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For: Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002;30:207-10. [PMID: 11752295 PMCID: PMC99122 DOI: 10.1093/nar/30.1.207] [Citation(s) in RCA: 9604] [Impact Index Per Article: 417.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
Number Cited by Other Article(s)
1
Chen Y, Li Y, Xu Y, Lv Q, Ye Y, Gu J. Revealing the role of natural killer cells in ankylosing spondylitis: identifying diagnostic biomarkers and therapeutic targets. Ann Med 2025;57:2457523. [PMID: 39853176 PMCID: PMC11770870 DOI: 10.1080/07853890.2025.2457523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 01/06/2025] [Accepted: 01/07/2025] [Indexed: 01/26/2025]  Open
2
Uusi-Mäkelä M, Harjula SKE, Junno M, Sillanpää A, Nätkin R, Niskanen MT, Saralahti AK, Nykter M, Rämet M. The inflammasome adaptor pycard is essential for immunity against Mycobacterium marinum infection in adult zebrafish. Dis Model Mech 2025;18:dmm052061. [PMID: 39916610 PMCID: PMC11972081 DOI: 10.1242/dmm.052061] [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: 08/14/2024] [Accepted: 02/03/2025] [Indexed: 03/25/2025]  Open
3
Zhang M, Yuan L, Yang X, Zhao X, Xie J, Liu X, Wang F. TRAF1 promotes the progression of Helicobacter pylori-associated gastric cancer through EGFR/STAT/OAS signalling. Life Sci 2025;373:123656. [PMID: 40287055 DOI: 10.1016/j.lfs.2025.123656] [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: 02/17/2025] [Revised: 04/11/2025] [Accepted: 04/21/2025] [Indexed: 04/29/2025]
4
Rajebhosale P, Jiang L, Ressa HJ, Johnson KR, Desai NS, Jone A, Role LW, Talmage DA. Diversification of dentate gyrus granule cell subtypes is regulated by Nrg1 nuclear back-signaling. Life Sci Alliance 2025;8:e202403169. [PMID: 40280713 PMCID: PMC12032840 DOI: 10.26508/lsa.202403169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2024] [Revised: 04/12/2025] [Accepted: 04/16/2025] [Indexed: 04/29/2025]  Open
5
Huang ZA, Ji GS, Yang S, Yang Y, Wu YC, Tian ZK, Song GS. Design, pharmacology, and toxicology of a novel chemically modified siRNA targeting hepatic angiotensinogen. MOLECULAR THERAPY. NUCLEIC ACIDS 2025;36:102542. [PMID: 40385635 PMCID: PMC12083919 DOI: 10.1016/j.omtn.2025.102542] [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: 12/20/2024] [Accepted: 04/14/2025] [Indexed: 05/20/2025]
6
Matboli M, Saad M, Ahmed MF, Helmy Hasanin A, Ellithy GM, Abdelwahab MS, Eltantawy EHB, Hamam GG, Hamoud AE, El-Shafei MM, Samir N. Febuxostat alleviate metabolic dysfunction-associated steatohepatitis in rat model via targeting inflammation, cell death, and intestinal barrier dysfunction. Biomed Pharmacother 2025;187:118086. [PMID: 40306176 DOI: 10.1016/j.biopha.2025.118086] [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: 03/18/2025] [Revised: 04/15/2025] [Accepted: 04/23/2025] [Indexed: 05/02/2025]  Open
7
Stapenhorst França F, Gensel JC. Redefining macrophage phenotypes after spinal cord injury: An open data approach. Exp Neurol 2025;388:115222. [PMID: 40113007 DOI: 10.1016/j.expneurol.2025.115222] [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: 11/20/2024] [Revised: 03/13/2025] [Accepted: 03/16/2025] [Indexed: 03/22/2025]
8
Fullstone T, Rohm H, Kaltofen T, Hierlmayer S, Reichenbach J, Schweikert S, Knodel F, Loeffler AK, Mayr D, Jeschke U, Mahner S, Kessler M, Trillsch F, Rathert P. Identification of FLYWCH1 as a regulator of platinum-resistance in epithelial ovarian cancer. NAR Cancer 2025;7:zcaf012. [PMID: 40191655 PMCID: PMC11970373 DOI: 10.1093/narcan/zcaf012] [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: 10/16/2024] [Revised: 02/20/2025] [Accepted: 03/25/2025] [Indexed: 04/09/2025]  Open
9
Cinnamon E, Stein I, Zino E, Rabinovich S, Shovman Y, Schlesinger Y, Salame TM, Reich-Zeliger S, Albrecht T, Roessler S, Schirmacher P, Lotem M, Ben-Neriah Y, Parnas O, Pikarsky E. RORc-expressing immune cells negatively regulate tertiary lymphoid structure formation and support their pro-tumorigenic functions. J Hepatol 2025;82:1050-1067. [PMID: 39710149 DOI: 10.1016/j.jhep.2024.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 11/28/2024] [Accepted: 12/07/2024] [Indexed: 12/24/2024]
10
Tasneem M, Gupta SD, Ahmed Jony MJ, Minkara M, Dey RK, Ferdoush J. Identification of key biomarker genes in liver hepatocellular carcinoma and kidney renal clear cell carcinoma progression: A shared high-throughput screening and molecular docking method with potentials for targeted therapeutic interventions. J Genet Eng Biotechnol 2025;23:100497. [PMID: 40390492 PMCID: PMC12049835 DOI: 10.1016/j.jgeb.2025.100497] [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: 09/20/2024] [Accepted: 04/14/2025] [Indexed: 05/21/2025]
11
Jeong J, Harris J, de Souza LL, Leonelli L. Combining the CowPEAsy Web Application With in Planta Agroinfiltration for Native Promoter Validation in Vigna unguiculata. PLANT, CELL & ENVIRONMENT 2025;48:4301-4311. [PMID: 39948050 PMCID: PMC12050393 DOI: 10.1111/pce.15431] [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: 05/28/2024] [Revised: 01/11/2025] [Accepted: 02/03/2025] [Indexed: 05/06/2025]
12
Jiang Y, Immadi MS, Wang D, Zeng S, On Chan Y, Zhou J, Xu D, Joshi T. IRnet: Immunotherapy response prediction using pathway knowledge-informed graph neural network. J Adv Res 2025;72:319-331. [PMID: 39097091 DOI: 10.1016/j.jare.2024.07.036] [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: 03/26/2024] [Revised: 07/10/2024] [Accepted: 07/30/2024] [Indexed: 08/05/2024]  Open
13
Xu Y, Zhang H, Jiao X, Zhang Y, Yin G, Wang C, Du Z, Liang M, Gao X, Gu Z, Jiang Y, Du B, Bi X. Dysregulations of C1QA, C1QB, C1QC and C5AR1 as candidate biomarkers of vascular dementia. NPJ AGING 2025;11:42. [PMID: 40414977 DOI: 10.1038/s41514-025-00228-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Accepted: 04/22/2025] [Indexed: 05/27/2025]
14
Huang Y, Yang T, Yang C, Tang B, Su B, Yang X. MiR-485-3p/MELK cascade mediates tumor progression in pancreatic cancer. Sci Rep 2025;15:17870. [PMID: 40404813 PMCID: PMC12098867 DOI: 10.1038/s41598-025-02586-8] [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: 12/28/2024] [Accepted: 05/14/2025] [Indexed: 05/24/2025]  Open
15
Pepler MAD, Mulholland EL, Montague FR, Elliot MA. Defining the networks that connect RNase III and RNase J-mediated regulation of primary and specialized metabolism in Streptomyces venezuelae. J Bacteriol 2025;207:e0002425. [PMID: 40227046 PMCID: PMC12096830 DOI: 10.1128/jb.00024-25] [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: 01/19/2025] [Accepted: 03/18/2025] [Indexed: 04/15/2025]  Open
16
Wilcken S, Koutsandrea PH, Bakker T, Kulik A, Orthwein T, Franz-Wachtel M, Harbig T, Nieselt KK, Forchhammer K, Brötz-Oesterhelt H, Macek B, Mordhorst S, Kaysser L, Gust B. The TetR-like regulator Sco4385 and Crp-like regulator Sco3571 modulate heterologous production of antibiotics in Streptomyces coelicolor M512. Appl Environ Microbiol 2025;91:e0231524. [PMID: 40183567 DOI: 10.1128/aem.02315-24] [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: 11/18/2024] [Accepted: 03/09/2025] [Indexed: 04/05/2025]  Open
17
Grossi E, Marchese FP, González J, Goñi E, Fernández-Justel JM, Amadoz A, Herranz N, Puchades-Carrasco L, Montes M, Huarte M. A lncRNA-mediated metabolic rewiring of cell senescence. Cell Rep 2025;44:115747. [PMID: 40408249 DOI: 10.1016/j.celrep.2025.115747] [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: 08/24/2023] [Revised: 03/21/2025] [Accepted: 05/06/2025] [Indexed: 05/25/2025]  Open
18
Bharati J, Kumar S, Buragohain BM, Das D, Devi SJ, Mohan NH, Gupta VK. Identification of differentially expressed genes and pathways in the post-ovulatory ampulla of cyclic pigs through a transcriptomics approach. Mol Biol Rep 2025;52:481. [PMID: 40397228 DOI: 10.1007/s11033-025-10605-0] [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] [Accepted: 05/13/2025] [Indexed: 05/22/2025]
19
Boshnakovska A, Pronto JR, Gall T, Aich A, Prochazka J, Nichtova Z, Sedlacek R, Sobitov I, Ainatzi S, Lenz C, Katschinski DM, Urlaub H, Voigt N, Rehling P, Kremer LS. SMIM20 promotes complex IV biogenesis and Ca2+ signaling in mice heart. Cell Rep 2025;44:115723. [PMID: 40402744 DOI: 10.1016/j.celrep.2025.115723] [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: 11/18/2024] [Revised: 03/18/2025] [Accepted: 04/29/2025] [Indexed: 05/24/2025]  Open
20
Auer F, Morcos MNF, Sipola M, Akhtar I, Moisio S, Vogt J, Haag R, Lahnalampi M, Tuononen TJ, Hanel A, Viitasalo A, Friedrich UA, Dahl A, Prexler C, Pandyra AA, Stepensky P, Takagi M, Borkhardt A, Heinäniemi M, Hauer J. Trajectories from single-cells to PAX5-driven leukemia reveal PAX5-MYC interplay in vivo. Leukemia 2025:10.1038/s41375-025-02626-2. [PMID: 40394211 DOI: 10.1038/s41375-025-02626-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 03/31/2025] [Accepted: 04/22/2025] [Indexed: 05/22/2025]
21
Deng J, Li P, Li S, Liang F, Hong M, Zhang T, Tan Y, Ren F, Zhang Y, Xu Z, Wang H. SYK identified by bioinformatics analysis promotes the proliferation of multiple myeloma. Expert Rev Hematol 2025:1-15. [PMID: 40387108 DOI: 10.1080/17474086.2025.2505724] [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: 02/09/2025] [Revised: 05/05/2025] [Accepted: 05/07/2025] [Indexed: 05/20/2025]
22
López-Paleta N, Moreno-Barbosa E, Velázquez-Castro J. A fast validation test of gene regulatory network models via the Fokker-Planck equation. J Biol Phys 2025;51:16. [PMID: 40388063 PMCID: PMC12089004 DOI: 10.1007/s10867-025-09681-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: 02/18/2025] [Accepted: 04/23/2025] [Indexed: 05/20/2025]  Open
23
Farrell C, Buhidma Y, Mumford P, Heywood WE, Hällqvist J, Flores-Aguilar L, Andrews EJ, Rahimzadah N, Taso OS, Doran E, Swarup V, Head E, Lashley T, Mills K, Toomey CE, Wiseman FK. Apolipoprotein E abundance is elevated in the brains of individuals with Down syndrome-Alzheimer's disease. Acta Neuropathol 2025;149:49. [PMID: 40387921 PMCID: PMC12089208 DOI: 10.1007/s00401-025-02889-0] [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: 02/19/2025] [Revised: 04/25/2025] [Accepted: 05/01/2025] [Indexed: 05/20/2025]
24
Mizrachi A, Sadeh M, Ben-Dor S, Dym O, Ku C, Feldmesser E, Zarfin A, Brunson JK, Allen AE, Jinkerson RE, Schatz D, Vardi A. Cathepsin X is a conserved cell death protein involved in algal response to environmental stress. Curr Biol 2025;35:2240-2255.e6. [PMID: 40233752 DOI: 10.1016/j.cub.2025.03.045] [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: 01/22/2025] [Revised: 03/12/2025] [Accepted: 03/21/2025] [Indexed: 04/17/2025]
25
Qu K, Gu J, Xu Z, Hepeng Y, Ning Q, Wu X. Alcohol consumption and esophageal cancer risk: unveiling DLEU2 as a key immune modulator through Mendelian randomization and transcriptomic analysis. Discov Oncol 2025;16:804. [PMID: 40383861 PMCID: PMC12086134 DOI: 10.1007/s12672-025-02660-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2024] [Accepted: 05/10/2025] [Indexed: 05/20/2025]  Open
26
Wang J, Chu Y, Hu G, Liang S, Cui Y, Zuo J, Luo Z, Chen X, Wang X, Yu Z, Zhang Z, Wang X. Piperlongumine Inhibits Malignant Progression of Esophageal Squamous Cells Through the PI3K/AKT Signaling Pathway. Biochem Genet 2025:10.1007/s10528-025-11139-7. [PMID: 40383869 DOI: 10.1007/s10528-025-11139-7] [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: 01/18/2025] [Accepted: 05/08/2025] [Indexed: 05/20/2025]
27
Prisinzano M, Seidita I, Bruni P, Petraglia F, Bernacchioni C, Meyer Zu Heringdorf D, Donati C. Characterization of functionally relevant G protein-coupled receptors in endometriotic epithelial cells. Cell Signal 2025;133:111876. [PMID: 40381972 DOI: 10.1016/j.cellsig.2025.111876] [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: 03/18/2025] [Revised: 05/07/2025] [Accepted: 05/15/2025] [Indexed: 05/20/2025]
28
Yang Y, Jing W, Zhang L, Zhang Y, Shang Y, Kuang Y. WDR62 affects the progression of ovarian cancer by regulating the cell cycle. Hereditas 2025;162:78. [PMID: 40369663 PMCID: PMC12076949 DOI: 10.1186/s41065-025-00444-1] [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: 01/05/2025] [Accepted: 05/02/2025] [Indexed: 05/16/2025]  Open
29
Toft K, Mardahl M, Hedberg-Alm Y, Anlén K, Tydén E, Nielsen MK, Honoré ML, Fromm B, Nielsen LN, Nejsum P, Thamsborg SM, Cirera S, Pihl TH. Evaluation of circulating microRNAs in plasma from horses with non-strangulating intestinal infarction and idiopathic peritonitis. Vet J 2025;313:106378. [PMID: 40374098 DOI: 10.1016/j.tvjl.2025.106378] [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: 01/07/2025] [Revised: 05/12/2025] [Accepted: 05/12/2025] [Indexed: 05/17/2025]
30
Ebelt ND, Loganathan S, Avsharian LC, Manuel ER. Transcriptomic analysis of non-leukemic cell subsets in azacytidine-responsive AML highlights pathways associated with adhesion, platelet aggregation, and angiogenesis in mice and humans. Mol Med 2025;31:185. [PMID: 40360989 PMCID: PMC12070539 DOI: 10.1186/s10020-025-01233-2] [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: 03/18/2025] [Accepted: 04/25/2025] [Indexed: 05/15/2025]  Open
31
Chen Y, Wang M. Revealing roles of PANoptosis-related genes in prognosis and molecular subtypes in lung squamous cell carcinoma by integrated bioinformatic analyses and experiments. Clin Exp Med 2025;25:154. [PMID: 40353888 PMCID: PMC12069423 DOI: 10.1007/s10238-025-01696-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: 02/19/2025] [Accepted: 04/14/2025] [Indexed: 05/14/2025]
32
Reierson MM, Acharjee A. Unsupervised machine learning-based stratification and immune deconvolution of liver hepatocellular carcinoma. BMC Cancer 2025;25:853. [PMID: 40349011 PMCID: PMC12066050 DOI: 10.1186/s12885-025-14242-5] [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: 12/06/2024] [Accepted: 04/29/2025] [Indexed: 05/14/2025]  Open
33
Pickard BS. A mechanism of global gene expression regulation is disrupted by multiple disease states and drug treatments. PLoS One 2025;20:e0317071. [PMID: 40341320 PMCID: PMC12061403 DOI: 10.1371/journal.pone.0317071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2024] [Accepted: 02/25/2025] [Indexed: 05/10/2025]  Open
34
Lei X, Qiu L, Chen Q, Liao L, Yu P, Wu W, Zhu Z, Li C, Lin G, Zhuang Z, Meng Y, Wang Y, Wang C, Du Y. Exploring the regulatory mechanism of CCNA2 in colorectal cancer: insights from multiomics and experimental analysis. J Biol Chem 2025:110216. [PMID: 40345591 DOI: 10.1016/j.jbc.2025.110216] [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: 05/11/2024] [Revised: 03/18/2025] [Accepted: 04/04/2025] [Indexed: 05/11/2025]  Open
35
Tsurukawa FK, Mao Y, Sanchez-Villalobos C, Khanna N, Crasto CJ, Lawrence JJ, Pal R. Cross study transcriptomic investigation of Alzheimer's brain tissue discoveries and limitations. Sci Rep 2025;15:16041. [PMID: 40341634 PMCID: PMC12062235 DOI: 10.1038/s41598-025-01017-y] [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: 12/02/2024] [Accepted: 05/02/2025] [Indexed: 05/10/2025]  Open
36
Bennett J, Levine AB, Nobre L, Negm L, Chung J, Fang K, Johnson M, Komosa M, Krumholtz S, Nunes NM, Rana M, Ryall S, Sheth J, Siddaway R, Bale TA, Bouffet E, Cusimano MD, Das S, Detsky J, Dirks P, Karajannis MA, Kongkham P, Giantini-Larsen A, Li BK, Lim-Fat MJ, Lin AL, Mason WP, Miller A, Perry JR, Sahgal A, Sait SF, Tsang DS, Zadeh G, Laperriere N, Nguyen L, Gao A, Keith J, Munoz DG, Tabori U, Hawkins C. A population-based analysis of the molecular landscape of glioma in adolescents and young adults reveals insights into gliomagenesis. NATURE CANCER 2025:10.1038/s43018-025-00962-x. [PMID: 40335748 DOI: 10.1038/s43018-025-00962-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 03/28/2025] [Indexed: 05/09/2025]
37
Yang J, Lin D, Liu D, Zhang D, Wang H. A PANoptosis-Based Signature for Survival and Immune Predication in Glioblastoma Multiforme. Ann Clin Transl Neurol 2025. [PMID: 40333895 DOI: 10.1002/acn3.70066] [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: 11/29/2024] [Revised: 03/27/2025] [Accepted: 04/14/2025] [Indexed: 05/09/2025]  Open
38
Dou T, Chen Y, Liu L, Zhang Y, Pei W, Li J, Lei Y, Wang Y, Jia H. Radiogenomic analysis of clinical and ultrasonic characteristics in correlation to immune-related genes in breast cancer. Sci Rep 2025;15:15918. [PMID: 40335526 PMCID: PMC12058982 DOI: 10.1038/s41598-025-00891-w] [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: 10/23/2024] [Accepted: 05/02/2025] [Indexed: 05/09/2025]  Open
39
Takahashi Y, Wang QS, Hasegawa T, Namkoong H, Inoue F, Fukunaga K, Imoto S, Miyano S, Okada Y. JOB: Japan Omics Browser provides integrative visualization of multi-omics data. BMC Genomics 2025;26:451. [PMID: 40335902 PMCID: PMC12057183 DOI: 10.1186/s12864-025-11639-1] [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: 10/22/2024] [Accepted: 04/25/2025] [Indexed: 05/09/2025]  Open
40
Brinkmeier ML, Cheung LYM, O'Connell SP, Gutierrez DK, Rhoads EC, Camper SA, Davis SW. Nucleoredoxin regulates WNT signaling during pituitary stem cell differentiation. Hum Mol Genet 2025;34:870-881. [PMID: 40044116 PMCID: PMC12056309 DOI: 10.1093/hmg/ddaf032] [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: 02/04/2025] [Accepted: 02/23/2025] [Indexed: 03/12/2025]  Open
41
Alavattam KG, Dickson BM, Hirano R, Dell R, Tsukiyama T. ChIP-seq Data Processing and Relative and Quantitative Signal Normalization for Saccharomyces cerevisiae. Bio Protoc 2025;15:e5299. [PMID: 40364978 PMCID: PMC12067309 DOI: 10.21769/bioprotoc.5299] [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: 02/10/2025] [Revised: 04/02/2025] [Accepted: 04/02/2025] [Indexed: 05/15/2025]  Open
42
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
43
Mia S, Siokatas G, Sidiropoulou R, Hoffman M, Fragkiadakis K, Markopoulou E, Elesawy MI, Roy R, Blair S, Kuwabara Y, Rapushi E, Chaudhuri D, Makarewich CA, Gao E, Koch WJ, Schilling JD, Molkentin JD, Marketou M, Drosatos K. Hepato-cardiac interorgan communication controls cardiac hypertrophy via combined endocrine-autocrine FGF21 signaling. Cell Rep Med 2025:102125. [PMID: 40339570 DOI: 10.1016/j.xcrm.2025.102125] [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: 05/14/2024] [Revised: 01/13/2025] [Accepted: 04/11/2025] [Indexed: 05/10/2025]
44
Golestanifar A, Lajmiri H, Saberiyan M. Integrative analysis of glioblastoma multiforme: the power of non-coding RNAs and hub genes in cancer research. Clin Exp Med 2025;25:138. [PMID: 40317362 PMCID: PMC12049400 DOI: 10.1007/s10238-025-01677-0] [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: 03/16/2025] [Accepted: 04/09/2025] [Indexed: 05/07/2025]
45
Golestanifar A, Masroor A, Khedri H, Zeini S, Nejatizadeh A. Dysregulated Long Non-coding RNAs SNHG15 and OTUD6B-AS1 in Systemic Lupus Erythematosus: Insights from Bioinformatics Analysis and Experimental Validation. Biochem Genet 2025:10.1007/s10528-025-11116-0. [PMID: 40314733 DOI: 10.1007/s10528-025-11116-0] [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: 01/21/2025] [Accepted: 04/20/2025] [Indexed: 05/03/2025]
46
Norden-Krichmar TM, Rotroff D, Schwantes-An TH, Bataller R, Goldman D, Nagy LE, Liangpunsakul S. Genomic approaches to explore susceptibility and pathogenesis of alcohol use disorder and alcohol-associated liver disease. Hepatology 2025;81:1595-1606. [PMID: 37796138 PMCID: PMC10985049 DOI: 10.1097/hep.0000000000000617] [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: 05/24/2023] [Accepted: 08/13/2023] [Indexed: 10/06/2023]
47
Ren Q, Ding K, Jiang W, Zhu W, Gao Y. Molecular crosstalk and potential causal mechanisms of rheumatoid arthritis and sarcopenia co-morbidity: A gene integration analysis. Exp Gerontol 2025;203:112729. [PMID: 40081680 DOI: 10.1016/j.exger.2025.112729] [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: 12/16/2024] [Revised: 02/28/2025] [Accepted: 03/09/2025] [Indexed: 03/16/2025]
48
Shen K, Lin J. Unraveling the Molecular Landscape of Neutrophil Extracellular Traps in Severe Asthma: Identification of Biomarkers and Molecular Clusters. Mol Biotechnol 2025;67:1852-1866. [PMID: 38801616 DOI: 10.1007/s12033-024-01164-z] [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: 12/05/2023] [Accepted: 04/08/2024] [Indexed: 05/29/2024]
49
Zheng L, Cao Y, Hao J, Yu Y, Lu W, Guo T, Yuan S. Investigation and validation of genes associated with endoplasmic reticulum stress in diabetic retinopathy using various machine learning algorithms. Exp Eye Res 2025;254:110317. [PMID: 40043935 DOI: 10.1016/j.exer.2025.110317] [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: 11/12/2024] [Revised: 01/20/2025] [Accepted: 02/27/2025] [Indexed: 04/08/2025]
50
Yang Y, Zhang Y, Liu K, Liu M, Zhang H, Guo M. IFI27, a potential candidate molecular marker for primary Sjogren's syndrome. Clin Rheumatol 2025;44:1949-1960. [PMID: 40146445 DOI: 10.1007/s10067-025-07409-9] [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: 08/13/2024] [Revised: 03/04/2025] [Accepted: 03/18/2025] [Indexed: 03/28/2025]
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