Pilot Study on the Profiling and Functional Analysis of mRNA, miRNA, and lncRNA in the Skeletal Muscle of Mongolian Horses, Xilingol Horses, and Grassland-Thoroughbreds by Wenqi Ding, Wendian Gong, Tugeqin Bou, Lin Shi, Yanan Lin, Huize Wu, Manglai Dugarjaviin, Dongyi Bai

“…Whole-transcriptome analysis identified 105 differentially expressed genes (DEGs) in the CY vs. …”
Get full text

Genome-wide identification, characterization, and expression analysis of the MADS-box gene family in grass pea (Lathyrus sativus) under salt stress conditions by Mohamed Abdelsattar, Ahmed E. Nassar, Khaled H. Mousa, Ahmed Hussein, Manal M. S. El-Baghdady, Khaled H. Radwan, Manar S. Ibrahim, Achraf El Allali, Aladdin Hamwieh, Alsamman M. Alsamman, Zakaria Kehel

“…Results In this study, a comprehensive analysis of all MADS-box genes in grass pea was performed at both the genomic and transcriptomic levels. …”
Get full text

Machine learning-driven multi-omics analysis identifies a prognostic gene signature associated with programmed cell death and metabolism in hepatocellular carcinoma by Xiang Li, Donghao Yin, Jiahao Geng, Yanyu Xu, Zijing Xu, Xuemeng Yang, Quanwei Li, Zimeng Shang, Zhiyun Yang, Zhong Xu, Jiabo Wang, Enxiang Zhang, Xinhua Song

“…In parallel, consensus clustering analysis was performed to assess the grouping efficiency of the model-associated genes. …”
Get full text

Integrated promoter-capture Hi-C and Hi-C analysis reveals fine-tuned regulation of the 3D chromatin architecture in colorectal cancer by Ajay Kumar Saw, Ayush Madhok, Anupam Bhattacharya, Anupam Bhattacharya, Soumyadeep Nandi, Sanjeev Galande, Sanjeev Galande

“…The primary goal is to examine how genomic structural alterations shape the epigenomic landscape in CRC and to assess their potential role in colorectal cancer susceptibility.Methods:PCHi-C and Hi-C datasets from multiple colorectal cancer (CRC) studies were integrated to enhance the resolution of chromatin interaction mapping. The analysis focused on identifying fine-scale interactions within topologically associated domains (TADs) while incorporating histone modification landscapes (H3K27ac, H3K4me3) and transcriptomic signatures from CRC cell lines and the TCGA database. …”
Get full text

Genome-Wide Identification of <i>UGT</i> Genes and Analysis of Their Expression Profiles During Fruit Development in Walnut (<i>Juglans regia</i> L.) by Danhua Shi, Jinyu Yang, Gengyang Li, Yuanting Zhou, Pei Yao, Yanyu Shi, Jieyun Tian, Xiaojun Zhang, Qunlong Liu

“…In conjunction with transcriptome analysis and quantitative expression, approximately 39% of <i>UGT</i> genes in walnut exhibited high expression levels during early fruit development. …”
Get full text

Unveiling the mechanisms of ultrasonic radiation-induced free radical stress on algal communities: Insights into growth inhibition, photosynthetic disruption, and antioxidant defen... by Xiaoge Wu, Tingting Shen, Xiaoyang Liu, Guangming Zhang, Xiaoqing Qian, Wenlan Yang

“…Transcriptomic analysis of Microcystis aeruginosa revealed a profound reprogramming of gene expression in response to sonication. …”
Get full text

Functional Analysis of Promoters, mRNA Cleavage, and mRNA Secondary Structure on <i>esxB-esxA</i> in <i>Mycolicibacterium smegmatis</i> by Ryan G. Peters, Jessica M. Kelly, Sarah Bibeau, Ying Zhou, Scarlet S. Shell

Get full text

Comprehensive pan-cancer analysis indicates UCHL5 as a novel cancer biomarker and promotes cervical cancer progression through the Wnt signaling pathway by Lingling Bao, Yuefei Wu, Zhengting Ren, Yi Huang, Yue Jiang, Kailang Li, Xin Xu, Yingquan Ye, Zhongxuan Gui

“…Abstract Background UCHL5 was initially recognized as a multifunctional molecule. While recent research has highlighted its involvement in tumor malignant biological behaviors, its specific role in promoting tumor cell apoptosis has drawn particular attention. …”
Get full text

Decoding regulatory programs underlying placode and dermal condensate cell fate commitment during hair follicle induction via single‐cell multi‐omics analysis by Fang Li, Minghao Li, Tongtong Zhang, Menghua Sui, Hasan Khatib, Xin Wang

“…The chromatin accessibility of Twist2, Enpp2, Dkk1, and Sox2 varied from fibroblasts (Fb) to pre‐DC lineage, while that of Edar, Lhx2, and Wnt10b varied from Epi to Pc lineage. …”
Get full text

The functional and clinical significance of nucleoporin NUP153 across human cancers: a systematic study based on multi-omics analysis and bench work validation by Youfu He, Youfu He, Qing Wang, Zhaorui Wang, Menghui Duan, Yu Zhou, Jing Huang, Qiang Wu, Feichang Wu, Chen Li

“…Single-cell analysis and spatial transcriptomics further revealed that NUP153 expression drives proliferative states in mucus-producing cells in gastric cancer, and its expression was associated with immune cell infiltration patterns, particularly neutrophil and macrophage distribution in the tumour microenvironment.ConclusionOur findings indicate that NUP153 is a critical factor in multiple cancers, especially gastric cancer, where its elevated expression holds promise as a diagnostic and prognostic biomarker. …”
Get full text

Proteomic Analysis Reveals That Dietary Supplementation with Fish Oil Enhances Lipid Metabolism and Improves Antioxidant Capacity in the Liver of Female <i>Scatophagus argus</i> by Jingwei He, He Ma, Dongneng Jiang, Tuo Wang, Zhiyuan Li, Gang Shi, Yucong Hong, Chunhua Zhu, Guangli Li

“…Comparative proteomic analysis of liver tissue identified significant differential protein expression between groups. …”
Get full text

RIOK1: A Novel Oncogenic Driver in Hepatocellular Carcinoma by Chunyan Ruan, Tianyu Shang, Sijia Zhang, Wenhong Ru, Yuefeng Yang, Yi Shen

“…Furthermore, integrated transcriptomic and proteomic analysis revealed that RIOK1 may promote HCC cell proliferation by affecting the cell cycle and DNA repair pathways. …”
Get full text

A temperature-induced metabolic shift in the emerging human pathogen Photorhabdus asymbiotica by Elena Lucy Carter, Nicholas R. Waterfield, Chrystala Constantinidou, Mohammad Tauqeer Alam

“…Most insect-restricted species display temperature restriction, unable to grow above 34°C, while Photorhabdus asymbiotica can grow at 37°C to infect mammalian hosts and cause Photorhabdosis. …”
Get full text

Identification and validation of shared biomarkers and drug repurposing in psoriasis and Crohn’s disease: integrating bioinformatics, machine learning, and experimental approaches... by Xiaolong Li, Xiaolong Li, Hui Cao, Mutian Niu, Mutian Niu, Qingbo Liu, Bin Liang, Junfeng Hou, Junfeng Hou, Jian Tu, Jian Tu, Jintao Gao, Jintao Gao

“…Immune infiltration analysis underscored the involvement of hub genes in immune regulation, while single-cell transcriptomic analysis revealed the cellular localization of these hub genes. …”
Get full text

Decoding disease–specific ageing mechanisms through pathway-level epigenetic clock: insights from multi-cohort validationResearch in context by Pan Li, Jijun Zhu, Shenghan Wang, Haowen Zhuang, Shunjie Zhang, Zhongting Huang, Fuqiang Cai, Zhijian Song, Yuxin Liu, Weixin Liu, Sebastian Freidel, Sijia Wang, Emanuel Schwarz, Junfang Chen

Get full text

Expression Analysis of the Extensive Regulation of Mitogen-Activated Protein Kinase (MAPK) Family Genes in Buckwheat (<i>Fagopyrum tataricum</i>) During Organ Differentiation and S... by Guoqing Dong, Zihao Gui, Yi Yuan, Yun Li, Dengxiang Du

“…Among these, <i>FtMAPK3</i>, <i>FtMAPK4</i>, and <i>FtMAPK8</i> demonstrated highly significant changes across both treatments. Transcriptome analysis confirmed these findings, suggesting that these three genes play pivotal roles in Tartary buckwheat’s response to abiotic stress and hold potential for molecular breeding improvements.…”
Get full text

Genome-wide identification and functional analysis of R2R3-MYB genes in Acer pseudosieboldianum: insights into low temperature stress response and anthocyanin biosynthesis by Shikai Zhang, Dong Zeng, Heng Zhang, Luwei Ding, Dongyuan Guo, Peilin Sun, Zhiming Han, Guanzheng Qu, Tuya Siqin, Xiangling You

“…Cis-regulatory element analysis identified 34 genes enriched in low-temperature response motifs, while transcriptomic and qPCR validation highlighted 22 cold-responsive and 14 leaf color-associated ApseMYB genes, including ApseMYB31 (28-fold induction at 4 °C) and ApseMYB16 (52-fold upregulation during leaf reddening). …”
Get full text

Identification of the disulfidptosis-related key gene CD2AP as a potential biomarker and new therapeutic target for LUAD patients by comprehensive multi-omics analysis by Zhiwu Lin, Jing Lv, Chuanqiang Dai, Yuanwei Zhai, Jiudong Jiang, Yang Gao, Rulin Li, Jiangang Fan, Yang Yu, Liang Wu, Yanchun Yang

“…We employed transcriptomics, methylation analysis, immune infiltration assays, and spatial transcriptomics. …”
Get full text

Efficacy, safety, and biomarker analysis of first-line immune checkpoint inhibitors with chemotherapy versus chemotherapy for advanced gastric cancer: a multicenter, retrospective... by Xue Zhang, Xin Dai, Aina Liu, Meili Sun, Lei Cong, Jing Liang, Zimin Liu, Zhen Li, Jinling Zhang, Jing Lv, Fangli Cao, Linli Qu, Haiyan Liu, Lu Yue, Yi Zhai, Fujun Yang, Jiahui Chu, Shuang Wang, Qian Xu, Jianyuan Zhou, Shulun Nie, Miao Huang, Ruitao Xu, Qiushi Wang, Xinyu Song, Di Zhang, Zhaodi Nan, Song Li, Lian Liu

Get full text

Whole blood RNA-seq analysis reveals the immunomodulatory effects of a supplemental multi-strain direct-fed microbial in the diet of newly weaned beef steers1 by Adekunle Ajiboye, Samanthia Johnson, Modoluwamu Idowu, Yarahy Leal, Taylor Sidney, Godstime Taiwo, Ibukun M. Ogunade, Christopher Ashwell

“…We examined the effects of a blend of live Saccharomyces cerevisiae, multiple probiotic bacteria, and their fermentation products on the whole blood transcriptome of newly weaned beef steers during a 56-d receiving period. …”
Get full text