Multiomic analysis identifies natural intrapatient temporal variability and changes in response to systemic corticosteroid therapy in chronic rhinosinusitis by Michael Hoggard, Bincy Jacob, David Wheeler, Melissa Zoing, Kevin Chang, Kristi Biswas, Martin Middleditch, Richard G. Douglas, Michael W. Taylor

“…Conclusions Understanding natural dynamics of CRS‐associated tissues is essential to provide baseline context for all studies on putative biomarkers, mechanisms, and subtypes of CRS. …”
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Fermentation Kinetics and Gene Expression Patterns in Adenosine Biosynthesis by <i>Bacillus subtilis</i> by Gengxuan Yan, Haoqiong Wu, Shumei Zhang, Chunyan Liu, Yuan Tian, Chong Yu

“…This research elucidates key regulatory nodes in the adenosine biosynthesis of <i>Bacillus subtilis</i> and provides theoretical support and candidate targets for the targeted modification of industrial strains through metabolic engineering strategies.…”
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Evolutionary origin of the frameshift sites in the ribosomal frameshifting genes of Euplotes by Ruan-lin Wang, Xiao-yan Liu, Qing-yao Meng, Xin Zhang, Yue-jun Fu, Ai-hua Liang

“…In this study, we explored the possible evolutionary origin of the frameshift sites by comparative transcriptome and genome analyses. Results We sequenced the transcriptomes of different Euplotes octocarinatus strains and performed comparative analyses of the frameshift sites. …”
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Metabolic profiling and gene expression analyses shed light on the cold adaptation mechanisms of Saposhnikovia divaricata (Turcz.) Schischk by Ming Jiang, Yue Pan, Kanchao Yu, Yanshi Ma, Ying Cui, Yang Liu, Jicheng Liu, Keyong Zhang, Hui Li

“…Therefore, we elucidated the SD response to cold stress by transcriptome and metabolome analysis. Cold stress induced chlorosis and wilting in plants, thus leading to added function of antioxidant enzymes and higher levels of malondialdehyde, proline, soluble sugars. …”
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SiCST1, a novel plant-specific protein of foxtail millet, confers cold stress tolerance in plants by Fan Yang, Jiaqi Qiao, Xiao Zhang, Zhuoya Zhang, Dongao Huo, Dongao Huo

“…In this study, we identified a novel plant-specific gene, SiCST1 (Cold Stress Tolerance in Setaria italica 1) in foxtail millet, through transcriptome deep sequencing (RNA-Seq) of cold-stressed seedlings. …”
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A network analysis of gene co-expression in post-mortem brain tissues identifying novel genes and biological pathways underlying major depression by Miaomiao Yan, Man Chen, Qin Jiang, Huilan Huang, Yigao Wu

“…However, the potential pathogenesis and target genes of the disease have not been well illustrated.MethodsWe identified differentially expressed genes(DEG) using the published transcriptome data GSE80655 from postmortem brain tissues of 69 MDD patients, 71 Bipolar Disorder (BD) patients, and 71 Schizophrenia(SZ) patients and 70 controls. …”
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Genome-wide characterization of the BBX gene family in perennial ryegrass and functional insights into the potentiality of LpBBX3 in drought and salt tolerance by Qingchun Liu, Yi Song, Yanfeng Liu, Xiao Xu, An Shao, Meng Wei, Yang He, Xinpei Zhang, Wei Wang

“…Transcription factor regulatory network analysis predicted several key families, including ERF, MYB, and NAC, as potential upstream regulators of LpBBX genes. Transcriptome analysis showed that LpBBXs exhibited diverse expression patterns in different tissues and responded positively to drought stress. …”
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Effects of Tannin Supplementation in Diet on the Resistance to Ammonia Stress of Pacific White Shrimp Litopenaeus vannamei by Xiuhong Zhang, Han Gong, Ping Chen, Jiajia Wang, Zhao Chen, Zhiqiang Chang, Jitao Li

“…In this study, we fed a diet containing 800 mg/kg of tannin on Litopenaeus vannamei for 56 days and then subjected to acute ammonia stress for 48 hr to investigate the effect of dietary tannin on the ammonia stress response of L. vannamei through transcriptomic and metabolomic analysis. The transcriptome analysis indicated that ammonia stress-induced differential expression of 4,185 genes, while tannin-fed shrimp only had 964 differentially expressed genes. …”
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V-ATPase contributes to the cariogenicity of Candida albicans- Streptococcus mutans biofilm by Qian Jiang, Mengmeng Xu, Hong Chen, Yao Zhang, Yuting Sun, Li Tao, Zheng Wang, Deqin Yang

“…This study revealed for the first time the regulating effect of V-ATPase on the cariogenicity of C. albicans-S. mutans biofilm and its potential mechanisms. The results may provide basis for new strategies of ecological prevention and treatment of dental caries.…”
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Integrating mRNA and miRNA Weighted Gene Co-Expression Networks with eQTLs in the Nucleus Accumbens of Subjects with Alcohol Dependence. by Mohammed Mamdani, Vernell Williamson, Gowon O McMichael, Tana Blevins, Fazil Aliev, Amy Adkins, Laura Hack, Tim Bigdeli, Andrew D van der Vaart, Bradley Todd Web, Silviu-Alin Bacanu, Gursharan Kalsi, COGA Consortium, Kenneth S Kendler, Michael F Miles, Danielle Dick, Brien P Riley, Catherine Dumur, Vladimir I Vladimirov

“…Cell-type-specific transcriptome analyses revealed two of the mRNA modules to be enriched for neuronal specific marker genes and downregulated in AD, whereas the remaining four mRNA modules were enriched for astrocyte and microglial specific marker genes and upregulated in AD. …”
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Muscle stem cells in Duchenne muscular dystrophy exhibit molecular impairments and altered cell fate trajectories impacting regenerative capacity by Jules A. Granet, Rebecca Robertson, Alessio A. Cusmano, Romina L. Filippelli, Tim O. Lorenz, Shulei Li, Moein Yaqubi, Jo Anne Stratton, Natasha C. Chang

“…Here, we used single-cell RNA-sequencing (scRNA-seq) to determine how dystrophin deficiency impacts the satellite cell transcriptome and cellular composition by comparing satellite cells from mdx and the more severe D2-mdx DMD mouse models. …”
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Identification and validation of the diagnostic biomarker MFAP5 for CAVD with type 2 diabetes by bioinformatics analysis by Qiang Shen, Lin Fan, Chen Jiang, Dingyi Yao, Xingyu Qian, Fuqiang Tong, Zhengfeng Fan, Zongtao Liu, Nianguo Dong, Chao Zhang, Jiawei Shi

“…Given that type 2 diabetes is an important risk factor for CAVD, we identified key genes associated with diabetes - related CAVD via various bioinformatics methods, which provide further potential molecular targets for CAVD with diabetes.MethodsThree transcriptome datasets related to CAVD and two related to diabetes were retrieved from the Gene Expression Omnibus (GEO) database. …”
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Discovering a novel glycosyltransferase gene CmUGT1 enhances main metabolites production of Cordyceps militaris by Rong-an He, Chen Huang, Chun-hui Zheng, Jing Wang, Si-Wen Yuan, Bai-Xiong Chen, Kun Feng

“…Therefore, in this study, we performed transcriptome analysis across four different developmental stages of C. militaris to target the putative glycosyltransferase gene CmUGT1, which plays important roles in metabolite production. …”
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Integrated omics profiling of individual variations in intestinal damage to the soybean allergen in piglets by Mengmeng Mi, Yaqing Zheng, Xin Fu, Nan Bao, Li Pan, Guixin Qin, Yuan Zhao

“…Soybean antigens affect the intestinal nutrient utilization and metabolism of piglets, which provides a scientific reference for the study of soybean antigen sensitization mechanisms, precision nutrition, disease prevention, and control of piglets, and also lays a foundation for human foodborne diseases.…”
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Genome-wide identification and expression profiling of the SWEET family in Actinidia polygama (Sieb. & Zucc.) Maxim. by Li Chen, Hui-Fang Song, Jia-Xin Liu, Xu-Xin Jiang, Jun Ai, Zhen-Xing Wang, Yun-Peng Wang

“…Although SWEET family members had been identified in many plants, transcriptome or genomics analysis of Actinidia polygama SWEET genes remains uncharacterized. …”
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Identification and expression analysis of bHLH transcription factors family in Rhododendron delavayi by WANG Hongfei1, OU Jing1*, WANG Xiaojing2, KE Ke3, FAN Yu1, ZHOU Yumei1, FAN Xinyue1

“…These research findings provide a theoretical basis for further investigations into the biological functions of RdbHLH genes and establish target gene resources for the breeding of superior horticultural varieties of R. delavayi.…”
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Plant long noncoding RNAs: why do we not know more? by Paulina Kościelniak, Łukasz Walas, Agata Konecka, Włodzimierz Buraczyk, Ewelina A. Klupczyńska

“…Key resources include GenBank, Ensembl, the 1000 Genomes Project, and GTEx, which provide detailed information on genome sequences, genetic variation, and gene expression in different tissues. …”
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Identifying Potential New Gene Expression-Based Biomarkers in the Peripheral Blood Mononuclear Cells of Hepatitis B-Related Hepatocellular Carcinoma by Vahdat Poortahmasebi, Ahmad Nejati, Mohammad Foad Abazari, Mohsen Nasiri Toosi, Azam Ghaziasadi, Nader Mohammadzadeh, Ahmad Tavakoli, Azam Khamseh, Navid Momenifar, Omid Gholizadeh, Mehdi Norouzi, Seyed Mohammad Jazayeri

“…Conclusion. This study provides us with new horizons into the biological process and potential prospective clinical diagnosis and prognosis of HCC in the near future.…”
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Genome-wide identification, expression analysis of the R2R3-MYB gene family and their potential roles under cold stress in Prunus sibirica by Xin Zhao, Shipeng Wang, Hongrui Zhang, Shengjun Dong, Jianhua Chen, Yongqiang Sun, Yueyuan Zhang, Quangang Liu

“…Protein interaction studies revealed collaborative regulation of the PsMYB proteins with Arabidopsis protein, and transcriptome analysis identified PsMYB genes that were highly expressed at low temperatures. …”
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Genome-Wide Identification and Analysis of the <i>CCT</i> Gene Family Contributing to Photoperiodic Flowering in Chinese Cabbage (<i>Brassica rapa</i> L. ssp. <i>pekinensis</i>) by Wei Fu, Xinyu Jia, Shanyu Li, Yang Zhou, Xinjie Zhang, Lisi Jiang, Lin Hao

“…The specific expression patterns of the <i>BrCMF</i> gene in different tissues, as well as the transcriptome and RT-qPCR results under different photoperiodic conditions, were further analyzed. …”
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