Comparative analysis of statistical and deep learning-based multi-omics integration for breast cancer subtype classification by Mahmoud M. Omran, Mohamed Emam, Mariam Gamaleldin, Asmaa M. Abushady, Mustafa A. Elattar, Mohamed El-Hadidi

“…Methods In this study, we conducted a multi-omics integration analysis on 960 BC patient samples, incorporating three omics layers: Host transcriptomics, epigenomics, and shotgun microbiome. …”
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Multi-omics analysis reveals the interplay between pulmonary microbiome and host in immunocompromised patients with sepsis-induced acute lung injury by Fan Lu, Ting Huang, Ruichang Chen, Haiyan Yin

“…Bronchoalveolar lavage fluid (BALF) was analyzed using metagenomic next-generation sequencing (mNGS) to assess the pulmonary microbiome, and transcriptomic sequencing evaluated host gene expression. …”
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Wnt/β-catenin signalling underpins juvenile Fasciola hepatica growth and development. by Rebecca Armstrong, Nikki J Marks, Timothy G Geary, John Harrington, Paul M Selzer, Aaron G Maule

“…Here, we identify five putative Wnt ligands and five Frizzled receptors in liver fluke transcriptomic datasets and find that Wnt/β-catenin signalling is most active in juveniles, the most pathogenic life stage. …”
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Targeting alveolar epithelial cell metabolism in pulmonary fibrosis: Pioneering an emerging therapeutic strategy by Tengkun Dai, Tengkun Dai, Yidan Liang, Yidan Liang, Xin Li, Xin Li, Jiamin Zhao, Jiamin Zhao, Guangqin Li, Qihong Li, Lin Xu, Lin Xu, Juanjuan Zhao, Juanjuan Zhao

“…Pulmonary fibrosis (PF) is a chronic and progressive lung disease, characterized by excessive deposition of fibrotic connective tissue within the lungs. Advances in transcriptomics, proteomics, and metabolomics have enhanced our understanding of PF’s pathogenesis. …”
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Multi-omics approaches for biomarker discovery and precision diagnosis of prediabetes by Jielin Song, Jielin Song, Jielin Song, Chuanfu Wang, Tong Zhao, Tong Zhao, Tong Zhao, Yu Zhang, Yu Zhang, Yu Zhang, Jixiang Xing, Jixiang Xing, Jixiang Xing, Xuelian Zhao, Xuelian Zhao, Xuelian Zhao, Yunsha Zhang, Yunsha Zhang, Yunsha Zhang, Zhaohui Zhang, Zhaohui Zhang, Zhaohui Zhang

“…Recent advancements in multi-omics technologies have provided unprecedented opportunities to identify biomarkers associated with prediabetes, offering novel insights into its diagnosis and management. …”
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An updated proteomic analysis of Drosophila haemolymph after bacterial infection by Samuel Rommelaere, Fanny Schüpfer, Florence Armand, Romain Hamelin, Bruno Lemaitre

“…Using an in-depth Mass Spectrometry-based proteomics approach, we provide a comprehensive characterization of the hemolymphatic proteome of adult flies upon bacterial infection. …”
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Integrative Single‐Cell Analysis Reveals Iron Overload‐Induced Senescence and Metabolic Reprogramming in Ovarian Endometriosis‐Associated Infertility by Yangshuo Li, Wei Zhou, Jie Ding, Di Song, Wen Cheng, Jin Yu, Shuai Sun, Shanshan Mei, Xiaolan Liang, Qianqian Zhao, Yanping Kuang, Mingqing Li, Zhexin Ni, Chaoqin Yu, Yue Gao

“…A single‐cell atlas of pre‐ovulatory follicular fluid from OEI patients reveals dynamic changes in iron metabolism and iron‐induced senescence phenotypes. Spatial transcriptomics using Stereo‐seq in iron‐overloaded mouse ovaries further identifies localized senescence features. …”
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Comprehensive resource for transcription readthrough events in healthy human tissues by Yang Mei, Ziqi Cheng, Yueqi Lu, Shiyi Wu, Xi Chen

“…The dataset encompasses the sequences, locations, expression profiles, and comprehensive annotation information of corresponding genes for RT transcripts. It provides a thorough elucidation of RT transcriptomics and its significance in gene regulation, offering a wealth of benchmark data to facilitate further research on RT transcripts.…”
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DGE-ontology: A quick and simple gene set enrichment analysis and visualisation tool by Michal Bukowski, Benedykt Wladyka

“…High-throughput quantification techniques provide considerable amounts of data. Making sense of such data requires not only thorough statistical analysis but a logical approach to data visualisation. …”
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Impact of Atrazine on Sucrose Sensitivity in Honey Bees by Xiexin Hu, Zixuan Xu, Jiachen Xu, Guiyi Ma, Yiren Pan, Minqi Cai, Zheguang Lin, Ting Ji, Kang Wang

“…This study investigated the effects of atrazine on honey bee sucrose sensitivity and clarified the underlying molecular mechanisms using transcriptomic analyses. Atrazine exposure reduced the sucrose sensitivity of honey bees substantially, likely through the inhibition of functional genes associated with cognition in the brain. …”
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Artificial intelligence-assisted RNA-binding protein signature for prognostic stratification and therapeutic guidance in breast cancer by Yunxia Zhao, Li Li, Shuqi Yuan, Zixin Meng, Jiayi Xu, Zhaogen Cai, Yijing Zhang, Xiaonan Zhang, Tao Wang

“…Low AIRS scores predicted better responses to immune checkpoint inhibitors, while drug sensitivity analysis highlighted panobinostat and paclitaxel as potential therapies for high-risk patients.ConclusionsThe AIRS model offers a robust tool for BC prognosis and treatment stratification, integrating genomic, transcriptomic, and single-cell data. It provides actionable insights for personalized therapy, paving the way for improved clinical outcomes. …”
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Study on the regulatory mechanism of NsdAsr on rimocidin biosynthesis in Streptomyces rimosus M527 by Yawen Xie, Yujie Jiang, Yongyong Zhang, Andreas Bechthold, Xiaoping Yu, Zheng Ma

“…Conclusion This study reveals NsdAsr’s dual role in limiting rimocidin production by suppressing metabolic precursors and modulating protein expression. Integrated transcriptomic and ChIP-seq analyses provide critical insights into its regulatory mechanisms.…”
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The role of transketolase in the immunotherapy and prognosis of hepatocellular carcinoma: a multi-omics approach by Xuan-Yu Gu, Zheng-Jun Zhou, Hua Yao, Jia-Li Yang, Jin Gu, Rui Mu, Li-Jin Zhao

“…Although these results provide insights into the potential involvement of TKT in immune cell infiltration and survival outcomes, further studies are required to fully elucidate its role in immunotherapy.…”
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Pan-genome analysis of the R2R3-MYB genes family in Brassica napus unveils phylogenetic divergence and expression profiles under hormone and abiotic stress treatments by Haiyan Fan, Haiyan Fan, Jiawei Li, Jiawei Li, Wencong Huang, Aoshuang Liang, Liqing Jing, Jintao Li, Qing-Yong Yang, Qing-Yong Yang, Kede Liu, Zhiquan Yang

“…Cis-element profiling highlighted enrichment in hormone-responsive and stress-related elements in the promoter regions of the R2R3-MYB genes. Transcriptomic analyses identified 283 hormone-responsive and 266 stress-responsive R2R3-MYB genes, and 30 co-regulated genes under drought and heat stress implicate their roles in combined stress adaptation.DiscussionThese findings provide the first pan-genome resource for R2R3-MYB genes in B. napus, which can serve as pivotal targets for enhancing stress resilience in rapeseed breeding programs.…”
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Molecular Characterization and Clinical Relevance of MGMT‐Silenced Pancreatic Cancer by Federico Nichetti, Marco Silvestri, Luca Agnelli, Andrea Franza, Chiara Pircher, Simone Rota, Paolo Ambrosini, Giuseppe Fotia, Jennifer Hüllein, Giovanni Randon, Panna Lajer, Federica Perrone, Elena Tamborini, Giuseppe Leoncini, Jorgelina Coppa, Michele Droz Dit Busset, Sara Pusceddu, Massimo Milione, Federica Morano, Filippo Pietrantonio, Giancarlo Pruneri, Vincenzo Mazzaferro, Daniel B. Lipka, Bruno Christian Köhler, Daniel Hübschmann, Stefan Fröhling, Filippo deBraud, Monica Niger

“…Experimental Design We leveraged sequencing data from The Cancer Genome Atlas (TCGA), the Clinical Proteomic Tumor Analysis Consortium 3 (CPTAC‐3), and the (Australian Pancreatic Cancer Genome Initiative) PACA‐AU cohorts to characterize MGMT‐silenced PAC. Genomic, transcriptomic, methylation, and clinical data were investigated, and findings were validated in silico using methylation, transcriptomic and drug sensitivity data from Cancer Cell Line Encyclopedia (CCLE) project, and in a real‐world cohort of PAC patients profiled for MGMT status at Istituto Nazionale Tumori of Milan (INT). …”
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PHF6 and RUNX1 mutations cooperate to accelerate leukemogenesis by Yueh-Chwen Hsu, Chi-Yuan Yao, Chang-Tsu Yuan, Chien-Chin Lin, Hsin-An Hou, Chein-Jun Kao, Chia-Lang Hsu, Wen-Chien Chou, Hwei-Fang Tien

“…We first analyzed the clinical, genetic, and transcriptomic features of our cohort of patients with acute myeloid leuemia (AML) focusing on these two mutations. …”
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Protective effect of exercise induced metabolite-3 in ischemia-reperfusion injury by Zijie CHENG, Xuejun WANG, Zimu WANG, Juying QIAN

“…Intracellular reactive oxygen species (ROS) levels were detected. Transcriptomic analysis was performed to identify potential signaling pathways and targets of EIM-3. …”
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Novel Lysosomal‐Associated Transmembrane Protein 4B‐Positive Stem‐Like Cell Subpopulation Characterizes High‐Risk Colorectal Cancer Subtypes by Yangyang Fang, Tianmei Fu, Ziqing Xiong, Qian Zhang, Wei Liu, Kuai Yu, Aiping Le

“…This study delineates tumor‐intrinsic stem‐like cell diversity and its prognostic implications through single‐cell transcriptomic profiling of 171,906 tumor epithelial cells (n = 152), integrated with bulk transcriptomic (n = 1389) and genomic (n = 1077) datasets. …”
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From Development to Regeneration: Insights into Flight Muscle Adaptations from Bat Muscle Cell Lines by Fengyan Deng, Valentina Peña, Pedro Morales-Sosa, Andrea Bernal-Rivera, Bowen Yang, Shengping Huang, Sonia Ghosh, Maria Katt, Luciana Andrea Castellano, Lucinda Maddera, Zulin Yu, Nicolas Rohner, Chongbei Zhao, Jasmin Camacho

“…In parallel, we performed transcriptomic and metabolic profiling of native pectoralis tissue in the closely related <i>Pteronotus parnellii</i> to define molecular programs supporting muscle specialization. …”
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Development of patient-specific iPSC-based epilepsy models and identification of differentially expressed genes for disease mechanisms by Jianfeng Wu, Siqi Huang, Lihao Chen, Yinghong Yang, Shunhan Zhang, Jiajia Xian, Jiajia Xian, Xiaoyan Ma, Xiaoyan Ma, Furong Ma, Shaoying Li, Shaoying Li, Yi Yang, Yingjun Xie, Xiaofang Sun

“…This suggests a potential role for these genes in the pathophysiology of epilepsy linked to CLCNKB mutations.DiscussionThe successful establishment of CLCNKB-mutant patient-specific iPSC lines and their transcriptomic characterization provide a valuable tool for studying the molecular basis of epilepsy. …”
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