Transcriptome-wide Identification and Expression Analysis of Brachypodium distachyon Transposons in Response to Viral Infection by Tuğba Gürkök

“…Transposable elements (TEs) are the most abundant group of genomic elements in plants that can be found in genic or intergenic regions of their host genomes. …”
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Integrated metabolome and transcriptome analysis of maize roots response to different degrees of drought stress by Yifan Wang, Luoluo Tong, Huiling Liu, Binyan Li, Renhe Zhang

“…Among these metabolites, lignin compounds emerged as the primary response to drought. Most lignin metabolites, including caffealdehyde, sinapyl alcohol, coniferaldehyde, p-coumaryl alcohol, and p-coumaric acid, showed a significant increase under MD but decreased under SD. …”
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Single-cell transcriptomic dynamics of scallop heart reveals the heterogeneous response to heat stress by Danyang Wang, Na Liu, Xiangfu Kong, Xinghai Zhu, Yangfan Wang, Jingjie Hu, Zhenmin Bao

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Host transcriptome response to Mycoplasma bovis and bovine viral diarrhea virus in bovine tissues by Anna K. Goldkamp, Randy G. Atchison, Shollie M. Falkenberg, Rohana P. Dassanayake, John D. Neill, Eduardo Casas

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Global transcriptome modulation by xenobiotics: the role of alternative splicing in adaptive responses to chemical exposures by Andrew J. Annalora, Jacki L. Coburn, Antony Jozic, Patrick L. Iversen, Craig B. Marcus

“…Conclusions This study demonstrates how xenobiotic structural features influence gene expression and splicing, revealing splicing patterns that expand our understanding of transcriptome diversity and function. By identifying regulatory mechanisms, including AHR activation, epitranscriptomic modulation, and crosstalk within SR protein networks, that shape adaptive responses to xenobiotic stress, this work offers insights into the splicing and transcriptional networks that maintain cellular homeostasis. …”
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Evaluating the response of Schizothorax prenanti to ammonia nitrogen stress using computer vision and transcriptomics by Yinhua Zhou, He Gao, Hejiao Li, Tianyi Shen, Yifan Yao, Zhilei Wang, Yuting Duan, Junting Li, Suxing Fu, Shidong Liu, Rongrong Liao, Haiping Liu, Luo Lei, Chaowei Zhou

“…Gill superoxide dismutase, catalase, and total antioxidant capacity activities were significantly decreased and malondialdehyde levels were increased. Transcriptomic analysis indicated that most differentially expressed genes (DEGs) in the M and H groups were enriched in pathways related to immune response, antioxidation, carbohydrate metabolism, and amino acid metabolism. …”
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Transcriptome Analysis Reveals Key Genes in Response to High-Temperature Stress in Rhododendron molle by Linshi Wu, Yan Liu, Xinyun Liu, Qiaoyun Li, Xinyu Yi, Chan Chen, Ling Wang, Juyang Liao

“…A Gene Ontology analysis (GO) revealed that these DEGs are mostly involved in stress response, catalytic activity, binding, transporter activity, and immune processes. …”
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Microalgae Pediastrum boryanum enhances growth and modulates physiology and transcriptome in Nile tilapia by Raghad E. Soliman, Ahmed Ateya, Mohamed Abou-El-Atta, Wasseem Emam, Mohamed M. Abdel-Rahim, Ashraf I. G. Elhetawy, Ahmed E. Elshafey, Radi A. Mohamed

“…Abstract The study aimed to explore the impact of dietary Pediastrum boryanum (PB) on growth performance, immune-physiological and transcriptome responses of Nile tilapia (Oreochromis niloticus). …”
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An Integrated Analysis of Transcriptomic and Metabolomic Effects Reveals Insights into Stress Responses in Largemouth Bass (<i>Micropterus salmoides</i>) Under MS-222 (Tricaine Met... by Ping Gao, Rimeng Chen, Deyun Ma, Shanshan Lin, Haodong Yu, Xuezhen Zhang

“…Methyl nicotinate and N-acetyl-L-phenylalanine were the most significantly upregulated in the gill and liver samples. …”
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Transcriptomic signatures of oxytosis/ferroptosis are enriched in Alzheimer’s disease by Antonio Currais, Kayla Sanchez, David Soriano-Castell, Nawab John Dar, K. Garrett Evensen, Salvador Soriano, Pamela Maher

“…The TrioSig signature was the most frequently found enriched, and bioinformatic analysis of its composition identified genes involved in the integrated stress response (ISR). …”
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Time-Series Transcriptome Analysis of the European Plum Response to Pathogen <i>Monilinia fructigena</i> by Raminta Antanynienė, Monika Kurgonaitė, Ingrida Mažeikienė, Birutė Frercks

“…Pathogenesis-related (PR) family and mildew resistance locus O (MLO-like) proteins were expressed the most during plum response to the pathogen. The plum initiates complex defense responses by significantly activating 23 pathways according to Kyoto Encyclopedia of Genes and Genomes (KEGG). …”
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Synthesis of transcriptomic studies reveals a core response to heat stress in abalone (genus Haliotis) by Roy Barkan, Ira Cooke, Sue-Ann Watson, Jan M. Strugnell

“…A substantial portion of publicly available studies has employed transcriptomic approaches to investigate abalone genetic response to heat stress. …”
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De novo transcriptome assembly and analysis of differential gene expression in response to drought in European beech. by Markus Müller, Sarah Seifert, Torben Lübbe, Christoph Leuschner, Reiner Finkeldey

“…GO term enrichment showed that mostly genes involved in lipid- and homeostasis-related processes were upregulated, whereas genes involved in oxidative stress response were downregulated in the stressed seedlings. …”
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Host Immune Response to Clinical Hypervirulent Klebsiella pneumoniae Pulmonary Infections via Transcriptome Analysis by Langhuan Lei, Xiaoli Zhang, Rui Yang, Haiming Jing, Yue Yuan, Zhifu Chen, Qiang Gou, Zhuo Zhao, Jinyong Zhang, Xingyong Wang

“…However, systematic immune response against K. pneumoniae has not been fully elucidated. …”
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Whole transcriptome analysis of breast tumors during neoadjuvant chemotherapy: association with response to preoperative chemotherapy by M. K. Ibragimova, M. M. Tsyganov, N. V. Litviakov

“…However, even in triple negative breast cancer, which is considered the most sensitive, it does not exceed 50 %. Therefore, the search for new genetic predictors of tumor response to preoperative treatment, as well as the assessment of tumor changes during neoadjuvant chemotherapy are highly relevant.Objective – to perform whole-transcriptome analysis of breast cancer during neoadjuvant chemotherapy depending on tumor response to preoperative treatment.Materials and methods. …”
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Physiological, biochemical, and transcriptomic responses to waterlogging stress in Panicum bisulcatum, an emerging weed in rice fields by Jinqiu Sun, Xiaoyue Yu, Yongjie Yang, Hongxing Xu, Mengjie Liu, Zhongxian Lü, Wei Tang

“…Following the identification of GAPDH as the most stable reference gene for normalization, quantitative real-time PCR analysis revealed significant upregulation of key pathway-related genes in P. bisulcatum under waterlogging stress, including LDH, GA20ox, GA2ox-1, SAM-synthase, ACO-1, and ACO-5. …”
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Transcriptomic–proteomic analysis reveals the regulatory mechanisms of Alfalfa (Medicago sativa) in response to Fusarium acuminatum by Zhidan Shi, Zhidan Shi, Hongxia Sun, Lifen Hao, Yongqing Yang, Chen Guo, Haiyan Huangfu, Hongli Huo, Lili Zhao, Jiuru Huangfu, Haijun Ding, Yongyu Fang, Ziqin Li, Yiding Niu

“…This study explores the response mechanism of alfalfa to Fusarium root rot. we used transcriptomic and proteomic methods to analyze differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) in alfalfa inoculated with Fusarium acuminatum on 0, 3, and 13 days. …”
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A transcriptomic survey of the impact of environmental stress on response to dengue virus in the mosquito, Aedes aegypti. by David S Kang, Martin S Barron, Diane D Lovin, Joanne M Cunningham, Matthew W Eng, Dave D Chadee, Jun Li, David W Severson

“…Here, we present the first whole transcriptome study to address the impact of environmental stress on A. aegypti response to dengue virus. …”
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An integrated physiological indicator and transcriptomic analysis reveals the response of soybean buds to high-temperature stress by Jiajia Li, Meiyan Wu, Haoran Chen, Wei Liao, Shu Yao, Ying Wei, Heng Wang, Qun Long, Xiaoyu Hu, Wei Wang, Guoji Wang, Lijuan Qiu, Xiaobo Wang

“…After HT treatment, changes in physiological indicators including hypocotyl length, enzyme activity and hormone content were detected; at the same time, the cotyledons, hypocotyls, and main roots were collected for transcriptome sequencing analysis. Analyzing the mechanisms of HT stress response in the bud stage of HD14 and JD36 at physiological and transcription levels. …”
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Transcriptome analysis of multiple tissues in the Babylonia areolata reveals the distinct response to Vibrio tubiashii infection by Chen Dai, Dapeng Luo, Qingming Liu, Jing Cui, Haohan Mi, Zuhao Zhang, Zhigang Tu, Minghui Shen

“…The GO and KEGG enrichment analyses showed distinct immune responses in different tissues. The DEGs in the gills were mostly associated with the cytoskeleton, focal adhesion, and ECM - receptor interaction and the DEGs in hemolymphocytes were mainly involved in catalytic activity, immune response, and the peroxisome pathway. …”
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