Identification and expression pattern analysis of the C2H2 family in the whole genome of Agaricus bisporus by Mengjiao Tao, Yanqi Han, Songhan Liu, Xin Zhang, Liyun Ye, Nanyi Li

“…Quantitative PCR validation further substantiated the transcriptome data, confirming the pivotal role of the AbC2H2 family in regulating the growth and developmental pathways in Agaricus bisporus. …”
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Identification and expression analysis of PAL genes related to chlorogenic acid synthesis in Vaccinium dunalianum Wight by Xiuhua An, Guoze Li, Aiyi Chen, Ping Zhao, Yong Ding

“…In this study, seven PAL genes (VdPAL1–VdPAL7) were cloned and analyzed through full-length transcriptome sequencing combined with reverse transcription polymerase chain reaction (RT-PCR) amplification in V. dunalianum. …”
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Genome-wide characterization and expression profiling of MADS-box family genes during organ development and drought stress in Camelina sativa L by Somayeh Tahmasebi, Parisa Jonoubi, Mohammad Majdi, Ahmad Majd, Parviz Heidari

“…The detailed annotation and comprehensive transcriptome profiling provided in this research yield essential insights into the functional roles that MADS-box genes perform in stress resistance, as well as their contributions to growth and developmental processes. …”
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Radiogenomic analysis of clinical and ultrasonic characteristics in correlation to immune-related genes in breast cancer by Tingyao Dou, Yaodong Chen, Lunhang Liu, Yaochen Zhang, Wanru Pei, Jing Li, Yan Lei, Yanhong Wang, Hongyan Jia

“…Further analysis of these genes provides new ideas for the diagnosis and treatment of breast cancer.…”
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Genome-wide identification of invertase genes in sweetpotato and its response to nitrogen and planting densities by Zheng-yu Hu, Pei-xin He, Yu-jie Li, Hong-Juan Liu, Rafiq Ahmad, Izhar Ali, Cheng-cheng Si

“…Conclusion These observations underscore the expansion of IbINVs in sweetpotato and provide a theoretical basis for optimizing the interaction between nitrogen application and planting density in sweetpotato, allowing for more efficient nitrogen use and improved growth.…”
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The study on cuproptosis in Alzheimer’s disease based on the cuproptosis key gene FDX1 by Guilin Chen, Erwei Xi, Xiaozhen Gu, Huili Wang, Qiqiang Tang

“…Previous studies have shown neuronal death in the brains of AD patients, but the role of cuproptosis and its associated genes in AD neurons remains unclear.MethodsIntersection analysis was conducted using the AD transcriptome dataset GSE63060, neuron dataset GSE147528, and reported cuproptosis-related genes to identify the cuproptosis key gene FDX1 highly expressed in AD. …”
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The origin and evolution of cultivated rice and genomic signatures of heterosis for yield traits in super-hybrid rice by Yiyong Zhao, Tao Li, Daliang Liu, Hao Yin, Liang Wang, Song Lu, Houlin Yu, Xinhao Sun, Taikui Zhang, Quanzhi Zhao

“…Conclusions Our study provides robust evidence for the independent domestication of indica and japonica rice subspecies and elucidates the genomic features associated with heterosis in super-hybrid rice. …”
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Dietary protein/lipid ratio affects the growth performance and one-carbon metabolism mediated by folate in juvenile razor clam Sinonovacula constricta by Yuxiang Zhu, Kai Liao, Yang Liu, Hailong Huang, Yang Zhang, Hui Ge, Deshui Chen, Bin Ma, Jilin Xu

“…The lipid level of clam exhibited an upward trend as the dietary protein/lipid ratio decreased, and the appropriate protein/lipid ratio enhanced the activities of amylase, catalase, and superoxide dismutase. Transcriptome analysis showed that the pyrimidine/purine metabolism and one carbon pool by folate in the clam fed P41L6 diet was downregulated relative to those fed P34L10 and P27L14 diets. …”
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Enhancing ovarian cancer prognosis with an artificial intelligence-derived model: Multi-omics integration and therapeutic implications by You Wu, Kunyu Wang, Yan Song, Bin Li

“…The model's performance and biological insights provide a foundation for advancing precision medicine in ovarian cancer. …”
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A miR-JL-5 inhibitor modulates the proliferation of Nosema ceranae in Apis cerana by Xu Han, Xu Han, Jin Hua Xiao, Wei Yu Yan, Xu Jiang He, Xu Jiang He, Zhi Jiang Zeng, Zhi Jiang Zeng

“…Our results provide insights into role that microRNA regulates the proliferation of N. ceranae in Apis cerana.…”
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Detection of favorable QTL alleles and candidate genes for high pH tolerance in Chinese shrimp Fenneropenaeus chinensis via association and linkage maps by Zhaoxia Li, Jinye Wang, Chuanshi Jia, Chenhui Guan, Yuying He

“…By integrating with transcriptome data and functional annotations, we further verified four candidate genes: TCPG, TMEM9, PSA7, and ZNF773. …”
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Echinococcus granulosus sensu lato promotes osteoclast differentiation through DUSP4-MAPK signaling in osseous echinococcosis by Haohao Sun, Yaqing Liu, Yaqing Liu, Yiping Huang, Kangjun Xiong, Zhendong Zhang, Weishan Wang, Yi Dai, Jing Li, Qi Li, Sibo Wang, Chenhui Shi

“…Osteoclast differentiation and bone resorption were assessed using TRAP staining and F-actin immunofluorescence. Transcriptome sequencing identified DUSP4 as a key regulator. …”
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Investigation of the Effects of Salinity Exposure on Immune Defense, Morphology, and Gene Expression in the Gills of <i>Macrobrachium nipponense</i> by Shubo Jin, Rong Zhou, Hongtuo Fu, Wenyi Zhang, Hui Qiao, Yiwei Xiong, Sufei Jiang

“…In addition, we found no obvious morphological changes in the gills, indicating that <i>M. nipponense</i> can adapt well to water environments with such salinity. Transcriptome profiling analysis identified 168, 434, and 944 differentially expressed genes (DEGs) when comparing S0 vs. …”
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Genome-Wide Identification of <i>UGT</i> Genes and Analysis of Their Expression Profiles During Fruit Development in Walnut (<i>Juglans regia</i> L.) by Danhua Shi, Jinyu Yang, Gengyang Li, Yuanting Zhou, Pei Yao, Yanyu Shi, Jieyun Tian, Xiaojun Zhang, Qunlong Liu

“…In conjunction with transcriptome analysis and quantitative expression, approximately 39% of <i>UGT</i> genes in walnut exhibited high expression levels during early fruit development. …”
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Prognostic risk model of six m7 g-related lncRNAs in lung adenocarcinoma by Kaijun Long, Kai Wang, Manjun Gao, Yao Wang, Yang Tang, Cheng Chen, Xixian Ke

“…This study aimed to explore the prognostic value of an m7G-related lncRNAs model in LUAD. Methods Transcriptome and clinical data of LUAD patients were downloaded from the TCGA database. …”
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Synergistic effects of 5-fluorouracil in combination with salinomycin promoted ferroptosis via inhibiting SLC7A11/GPX4 in colorectal cancer by Can Wang, Junyang Wang, Fei Xing, Ning Liu, Xudong Wang

“…Wound healing and migration and invasion experiments were used to identify changes in migration and invasion capabilities under the influence of different drugs. Transcriptome sequencing is used to explore the molecular mechanisms of drugs. …”
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DTC-m6Am: A Framework for Recognizing N6,2′-O-dimethyladenosine Sites in Unbalanced Classification Patterns Based on DenseNet and Attention Mechanisms by Hui Huang, Fenglin Zhou, Jianhua Jia, Huachun Zhang

“…In this study, we present a robust and reliable deep learning model, DTC-m6Am, for identifying m6Am sites across the transcriptome. …”
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Identification and analysis of major latex protein (MLP) family genes in Rosa chinensis responsive to Botrytis cinerea infection by RNA-seq approaches by Haoyuan Chen, Qingkui Li, Peilei Cheng, Taotao Yan, Chunlan Dong, Zhe Hou, Peihuang Zhu, Changbing Huang

“…In summary, our research results underscore the potential importance of the RcMLP gene family in response to B. cinerea infection and provide comprehensive basis for further function exploration of the MLP gene family in rose resistance to fungal infections.…”
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Viral-mediated knockdown of Atxn2 attenuates TDP-43 pathology and muscle dysfunction in the PFN1C71G ALS mouse model by Zachary C. E. Hawley, Xueying Li, Dora Bodnar, Yuanzheng Gu, Yi Luo, Daniel Ferretti, Adam Sheehy, Rachelle Driscoll, Maria I. Zavodszky, Shaolong Cao, Isabel Isaza, Luke Jandreski, Yuqing Liu, Thomas Carlile, Shih-Ching Lo, Anna Grimard, Shawn Bourque, Aditya Utturkar, Samantha Desmarais, H. Moore Arnold, Dann Huh, Edward Guilmette, Deborah Y. Kwon

“…Notably, impaired regulation of the PFN1C71G skeletal muscle transcriptome exceeds that of the spinal cord and is also improved by Atxn2 reduction in the CNS. …”
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CNGC20 plays dual roles in regulating plant growth and immunity in Brassica napus by Yingying Tan, Guowei Huang, Haiyan Fan, Tao Wu, Zhilin Guan, Kede Liu

“…The enhanced immunity improves the resistance to Leptosphaeria biglobosa and Sclerotinia sclerotiorum. Transcriptome analysis further revealed that CNGC20 plays dual roles in regulating plant growth and immunity via the brassinosteroid and auxin signaling pathways. …”
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