Predicting antimicrobial mechanism-of-action from transcriptomes: A generalizable explainable artificial intelligence approach. by Josh L Espinoza, Chris L Dupont, Aubrie O'Rourke, Sinem Beyhan, Pavel Morales, Amy Spoering, Kirsten J Meyer, Agnes P Chan, Yongwook Choi, William C Nierman, Kim Lewis, Karen E Nelson

“…We evaluated our methods using whole transcriptome responses from Escherichia coli challenged with 41 known antibiotics and 9 crude extracts while depositing 122 transcriptomes unique to this study. …”
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Deciphering the cellular and molecular landscape of cervical cancer progression through single-cell and spatial transcriptomics by Peng Xia, Juanhong Zhou, Rong Shen, Degui Wang

“…This study employed an integrated approach combining single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (stRNA-seq) to comprehensively characterize the tumor microenvironment (TME) across different stages of cervical cancer development. …”
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Transcriptome profiling reveals key genes in eggplant (Solanum melongena) roots under salt stress by Hongmei Sun, Yong Wang, Lianbin Cao, Yihan Wang, Zhaoyang Wei, Li Song, Jun Jiang, Junhe Liu, Shilin Tian

“…Taken together, this study provides important candidate genes linked to salt tolerance in eggplant roots, offering a foundation for further in-depth study of resistance mechanisms in eggplant ZH171.…”
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Optimization of Protoplast Preparation Conditions in <i>Lyophyllum decastes</i> and Transcriptomic Analysis Throughout the Process by Xiaobin Li, Ying Qin, Yufei Kong, Samantha Chandranath Karunarathna, Yunjiang Liang, Jize Xu

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Transcriptomic Responses of Gonadal Development to Photoperiod Regulation in Amur Minnow (<i>Phoxinus lagowskii</i>) by Mingchao Zhang, Yingdong Li

“…High-throughput RNA sequencing was used to analyze transcriptomic responses of gonadal tissues under three photoperiod regimes: natural light (12L:12D), continuous light (24L:0D), and continuous darkness (0L:24D) over a 9-week experimental period. …”
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Transcriptome Analysis and Sensory Evaluation of Thai Native Chicken Raised in Conventional and Free-Range Conditions by P. Seritrakul, P. Poommarin

“…At 6 months, blood samples were collected for transcriptome analysis and verified by quantitative real-time PCR. …”
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Transcriptome of <i>Kurthia gibsonii</i> TYL-A1 Revealed the Biotransformation Mechanism of Tylosin by Ye Wang, Cuizhu Zhao, Boyu Zhao, Xinran Duan, Peng Hao, Xiaojun Liang, Lianyu Yang, Yunhang Gao

“…In conclusion, this study provides novel insights regarding the degradation of TYL by <i>K. gibsonii</i> TYL-A1.…”
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DRaCOon: a novel algorithm for pathway-level differential co-expression analysis in transcriptomics by Fernando M. Delgado-Chaves, Ferdinand Spurny, Tanja Laske, Mhaned Oubounyt, Jan Baumbach

“…Crucially, DRaCOoN also provides a benchmarking framework for comprehensive method evaluation. …”
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Transcriptome sequencing and screening of anthocyanin related genes in purple potato tubers (Solanum tuberosum L.) by Xiaojuan Wu, Yanhong Ma, Peijie Wang, Juan Wu, Nan Li, Zhicheng Zhang, Rui Xie, Dan Wang, Hushuai Nie

“…Conclusion The key genes involved in anthocyanin synthesis in potato tubers were identificated, it provides new insights for molecular breeding new cultivars. …”
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De novo transcriptome assembly and discovery of drought-responsive genes in white spruce (Picea glauca). by Zoé Ribeyre, Claire Depardieu, Julien Prunier, Gervais Pelletier, Geneviève J Parent, John Mackay, Arnaud Droit, Jean Bousquet, Philippe Nolet, Christian Messier

“…In this study, we examined the transcriptome of white spruce (Picea glauca (Moench) Voss) to identify key genes and metabolic pathways involved in the species' response to water stress. …”
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Transcriptomic Analysis on Developing Seed Uncovers Candidate Genes Associated with Seed Storage Protein in Soybean by Li Hu, Huibin Huang, Wenjun Li, Runqing Duan, Dongyan Li, Xianzhi Wang

“…Merr.] is a globally significant crop that provides essential meal protein and vegetable oil for human consumption. …”
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GATA3 differentially regulates the transcriptome via zinc finger 2-modulated phase separation by Yatao Chen, Yajie Wan, Xiaoying Pei, Ziqi Wei, Tan Wang, Jun Zhang, Liming Chen

“…Therefore, GATA3 demonstrates a principle of how a transcription factor differentially regulates the transcriptome via DBD-modulated PS.…”
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Transcriptome analysis of Petunia axillaris flowers reveals genes involved in morphological differentiation and metabolite transport. by Ikuko Amano, Sakihito Kitajima, Hideyuki Suzuki, Takao Koeduka, Nobukazu Shitan

“…Our systematic analysis provides comprehensive transcriptomic information regarding morphological differentiation and metabolite transport in the Petunia flower and lays the foundation for establishing the specific mechanisms that control secondary metabolite biosynthesis in plants.…”
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The dynamic transcriptome reveals response patterns to black shank disease in tobacco (Nicotiana tabacum L.) by Zhijun Tong, Zuoqian Fan, Tianyu Du, Dunhuang Fang, Xueyi Sui, Chuyu Ye, Qian-Hao Zhu, Longjiang Fan, Bingguang Xiao, Enhui Shen

“…Several transcripts were identified to be potential candidates for further functional characterization. Our findings provide invaluable insights into the dynamic transcriptome in defense responses of tobacco against P. nicotianae infection.…”
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Single-cell transcriptomics and tissue metabolomics uncover mechanisms underlying wooden breast disease in broilers by Di Zhao, Zehe Song, Li Shen, Tian Xia, Qingyuan Ouyang, Haihan Zhang, Xi He, Kelang Kang

“…When WB occurs, myocytes and endothelial cells undergo apoptosis, macrophages are activated and exert immune functions, satellite cells participate in muscle rebuilding and repair, and the content of metabolites undergoes significant changes. This cell transcriptome profile provides an essential reference for future studies on the development and remodeling of WB.…”
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Combined transcriptomics and metabolomics to reveal the effects of copper exposure on the liver of rainbow trout(Oncorhynchus mykiss) by Junhao Lu, Jinqiang Quan, Jing Zhou, Zhe Liu, Jieping Ding, Tingting Shang, Guiyan Zhao, Lanlan Li, Yingcan Zhao, Xiangru Li, Jiajun Wu

“…We investigated the effects of Cu2+(75 μg/L, 150 μg/L, and 300 μg/L) on the rainbow trout liver. Combination of transcriptome and metabolome analyses, the regulatory mechanisms of the liver under Cu stress were elucidated. …”
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Integration of phospho-signaling and transcriptomics in single cells reveals distinct Th17 cell fates by Seth D. Fortmann, Awalpreet S. Chadha, Blake F. Frey, Asif Elahi, Vidya Sagar Hanumanthu, Shanrun Liu, Andrew Goldsborough, P. Brent Ferrell, Jr., Maria B. Grant, Casey T. Weaver, Robert S. Welner

“…Summary: Single-cell RNA sequencing (scRNA-seq) provides the resolution and scale necessary to identify transcriptional programs but fails to capture post-transcriptional information critical to decipher signaling networks and cellular states. …”
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Transcriptome sequencing reveals the potential mechanisms of dietary lutein regulation on chicken leg muscle development by Tuanhui Ren, Meng Xu, Wujian Lin, Wen Luo, Xiquan Zhang

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Age-Related Meat Flavor Precursors of Naturally Grazed Sunit Sheep: Metabolomics and Transcriptomics Approaches by Yajuan Huang, Xige He, Yunfei Han, Lu Chen, Xueting Yu, Jin Li, Xueyan Yun, Rina Sha, Gerelt Borjigin

“…The longissimus dorsi muscle was sampled from each group and subjected to metabolomics and transcriptomics analyses. A total of 395 differential metabolites (DMs) and 1482 differentially expressed genes (DEGs) were detected across the age groups. …”
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Identification of Candidate Genes for Hypoxia Tolerance in Rice by Genome-Wide Association Analysis and Transcriptome Sequencing by Chenghang Tang, Di Bai, Xingmeng Wang, Guohui Dou, Jiaqi Lv, Yaling Bao, Nansheng Wang, Linjun Yu, You Zhou, Jinguo Zhang, Dezhuang Meng, Jun Zhu, Yingyao Shi

“…By comparing the results of GWAS and transcriptome sequencing, the candidate genes were further screened and analyzed.As a result, a total of 86 genes related to hypoxic germination tolerance were detected by GWAS, and 51 genes were mapped by GWAS and transcriptome sequencing. …”
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