Integrated Multi-Omics Analysis to Investigate the Molecular Mechanisms Underlying the Response of <i>Auricularia heimuer</i> to High-Temperature Stress by Fang Lu, Xin Sun, Xiaodong Dai, Piqi Zhang, Yinpeng Ma, Yafei Xu, Lei Wang, Jiechi Zhang

“…In this study, we analyzed the physiological, transcriptomic, and metabolomic results of <i>A. heimuer</i> (variety “Hei29”) under high-temperature stress. …”
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Multi-tissue network analysis reveals the effect of JNK inhibition on dietary sucrose-induced metabolic dysfunction in rats by Hong Yang, Cheng Zhang, Woonghee Kim, Mengnan Shi, Metin Kiliclioglu, Cemil Bayram, Ismail Bolar, Özlem Özdemir Tozlu, Cem Baba, Nursena Yuksel, Serkan Yildirim, Shazia Iqbal, Jihad Sebhaoui, Ahmet Hacımuftuoglu, Matthias Uhlen, Jan Boren, Hasan Turkez, Adil Mardinoglu

“…In this study, we challenged rats with sucrose-sweetened water and investigated the potential effects of JNK inhibition by employing network analysis based on the transcriptome profiling obtained from hepatic and extrahepatic tissues, including visceral white adipose tissue, skeletal muscle, and brain. …”
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Unlocking the Potential of RNA Sequencing in COVID-19: Toward Accurate Diagnosis and Personalized Medicine by Heba M. Saad Eldien, Abdulrahman H. Almaeen, Ahmed Abo El Fath, Ahmed E. Taha, Rehab Ahmed, Hassabelrasoul Elfadil, Helal F. Hetta

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Integrated Cytological, Physiological, and Comparative Transcriptome Profiling Analysis of the Male Sterility Mechanism of ‘Xinli No.7’ <i>Pear</i> (<i>Pyrus</i> sp.) by Hao Li, Xiangyü Li, Yüjia Luo, Quanhui Ma, Zhi Luo, Jiayuan Xuan, Cuiyun Wu, Fenfen Yan

“…These findings provide theoretical insights into the molecular mechanisms of male sterility in ‘Xinli No.7’, supporting future genetic and breeding applications.…”
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Effects of High Temperature at Grain Filling Stage on Grain Quality and Gene Transcription in Heat-Sensitive Versus Heat-Tolerant Rice Cultivars by Yujian Guo, Hui Luo, Jiajie Yi, Yuqi Zhu, Xiaojie Ma, Yubing Jiang, Yanjiao Peng, Yunhua Xiao, Guilian Zhang, Xiong Liu, Huabing Deng

“…We selected these two varieties for transcriptome analysis after 14 days of HT treatment and found that the number of differentially expressed genes (DEGs) in 8XR274 was significantly less than that in 5W0076. …”
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Integrative RNA-seq and ATAC-seq analysis unveils antioxidant defense mechanisms in salt-tolerant rice variety Pokkali by Qiaoyu Yang, Yutong Zheng, Xitao Li

“…The identification of key genes involved in redox regulation provides valuable insights into the molecular basis of salt tolerance, offering potential targets for the genetic improvement of salt-sensitive rice varieties through breeding programs.…”
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A comprehensive analysis of the effect of quorum-sensing molecule 3-oxo-C12-homoserine lactone on Candida auris and Candida albicans by Fruzsina Kovács, Ágnes Jakab, Noémi Balla, Zoltán Tóth, Dávid Balázsi, Lajos Forgács, Andrea Harmath, Aliz Bozó, Ágota Ragyák, László Majoros, Renátó Kovács

“…In conclusion, the obtained findings on C. auris do not provide clear evidence that HSL mediated effects have any favourable consequences in terms of P. aeruginosa-C. auris co-colonisation and/or co-infections.…”
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Drought priming-induced low temperature stress tolerance in wheat: insight into stress memory dynamics by Yi Wang, Lihao Zheng, Jiamin Song, Jian Cai, Qin Zhou, Yingxin Zhong, Dong Jiang, Xiao Wang

“…Here, we integrated physiological, transcriptomic, and metabolomic analyses to identify key stress memory genes or metabolites associated with priming-induced low temperature tolerance in wheat. …”
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Analysis of 1,25-dihydroxyvitamin D genomic action in human enteroids and colonoids reveals multiple regulatory effects of vitamin D in human intestinal physiology by Zachary K. Criss, Kali Deans-Fielder, James C. Fleet, Sylvia Christakos, Noah Shroyer

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Incorporating gene expression and environment for genomic prediction in wheat by Jia Liu, Jia Liu, Andrew Gock, Kerrie Ramm, Sandra Stops, Tanya Phongkham, Adam Norman, Russell Eastwood, Eric Stone, Shannon Dillon

“…We demonstrate that combining less costly environmental covariates with conventional genomic data provides a practical alternative with similar gains to the transcriptome when environments are well characterised.…”
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The functions of DNA methyltransferases during the feeding and development of Haemaphysalis longicornis are potentially associated with lysosome pathways by Zhijun Yu, Tingwei Pei, Xinyue Shi, Chuks F. Nwanade, Ziyan Bing, Ziwen Gao, Jianglei Meng, Lu Li, Jingze Liu

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Alternative mRNA splicing in anthracycline-induced cardiomyopathy – a COG-ALTE03N1 report by Purnima Singh, David K. Crossman, Changde Cheng, Patrick J. Trainor, Noha Sharafeldin, Xuexia Wang, Liting Zhou, Lindsey Hageman, Saro H. Armenian, Frank M. Balis, Douglas S. Hawkins, Frank G. Keller, Melissa M. Hudson, Joseph P. Neglia, Jill P. Ginsberg, Wendy Landier, Smita Bhatia

“…Our findings suggest that differential alternative splicing events can provide additional insight into the peripheral blood transcriptomic landscape of anthracycline-induced cardiomyopathy. …”
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Combination of spatial transcriptomics analysis and retrospective study reveals liver infection of SARS-COV-2 is associated with clinical outcomes of COVID-19Research in context by Shiqi Chen, Yi Zhang, Asha Ashuo, Shu Song, Lunzhi Yuan, Weixia Wang, Cong Wang, Zunguo Du, Yangtao Wu, Dan Tan, Chenlu Huang, Jingna Chen, Yaming Li, Jinjin Bai, Huilin Guo, Zehong Huang, Yi Guan, Ningshao Xia, Zhenghong Yuan, Jiming Zhang, Quan Yuan, Zhong Fang

“…The 10x Genomics Visium CytAssist Spatial Gene Assay was designed to analyze liver transcriptomics. TCR CDR3 sequences were analyzed in DNA from liver tissues. …”
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Transcriptomic Profiling of <i>Misgurnus anguillicaudatus</i> Reveals the Anti-Inflammatory Action of <i>Lonicera japonica</i> Extract in Response to Lipopolysaccharide Challenge by Yue Zhao, Chen Wang, Qiuning Liu

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Epigenomic landscapes define differential Janus kinases inhibitor sensitivity in IFN-γ-primed human macrophages by Geunho Kwon, Yebin Park, Keunsoo Kang, Kyung-Hyun Park-Min, Kyuho Kang

“…Our findings elucidate JAKi responsiveness mechanisms through IFN-γ-induced epigenomic remodeling, providing insights into inflammatory regulation in RA and suggesting strategies to overcome JAKi resistance.…”
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Progress in multi-omics studies of osteoarthritis by Yuanyuan Wei, He Qian, Xiaoyu Zhang, Jian Wang, Heguo Yan, Niqin Xiao, Sanjin Zeng, Bingbing Chen, Qianqian Yang, Hongting Lu, Jing Xie, Zhaohu Xie, Dongdong Qin, Zhaofu Li

“…Collectively, this study encapsulates the pivotal advances in current OA research and prospects for future investigation, providing invaluable references for a deeper understanding and treatment of OA. …”
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Cadmium Exposure Disrupts Uterine Energy Metabolism and Coagulation Homeostasis During Labor in Institute of Cancer Research Mice: Insights from Transcriptomic Analysis by Yueyang Wang, Yichen Bai, Yi Wang, Yan Cai

“…<b>Conclusion:</b> This study successfully established a Cd exposure-induced uterine injury model, providing valuable references for human reproductive health research.…”
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Global Transcriptome and Correlation Analysis Reveal Cultivar-Specific Molecular Signatures Associated with Fruit Development and Fatty Acid Determination in Camellia oleifera Abel by Shaofeng Peng, Jia Lu, Zhen Zhang, Li Ma, Caixia Liu, Yongzhong Chen

“…The multiple phenotypic data revealed the dynamic law of changes during the picking stage. Transcriptomic analysis identified a large number of potential key regulatory factors that can control the oil content of dried kernels, oleic acid, linoleic acid, linolenic acid, fresh seed rate, and kernel-to-seed ratio, thereby providing a new insight into the molecular networks underlying the picking stage of oil-tea Camellia, which provides a theoretical basis for the optimal fruit picking point.…”
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Combined Network Pharmacology, Transcriptomics and Metabolomics Strategies Reveal the Mechanism of Action of Lang Chuang Wan to Ameliorate Lupus Nephritis in MRL/lpr Mice by Cuicui Li, Guoxin Ji, Xinru Zhang, Hang Yu, Zhimeng Li, Bo Yang, Zhuangzhuang Yao, Shilei Wang, Tongwei Jiang, Shumin Wang

“…Then, we further explored the mechanisms of action through network pharmacology, transcriptomics, and metabolomics, and validated with Western blot. …”
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Integrated transcriptome analysis and combinatorial machine learning to construct a homeostatic model of acetylation for ccRCC and validate the key gene GCNT4 by Baohua Zhu, Ziyang Mo, Yi Bao, Xinxin Gan, Linhui Wang

“…Conclusion This study constructed a ccRCC acetylation homeostasis model via transcriptome analysis and machine learning, validating GCNT4 as a key gene. …”
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