The Effect of Gut Microbiome Perturbation on the Bioavailability of Glycyrrhizic Acid in Rats by Tiantian Shi, Huifang Li, Zihao Zhang, Yuying Zang, Shu Jiang, Tianjie Yuan

“…Pharmacokinetic parameters were evaluated by LC-MS, and 16S rRNA sequencing was applied to analyze the gut microbiome composition. The transcriptome analysis of Caco-2 cells was used to elucidate the regulation mechanism of polar metabolites resulting from gut microbiome perturbation. …”
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Genome-Wide Analysis Reveals Expansion and Positive Selection of Monocarboxylate Transporter Genes Linked to Enhanced Salinity and Ammonia Tolerance in <i>Sinonovacula constricta</... by Yiping Meng, Liyuan Lv, Hanhan Yao, Zhihua Lin, Yinghui Dong

“…Moreover, positive selection analysis revealed three positive selection sites in the <i>MCT</i> amino acid sequences sites. Multi-transcriptome analyses and the temporal expression patterns displayed that <i>ScSMCTs</i> and <i>ScMCTs</i> play distinct roles in response to salinity and ammonia stressors. …”
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Bacterial communities associated with ambrosia beetles: current knowledge and existing gaps by Juan Carlos Cambronero-Heinrichs, Juan Carlos Cambronero-Heinrichs, Peter H. W. Biedermann, Laura Besana, Andrea Battisti, Davide Rassati

“…In this review, we synthesize current knowledge on the bacterial microbiota of ambrosia beetles, identify critical gaps in the field, and provide recommendations for future research. To date, eight metabarcoding studies have explored bacterial communities in ambrosia beetles, analyzing a total of 13 species, mostly within the tribe Xyleborini (Scolytinae). …”
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Machine learning-based identification of co-expressed genes in prostate cancer and CRPC and construction of prognostic models by Changhui Fan, Zhiheng Huang, Han Xu, Tianhe Zhang, Haiyang Wei, Junfeng Gao, Changbao Xu, Changhui Fan

“…Abstract The objective of this study was to employ machine learning to identify shared differentially expressed genes (DEGs) in prostate cancer (PCa) initiation and castration resistance, aiming to establish a robust prognostic model and enhance understanding of patient prognosis for personalized treatment strategies. mRNA transcriptome data associated with Castration-Resistant Prostate Cancer (CRPC) were obtained from the GEO database. …”
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Cloning, structural and function analysis of MiMYB44L gene in kernels of Macadamia integrifolia by XU Peng, TAN Qiujin, SONG Haiyun, ZHENG Shufang, YANG Xiaozhou, HUAN Xiuju, ZHANG Tao, ZHOU Chunheng, WEI Yuanrong, WANG Wenlin*

“…In order to further explore the main regulatory genes related to nutrient formation in M. integrifolia kernels, transcriptomics, gene cloning, fluorescence quantification PCR and bioinformatics techniques were used to screen potential regulatory genes from the kernel transcriptomes of ‘Guire No. 1' and ‘A4', which have significantly different nutrient contents in M. integrifolia kernels. …”
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Genome-wide identification and expression analysis of the JMJ-C gene family in melon (Cucumis melo L.) reveals their potential role in fruit development by Wuyun Jin, Wei Yan, Ming Ma, Agula Hasi, Gen Che

“…Conclusions This study provides a comprehensive understanding of the gene structure, classification, and evolution of JMJ-C in melon and supports the clarification of the JMJ-C functions in further research.…”
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Identification of a novel chemotherapy benefit index for patients with advanced ovarian cancer based on Bayesian network analysis. by Shuxiao Ma, Lu Zhou, Yi Liu, Hui Jie, Min Yi, Chenglin Guo, Jiandong Mei, Chuan Li, Lei Zhu, Senyi Deng

“…<h4>Methods</h4>Based on The Cancer Genome Atlas (TCGA) transcriptome data, we conducted correlation and Bayesian network analyses to identify key genes strongly associated with chemotherapy prognosis. …”
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Molecular Adjuvant Potential of <i>GCSF</i> and <i>MCSF</i> in Starry Flounder Challenged with <i>Streptococcus parauberis</i> by Min-Young Sohn, Gyoungsik Kang, Kyung-Ho Kim, Ha-Jeong Son, Chan-Il Park

“…In this study, we performed transcriptome sequencing using next-generation sequencing (NGS) to identify and characterize granulocyte colony-stimulating factor (<i>GCSF</i>) and macrophage colony-stimulating factor (<i>MCSF</i>) in starry flounder (<i>Platichthys stellatus</i>). …”
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Deciphering hypoxia’s role in hepatocellular carcinoma prognosis with single-cell approaches by Jun Liang, Di Chen, Huiyu Liang

“…Conclusion Key transcription factors like NOP58, MED8 play pivotal roles in hypoxia-induced HCC invasion and metastasis, and a predictive model based on these factors forecasts HCC survival. Our findings provide novel molecular markers and therapeutic targets for HCC, highlighting the importance of considering the hypoxia TME in diagnostic and treatment strategies.…”
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Genome-Wide Identification of Cucumber <i>Lhc</i> Genes’ Family and Their Expression Analysis by Yongmei Miao, Kaijing Zhang

“…Analysis of the <i>cis</i>-acting elements in <i>CsLhc</i> promoters revealed their potential involvement in stress responses. Transcriptome data indicated that <i>CsLhcs</i> are minimally expressed in male flowers and roots, but highly expressed in other organs. …”
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Genome-wide identification, evolution, and expression analysis of StNRT (nitrate and peptide transporter) gene family in potato (Solanum tuberosum L.) by Zuxin He, Jian Wang, Weixiu Zhou, Heng Guo, Tiancang Na

“…Results Bioinformatics and transcriptome analyses of the StNRT gene family were conducted to dissect the structure, evolution, and expression of the StNRTs in Solanum tuberosum L. …”
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Key gene screening and diagnostic model establishment for acute type a aortic dissection by Yue Pan, Zhiming Yu, Xiaoyu Qian, Xuesong Zhang, Qun Xue, Weizhang Xiao

“…The multi-omics diagnostic model provides a novel tool for early screening, potentially reducing mortality through timely intervention. …”
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Characterizing genetic pathways unique to autism spectrum disorder at multiple levels of biological analysis by Lukas S. Schaffer, Sophie Breunig, Jeremy M. Lawrence, Isabelle F. Foote, Andrew D. Grotzinger

“…Finally, we implemented Transcriptome-Wide SEM (T-SEM) to explore patterns of gene-expression associated with uASD. …”
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Genome-wide identification, evolutionary analysis of 4CL gene family and expression analysis in banana by Mengge Wang, Liang Jia, Yanying Liu, Chunyu Zhang, Yukun Chen, Yuling Lin, Yuji Huang, Zhongxiong Lai

“…All protein members can interact with each other.Transcriptome expression analysis showed that Ma4CL3-2 expression was down-regulated and Ma4CL11-1 expression was up-regulated. …”
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Identification and Analysis of Stress-Associated Protein (SAP) Transcription Factor Family Members in <i>Pinus massoniana</i> by Yulu Zhao, Xingyue Ren, Jingjing Zhang, Wenya Yu, Qiong Yu, Kongshu Ji

“…The identification and preliminary analysis of <i>PmSAP</i> genes provided a theoretical foundation for understanding stress resistance mechanisms in <i>P. massoniana.…”
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Variant calling from RNA-Seq data reveals allele-specific differential expression of pathogenic cancer variants by Audrey Bollas, Jeffrey Gaither, Kathleen M. Schieffer, Peter White, Elaine R. Mardis

“…RNA sequencing (RNA-Seq) has become a crucial assay in cancer research, offering insights beyond those provided by DNA sequencing. This study introduces VarRNA, a novel method that utilizes RNA-Seq data to classify single nucleotide variants and insertions/deletions from tumor transcriptomes. …”
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A resource of longitudinal RNA-seq data of Holstein cow rumen, duodenum, and colon epithelial cells during the lactation cycle by Yahui Gao, George E. Liu, Li Ma, Cong-jun Li, Ransom L Baldwin

“…These tissues each serve critical and distinct roles in the digestion and absorption of nutrients and are all vital for providing the necessary substrates required for milk production. …”
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Matured hiPSC-derived cardiomyocytes possess dematuration plasticity by Fang Meng, Maxwell Kwok, Yen Chin Hui, Ruofan Wei, Alejandro Hidalgo-Gonzalez, Anna Walentinsson, Henrik Andersson, Frederik Adam Bjerre, Qing-Dong Wang, Ditte C. Andersen, Ellen Ngar-Yun Poon, Daniela Später, David C. Zebrowski

“…ScRNA transcriptome analysis supported that matured hiPSC-CMs treated with either nitrendipine or 1-NA-PP1 undergo dematuration. …”
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Application of single-cell sequencing technology to the study of embryonic developmental toxicity of emerging contaminants: Progress and perspectives by Weizhao CAO, Yunhui ZHANG

“…In recent years, single-cell RNA sequencing (scRNA-seq) technology has enabled the analysis of transcriptomes at the single-cell level, revealing cellular heterogeneity and the complexity of intercellular communication. …”
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Identification of a PANoptosis-related gene signature reveals therapeutic potential of SFRP2 in pulmonary arterial hypertension by Li Li, Mukamengjiang Juaiti

“…The immune landscape in PAH was characterized using the CIBERSORT algorithm, providing insights into immune cell composition and its role in disease progression. …”
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