Comparative study on the mechanism of yellow petal formation in Paphiopedilum armeniacum: an integrated transcriptomic and metabolomic analysis of three Paphiopedilum species by Yaqin Ye, Yanting Chang, Yanjun Ma, Yayun Deng, Wenbo Zhang, Tiankui Chu, Hanchen Tian, Baokun Yan, Pengda Zhao, Zehui Jiang, Tao Hu

“…Conclusions These works elucidate the expression patterns and regulatory roles of carotenoid-related genes in metabolic pathways during P. armeniacum blooming, providing new insights into the molecular mechanisms of carotenoid-mediated plant coloration.…”
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Systematic evaluation of the isolated effect of tissue environment on the transcriptome using a single-cell RNA-seq atlas dataset by Daigo Okada, Jianshen Zhu, Kan Shota, Yuuki Nishimura, Kazuya Haraguchi

“…These atlases encompass data from diverse tissues and cell-types, providing insights into the landscape of cell-type-specific gene expression. …”
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A systems biology framework integrating cross-species transcriptomics and PPI networks for Xylella fastidiosa resistance gene identification by Aparna S. Balan, Giorgia Tranchina, Floriana Bonanno, Tiziano Caruso, Francesco Paolo Marra, Claudio Di Vaio, Annalisa Marchese

“…Through cross-species transcriptomic analysis of Olea europaea, Prunus dulcis, Vitis vinifera, and Medicago sativa, we identified a novel core resistance network consisting of 18 conserved genes against Xylella fastidiosa, alongside 1852 divergent expression patterns. …”
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Transcriptome and Physiological Analyses of Resistant and Susceptible Pepper (<i>Capsicum annuum</i>) to <i>Verticillium dahliae</i> Inoculum by Xinmin Huang, Liming He, Huimin Tan, Jiayi Liu, Qiucheng Qiu, Qidi Sun, Lejun Ouyang, Hanbing Han, Qinqin He

“…We performed physiological and transcriptome analysis using resistant and susceptible pepper cultivars inoculated with <i>V. dahliae</i>. …”
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Transcriptomic Differences Between Human Trabecular Meshwork Stem Cells and Trabecular Meshwork Cells Reveal Specific Biomarker Profiles by Rong Du, Ajay Kumar, Enzhi Yang, Jingxue Zhang, Ningli Wang, Yiqin Du

“…In this study, we performed a comprehensive transcriptomic comparison of human TMSCs and human TM cells (TMCs) using RNA sequencing and microarray analyses, followed by qPCR validation. …”
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Patient-centered brain transcriptomic and multimodal imaging determinants of clinical progression, physical activity, and treatment needs in Parkinson’s disease by Quadri Adewale, Ahmed Faraz Khan, Sue-Jin Lin, Tobias R. Baumeister, Yashar Zeighami, Felix Carbonell, Daniel Ferreira, Yasser Iturria-Medina

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Integrated transcriptome and metabolome analysis revealed differential drought stress response mechanisms of wheat seedlings with varying drought tolerance by Xiaorui Guo, Liangjie Lv, Aiju Zhao, Wei Zhao, Yuping Liu, Zetong Li, Hui Li, Xiyong Chen

“…Results This study analyzed the transcriptome and metabolome of wheat seedlings with varying drought tolerance (drought-tolerant T13, control CK, and drought-susceptible T2) under drought stress. …”
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Dual Transcriptome of Post-Germinating Mutant Lines of <i>Arabidopsis thaliana</i> Infected by <i>Alternaria brassicicola</i> by Mailen Ortega-Cuadros, Laurine Chir, Sophie Aligon, Nubia Velasquez, Tatiana Arias, Jerome Verdier, Philippe Grappin

“…Building upon recent reports that highlighted the involvement of indole pathways in seeds infected by <i>Alternaria</i>, this study provides transcriptomic resources to further elucidate the role of these metabolic pathways during the interaction between seeds and fungal pathogens. …”
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Ferulic acid and N-Feruloylserotonin ameliorate LPS-induced intestinal inflammation via modulation of gut microbiota, metabolome, and transcriptome by Xiangdong Hu, Xiangdong Hu, Xiangdong Hu, Xuebing Han, Xuebing Han, Gang Liu, Guiping Guan, Chenmei Xia

“…This work establishes a mechanistic foundation for deploying ferulic acid and N-Feruloylserotonin in intestinal health preservation and inflammatory disease prevention, while providing novel insights into microbiota-homeostasis crosstalk.…”
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Integrated spatial and single cell transcriptomics identifies PRKDC as a dual prognostic biomarker and therapeutic target in hepatocellular carcinoma by Wenpeng Pang, Yunyong Wang, Xiaohang Lu, Minpeng Li, Fuli Long, Songlin Chen, Yuan Yu, Mingfen Li, Hongsheng Lin

“…Taken together, we first to integrate spatial transcriptomics and single-cell transcriptomics and bulk RNA-seq to reveal that PRKDC is a reliable prognostic biomarker and a potential therapeutic target. …”
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Time-coexpress: temporal trajectory modeling of dynamic gene co-expression patterns using single-cell transcriptomics data by Shuyi Yang, Anderson Bussing, Giampiero Marra, Michelle L. Brinkmeier, Sally A. Camper, Shannon W. Davis, Yen-Yi Ho

“…Abstract Background The rapid advancement of single-cell RNA sequencing (scRNAseq) technology provides high-resolution views of transcriptomic activity within individual cells. …”
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Phenotypic and Transcriptomic Analysis Revealed a Lack of Risk Perception by Native Tadpoles Toward Novel Non‐Native Fish by Yuanfei Wang, Yudong Zhu, Liuyang He, Haoqi Yu, Xiuqin Lin, Jianghong Ran, Feng Xie

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Transcriptome Profiling Reveals Genetic Basis of Muscle Development and Meat Quality Traits in Chinese Congjiang Xiang and Landrace Pigs by Jiada Yang, Qiaowen Tang, Chunying Sun, Qiuyue Li, Xiaoyu Li, Lu Hou, Yi Yang, Kang Yang

“…(1) Objectives: Understanding the genetic basis of muscle development and meat quality traits in divergent pig breeds is crucial for advancing precision breeding strategies. (2) Methods: This study investigated transcriptome differences in the <i>longissimus dorsi</i> muscle between Chinese Congjiang Xiang (CX) and Landrace (LAN) pigs. …”
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Integrated Transcriptomic and Proteomic Analyses Reveal CsrA-Mediated Regulation of Virulence and Metabolism in <i>Vibrio alginolyticus</i> by Bing Liu, Huizhen Chen, Kai Sheng, Jianxiang Fang, Ying Zhang, Chang Chen

“…Our findings establish CsrA as a global regulator in <i>V. alginolyticus</i>, expanding the known targets of CsrA and providing new insights into its regulatory roles.…”
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Transgenerational toxicity assessment of [C8mim]Br: Focus on early development, antioxidant defense, and transcriptome profiles in zebrafish by Fei Zhao, Ying Shen, Zhongjun Ma, Huiqing Tian, Bingkun Duan, Yihua Xiao, Changqing Liu, Xueqing Shi, Dong Chen, Wei Wei, Rui Jiang, Penghao Wei

“…Overall, this transgenerational toxicity assessment underscores the adverse outcomes of parental [C8mim]Br exposure on unexposed offspring, providing a crucial aspect of the ecological risks of [C8mim]Br.…”
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Integrated Transcriptomic and Targeted Metabolomic Analyses Elucidate the Molecular Mechanism Underlying Dihydromyricetin Synthesis in <i>Nekemias grossedentata</i> by Fuwen Wu, Zhi Feng, Zhi Yao, Peiling Zhang, Yiqiang Wang, Meng Li

“…This study aimed to elucidate the molecular mechanisms underlying the substantial synthesis of DHM in <i>N. grossedentata</i>, providing a theoretical foundation for enhancing DHM production and developing <i>N. grossedentata</i> resources.…”
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A four-gene signature identified by integrated transcriptomic analysis for differential diagnosis and prognosis of uterine smooth muscle tumors by Huiyi Hu, Huiyi Hu, Yuanqun Chen, Bo Hong, Jia Liu, Yuchen Jiang, Zhiying Yu, Zhi-Jie Xiao, Zhi-Jie Xiao, Jing Li, Jing Li

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Integrative transcriptome and WGCNA analysis reveal key genes mainly in response to Alternaria alternata in Populus simonii × P. nigra by Siyuan Liu, Siyuan Liu, Siyuan Liu, Lijuan Dai, Guanzheng Qu, Xinming Lu, Hong Pan, Xiaoyu Fu, Airong Dong, Airong Dong, Libin Yang

“…Additionally, we analyzed the gene expression regulation and defense mechanisms of Populus simonii × P. nigra adversity stress, providing new insights into how plants respond to biological stress.…”
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Spatial transcriptomics reveals prognostically LYZ + fibroblasts and colocalization with FN1 + macrophages in diffuse large B-cell lymphoma by Liyuan Dai, Ning Lou, Liling Huang, Lin Li, Le Tang, Yuankai Shi, Xiaohong Han

“…Methods This study is a multi-omics approach, integrating spatial transcriptomics (n = 11), bulk transcriptomics (n = 2,499), immunohistochemistry (IHC, n = 37), multiplex immunofluorescence (mIF, n = 56), and plasma samples (n = 240) to identify and characterize fibroblast and tumor-associated macrophage subtypes in the TME. …”
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Transcriptomic Changes and Pathological Mechanisms in Familial and Sporadic Idiopathic Restless Legs Syndrome: Implications for Inflammation and Cell Adhesion Molecules by He XR, Song JM, Zhao JP, Zhang J, Feng JT, Chen SQ, Zhou ZY, Wang HM, Zhang Y, Feng Y, Wu YC, Zhu XY

“…These findings further support the association between RLS, inflammation, and synaptic transmission, providing insights into potential diagnostic and therapeutic strategies targeting these pathways.Keywords: restless legs syndrome, peripheral blood mononuclear cells, bioinformatics, transcriptomics, inflammation, message-RNA sequencing…”
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