Identification of disulfidptosis in esophageal squamous cell carcinoma based on single-cell and bulk RNA-seq data to predict prognosis and treatment response by Xiaodan Zhang, Xiaodan Zhang, Jianting Du, Jianting Du, Xiao Lin, Xiao Lin, Shuliang Zhang, Shuliang Zhang, Taidui Zeng, Taidui Zeng, Maohui Chen, Maohui Chen, Guanglei Huang, Guanglei Huang, Chun Chen, Chun Chen, Bin Zheng, Bin Zheng

“…Subsequently, univariate Cox, multivariate Cox, and LASSO-Cox regression analysis were used to establish risk stratification models. The transcriptome data of the TCGA-ESCC cohort and the GSE160269 single-cell sequencing dataset were integrated to verify the biological significance of the model, and further analyze the heterogeneity of the tumor immune microenvironment, explore the differences in the intercellular communication network, and screen potential targeted drugs, providing a theoretical basis for subsequent translational research.ResultsWe identified two distinct patterns of disulfidptosis expression with significant differences in overall survival. …”
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Identification and comparative analysis of genes in response to cold stress between two mainly cultivated tetraploid cottons by QI Bowen, GUO Menglan, LU Hejun, MEI Huan, ZHAO Ting, FANG Lei

“…It was found that their expression levels were highly correlated with the expression levels of transcriptome. This study is helpful to analyze the molecular mechanism of different cold tolerance of TM-1 and Hai7124 and provide important genetic resources for the improvement of cold tolerance in cotton breeding.…”
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Fenaminosulf Promotes Growth and Gall Formation in <i>Zizania latifolia</i> Through Modulation of Physiological and Molecular Pathways by Chaohong Ding, Ruifang Ma, Liqiu Wang, Xinyan Lan, Limin Chen, Jinxing Zhu, Lailiang Wang

“…In contrast, higher FM concentrations (2.5 g/L and 5 g/L) inhibited vegetative growth but significantly enhanced gall formation, particularly at 2.5 g/L, indicating that FM can redirect plant resources or alter susceptibility to favor the fungal interaction under specific conditions. Transcriptomic analysis provided mechanistic insights, revealing extensive gene expression reprogramming, especially under high FM treatment (5 g/L). …”
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Integrated multi-omics analysis reveals the immunotherapeutic significance of tumor cells with high FN1 expression in ovarian cancer by Xinyi Zhang, Zhikai Xiahou, Fu Zhao, Qing Wu, Wei Nie, Shouyan Wang

“…Meanwhile, this study provided new insights into the heterogeneity of tumor cells and suggested a potential therapeutic target, FN1, which could be helpful for precise immunotherapy of ovarian cancer.…”
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Genomics—based approaches may assist in the verification and accelerate responsible deployment of marine carbon dioxide removal by Sharon E. Hook, Levente Bodrossy, Elizabeth A. Brewer, Anusuya Willis

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A single cell atlas of the human liver tumor microenvironment by Hassan Massalha, Keren Bahar Halpern, Samir Abu‐Gazala, Tamar Jana, Efi E Massasa, Andreas E Moor, Lisa Buchauer, Milena Rozenberg, Eli Pikarsky, Ido Amit, Gideon Zamir, Shalev Itzkovitz

“…Our analysis provides a resource for understanding human liver malignancies and may expose potential points of interventions.…”
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A scRNA-seq reference contrasting living and early post-mortem human retina across diverse donor states by Luning Yang, Yiwen Tao, Qi Pan, Tengda Cai, Yunyan Ye, Jianhui Liu, Yang Zhou, Yongqing Shao, Quanyong Yi, Zen Huat Lu, Lie Chen, Gareth McKay, Richard Rankin, Weihua Meng

“…Although single-nucleus RNA-seq expands the utility of frozen samples, it provides a nuclear-centric view, potentially missing key cytoplasmic information and transient biological processes. …”
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SmilODB: a multi-omics database for the medicinal plant danshen (Salvia miltiorrhiza, Lamiaceae) by Yong-Hui Liu, Wen-Qiong Zeng, Si-Fan Tao, Yi-Nuo Du, Fei-Hong Yu, Zhe-Chen Qi, Dong-Feng Yang

“…Although various omics resources have been published, there remains a lack of an integrated platform to unify genomic, transcriptomic, proteomic, and metabolomic data.MethodsTo address this gap, we constructed the S. miltiorrhiza Multi-omics Database (SmilODB, http://www.isage.top:56789/), which systematically integrates publicly available genome assemblies, transcriptome datasets, metabolic pathway annotations, and protein structural predictions. …”
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Gibberellin-induced germination enhancement in Chinese sour jujube seeds under cold stress by Qiang Chen, Guolong Li, Jinao Duan, Zhishu Tang, Zhongxing Song, Hongbo Liu, Xinbo Shi

“…This study clarified the GA3-mediated cold-resistant mechanisms of Chinese sour jujube, which provided a basis for breeding cold-resistant varieties and optimizing germination scheme under low temperature stress.…”
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Multi-omics and single-cell approaches reveal molecular subtypes and key cell interactions in hepatocellular carcinoma by Xueqing Zou, Xueqing Zou, Yongmei Wang, Mingyuan Luan, Yizheng Zhang

“…In summary, our novel multi-omics classification of HCC provides valuable insights into tumor heterogeneity and prognosis, offering potential clinical applications for precision oncology.…”
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Interplay between MRI radiomics and immune gene expression signatures in oral squamous cell carcinoma by Anna Corti, Deborah Lenoci, Valentina D. A. Corino, Davide Mattavelli, Marco Ravanelli, Tito Poli, Stefano Cavalieri, Lisa Licitra, Loris De Cecco, Luca Mainardi

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Combination Therapy of Half-Dose Resmetirom and Metformin Attenuates Metabolic Dysfunction-Associated Steatohepatitis Through Improving Cholesterol Metabolism and Inflammation by Wenxiu Liu, Fan Yao, Jinghan Wang, Nan Shao, Xinxin Cao, Zhengqi Dong, Bin Zhang, Xiaobo Sun

“…<b>Methods</b>: In this study, half-dose Res and low-dose metformin (Met) (referred to as RM) were administered in combination to treat MASH models in vitro and in vivo. We utilized transcriptome and lipidomics sequencing to assess the efficacy of RM in improving MASH. …”
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Identification of sex-linked markers and genes in Portuguese oyster (Magallana angulata) by Xiaoyan Zhou, Yue Ning, Jingyi Xie, Yi Han, Chaonan Tang, Caiyuan Su, Qijuan Wan, Qisheng Wu, Xiang Guo, Jianfei Qi, Yizhou Ke, Hui Ge, Mingyi Cai

“…SNP annotation revealed 57 genes around these sex-associated SNPs. Transcriptomic analysis identified 8,635 differentially expressed genes (DEGs) between male and female gonads, of which 12 overlapped with GWAS-identified genes. …”
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The Dysregulation of Tuning Receptors and Transcription Factors in the Antennae of <i>Orco</i> and <i>Ir8a</i> Mutants in <i>Aedes aegypti</i> Suggests a Chemoreceptor Regulatory M... by Matthew M. Cooke, Michael S. Chembars, Ronald Jason Pitts

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Genome-wide identification of chitinase gene family in Hordeum vulgare: insights into stress response mechanisms and evolutionary dynamics by Irfan Ali Sabir, Farhan Nabi, Muhammad Aamir Manzoor, Fazal Ullah, Muhammad Saeed, Abeer Hashem, Jawaher Alkahtani, Elsayed Fathi Abd-Allah, Muslim Qadir

“…Conclusion These findings provide a comprehensive overview of the HvCHT genes role in barley defense mechanisms, underlining their regulatory functions in biotic and abiotic stressors. …”
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Multi-omics characterization of oncosis in spinal cord injury by Zhipeng Jiang, Youwei Guo, Zihan Wang, Jinhao Ouyang, Hailong Huang, Haoxuan Huang, Tianqian Shen, Lei Wang, Wen Yin, Xingjun Jiang, Caiping Ren

“…Single-cell RNA sequencing and spatial transcriptomics revealed specific cell-type specificity and lesion-centered spatial enrichment of these genes. …”
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RNA-binding proteins regulate immune-related alternative splicing in inherited salt-losing tubulopathies by Fuhui Ma, Yanrong Ma, Mayinu Yusufu, Reziwanguli Wusiman, Shuqing Xing, Xiangxin Song, Suli Li, Yanying Guo

“…RNA sequencing (RNA-seq) was performed to obtain transcriptomic profiles, followed by analysis of gene expression patterns and alternative splicing events (ASEs). …”
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Transcriptional and Physiological Responses of <i>Saccharomyces cerevisiae</i> CZ to Octanoic Acid Stress by Zhi-Hai Yu, Ming-Zhi Shi, Wen-Xuan Dong, Xiao-Zhu Liu, Wei-Yuan Tang, Ming-Zheng Huang

“…This work emphasizes the critical role of strain-specific regulatory networks in octanoic acid resistance and provides insights for optimizing yeast robustness through targeted engineering of membrane stability and metabolic adaptability. …”
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Qingwen Hufei Granules Attenuate Lipopolysaccharide-Induced Acute Lung Injury by Suppressing NLRP3 Inflammasome-Dependent Pyroptosis by Long K, Yang Y, Wang Y, Wang B, Zhou H, Liu Y, Li Y, Yang S, Cao L, Huang T, Liu Y, Zhang H

“…Keywords: acute lung injury, lipopolysaccharide, Qingwen Hufei granules, transcriptomics, NOD-like receptor-signaling pathway…”
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Tumor gene expression signatures associated with outcome in large B−cell lymphoma treated with CD19-directed CAR T−cell therapy (axicabtagene ciloleucel) by Yuan Tian, Justin Budka, Frederick L. Locke, Jason R. Westin, Christina To, Gayatri Tiwari, Daqin Mao, Davide Bedognetti, Rhine R. Shen, Jorge Andrade, Simone Filosto

“…IntroductionCAR T cell therapy provided transformative outcomes for patients with B-cell lymphoma; however, a large fraction of patients remains at risk for relapse, underlying the need to uncover mechanisms of resistance and predictive biomarkers. …”
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