Telomere-to-telomere Phragmites australis reference genome assembly with a B chromosome provides insights into its evolution and polysaccharide biosynthesis by Jipeng Cui, Rui Wang, Ruoqing Gu, Minghui Chen, Ziyao Wang, Li Li, Jianming Hong, Suxia Cui

“…Based on multi-tissue transcriptomic data, we identified structural genes in the biosynthetic pathway of pharmacologically active Phragmitis rhizoma polysaccharides with essential roles in rhizome development. …”
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Identification of differentially expressed genes and proteins related to diapause in Lymantria dispar: Insights for the mechanism of diapause from transcriptome and proteome analys... by Qing Xie, Xiaofan Ma, Yafei Li, Wenzhuai Ji, Fengrui Dou, Xiue Zhu, Juan Shi, Yixia Cao

“…This study elucidates the diapause mechanism of spongy moth at the gene and protein levels, providing theoretical insights into the early and precise prevention and control of spongy moth. …”
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An annotated CNS transcriptome of the medicinal leech, Hirudo verbana: De novo sequencing to characterize genes associated with nervous system activity. by Adam J Northcutt, Eva K Fischer, Joshua G Puhl, Karen A Mesce, David J Schulz

“…Here, we generated the first de novo transcriptome assembly from the entire central nervous system of Hirudo verbana, with the goal of providing a molecular resource, as well as to lay the foundation for a comprehensive discovery of genes fundamentally important for neural function. …”
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Integrating Molecular Perspectives: Strategies for Comprehensive Multi-Omics Integrative Data Analysis and Machine Learning Applications in Transcriptomics, Proteomics, and Metabol... by Pedro H. Godoy Sanches, Nicolly Clemente de Melo, Andreia M. Porcari, Lucas Miguel de Carvalho

“…With the advent of high-throughput technologies, the field of omics has made significant strides in characterizing biological systems at various levels of complexity. Transcriptomics, proteomics, and metabolomics are the three most widely used omics technologies, each providing unique insights into different layers of a biological system. …”
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Development of a MVI associated HCC prognostic model through single cell transcriptomic analysis and 101 machine learning algorithms by Jiayi Zhang, Zheng Zhang, Chenqing Yang, Qingguang Liu, Tao Song

“…Lastly, we investigated immunotherapy responses and drug sensitivities between risk groups, providing novel therapeutic insights for liver cancer.…”
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Transcriptomics and Metabolomics Explain the Crisping Mechanisms of Broad Bean-Based Crisping Diets on Nile Tilapia (<i>Orechromis niloticus</i>) by Xiaogang He, Haoming Shu, Tian Xu, Minhui Yu, Honglin Li, Yanru Hu, Jiajun Mo, Chunxiang Ai

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A Novel Method to Profile Transcripts Encoding SH2 Domains in the <i>Patiria miniata</i> Mature Egg Transcriptome by Lauren Bates, Emily Wiseman, Alexis Whetzel, David J. Carroll

“…This work furthers research into egg activation by providing possible target proteins for future experiments and a novel method for identifying specific proteins of interest within a de novo transcriptome.…”
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Transcriptomic Analysis of the Spleen from Asian Seabass (<i>Lates calcarifer</i>) Infected with Infectious Spleen and Kidney Necrosis Virus by Hong-Yi Xin, Lim Xin Ying, Lee Ching Pei Carmen, Mookkan Prabakaran

“…Next-generation sequencing identified differentially expressed genes, providing a comprehensive overview of the transcriptional landscape in the spleen of ISKNV-infected fish. …”
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Molecular mechanisms of flowering time differentiation revealed by transcriptomic sequencing and de novo analysis in Chinese invasive populations of Ambrosia artemisiifolia by Xiao-Feng Yang, Xiao-Meng Li, Pär K. Ingvarsson, Chao Xi, Wan-Jin Liao

“…Differentially expressed genes (DEGs) across sampling times and flowering time groups were identified through transcriptome sequencing and analyses of DGE and WGCNA, and were partially annotated to circadian rhythm, light response and hormone response through GO enrichment. …”
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Extracellular vesicle-derived miRNA-mediated cell–cell communication inference for single-cell transcriptomic data with miRTalk by Xin Shao, Lingqi Yu, Chengyu Li, Jingyang Qian, Xinyu Yang, Haihong Yang, Jie Liao, Xueru Fan, Xiao Xu, Xiaohui Fan

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Integrated physiological, biochemical and transcriptomic analyses elucidate the response of alpine plant Lamiophlomis rotata (Benth.) Kudo to Low-Nitrogen stress by Liwen Zhong, Tingju Li, Jiasen Zhang, Jie Zhang, Jielin Zhang, Ling Li, Guopeng Chen, Shihong Zhong, Rui Gu

“…The species demonstrated nitrogen conservation strategies through enhanced assimilation and metabolic diversion into secondary biosynthesis, providing critical insights for alpine medicinal plant cultivation.…”
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Unravelling turbot (Scophthalmus maximus) resistance to Aeromonas salmonicida: transcriptomic insights from two full-sibling families with divergent susceptibility by Patricia Pereiro, Ricardo Tur, Miguel García, Antonio Figueras, Beatriz Novoa

“…Additionally, many DEGs overlapped with previously identified quantitative trait loci (QTLs) associated with resistance to A. salmonicida, providing further insights into the genetic basis of disease resistance. …”
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Claroideglomus etunicatum enhances Pteris vittata L. arsenic resistance and accumulation by mediating the rapid reduction and transport of arsenic in roots by Guofei Pan, YueZhen Xu, WeiZhen Li, Linyan Zan, Xueli Wang

“…To understand how AMF mediate P. vittata arsenic metabolism under arsenic stress, we performed P. vittata root transcriptome analysis before and after Claroideglomus etunicatum (C. etunicatum) colonization. …”
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Integrated single-cell and transcriptome sequencing to construct a prognostic model of M2 macrophage-related genes in prostate cancer by TANG Kairan, FENG Chengling, HAN Bangmin

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Lipidomics and Transcriptomics Revealed Dietary Complex Plant Extracts Improve Lipid Composition of <i>Longissimus dorsi Muscle</i> in Sheep by Hui Guo, Ruixue Nie, Wenwen Wang, Tao Guo, Chang Gao, Jinju Mao, Yuchao Hu, Na Liu, Xiaoping An, Yang Jia, Jingwei Qi, Yuan Wang

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Transcriptomics-based analysis of neurotoxic and reproductive effects in turbot (Scophthalmus maximus) after exposure to tris (2-chloroethyl) phosphate (TCEP) by Xiaoqian Zhou, Weifeng Liu, Bailin Cong, Aifang Deng, Jing Lin, Linlin Zhao, Shenghao Liu

“…This study aimed to investigate the toxic effects of TCEP on turbot by integrating physio-biochemical and transcriptomic analyses. Results TCEP exposure induced severe neuroendocrine disrupting effects in turbot. …”
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Genome-wide identification and transcriptome analysis of the cytochrome P450 genes revealed its potential role in the growth of Flammulina filiformis by Xun Liu, Xinmin Liang, Jing Han, Yuqin Cui, Mengting Lei, Bo Wang, Dinghong Jia, Weihong Peng, Xiaolan He

“…Conclusions These results provide a foundation for further exploration of the molecular evolution mechanism and potential functions of the CYP450 genes of F. filiformis in the regulation of growth and development.…”
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Liver Transcriptome Analysis Reveals a Potential Mechanism of Heat Stress Increasing Susceptibility to <i>Salmonella</i> Typhimurium in Chickens by Qi Zhang, Yvqing Zhu, Zixuan Wang, Qinghe Li, Guiping Zhao, Qiao Wang

“…By integrating inflammatory phenotypes, liver transcriptome profiles, and weighted gene co-expression network analysis (WGCNA), we systematically investigated the key regulatory factors through which heat stress affects host susceptibility to <i>Salmonella</i>. …”
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Integrated Metabolome and Transcriptome Analysis Reveals the Key Bitter Substances of <i>Pleioblastus amarus</i> Shoots at Different Developmental Stages by Limei Gong, Weijin Shi, Chunyan Mou, Shixing Zhou, Lin Xiao, Hongling Hu, Lihua Tu, Guirong Hou, Wei Ding, Congde Huang, Gang Chen

“…This research highlights key compounds and genes related to bitterness, providing a basis for future research on enhancing the nutritional value and flavor of <i>P. amarus</i> shoots.…”
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Comprehensive transcriptomic and metabolomic analyses reveal developmental changes in one-year-old and two-year-old Polygonatum cyrtonema hua by Liang Wu, Yuqin Qiu, Yuting Fang, Can Huang, Dawei Song, Duohui Li, Li Zhao, Haiyang Zhao, Lamei Qi, Lishang Dai

“…Overall, this study study integrates multi-omics techniques to demonstrate age-related changes in metabolites and genes profiles in P. cyrtonema, providing valuable insights for the identification of candidate genes involved in the biosynthesis of active substances.…”
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