Pulsed Electric Field Treatment Modulates Gene Expression and Stress Responses in Fusarium-Infected Malting Barley by Pavel Svoboda, Jaroslava Ovesná, Štěpán Helmer, Milena Stránská

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Examining parent-of-origin effects on transcription and RNA methylation in mediating aggressive behavior in honey bees (Apis mellifera) by Sean T. Bresnahan, Ellen Lee, Lindsay Clark, Rong Ma, Michael Markey, Juliana Rangel, Christina M. Grozinger, Hongmei Li-Byarlay

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Molecular Mechanism During Mycelium Subculture Degeneration of <i>Volvariella volvacea</i> by Lidan Feng, Lujuan Wang, Yuanxi Lei, Jie Li, Fengyun Zhao

“…These findings could form a theoretical basis for the degeneration mechanism of <i>V. volvacea,</i> and also provide a basis for the molecular function study of the genes related to strain degradation.…”
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Investigation of the therapeutic effects and mechanisms of Houpo Mahuang Decoction on a mouse model of chronic obstructive pulmonary disease by Shanlan Li, Ziqi Dai, Tong Zhang, Zhuoqian Guo, Feng Gao, Xuehao Cheng, Jin An, Yixuan Lin, Xiaomin Xiong, Nan Wang, Guanghui Jiang, Bing Xu, Haimin Lei

“…Network pharmacology and transcriptomics further revealed the mechanism, indicating that the IL-17 signaling pathway might been instrumental in the inhibitory effect of HPMHD on mouse model of COPD. …”
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Multi-omics analysis identified macrophages as key contributors to sex-related differences in ulcerative colitis by Xiaojie Fang, Jiahao Yang, Liu Yang, Yiyou Lin, Yanyan Li, Xin Yin, Xiaobing Dou, Chenyun Miao

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Multi-omics analysis of Taiwanofungus gaoligongensis: effects of different cultivation methods on secondary metabolites by Tingwen He, Tingwen He, Tingwen He, Xiaolong Yuan, Liangjun Xiao, Tanggeran Hu, Yi Wang, Xiaolei Zhao, Xiaolei Zhao, Xiaolei Zhao, Lu Li, Lu Li, Chengbo Peng, Chengbo Peng, Chengbo Peng, Hongling Zhang, Hongling Zhang, Hongling Zhang, Yuan Zheng, Yuan Zheng, Yuan Zheng, Yuan Zheng

“…In addition, the levels of steroids, phenolic compounds, and flavonoids were also significantly increased in NZJB and XZJB. Transcriptome analysis revealed significant differences in the expression of genes involved in the biosynthesis of antcins and antrodin C across the different cultivation methods. …”
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Integrative genomic analysis identifies novel causal genes of Hodgkin’s and non-Hodgkin’s lymphoma by Patrick Shi, Ancha Baranova, Hongbao Cao

“…Methods We conducted integrative genomic analyses, including a transcriptome-wide association study (TWAS), a proteome-wide association study (PWAS), and a summary-data-based Mendelian randomization (SMR), to identify causal genes for NHL and HL. …”
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Transcriptional analysis of metastatic hormone-naïve prostate cancer primary tumor biopsies reveals a relevant role for SOX11 in prostate cancer cell dissemination by Natalia Martin-Martin, Saioa Garcia-Longarte, Jon Corres-Mendizabal, Uxue Lazcano, Ianire Astobiza, Laura Bozal-Basterra, Nicolas Herranz, Hielke van Splunder, Onintza Carlevaris, Mikel Pujana-Vaquerizo, María Teresa Blasco, Ana M. Aransay, Antonio Rosino, Julian Tudela, Daniel Jimenez, Alberto Martinez, Andrei Salca, Aida Santos-Martín, Sofía Rey, Aitziber Ugalde-Olano, David Gonzalo, Mariona Graupera, Roger R. Gomis, Joaquin Mateo, Miguel Unda, Enrique Gonzalez-Billalabeitia, Ana Loizaga-Iriarte, Isabel Mendizabal, Arkaitz Carracedo

“…Despite the extensive characterization of localized and metastatic castration-resistant prostate cancer, the molecular characteristics of mHNPC remain largely unexplored. Results Here, we provide the first extensive transcriptomics characterization of primary tumor specimens from patients with mHNPC. …”
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Multi-omics analysis of the mechanisms of abundant theacrine and EGCG3"Me in tea (Camellia sinensis) by Yanyu Zhu, Mengya Gu, Wentao Yu, Longhua Liao, Shuilian Gao, Shuyan Wang, Hongzheng Lin, Wenjing Gui, Youliang Zhou, Zhiming Chen, Jingde Zeng, Naixing Ye

“…Through integrated transcriptome-proteome-metabolome analysis, SAMS3, APRT1, IMPDH, and TCS1 were identified as critical enzymes for theacrine synthesis; while CHI1, CHI2, FLS2 and LAR1 were key for EGCG3"Me synthesis. …”
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gdGSE: An algorithm to evaluate pathway enrichment by discretizing gene expression values by Jiangti Luo, Qiqi Lu, Mengjiao He, Xiaobo Zhang, Xiang Yang, Xiaosheng Wang

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Obesity and cervical intraepithelial neoplasia: regulation of mitochondrial energy metabolism via the Kisspeptin/GPR54 signaling pathway by Jiajia Pan, Yuanyuan Chen, Yan Ye, Peipei Li, Feifei Ni, Haizhen He

“…Methods A clinical analysis of 980 samples was conducted to assess the correlation between Body Mass Index (BMI) and CIN grade. Transcriptomic analysis identified KISS1R as a key gene. …”
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GeNetFormer: Transformer-Based Framework for Gene Expression Prediction in Breast Cancer by Oumeima Thaalbi, Moulay A. Akhloufi

“…<i>Conclusions:</i> Our results show that GeNetFormer provides improvements over other models such as ST-Net and show how transformer architectures are capable of analyzing spatial transcriptomics data to advance cancer research.…”
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Spatiotemporal dynamic changes of meningeal microenvironment influence meningeal lymphatic function following subarachnoid hemorrhage: from inflammatory response to tissue remodeli... by Bingrui Zhu, Changming Liu, Ming Luo, Jiarui Chen, Sixuan Tian, Tiantong Zhan, Yibo Liu, Haocheng Zhang, Zhen Wang, Jianmin Zhang, Yuanjian Fang, Sheng Chen, Xiaoyu Wang

“…Methods We employed bioinformatics analysis of single-cell RNA sequencing and spatial transcriptomics to characterize the spatiotemporal dynamic changes in the early meningeal microenvironment post-SAH. …”
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Unveiling the role of TCF19 in intervertebral disc degeneration with single-cell and bulk RNA sequencing by Xianwei He, Liwei Wu, Hao Zhou

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Long-read RNA-sequencing reveals transcript-specific regulation in human-derived cortical neurons by Jishu Xu, Michaela Hörner, Elena Buena Atienza, Kalaivani Manibarathi, Maike Nagel, Stefan Hauser, Jakob Admard, Nicolas Casadei, Stephan Ossowski, Rebecca Schuele

“…Long-read RNA sequencing has transformed transcriptome analysis by enabling comprehensive mapping of full-length transcripts, providing an unprecedented resolution of transcript diversity, alternative splicing and transcript-specific regulation. …”
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PLXDC1+ Tumor‐Associated Pancreatic Stellate Cells Promote Desmoplastic and Immunosuppressive Niche in Pancreatic Ductal Adenocarcinoma by Yanhua Du, Yizhou Zhao, Judong Li, Jiaxin Wang, Shenglan You, Yao Zhang, Li Zhang, Jihong Yang, Hamid Alinejad‐Rokny, Shujie Cheng, Chenghao Shao, Duowu Zou, Youqiong Ye

“…Overall, this study provides key insights into PSCs in PDAC and potential therapeutic targets.…”
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<i>Bacillus velezensis</i> Isolate X5 Stimulates the Resistance of Resistant and Susceptible Banana Varieties to Foc Through Different Mechanisms by Yunlong Xu, Jun Wang, Guangxiang Tian, Changcong Liang, You Zhou, Lijia Guo, Yang Yang, Laying Yang

“…From the perspectives of metabolism, transcriptome, and key genes in important pathways, this study analyzed the composition and content changes of other types of signaling molecules, such as free amino acids and soluble sugars, in resistant/susceptible varieties. …”
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Cancer stem cells and tumor-associated macrophages as mates in tumor progression: mechanisms of crosstalk and advanced bioinformatic tools to dissect their phenotypes and interacti... by Francesco Verona, Sebastiano Di Bella, Roberto Schirano, Camilla Manfredi, Francesca Angeloro, Giulia Bozzari, Matilde Todaro, Matilde Todaro, Giuseppe Giannini, Giuseppe Giannini, Giorgio Stassi, Veronica Veschi

“…Nowadays, the integration of biological and computational data obtained by cutting-edge technologies (single-cell RNA sequencing, spatial transcriptomics, trajectory analysis) has significantly improved the comprehension of the biunivocal multicellular dialogue, providing a comprehensive view of the heterogeneity and dynamics of CSCs, and uncovering alternative mechanisms of immune evasion and therapeutic resistance. …”
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Spatiotemporal dynamics of benzylisoquinoline alkaloid gene expression and co-expression networks during Papaver Somniferum developmental stages by Zishi Wang, Quanzheng Yun, Jinyuan Hu, Zhen Wei, Deri Feng, Ning Li, He Xu, Lihong Fu, Zhenlong Wang, Shujin Li, Fangru Liu, Yan Wang, Bin Cong, Baishi Wang

“…This study employs transcriptome sequencing and weighted gene co-expression network analysis (WGCNA) to investigate the spatiotemporal expression patterns and regulatory networks of BIA-related genes across developmental stages and organs. …”
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Cathepsin D inhibits AGEs-induced phenotypic transformation in vascular smooth muscle cells by Xingmin He, Songhao Tian, Lixia Bu, Xinna Zhao, Liqiang Zheng, Peigang Zhang, Renwei Guo, Mingfeng Ma

“…This study highlights the critical role of CTSD in the phenotypic transformation of VSMCs induced by AGEs and provides a new perspective for cardiovascular and cerebrovascular disease treatment. …”
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