Mutagenesis of Highland barley (Hordeum vulgare L. Var. nudum) using nitrogen ion beam implantation: screening of phenotypic variations and comparative transcriptome analysis by Hao-Yue Yu, You-Huan Zhang, Hang Li, Hong Feng

“…These findings provide critical insights into the genetic and molecular mechanisms driving high-yield and stress-resilient traits in highland barley.…”
Get full text

Effect of paternal exposure to glyphosate and microcystin-LR on zebrafish (Danio rerio) fathers and progeny: An integrated investigation based on behavioral, histopathological, bio... by Wei Liu, Yanlei Yang, Jingyu Han, Yiyi Feng, Junguo Ma, Xiaoyu Li

“…Overall, these findings collectively provide robust evidence of intergenerational effects resulting from exposure to individual and combined GLY and MC-LR, especially regarding persistent impacts on behavioral parameters, which should be emphasized in future ecological and health risk assessments.…”
Get full text

Disclosing antifungal activity of Huangqin decoction upon Trichophyton mentagrophytes and exploring its potential inhibitory mechanisms through transcriptome sequencing and qRT-PCR by Su-Qing Yang, You-Jin Ge, Cheng-Ying Shen

“…Given the valued advantages of TCM such as broad-spectrum antifungal activity, low incidence of drug resistance and low toxicity, this study investigated the antifungal activity of HQD against T. mentagrophytes and explored the potential inhibitory mechanism, aimed to provide new clues for the treatment of dermatophytosis. …”
Get full text

Integrated metabolome and transcriptome analysis reveals potential mechanism during the bud dormancy transition of Astragalus membranaceus (Fisch.) Bge. var. mongholicus (Bge.) Hsi... by Huan Guan, Huan Guan, Yuhuan Zhao, Yuhuan Zhao, Qing Chen, Qianqian Zhang, Qianqian Zhang, Pengpeng Yang, Pengpeng Yang, Shuying Sun, Shuying Sun, Guilin Chen, Guilin Chen

“…A total of 1,069 differentially accumulated metabolites (DAMs) participated in amino acid and carbohydrate metabolism. Transcriptome analysis revealed 16,832 differentially expressed genes (DEGs). …”
Get full text

Single-Cell and Single-Nuclei transcriptomics profiling reveals dynamic cellular features in tumor-related adipose microenvironment of breast cancer patients with high BMI by Xiaoxiao Hu, Fang Jia, Lili Li, Wuzhen Chen, Leyi Zhang, Jun Pan, Sangsang Zhu, Zhen Wang, Jian Huang

“…Materials and methods: We unveiled a comprehensive cell atlas by employing single-cell (N = 27) and single-nuclei (N = 6) transcriptomics to address dynamic changes of immune and stromal cell components within WAT in high BMI population. …”
Get full text

Adaptive Responses of Large Yellow Croaker <i>Larimichthys crocea</i> to Ocean Acidification: Integrative Analysis of Gill and Kidney Transcriptomics and Antioxidant Enzyme Activit... by Ting Ye, Xiaoyan Zhang, Feng Liu, Xiao Liang, Dandan Guo, Bao Lou, Zhigang Xie

“…The lowest MDA content and the highest antioxidant enzyme activities (CAT, SOD, GSH-Px) were observed in <i>L. crocea</i> at pH 7.8, suggesting pH 7.8 was optimal for <i>L. crocea</i>. Transcriptomic analysis revealed distinct gene expression patterns between the gills and kidneys under acidification stress. …”
Get full text

Genetic and transcriptomic analyses of early-onset colon cancer (EOCC): a post hoc analysis of 2973 patients from two adjuvant randomized trials by A. Gandini, C. Gallois, H. Blons, C. Mulot, N. Agueeff, C. Lepage, R. Guimbaud, L. Mineur, J. Desramé, B. Chibaudel, A. de Reyniès, T. André, P. Laurent-Puig, J. Taieb

Get full text

Deciphering low-dose radiation-induced cytotoxic effects:The application of integrative transcriptomics and metabolomics analysis in lung organoid-based 3D in vitro model by Lihui Xuan, Jinhua Luo, Huiji Pan, Dafei Xie, Xin Huang, Yang Han, Chenjun Bai, Hua Guan, Ruixue Huang, Ping-Kun Zhou

“…In summary, our combined transcriptomic and metabolomic analysis of lung organoids provides an effective approach to understanding the biological effects of low-dose radiation exposure.…”
Get full text

Explore autophagy-related lncRNA-miRNA-mRNA ceRNA networks for diagnosis of early-onset schizophrenia through transcriptome analysis by Wei Hu, Wei Hu, Xinzhe Du, Xinzhe Du, Xinxia Wang, Xinxia Wang, Kexin Zhang, Kexin Zhang, Junxia Li, Junxia Li, Yao Gao, Yao Gao, Ting An, Hong Zhang, Yu Zhang, Zhiyong Ren, Yong Xu, Yong Xu, Yong Xu, Sha Liu, Sha Liu

“…Furthermore, all three diagnostic lncRNAs and five hub mRNAs were positively correlated with at least two types of immune infiltration.ConclusionThrough transcriptome analysis, we searched for diagnostic autophagy-related ceRNA networks, which provided valuable candidates for the early diagnosis of EOS.…”
Get full text

Identification of key genes associated with residual feed intake in small-sized meat ducks through integrated analysis of mRNA and miRNA transcriptomes by Dandan Geng, Chunyou Yuan, Xiaofan Li, Chenxiao Wang, Qixin Guo, Yong Jiang, Zhixiu Wang, Guohong Chen, Guobin Chang, Hao Bai

“…Hypothalamic samples from 6 HRFI and 6 LRFI ducks underwent transcriptomic analysis, including differential gene expression, gene ontology, Kyoto Encyclopedia of Genes and Genomes pathway analysis, weighted gene co-expression network analysis, and miRNA target prediction. …”
Get full text

Integrated Analysis Reveals Genetic Basis of Growth Curve Parameters in an F₂ Designed Pig Population Based on Genome and Transcriptome Data by Zhaoxuan Che, Jiakun Qiao, Fangjun Xu, Xinyun Li, Yunxia Zhao, Mengjin Zhu

“…However, the ability of single genome-wide association analysis (GWAS) and transcriptome analyses to identify valuable genes and variants is limited. …”
Get full text

Integration of Bulk and Single-Cell Transcriptomics Reveals BCL2L14 as a Novel IGKC+ T Cell-Associated Therapeutic Target in Breast Cancer by He J, Akhtar A, Li J, Wei Q, Yuan Y, Ran J, Ma Y, Chen D

Get full text

Integrated proteomics and transcriptomics analysis reveals key regulatory genes between ER-positive/PR-positive and ER-positive/PR-negative breast cancer by Zhengjia Lu, Jiao Yang, Yang Feng, Jia Ming

“…Kaplan–Meier curves, Gene Set Enrichment Analysis (GSEA), immune cell infiltration analysis, and OncoPredict drug sensitivity predictions were conducted to provide insights into the underlying mechanisms and clinical treatment strategies for this patient cohort. …”
Get full text

RNA-Seq data provide new insights into the molecular regulation of breast muscle glycogen reserves, a key factor in muscle function and meat quality in chickens by Philippe Bochereau, Sarah Maman Haddad, Elisabeth Le Bihan-Duval, Cécile Berri

Get full text

Opportunities, challenges and future perspectives of using bioinformatics and artificial intelligence techniques on tropical disease identification using omics data by S. M. Vidanagamachchi, K. M. G. T. R. Waidyarathna

Get full text

Prediction of hub genes in pulpal inflammation and regeneration using autoencoders and a generative AI approach by Pradeep K. Yadalam, Jogikalmat Krithikadatta, Prabhu M. Natarajan, Carlos M. Ardila

“…Abstract Pulpal inflammation and regeneration are crucial for enhancing endodontic treatment outcomes. Transcriptomic studies highlight the involvement of proinflammatory cytokines, NF-κB signaling, and stem cell activity. …”
Get full text

Insights into human melanocyte development and characteristics through pluripotent stem cells combined with single-cell sequencing by Jie Yang, Zihan Wang, Hang Zhou, Yuyun Xiong, Yumei Li, Yun-wen Zheng, Liping Liu

Get full text

The promising role of nanopore sequencing in cancer diagnostics and treatment by Xinming Su, Qingyuan Lin, Bin Liu, Chuntao Zhou, Liuyi Lu, Zihao Lin, Jiahua Si, Yuemin Ding, Shiwei Duan

“…Cancer arises from genetic alterations that impact both the genome and transcriptome. The utilization of nanopore sequencing offers a powerful means of detecting these alterations due to its unique capacity for long single-molecule sequencing. …”
Get full text

Metabolome and Transcriptome Analysis Reveals Molecular Mechanisms of Soil Amendment (Volcanic Ash) Alleviating Salt–Alkali Stress in Melons (<i>Cucumis melo</i> L.) by Lina Fu, Xiaoxin Tian, Wei Wang, Chunyan Wu

“…Our research elucidated the molecular mechanism of salt–alkali tolerance in thin-skinned melons, providing new references for improving salt–alkali tolerance and improving salt–alkali soil in the future.…”
Get full text

Transcriptome Analysis of the <i>CML</i> Gene Family in <i>Bletilla striata</i> and Regulation of Militarine Synthesis Under Sodium Acetate and Salicylic Acid Treatments by Kunqian Li, Mengwei Xu, Qingqing Li, Hongwei Li, Ya Xu, Delin Xu

Get full text