Molecular landscape of sex- and modality-specific exercise adaptation in human skeletal muscle through large-scale multi-omics integration by Macsue Jacques, Shanie Landen, Adam P. Sharples, Andrew Garnham, Ralf Schittenhelm, Joel Steele, Aino Heikkinen, Elina Sillanpää, Miina Ollikainen, James Broatch, Navabeh Zarekookandeh, Ola Hanson, Ola Ekström, Olof Asplund, Séverine Lamon, Sarah E. Alexander, Cassandra Smith, Carlie Bauer, Mary N. Woessner, Itamar Levinger, Andrew E. Teschendorff, Linn Gillberg, Ida Blom, Jørn Wulff Helge, Nicholas R. Harvey, Larisa M. Haupt, Lyn R. Griffiths, Atul S. Deshmukh, Kirsi H. Pietiläinen, Päivi Piirilä, Robert A.E. Seaborne, Marie Klevjer, Anja Bye, Ulrik Wisløff, Bernadette Jones-Freeman, Nir Eynon

“…Minimal sex differences were observed, while modality-specific analysis highlighted distinct pathways for aerobic and resistance exercise, contrasting with muscle disuse patterns. …”
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GmBSK1-GmGSK1-GmBES1.5 regulatory module controls heat tolerance in soybean by Ze-Hao Hou, Yuan Gao, Jia-Cheng Zheng, Meng-Jie Zhao, Ying Liu, Xiao-Yu Cui, Zhi-Yong Li, Ji-Tong Wei, Tai-Fei Yu, Lei Zheng, Yuan-Chen Jiao, Shu-Hui Yang, Jia-Min Hao, Jun Chen, Yong-Bin Zhou, Ming Chen, Lijuan Qiu, You-Zhi Ma, Zhao-Shi Xu

“…Methods: Transgenic technology and CRISPR/Cas9 technology were used to generated GmBSK1-OE, GmBES1.5-OE and gmbsk1 transgenic soybean plants, and transcriptome analysis, LUC activity assay and EMSA assay were carried out to elucidate the potential molecular mechanism underlying GmBSK1-GmBES1.5-mediated heat stress tolerance in soybean. …”
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The involvement of Argonaute molecule PIWI in the antiviral immunity of oyster Crassostrea gigas by Yuhao Jin, Xue Qiao, Yuqing Zeng, Yiqing Wang, Lilin Hou, Xinyu Zhao, Sicong Wang, Lingling Wang, Linsheng Song

“…The predicted CgPIWI protein consists of a N domain, a PAZ domain, a MID domain and a PIWI domain, and shared identity ranging from 27.04% to 70.37% with other PIWIs. Transcriptome analysis showed that CgPIWI was highly expressed in embryonic period (from egg to blastula stage) and then gradually decreased with the development process (from blastula to early D-larva stage). …”
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Expression Profiling of a Heterogeneous Population of ncRNAs Employing a Mixed DNA/LNA Microarray by Konstantinia Skreka, Marek Zywicki, Michael Karbiener, Alexander Hüttenhofer, Marcel Scheideler, Mathieu Rederstorff

“…However, LNA microarrays are quite expensive for high-throughput studies targeting longer ncRNAs, while DNA arrays do not provide satisfying results for the analysis of small RNAs. …”
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Identification of therapeutic targets in lung adenocarcinoma using Mendelian randomization and multi-omics by Yue Li, Keru Ma, Hao Wang, Zongying Liu, Zhuying Li

“…The prognostic relevance of the identified candidate targets was assessed using transcriptomic data. Functional interactions were explored via protein–protein interaction network analysis, while single-cell analyses were employed to determine cell-specific expression patterns and differentiation trajectories. …”
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Succinylation-related molecular activities in cancer: metabolic adaptations, immune landscape, and prognostic significance in colorectal cancer by Zhihang Jiang, Zhihang Jiang, Xiaoqing Li, Xiaoqing Li, Long Hu, Zheng Jiang

“…A systematic pan-cancer analysis of succinylation-related molecular activities is needed.MethodsBulk transcriptomic, single-cell RNA sequencing, and spatial transcriptomic data across pan-cancer from TCGA, GEO, TISCH, and multiple other databases were analyzed. …”
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Screening and regulatory mechanism exploration of M1 macrophage polarization and efferocytosis-related biomarkers in coronary heart disease by Hong Gao, Junhua Li, Jianxin Huang, Xiaojie Jiang

“…Immune infiltration analysis indicated IL13RA1 all had a positive correlation with M0 macrophage, while had a negative correlation with. …”
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FPR3 orchestrates macrophage polarization in breast cancer: multi-omics dissection of prognostic relevance and therapeutic targeting by Ying Chen, Xin Tang, Liran Zhu, Yi Wang, Gaopeng Li, Wulin Yang

“…Methods A comprehensive analysis integrating bulk RNA-seq transcriptomics, methylomics, single-cell transcriptomics, and spatial single-cell transcriptomics data was conducted to elucidate the distinctive characteristics of FPRs in breast cancer. …”
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Effect of age and sex differences on the abundances of neuronal, glial, and endothelial cells in non-diseased brain tissue. by Arttu Autio-Kimura, Tapio Nevalainen, Mikko Hurme

“…An age-associated decrease in neuronal proportions was only observed in male donors, while no significant change was found in females. …”
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Chromosome number variation and phylogenetic divergence of East Asian Cirsium sect. Onotrophe subsect. Nipponocirsium (Compositae), with a new species from Taiwan by Chih-Yi Chang, Pei-Chun Liao, Hsy-Yu Tzeng, Junko Kusumi, Zhi-Hui Su, Yen-Hsueh Tseng

“…Cirsium pengii diverged around 0.47 Myr, while tetraploid species C. kawakamii and C. tatakaense diverged around 0.35 Myr. …”
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Progression of Ankle Osteoarthritis Is Associated with Distinct Synovial Phenotypes by Julia Matthias MD, Michael A. David PhD, Sara E. Buckley DO, Nathaniel Zona BA, Michael Zuscik PhD, Kenneth Hunt MD

“…Methods: Synovial samples from patients undergoing routine ankle procedures (IRB-approved) were harvested for bulk RNA sequencing and digital histopathological (DH) analysis. Standard Gene Ontology (GO) analysis was used to identify enriched gene pathways. …”
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Multi-omics landscape of alternative splicing in diffuse midline glioma reveals immune- and neural-driven subtypes with implications for spliceosome-targeted therapy by Chaxian Liu, Chaxian Liu, Chaxian Liu, Chaxian Liu, Chaxian Liu, Yue Liu, Yue Liu, Yue Liu, Yue Liu, Yue Liu, Hao Lin, Hao Lin, Hao Lin, Hao Lin, Hao Lin, Chufan Zhang, Chufan Zhang, Chufan Zhang, Bilong Zhang, Bilong Zhang, Bilong Zhang, Haikun Song, Haikun Song, Haikun Song, Xiaomin Fan, Yi Lyu, Hui Yang, Hui Yang, Hui Yang, Hui Yang, Hui Yang, Ying Mao, Ying Mao, Ying Mao, Ying Mao

“…Given its potential impact on gene regulation and tumor progression, a comprehensive analysis of alternative splicing could provide novel insights into targeted or immune therapeutic strategies, complementing existing transcriptomic studies of DMG.MethodsTo investigate the alternative splicing landscape of DMG, we performed transcriptome sequencing (RNA-seq) on patient-derived H3WT and H3K27-altered DMG cell lines, integrating these data with RNA-seq and single-cell transcriptomic (scRNA-seq) datasets from published sources. …”
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EIF4A3 Promotes Muscle Atrophy and Aging by Inhibiting the FAK Pathway Through NEDD9 mRNA Destabilization by Qian Li, Xiaohang Yin, Wensi Wan, Yi Zhou, Siqi Wang, Yuwei Yan, Jingying Chen, Xinyi Ren, Junli Gao, Yuying Chen, Yanan Zhang, Caiyue Cui, Emeli Chatterjee, Guoping Li, Ming Wu, Yan Zhang, Dongchao Lu, Tingting Yang, Yongjun Zheng, Jin Li

“…Methods Single‐cell transcriptome analysis and western blot were employed to analyse EJC expression in muscle atrophy. …”
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Watkins wheat landraces decode nitrogen-driven biomass trade-offs: GWAS exposes root-shoot dialectics and elite landraces for resilient agriculture by Abdul Waheed, Muhammad Shahid Iqbal, Zareen Sarfraz, Junliang Hou, Yanping Wei, Bo Song, Shifeng Cheng

“…Multivariate analysis was performed to classify biomass allocation strategies among the landraces.ResultsPhenotypic analysis revealed stark differences in root-shoot allocation strategies under LN and NN conditions. …”
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An in vitro neurobacterial interface reveals direct modulation of neuronal function by gut bacteria by Juan Lombardo-Hernandez, Jesús Mansilla-Guardiola, Riccardo Aucello, Cristian Botta, Maria Teresa García-Esteban, Antonio Murciano-Cespedosa, David Muñoz-Rodríguez, Elisa Quarta, Álvaro Mateos González, Carmen Juan-Llamas, Kalliopi Rantsiou, Stefano Geuna, Luca Cocolin, Celia Herrera-Rincon

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Integration of single-cell sequencing and mendelian randomization reveals novel causal pathways between monocytes and hepatocellular carcinoma by Jiang Yu, Jing Yu, Zhou Kang, Yong Peng

“…Methods This investigation employed single-cell transcriptomic analysis of human hepatic innate lymphoid cells (ILCs) to identify monocyte subpopulations and their cellular markers. …”
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Ferroptosis-related hub genes and immune cell dynamics as diagnostic biomarkers in age-related macular degeneration by Jinquan Chen, Zhao Long, Dandan Shi, Qian Zhang, H. Peng

“…Finally, we performed a functional enrichment analysis of these hub genes. Results In the macula of patients with AMD, 452 DEGs were identified, while in the peripheral retina, 222 DEGs were discovered. …”
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Exploring T-cell metabolism in tuberculosis: development of a diagnostic model using metabolic genes by Shoupeng Ding, Chunxiao Huang, Jinghua Gao, Chun Bi, Yuyang Zhou, Zihan Cai

“…Clinical validation substantiated the differential expression patterns of T-cell-related metabolic differentially expressed genes (TCM–DEGs; p < 0.05), while the nomogram predictive model achieved exceptional discriminative capacity (C-index = 0.944), demonstrating superior clinical applicability through decision curve analysis. …”
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Gene Ranking of RNA-Seq Data via Discriminant Non-Negative Matrix Factorization. by Zhilong Jia, Xiang Zhang, Naiyang Guan, Xiaochen Bo, Michael R Barnes, Zhigang Luo

“…RNA-sequencing is rapidly becoming the method of choice for studying the full complexity of transcriptomes, however with increasing dimensionality, accurate gene ranking is becoming increasingly challenging. …”
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Single-Cell RNA Sequencing Identifies Crucial Genes Influencing the Polarization of Tumor-Associated Macrophages in Liver Cancer by Kedong Xu, Mingyi Dong, Zhengqiang Wu, Linfei Luo, Fei Xie, Fan Li, Hongyan Huang, Fenfen Wang, Xiaofeng Xiong, Zhili Wen

“…Employing trajectory analysis, survival analysis, and immune infiltration correlation, we scrutinized and validated genes likely directing M2 polarization. …”
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