rex DA, Schuster D, Neely BA, Rosano GL, Volkmar N, Momenzadeh A, Peters-Clarke TM, Egbert SB, Kreimer S, Doud EH, Crook OM, Yadav AK, Vanuopadath M, Hegeman AD, Mayta M, Duboff AG, Riley NM, Moritz RL, Meyer JG. Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry. ACS MEASUREMENT SCIENCE AU 2024;4:338-417. [PMID: 39193565 PMCID: PMC11348894 DOI: 10.1021/acsmeasuresciau.3c00068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 05/03/2024] [Accepted: 05/03/2024] [Indexed: 08/29/2024]
16
Zhou Z, Zhu F, Ma S, Tan C, Yang H, Zhang P, Xu Y, Qin R, Luo Y, Chen J, Pan P. Design of Cryptococcus neoformans multi-epitope vaccine based on immunoinformatics method. Med Mycol 2024;62:myae080. [PMID: 39122658 DOI: 10.1093/mmy/myae080] [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: 03/23/2024] [Revised: 07/01/2024] [Accepted: 08/08/2024] [Indexed: 08/12/2024]  Open
17
Zheng X, Shen J, Jiang H, Tian M, Wang Q, Guo K, Chen R, Xia Q, Yan Q, Du L, Duan S. Exploring the multifaceted role of GCN1: Implications in cellular responses and disease pathogenesis. Biomed Pharmacother 2024;175:116681. [PMID: 38705128 DOI: 10.1016/j.biopha.2024.116681] [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: 02/04/2024] [Revised: 04/21/2024] [Accepted: 04/29/2024] [Indexed: 05/07/2024]  Open
18
Omenn GS, Lane L, Overall CM, Lindskog C, Pineau C, Packer NH, Cristea IM, Weintraub ST, Orchard S, Roehrl MHA, Nice E, Guo T, Van Eyk JE, Liu S, Bandeira N, Aebersold R, Moritz RL, Deutsch EW. The 2023 Report on the Proteome from the HUPO Human Proteome Project. J Proteome Res 2024;23:532-549. [PMID: 38232391 PMCID: PMC11026053 DOI: 10.1021/acs.jproteome.3c00591] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
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