Multi-omics characterization of a lytic phage targeting Listeria monocytogenes by Stevan Cucić, Leena Putzeys, Maarten Boon, Dion Lepp, Rob Lavigne, Cezar M. Khursigara, Hany Anany

“…Profound changes in the host transcriptome became evident 5 min post-infection. GO enrichment and KEGG pathway analysis indicate a downregulation of host transcription factor expression and an upregulation of translation, cobalamin biosynthesis, and propanediol metabolism. …”
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The impact of Sarcocystis infection on lamb flavor metabolites and its underlying molecular mechanisms by Kang Zhang, Huan Teng, Huan Teng, Li Zhu, Bin Ni, Lai Jiewei, Li Shanshan, Zhao Yunong, Xiao Guo, DanQu Lamu

“…Phenolic and acidic metabolites were markedly upregulated, intensifying bitterness and sourness, while ketone and lactone metabolites were downregulated, reducing fatty and creamy aromas. Transcriptomic analysis identified 574 DEGs, including upregulated genes such as MAPK12, COX6A2, and RXRA, which are involved in lipid metabolism, fatty acid oxidation, and thermogenesis, and downregulated genes such as COX2, COX3, and ADIPOQ, which are associated with mitochondrial function and energy metabolism. …”
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Design and synthesis of 3,4-seco-Lupane triterpene derivatives: targeting tumor angiogenesis and inducing apoptosis in triple-negative breast cancer by Chunyu Gao, Chunyu Gao, Hongbo Teng, Hongbo Teng, Wenxin Zhang, Wenxin Zhang, Yaru Zhao, Yaru Zhao, Chunguo Cui, Zerbo Patrice, Liyan Wang, Liyan Wang, Yan Zhao, Yan Zhao

“…With the help of transcriptomics, the mechanism of action was explored and verified. …”
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Integrated multiomics analysis identifies PHLDA1+ fibroblasts as prognostic biomarkers and mediators of biological functions in pancreatic cancer by Rui Wang, Rui Wang, Guan-Hua Qin, Guan-Hua Qin, Yifei Jiang, Fu-Xiang Chen, Fu-Xiang Chen, Zi-Han Wang, Zi-Han Wang, Lin-Ling Ju, Lin Chen, Da Fu, En-Yu Liu, Su-Qing Zhang, Wei-Hua Cai

“…Here, we introduce a novel 7-gene risk model that not only robustly stratifies PC patients but also unveils the unique role of PHLDA1 as a key mediator in tumor-stroma crosstalk.MethodsBy integrating single-cell RNA sequencing (scRNA-seq), spatial transcriptomics, and bulk RNA sequencing data, we comprehensively characterized the heterogeneity of CAFs in PC. …”
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Integrative Omics Analysis Reveals Mechanisms of Anthocyanin Biosynthesis in Djulis Spikes by Chunmei Zheng, Wenxuan Ge, Xueying Li, Xiuzhang Wang, Yanxia Sun, Xiaoyong Wu

“…This research initially detected the anthocyanin content at different developmental stages of the spike and subsequently utilized an integrative approach, combining targeted metabolomics, transcriptomics, and untargeted metabolomics analyses, to elucidate the mechanisms of anthocyanin biosynthesis in the spikes of djulis. …”
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Molecular subtype of recurrent implantation failure reveals distinct endometrial etiology of female infertility by Jing Yang, Lingtao Yang, Ying Zhou, Fengyang Cao, Hongkun Fang, Huan Ma, Jun Ren, Chunyu Huang, Lianghui Diao, Qiyuan Li, Qionghua Chen

“…Methods We conducted a comprehensive computational analysis integrating publicly available endometrial transcriptomic datasets with prospectively collected samples. …”
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ABA Enhances Drought Resistance During Rapeseed (<i>Brassica napus</i> L.) Seed Germination Through the Gene Regulatory Network Mediated by ABA Insensitive 5 by Dan Luo, Qian Huang, Manyi Chen, Haibo Li, Guangyuan Lu, Huimin Feng, Yan Lv

“…Additionally, TFs involved in regulating the glutathione metabolism pathway were identified, providing insights into the collaboration of <i>ABI5</i> with other TF. …”
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Genus-Wide Pan-Genome Analysis of <i>Oryza</i> Calcium-Dependent Protein Kinase Genes and Their Related Kinases Highlights the Complexity of Protein Domain Architectures and Expres... by Fu Shi, Li Li, Mingjie Chen, Junli Chang, Min Tu, Guangyuan He, Yin Li, Guangxiao Yang

“…This study utilized evolutionary genomics approaches and provided the pan-genome repertoires of <i>CPKs</i> and their related kinases in 34 <i>Oryza</i> genomes by leveraging the rich genomics resources of the <i>Orzya</i> genus. …”
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Transcriptome analysis and reverse engineering verification of SNZ3Val125Ile and Pho3Asn134Asp revealed the mechanism of adaptive laboratory evolution to increase the yield of tyro... by Na Song, Huili Xia, Xiaoxue Yang, Siyao Liu, Linglong Xu, Kun Zhuang, Lan Yao, Shihui Yang, Xiong Chen, Jun Dai

“…Further reverse engineering verified that the mutation of SNZ3 promoted tyrosol synthesis in S. cerevisiae in glucose-rich medium. This study provides a theoretical basis for the metabolic engineering of S. cerevisiae to synthesise tyrosol and its derivatives. …”
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A single-cell landscape of the regenerating spinal cord of zebrafish by Lei Yao, Xinyi Cai, Saishuai Yang, Yixing Song, Lingyan Xing, Guicai Li, Zhiming Cui, Jiajia Chen

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Association Between Autoimmune Thyroid disease and Oral Lichen Planus: A Multi-Omic Genetic Analysis by Jie Ni, Xinjian Ye, Yitong Chen, Haizhou Fu, Ziqiong Wu, Haiping Lu, Qianming Chen

“…Conclusion: Our study provides novel evidence of a possible genetic association between AITD and OLP. …”
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Molecular Mechanisms of Gene Expression Regulation in Response to Heat Stress in <i>Hemerocallis fulva</i> by Boyan Chu, Weixue Liu, Jinxia Li, Xiaofei Zhang, Ping Li

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The mechanism of telomerase Cajal body protein 1 regulating senescence of mouse bone marrow mesenchymal stem cells by Shu-qian Lin, Nini Tian, Xiang Yao, Xing-hua Pan, Zi-an Li, Qiang Wang, Jin Gao, Xi-long Zhao, Guang-ping Ruan

“…This study confirmed that the expression of TCAB1 is closely related to the senescence of BMSC through molecular level, which provides a new technique for the clinical treatment of cell senescence.…”
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Identification of potential drug targets for pelvic organ prolapse using a proteome-wide Mendelian randomization approach by Ziwei Xie, Yuxin Feng, Yue He, Yingying Lin, Xiaohong Wang

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Enhancing TREM2 expression activates microglia and modestly mitigates tau pathology and neurodegeneration by Kai Chen, Fuyao Li, Shuwen Zhang, Yixing Chen, Tadafumi C. Ikezu, Zonghua Li, Yuka A. Martens, Wenhui Qiao, Axel Meneses, Yiyang Zhu, Gisela Xhafkollari, Guojun Bu, Na Zhao

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RnaXtract, a tool for extracting gene expression, variants, and cell-type composition from bulk RNA sequencing by Sophiane G. Bouirdene, Simon Gotty, Mickaël Leclercq, Charles Joly-Beauparlant, Emeric Texeraud, Steve Bilodeau, Arnaud Droit

“…Abstract RNA sequencing (RNA-seq) is a widely used method in transcriptomics research, offering insights into gene expression, variant discovery, and, when deconvoluted, the cellular composition of complex tissues. …”
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Morphotype-Specific Antifungal Defense in <i>Cacopsylla chinensis</i> Arises from Metabolic and Immune Network Restructuring by Jiayue Ji, Xin Gao, Zengli Hu, Ruiyan Ma, Longlong Zhao

“…These findings advance our understanding of <i>C. chinensis</i>/<i>B. bassiana</i> interactions, providing a basis for elucidating immune regulation in seasonally polymorphic insects. …”
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The Construction of ceRNA Regulatory Network Unraveled Prognostic Biomarkers and Repositioned Drug Candidates for the Management of Pancreatic Ductal Adenocarcinoma by Busra Aydin, Keziban Okutan, Ozge Onluturk Aydogan, Raghu Sinha, Beste Turanli

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Characterization of the WRKY family transcription factors in Astragalus membranaceus and their expression under drought stress by Jiemin Wang, Zhengpu Rong, Weihong Shi, Ye Zhang, Wenshuai Wang, Yuguang Zheng, Xiaowei Han, Huigai Sun

“…This study conducted a genome-wide identification of the Astragalus membranaceus (A. membranaceus) WRKY TF family, aiming at providing essential stress-tolerance genes for molecular breeding in A. membranaceus. …”
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Revealing the dynamic changes of metabolites and molecular mechanisms of chlorogenic acid accumulation during the leaf development of Vaccinium dunalianum based on multi-omic analy... by Anmian Zhang, Jiaxin Liu, Weicheng Li, Lihong Yang, Wenjin Duan, Ping Zhao, Zhiyu Pu, Yong Ding

“…Additionally, this study also reveals V. dunalianum holds promise as a natural antioxidant source for functional foods, providing data support for network pharmacology.…”
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