Transcriptomic and metabolomic insights into flavor variations in wild and cultivated Agaricus bisporus by Zhi-Xin Cai, Zhi-Heng Zeng, Wen-Zhi Chen, Zhong-Jie Guo, Yuan-Ping Lu, Jian-Hua Liao, Hui Zeng, Mei-Yuan Chen

“…These findings not only elucidate the impact of artificial cultivation on metabolic reprogramming in A. bisporus but also provide critical molecular targets for targeted breeding of strains with enhanced flavor and nutritional value, offering practical significance for advancing the edible fungi industry.…”
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HSPB1 Orchestrates the Inflammation-Associated Transcriptome Profile of Atherosclerosis in HUVECs by Gang Zhao, Li Zhao, Yulin Miao, Lei Yang, Lizhen Huang, Zhipeng Hu

“…Cellular phenotype was then assessed and transcriptome data (RNA-seq) was analyzed to identify the potential targets regulated by HSPB1. …”
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Study on yolk iron transportation in chick embryo eggs based on transcriptomics by Lulu Ma, Zhaowei Cui, Shuaishuai Wei, Jiaying Huo, Shijian Dong, Shugang Li

“…Chick embryo eggs have a complete system of iron release, delivery, and uptake and thus provide a useful tool to study the fast transportation and absorption of iron. …”
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Identification of predictors for bacterial meningitis diagnosis based on transcriptomics and genetic analysis by Hexiang Jiang, Xibing Yu, Jingyan Fan, Houhui Song, Yang Yang

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Transcriptomic Regulatory Mechanisms of Isoflavone Biosynthesis in <i>Trifolium pratense</i> by Kefan Cao, Sijing Wang, Huimin Zhang, Yiming Ma, Qian Wu, Fan Huang, Mingjiu Wang

“…In this study, we systematically analyzed 500 accessions of <i>T. pratense</i> for isoflavone content and performed RNA-seq-based transcriptomic profiling to investigate the molecular mechanisms underlying isoflavone biosynthesis. …”
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Single−cell transcriptomic landscape of sciatic nerve after transection injury by Yiben Ouyang, Mingqian Yu, Tieyuan Zhang, Haofeng Cheng, Liang Zuo, Haolin Liu, Yanjun Guan, Ao Liu, Jiajie Chen, Ruichao He, Sice Wang, Tianqi Su, Yixiao Tan, Yuhui Cu, Xiaochun Zhang, Xiaoyang Fu, Junli Wang, Jinjuan Zhao, Jiang Peng, Yu Wang

“…Together, this work provides a time−resolved single−cell atlas of peripheral nerve regeneration, defines key regulatory circuits within the immune–NF–Gli axis, and identifies phase−specific therapeutic targets—such as early Mac heterogeneity, NF4−mediated matrix remodeling, and Schwann cell remyelination—for enhancing functional recovery following severe nerve injury.…”
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Machine Learning-Driven Transcriptome Analysis of Keratoconus for Predictive Biomarker Identification by Shao-Hsuan Chang, Lung-Kun Yeh, Kuo-Hsuan Hung, Yen-Jung Chiu, Chia-Hsun Hsieh, Chung-Pei Ma

“…<b>Objective:</b> This study employed multiple machine learning algorithms to analyze the transcriptomes of keratoconus patients, identifying feature gene combinations and their functional associations, with the aim of enhancing the understanding of keratoconus pathogenesis. …”
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Sexual dimorphism in lung transcriptomic adaptations in fetal alcohol spectrum disorders by Vishal D. Naik, Dylan J. Millikin, Daniel Moussa, Hong Jiang, Alexander L. Carabulea, Joseph D. Janeski, Jiahui Ding, Kang Chen, Marta Rodriguez-Garcia, Sunil Jaiman, Stephen A. Krawetz, Gil Mor, Jayanth Ramadoss

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The BeeBiome data portal provides easy access to bee microbiome information by Valentine Rech de Laval, Benjamin Dainat, Philippe Engel, Marc Robinson-Rechavi

“…While each of these datasets by itself has provided important insights, the integration of such datasets provides an unprecedented opportunity to obtain a global picture of the microbes associated with bees and their link to bee health. …”
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Genomic and Transcriptomic Analysis to Explore the Biological Characteristics of <i>Cyclocybe chaxingu</i> by Qiang Yang, Haiyan Song, Ge Su, Xuncheng Wang, Haijing Hu, Zhijun Zhai, Minghui Chen, Jianping Zhou, Hua Yin, Yang Gao, Dianming Hu

“…Transcriptomic analysis revealed distinct gene expression patterns in mycelia, stipe, and cap, reflecting their functional specialization. …”
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SpaMask: Dual masking graph autoencoder with contrastive learning for spatial transcriptomics. by Wenwen Min, Donghai Fang, Jinyu Chen, Shihua Zhang

“…Recent advancements in spatial resolved transcriptomics (SRT) have enabled the analysis of gene expression while preserving the spatial context within tissues. …”
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SCNT: an R package for data analysis and visualization of single-cell and spatial transcriptomics by Jianbo Qing, Jialu Wu, Yafeng Li, Junnan Wu

“…The SCNT (Single-Cell, Single-Nucleus, and Spatial Transcriptomics Analysis and Visualization Tools) package was developed to address these challenges by providing an efficient and user-friendly tool for processing, analyzing, and visualizing SC and ST data. …”
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Transcriptomic HEPN1 signatures predict treatment response in low grade glioma by Lei Jiao, Shuhua Fang, Jianbo Zhang

“…Conclusion The system elucidates the mechanism of iron death related genes in glioma heterogeneity, providing an important theoretical basis for precise treatment of gliomas.…”
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Transcriptomic and Lipidomic Characteristics of Subcutaneous Fat Deposition in Small-Sized Meat Ducks by Hao Zheng, Cui Wang, Ao Zhou, Xing Chen

“…Furthermore, the transcriptomic analysis identified 265 differentially expressed genes (DEGs), including 119 down-regulated and 146 up-regulated genes. …”
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Transcriptome analysis of heterografting on key medicinal compounds accumulation in Ziziphi Spinosae Semen by Xiangrui Fu, Yinfeng Yu, Zikang Lu, Chaohui Wang, Lanping Guo, Yuping Yan, Donglai Ma, Xian Gu

“…Conclusions This study enhances understanding of the molecular mechanisms underlying the effects of heterografting on ZSS quality, providing significant implications for the cultivation and improvement of the quality of medicinal ZSS.…”
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Single-cell transcriptomes reveal spatiotemporal heat stress response in maize roots by Ting Wang, Fanhua Wang, Shuhan Deng, Kailai Wang, Dan Feng, Fan Xu, Weijun Guo, Jia Yu, Yue Wu, Hada Wuriyanghan, Shang-Tong Li, Xiaofeng Gu, Liang Le, Li Pu

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Recent Advances in Transcriptome Analysis Within the Realm of Low Arsenic Rice Breeding by Guanrong Huang, Guoping Yu, Huijuan Li, Haipeng Yu, Zengying Huang, Lu Tang, Pengfei Yang, Zhengzheng Zhong, Guocheng Hu, Peng Zhang, Hanhua Tong

“…Finally, the challenges associated with applying transcriptome analysis to low-As breeding are deliberated upon, and future research directions are envisioned, with the aim of providing references to expedite high-yield and low-arsenic breeding in rice.…”
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Proteomics and transcriptomics combined reveal specific immunological markers in autoimmune thyroid disease by Xia Chen, Hui Chen

“…This study employs a combination of proteomics and transcriptomics analysis to identify and validate specific immune response markers in patients with hyperthyroidism and hypothyroidism, thereby providing a scientific basis for the clinical diagnosis and treatment of AITD.MethodsBy collecting serum and whole blood tissue samples from patients with hyperthyroidism, hypothyroidism, and healthy controls, this study utilizes a combination of transcriptomics and proteomics to analyze changes in immune-related signaling molecules in patients. …”
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Cross-species transcriptome-wide meta-analysis of anterior cruciate ligament rupture by Livia Beccacece, Stefano Pallotti, Yiyun Li, Jie Huang, Leonardo Pasotti, Valerio Napolioni

“…This study aims to identify cross-species responses to ACL rupture providing insights on its molecular basis. We analyzed five publicly available transcriptomic datasets from Homo sapiens, Mus musculus, Canis lupus familiaris, and Oryctolagus cuniculus. …”
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Unraveling the transcriptomic effects of leucine supplementation on muscle growth and performance in basketball athletes. by Sinan Wang, Weishuai Guo, Rui Dong

“…WGCNA highlighted a key module associated with muscle growth, enriched in cytoskeletal pathways. qPCR validation confirmed the upregulation of cytoskeleton-related genes, supporting the transcriptomic findings. These results suggest that leucine enhances muscle adaptation by regulating cytoskeletal dynamics, providing molecular insights into its role in improving athletic performance.…”
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