Circular Nucleic Acids Act as an Oncogenic MicroRNA Sponge to Inhibit Hepatocellular Carcinoma Progression by Qianyi Zhang, Pengcheng Sun, Guang Hu, Xuanyao Yu, Wen Zhang, Xuan Feng, Lan Yu, Pengfei Zhang

“…First, we identified tumor suppressor genes (TSGs) with abnormally low expression in hepatocellular carcinoma (HCC) tumor cells by transcriptomic analysis and targeted the upstream cancer miRNA clusters of these TSGs. …”
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Estimation of genetic parameters and genome-wide association study for carcass traits in native chickens by Xianghua Zhu, Houxue Cui, Nanxi Dong, Lu Liu

“…Conclusion In general, the findings in this study could facilitate the understandings of genetic mechanisms of carcass traits in chickens, and provide important variants and genes set for genomic breeding.…”
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Screening of qPCR Reference Genes in Quinoa Under Cold, Heat, and Drought Gradient Stress by Qiuwei Lu, Xueying Wang, Suxuan Dong, Jinghan Fu, Yiqing Lin, Ying Zhang, Bo Zhao, Fuye Guo

“…Crucially, normalization with unstable genes (<i>DHDPS96</i> and <i>EF03</i>) distorted expression profiles. This work provides validated reference standards for quinoa transcriptomics under abiotic stresses.…”
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Computational analysis of DEHP’s oncogenic role in colorectal cancer by Zhou Zhu, Jian Qin, Chungang He, Shuangyou Wang, Yaolin Lu, Shuai Wang, Xiaogang Zhong

“…Methods We integrated transcriptomic data from TCGA-COADREAD (41 normal and 476 cancer tissues) and GEO datasets (GSE32323 and GSE21510) to identify differentially expressed genes (DEGs) using the `limma` package. …”
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Virocell resource manipulation under nutrient limitation by Morgan M. Lindback, Cristina Howard-Varona, Jane Fudyma, Malak Tfaily, Matthew B. Sullivan, Melissa B. Duhaime

“…Here, we leverage transcriptomic, proteomic, and endo- and exo-metabolomic data from two Pseudoalteromonas virocells independently infected by unrelated dsDNA viruses, PSA-HS2 (HS2-virocells) and PSA-HP1 (HP1-virocells), to examine how phosphate limitation affects virocell resource manipulation intra- and extracellularly. …”
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Genome-Wide Identification of <i>PP2C</i> Gene Family in Oat (<i>Avena sativa</i> L.) and Its Functional Analyses in Response to ABA and Abiotic Stresses by Panpan Huang, Kuiju Niu, Jikuan Chai, Wenping Wang, Yanming Ma, Yanan Cao, Guiqin Zhao

“…Collectively, this study provides the first comprehensive genomic and functional characterization of the <i>PP2C</i> family in oat, offering valuable insights into their evolutionary diversification and functional specialization.…”
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Genome-Wide Identification and Expression of Neuropeptides and Their Expression Patterns After RNAi of CHH Genes in Pacific White Shrimp <i>Litopenaeus vannamei</i> by Long Zhang, Lichao Sun, Guanghao Song, Beibei Wang, Yanting Cui, Fei Liu, Yuquan Li, Zhongkai Wang

“…Furthermore, comparative transcriptomic analysis of the eyestalk revealed that the expression of the majority of neuropeptide genes was downregulated following the suppression of CHH and VIH gene expression. …”
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Unraveling shared diagnostic genes and cellular microenvironmental changes in endometriosis and recurrent implantation failure through multi-omics analysis by Dongxu Qin, Yongquan Zheng, Libo Wang, Zhenyi Lin, Yao Yao, Weidong Fei, Caihong Zheng

“…In this study, we integrated transcriptomic and single-cell sequencing data from the Gene Expression Omnibus (GEO) database to identify shared diagnostic genes and alterations in the cellular microenvironment between EMs and RIF. …”
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Effects of Mulberry Leaf Extract on the Liver Function of Juvenile Spotted Sea Bass (Lateolabrax maculatus) by Sishun Zhou, Hao Lin, Lumin Kong, Jianrong Ma, Zhongying Long, Huihui Qin, Zhangfan Huang, Yi Lin, Longhui Liu, Zhongbao Li

“…Through comparative transcriptomic analysis, it was indicated that ELM enhanced the hepatic lipids and carbohydrates metabolism ability, as manifested in the upregulation of expression of phosphatidate phosphatase, glucuronosyltransferase, inositol oxygenase, carbonic anhydrase, and cytochrome c oxidase subunit 2. …”
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Metabolic reprogramming and prognostic insights in molecular landscapes driven by glycolysis in ovarian cancer by Mingwei Wang, Qiaohui Ying, Yuncan Xing, Shuchang Dai, Jue Wang, Zhong Liu

“…Identifying glycolysis-related biomarkers could provide novel insights into prognosis and potential therapeutic targets for OC.The transcriptomic and clinical information of OC patients were obtained from The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), and Gene Expression Omnibus (GEO) databases. …”
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Oil trait and multi-omic analyses reveal the regulatory network of triacylglycerol and fatty acid accumulation in hexaploid Camellia oleifera across different harvesting stages by Jugang Wang, Jian Song, Xiaomin Gao, Jiali Wang, Tianyu Huang, Manmei Zeng, Zhoujun Zhu, Min Liu, Zuhua Wang

“…In this study, we combined oil trait measurements with multi-omics analyses (global transcriptomics, miRNA sequencing, proteomics, and metabolomics) across 3 harvest stages, using the hexaploid C. oleifera ‘Changlin 40’ genome as reference. …”
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Effects of valproate on the entry of inert hydrophilic markers and expression of tight junction associated genes in the neonatal brain and choroid plexus of a rat model of epilepsy... by Fiona Qiu, Katarzyna M. Dziegielewska, Mark D. Habgood, Yifan Huang, Norman R. Saunders

“…Brain cortex and choroid plexus transcriptomes from both rat strains were examined and compared for the expression of tight junction associated proteins. …”
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Innate immune pathway activation to modulate mesenchymal stromal cell (MSC) interactions with synovium and cartilage by Peter Linde, Lyndah Chow, Isabella Sabino, Zoë Williams, Renata Impastato, Steven Dow, Lynn Pezzanite

“…These results indicate that in vitro modeling of target cell responses to “licensed” MSC can provide new information on the MSC and target cell interactions, though ultimately the functional impacts of activated MSC need to be evaluated using in vivo models.…”
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Regulatory role of lncRNA MSTRG.11540.1 on the novel-m1192-3p/CYP2C70 axis in modulating albendazole resistance in Haemonchus contortus by Xindi Chen, Tengyu Wang, Xu Yan, Ya Su, Wa Gao, Chunxia Liu, Huilin Kou, Yu Yu, Xianran Meng, Wenlong Wang, Wenrui Guo

“…Furthermore, an egg hatch assay (EHA) was conducted to assess the impact of the lncRNA-mediated ceRNA axis on albendazole resistance. The aim was to provide insights into the molecular mechanisms by which lncRNAs may regulate drug resistance in H. contortus. …”
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Evaluating methods for integrating single-cell data and genetics to understand inflammatory disease complexity by Hope A. Townsend, Hope A. Townsend, Kaylee J. Rosenberger, Kaylee J. Rosenberger, Lauren A. Vanderlinden, Lauren A. Vanderlinden, Jun Inamo, Jun Inamo, Fan Zhang, Fan Zhang, Fan Zhang

“…Overall, while noting evolving single-cell technologies, our study provides key findings for integrating expanding fine-grained scRNA-seq, GWAS, and noncoding SNP resources to unravel the complexities of inflammatory diseases.…”
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Species-specific gene regulatory network rewiring mediated by the GATA-type regulator NsdD in Aspergillus by Heungyun Moon, Mi-Kyung Lee, Junha Shin, Sung Chul Park, Julio C. Rivera Vazquez, Daniel Amador-Noguez, Nancy P. Keller, Hee-Soo Park, Kap-Hoon Han, Jae-Hyuk Yu

“…To address this gap, we have conducted network-based multiomics analyses in two distantly related species, Aspergillus nidulans and Aspergillus flavus. Transcriptomic profiling reveals that NsdD regulates gene expression in a cell type- and species-specific manner. …”
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A phase separation-related gene signature for prognosis prediction and immunotherapy response evaluation in gastric cancer with targeted natural compound discovery by Yanjuan Jia, Yuanyuan Ma, Zhenhao Li, Wenze Zhang, Rukun Lu, Wanxia Wang, Chaojun Wei, Chunyan Wei, Yonghong Li, Xiaoling Gao, Tao Qu

“…These findings advance the understanding of PS regulation in GC and provide a framework for personalized therapy.…”
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Gene Expression Profiling of Mediators Associated with the Inflammatory Pathways in the Intestinal Tissue from Patients with Ulcerative Colitis by Gabriela Fonseca Camarillo, Emilio Iturriaga Goyon, Rafael Barreto Zuñiga, Lucero Adriana Salazar Salas, Ana Elena Peredo Escárcega, Jesús K. Yamamoto-Furusho

“…The aim of this study was to analyze a transcriptomic panel of mediators associated with the inflammatory pathways in the colonic mucosa of UC patients. …”
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Xanthosine alleviates myocardial ischemia–reperfusion injury through attenuation of cardiomyocyte ferroptosis by Yang Xu, Wenfeng Zhou, Zhongguo Fan, Yiwei Cheng, Yujia Xiao, Yu Liu, Xinxin Li, Zhenjun Ji, Yi Fan, Genshan Ma

“…Integrated drug affinity responsive target stability (DARTS)-based drug target screening and RNA-seq transcriptomic profiling elucidate XTS-mediated mechanisms against I/R injury. …”
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Mapping the rapid growth of multi-omics in tumor immunotherapy: Bibliometric evidence of technology convergence and paradigm shifts by Huijing Dong, Xinmeng Wang, Yumin Zheng, Jia Li, Zhening Liu, Aolin Wang, Yulei Shen, Daixi Wu, Huijuan Cui

“…While omics technologies (genomics, transcriptomics, proteomics, metabolomics)provide multidimensional molecular profiling, their synergistic potential with immunotherapy remains underexplored in large-scale trend analyses. …”
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