Investigating age-related dynamics and transcriptional signatures of CD8⁺HLA-DR⁺ regulatory T lymphocytes: perspectives in understanding immune system aging by K. S. Matveeva, S. A. Rybtsov, D. V. Shevyrev

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Inflammatory factor CCL2 enhances the interaction between monocyte-macrophage cells and liver parenchymal cells to promote liver inflammation and fibrosis in biliary atresia by Xin Li, Shaowen Liu, Tengfei Li, Qianhui Yang, Yuqiang Chen, Yu Meng, Zhiru Wang, Yilin Zhao, Shujian Zhang, Liang Ge, Alimujiang Abudureyimu, Jianghua Zhan

“…Single-cell RNA sequencing (scRNA-seq), spatial transcriptomics (ST), and Mendelian randomization (MR) were integrated for analysis. …”
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Software and Resources of Modern Programming Languages for Bioinformatics and Computational Vaccinology Research of the New Coronavirus Infection by M. V. Sprindzuk, A. S. Vladyko, L. P. Titov, A. P. Konchits

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Cell-specific transcriptional signatures of vascular cells in Alzheimer’s disease: perspectives, pathways, and therapeutic directions by Soumilee Chaudhuri, Minyoung Cho, Julia C. Stumpff, Paula J. Bice, Özkan İş, Nilüfer Ertekin-Taner, Andrew J. Saykin, Kwangsik Nho

“…Additionally, the understudied niche of cerebrovascular cells, such as endothelial and mural cells, and their subtypes have been scrutinized for understanding cellular and transcriptional heterogeneity in AD. Here, we provide an overview of rich transcriptional signatures derived from recent single-cell and single-nucleus transcriptomic studies of human brain vascular cells and their implications for targeted therapy for AD. …”
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Nano-Titanium Dioxide Regulates the Phenylpropanoid Biosynthesis of Radish (<i>Raphanus sativus</i> L.) and Alleviates the Growth Inhibition Induced by Polylactic Acid Microplastic... by Lisi Jiang, Wenyuan Li, Yuqi Zhang, Zirui Liu, Yangwendi Yang, Lixin Guo, Chang Guo, Zirui Yu, Wei Fu

“…A total of 1673 differentially expressed genes (DEGs, 844 upregulated genes, and 829 downregulated genes) were detected by transcriptome analysis. Metabolomics analysis showed that 5041 differential metabolites were involved; they mainly include terpenoids, fatty acids, alkaloids, shikimic acid, and phenylpropionic acid. …”
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Construction of a Dataset for All Expressed Transcripts for Alzheimer’s Disease Research by Zhenyu Huang, Bocheng Shi, Xuechen Mu, Siyu Qiao, Gangyi Xiao, Yan Wang, Ying Xu

“…<b>Conclusions</b>: The newly developed transcriptome resource and the associated analysis tools offer a valuable contribution to AD research, providing deeper insights into the disease’s molecular mechanisms. …”
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Machine learning using scRNA-seq Combined with bulk-seq to identify lactylation-related hub genes in carotid arteriosclerosis by Gaoyan Liu, Ye Song, Shanxue Yin, Bo Zhang, Peng Han

“…By combining scRNA-seq and Bulk transcriptome data in this study, three lactylation-associated genes SOD1, DDX42 and PDLIM1 were identified in carotid atherosclerosis samples, providing targets for the diagnosis and treatment of carotid atherosclerosis samples.…”
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Predicting prognosis and immunotherapy response of ferroptosis-related genes in colorectal cancer by Hongyun Wei, Keyu Ren, Yanchun Jin, Yao Wen, Bin Cao, Yu Gan, Ying Shi, Zhihong Wu, Linlin Chen

“…Abstract To identify ferroptosis markers, which were associated with prognosis and immune response in colorectal cancer (CRC), we integrated spatial transcriptome, single-cell transcriptome, and bulk transcriptome data for analysis, and this multi-omics integration approach is an innovation that distinguishes this study from previous ones. …”
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Identification of novel potential biomarkers using bulk RNA and single cells to build a neural network model for diagnosis of liver cancer by Yingzheng Gao, Jiahao Chen, Weidong Du

“…We used multiple machine algorithms to find hub genes related to liver cancer, and constructed new artificial neural network models based on their transcriptome expression patterns to assist in the diagnosis of liver cancer. …”
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Genome-wide study and expression analysis of soybean ERF transcription factors and overexpression of GmERF205 enhances drought resistance in soybean by Nan Wu, Yongqi Feng, Tao Jiang, Zhaobo Li, Yulan Liu, Minghao Yuan

“…And the transcriptome results were validated by fluorescence qRT-PCR. …”
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Effects of high-temperature stress on gene expression related to photosynthesis in two jujube (Ziziphus jujuba Mill.) varieties by Lei Yang, Xiaojuan Yang, Bingqi Shen, Juan Jin, Lili Li, Dingyu Fan, Subina Xiaokelaiti, Qing Hao, Jianxin Niu

“…This study unveils critical photosynthetic genes involved in heat stress, providing a theoretical foundation for comprehending the molecular mechanisms underlying jujube heat tolerance.…”
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Comprehensive analysis of bioinformatics and system biology reveals the association between Girdin and hepatocellular carcinoma. by Tengda Huang, Hongying Chen, Hongyuan Pan, Tian Wu, Xiangyi Ren, Liwen Qin, Kefei Yuan, Fang He

“…<h4>Conclusion</h4>This study reveals the association between Girdin and hepatocellular carcinoma, providing novel clues for future research and treatment of hepatocellular carcinoma.…”
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Fibro-adipogenic progenitor cells in skeletal muscle unloading: metabolic and functional impairments by Margarita Sorokina, Danila Bobkov, Natalia Khromova, Natalia Vilchinskaya, Boris Shenkman, Anna Kostareva, Renata Dmitrieva

“…Abstract Background Skeletal muscle resident fibro-adipogenic progenitor cells (FAPs) control skeletal muscle regeneration providing a supportive role for muscle stem cells. …”
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Knockdown of human-specific lncRNA MEK6-AS1 improves osteogenic differentiation of senescent mesenchymal stem cells by CHEN Yunhua, LI Di, ZHAO Xiaoyan, CHEN Ming, LI Hongling, ZHAO Chunhua

“…RT-qPCR was used to detect the expression of MEK6-AS1 during senescence and osteogenic differentiation of human MSCs (hMSCs); Lentiviral knockdown technology was used to regulate the expression of MEK6-AS1 in the MSCs replicative senescence model. Transcriptome sequencing technology was utilized to analyze the effects of MEK6-AS1 on the transcriptome of hMSCs especially on genes and pathways related to osteogenic differentiation. …”
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Integrative omics analysis reveals the genetic basis of fatty acid composition in Brassica napus seeds by Yuting Zhang, Yunhao Liu, Zhanxiang Zong, Liang Guo, Wenhao Shen, Hu Zhao

“…Comparative analysis of transcriptome profiles suggests that BnaA09.PYRD may influence fatty acid composition by regulating energy metabolism during seed development. …”
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Early Regulation of Profibrotic Genes in Primary Human Cardiac Myocytes by Trypanosoma cruzi. by Aniekanabassi N Udoko, Candice A Johnson, Andrey Dykan, Girish Rachakonda, Fernando Villalta, Sammed N Mandape, Maria F Lima, Siddharth Pratap, Pius N Nde

“…Primary human cardiomyoctes (PHCM) exposed to invasive T. cruzi trypomastigotes were used for transcriptome profiling and downstream bioinformatic analysis to determine fibrotic-associated genes regulated early during infection process (0 to 120 minutes). …”
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Research on the construction of corneal endothelium transplantation with acellular amniotic membrane as a scaffold by Ya-Nan Chen, Rui-Qin Guo, Bo-Yu Liang, Hong-Qin Ke, Meng-Jie Dong, Ming-Fang He, Ji Yang, Hai Liu

“…Functional validation included immunofluorescence detection of tight junction proteins (ZO-1), transcriptome sequencing (RNA-seq), and quantitative PCR (qPCR) to analyze the expression of genes regulating barrier function, ion transport, and extracellular matrix synthesis. …”
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Phenylacetylglutamine produced from injury lung alveolar epithelial cells promotes the function of BMSCs by regulating NONRATT006276.2/Mapt pathway by Tianyun Yang, Juan Peng, Rongrong Ren, Lin Song

“…Abstract Mesenchymal stem cell (MSC)-based therapy regenerates damaged structures of the respiratory system and restores lung function, thus providing a promising therapeutic approach for chronic obstructive pulmonary disease. …”
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multiDGD: A versatile deep generative model for multi-omics data by Viktoria Schuster, Emma Dann, Anders Krogh, Sarah A. Teichmann

“…We present multiDGD, a scalable deep generative model providing a probabilistic framework to learn shared representations of transcriptome and chromatin accessibility. …”
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Identification of novel proteins associated with intelligence by integrating genome-wide association data and human brain proteomics. by Zheng Zhang, Yousong Zhu, Junlong Zhang, Wenbin He, Cheng Han

“…This study aimed to bridge this gap by integrating intelligence GWAS data with human brain proteomics and transcriptomics. We conducted proteome-wide (PWAS) and transcriptome-wide (TWAS) association studies, along with enrichment and protein-protein interaction (PPI) network analyses. …”
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