Integrating transcriptomics and hybrid machine learning enables high-accuracy diagnostic modeling for nasopharyngeal carcinoma by Hehe Wang, Junge Zhang, Peng Cheng, Lujie Yu, Chunlin Li, Yaowen Wang

“…This study aimed to develop robust machine learning (ML)-driven diagnostic models and identify key biomarkers through integrated analysis of multi-cohort transcriptomic data. Methods Seven NPC transcriptomic datasets (GSE12452, GSE40290, GSE53819, and GSE64634 were merged to form the training cohort, while GSE13597, GSE34573, and GSE61218 served as independent external validation sets) were integrated and preprocessed using ComBat for batch effect correction. …”
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Transcriptomic Deconvolution in Acute Myocardial Infarction: Exploring Diagnostic Potential and Validation Through Blood Counts by Murilo de Queiroz Ramos, José Victor Almeida Guimarães, Diego Moura Tanajura, Kiyoshi Ferreira Fukutani, Hanjia Gao

“…The keyword “myocardial infarction” was searched in the Gene Expression Omnibus database, and only transcriptomes from peripheral blood studies of patients with AMI within 12 h of symptom onset were included. …”
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Transcriptomics Uncovers Pathways Mediating Low-Nitrogen Stress Tolerance in Two Foxtail Millet Varieties by Jirong Wu, Lu Chen, Zhenrong Yang, Juan Lu, Jinwen Yang, Ning Li, Huawei Shi

“…In this study, the LN tolerance of 50 foxtail millet genotypes was assessed through field trials and seedling hydroponic experiments. Subsequently, transcriptome analysis was performed on one highly sensitive genotype, named Maotigu, and on one highly tolerant genotype, named Dahuanggu, under LN (0.1 mmol/L) and control (5 mmol/L) conditions in seedling hydroponic experiments. …”
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Transcriptome alterations in long-term mining region residents: Insights into immune response and molecular pathways by Ani Stepanyan, Arsen Arakelyan, Jonathan Schug

“…Transcriptomic analysis of peripheral blood mononuclear cells was performed by mRNA sequencing. …”
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Transcriptomic Profile of Early Antral Follicles: Predictive Somatic Gene Markers of Oocyte Maturation Outcome by Alessia Peserico, Barbara Barboni, Chiara Camerano Spelta Rapini, Chiara Di Berardino, Giulia Capacchietti, Angelo Canciello, Fani Konstantinidou, Marisa Donato, Liborio Stuppia, Valentina Gatta

“…Meiosis resumption involved ECM remodeling, hypoxia, and relaxin signaling activation, while proliferative and metabolic pathways were downregulated. …”
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Integrating metabolomics and transcriptomics comprehensively reveals the global metabolic differences in three species of Nitraria berries by Yanhong Li, Shengyan Wang, Qing Zhao, Qian Wang, Zufan Yang, Qiangqiang Jia

“…This study combined metabolomics and transcriptomics to explore the differences among three species of Nitraria berries. …”
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The rat mammary gland undergoes dynamic transcriptomic and lipidomic modifications from pre-puberty to adulthood by David Tovar-Parra, Alec McDermott, Melany N. Juarez, Jysiane Cardot, Mame Sokhna Sylla, Line Berthiaume, Géraldine Delbès, Martin Pelletier, Étienne Audet-Walsh, Isabelle Plante

“…Significant differences in adipocyte number and size were observed between PND21, PND46, and PND90. Transcriptomic analysis revealed that 1563 genes changed significantly between PND21 and PND46, with only 14 genes altered between PND46 and PND90. …”
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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

“…Under waterlogging stress, the activities of key anaerobic respiration enzymes (alcohol dehydrogenase [ADH], pyruvate decarboxylase [PDC], and lactate dehydrogenase [LDH]), malondialdehyde (MDA) content, and antioxidant enzyme activities (superoxide dismutase [SOD], peroxidase [POD], and catalase [CAT]) were significantly increased. Comparative transcriptomic analysis at two waterlogging time points identified 11,986 and 1295 differentially expressed genes (DEGs) at 1 day and 7 days, respectively. …”
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Variational graph autoencoder for reconstructed transcriptomic data associated with NLRP3 mediated pyroptosis in periodontitis by Pradeep K. Yadalam, Prabhu Manickam Natarajan, Carlos M. Ardila

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Methanol fixation and tagmentation of RNA/DNA hybrids directly enable single-cell transcriptome sequencing by Tao Xu, Yicong Xu, Ziyang An, Yiheng Li, Jiawen Yang, Weixing Zhang, Jin Xu

“…While full-length single-cell transcriptome sequencing methods, such as Smart-seq, offer more comprehensive information, but are restricted by low-throughput. …”
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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

“…The transcriptome assembly and gene expression analysis identified a total of 33,287 transcripts corresponding to 18,934 annotated unique genes, including 4,425 genes that are uniquely responsive to drought. …”
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Phylogeny and species delimitation of ciliates in the genus Spirostomum (class Heterotrichea) using single-cell transcriptomes by Shahed Uddin Ahmed Shazib, Auden Cote-L’Heureux, Ragib Ahsan, Sergio A. Muñoz-Gómez, JunMo Lee, Laura A. Katz, Mann Kyoon Shin

“…Results Phylogenomic analysis of 37 Spirostomum specimens (25 newly generated transcriptomes and 12 from GenBank) and 265 protein-coding genes provides robust insight into the evolutionary relationships among Spirostomum species. …”
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Dynamic transcriptome and metabolome analyses of two sweet corn lines under artificial aging treatment by Zili Zhang, Ruichun Yang, Lei Gao, Shilin Huang, Feng Jiang, Qingchun Chen, Pengfei Liu, Faqiang Feng

“…However, there were few researches involving in the metabolome and transcriptome of artificial aging seeds. Results Using two inbred lines with significant differences in seed artificial aging tolerance, RNA sequencing and non-targeted metabolomic analysis were employed to extensively evaluate transcripts and metabolites in seeds that underwent artificial aging. …”
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An organ‐specific transcriptome atlas of Curcuma wenyujin: MicroRNAs, phasiRNAs, and metabolic pathways by Xiaoxia Ma, Yinju Tang, Zedi Feng, Xiu Yin, Yijun Meng, Xiaopu Yin, Tian Xie

“…Analysis of the enzyme‐coding genes of the β‐elemene biosynthetic pathway showed that the downstream genes were tuber‐specific, while the upstream genes were not. …”
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Dissecting tumor cell programs through group biology estimation in clinical single-cell transcriptomics by Shreya Johri, Kevin Bi, Breanna M. Titchen, Jingxin Fu, Jake Conway, Jett P. Crowdis, Natalie I. Vokes, Zenghua Fan, Lawrence Fong, Jihye Park, David Liu, Meng Xiao He, Eliezer M. Van Allen

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Comparative Transcriptomic Analyses of Anthocyanin Biosynthesis Genes in Eggplant Under Low Temperature and Weak Light by Baoying Shen, Hongqi Wu, Xinxin Xie, Bo Zhao, Peiqiang Chen, Deyong Ao, Heli Pan, Biying Lin

“…The effects of low temperature and weak light on the anthocyanin content in various parts of the eggplant were analyzed, and transcriptome analysis was performed on the eggplant peel under the treatments of low temperature, weak light, and the combination of low temperature and weak light using RNA sequencing. …”
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Insights into growth retardation and dwarfism caused by goose parvovirus in goslings: a transcriptomic profiling study by Keshan Zhang, Guangliang Gao, Zhuping Chen, Hongyuan Zhang, Xianzhi Zhao, Qin Li, Lin Ma, Lecheng Wang, Yi Luo, Qigui Wang

“…In addition, GPV infection inhibited the proliferation of goose embryo fibroblasts and induced apoptosis, as demonstrated by transcriptomic analysis, which identified 285 differentially expressed genes (DEGs). …”
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Proteomic and transcriptomic analyses identify apo-transcobalamin-II as a biomarker of overall survival in osteosarcoma by Ryan A. Lacinski, Ryan A. Lacinski, Sebastian A. Dziadowicz, Sebastian A. Dziadowicz, Clark A. Roth, Li Ma, Li Ma, Vincent K. Melemai, Brody Fitzpatrick, Edwin Chaharbakhshi, Tanya Heim, Ines Lohse, Karen E. Schoedel, Gangqing Hu, Gangqing Hu, Nicolas J. Llosa, Kurt R. Weiss, Brock A. Lindsey

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Multi-omics analysis of the mechanisms of abundant theacrine and EGCG3"Me in tea (Camellia sinensis) by Yanyu Zhu, Mengya Gu, Wentao Yu, Longhua Liao, Shuilian Gao, Shuyan Wang, Hongzheng Lin, Wenjing Gui, Youliang Zhou, Zhiming Chen, Jingde Zeng, Naixing Ye

“…Through integrated transcriptome-proteome-metabolome analysis, SAMS3, APRT1, IMPDH, and TCS1 were identified as critical enzymes for theacrine synthesis; while CHI1, CHI2, FLS2 and LAR1 were key for EGCG3"Me synthesis. …”
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Transcriptomic Responses to Rapid Cold Hardening in Tomato Leafminer Adults: Implications for Tomato Leafminer Management by Yan Zhao, Farman Ullah, Jiayi Shi, Yingjie Hu, Yuyang Jiang, Youming Hou

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