Multi-omics reveals the inhibition of asexual reproduction in the jellyfish Aurelia coerulea polyp by Bacillus pacificus by Hao Sun, Xuerui Liu, Manzoor Ahmad, Xiangrui Guo, Zhen Yu, Ye Zhao, Pingping Shen, Yanying Zhang, Zhijun Dong

“…Therefore, we aimed to elucidate these processes by performing a coculture experiment coupled with analyses utilizing high-throughput sequencing, transcriptomics, metabolomics, and fluorescence in situ hybridization. …”
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SPINK1 facilitates tumor progression via the EGFR/JAK/STAT3 axis in oral squamous cell carcinoma: insights from single-cell RNA sequencing by Mingyan Bao, Zhangui Tang

“…SPINK1 knockdown led to a significant reduction in EGFR and STAT3 phosphorylation levels, whereas exogenous supplementation of EGFR effectively rescued this phenotype.ConclusionSPINK1 has been established as a novel therapeutic target in OSCC, with its dual role in tumorigenesis and immune modulation providing a molecular foundation for developing targeted therapeutic modalities and precision oncology strategies.…”
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A novel computational approach for predicting complex phenotypes in Drosophila (starvation-sensitive and sterile) by deriving their gene expression signatures from public data. by Dobril K Ivanov, Gerrit Bostelmann, Benoit Lan-Leung, Julie Williams, Linda Partridge, Valentina Escott-Price, Janet M Thornton

“…Many research teams perform numerous genetic, transcriptomic, proteomic and other types of omic experiments to understand molecular, cellular and physiological mechanisms of disease and health. …”
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The future of immunohistochemistry: advancing precision medicine through artificial intelligence-driven spatial proteomics and multiplexed diagnostic technologies by Ruby Dhar, Arun Kumar, Subhradip Karmakar

“…The application of IHC is rapidly broadening beyond conventional single-marker analyses to include advanced multiplexed spatial proteomics techniques that allow for the detection of 40 or more protein markers simultaneously within intact tissue structures at subcellular precision, providing new insights into the tumor microenvironment and cellular interactions. …”
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CRISPR/Cas9-based discovery of ccRCC therapeutic opportunities through molecular mechanism and immune microenvironment analysis by Bo Han, Weiyang Liu, Wanhui Wang, Zhuolun Li, Bosen You, Dongze Liu, Yunfeng Nan, Tiankai Ding, Zhou Dai, Yantong Zhang, Wei Zhang, Qing Liu, Xuedong Li

“…This multi-omics-driven model elucidates MELK-mediated mechanisms and their interactions with the tumor microenvironment, providing novel strategies for risk stratification and targeted therapy. …”
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Targeting PIK3CB/YAP1 improves the sensitivity of paclitaxel by suppressing aging in head and neck squamous tumor cells by Junzhi Liu, Huimin Li, Ruotong Sun, Guoguang Ying, Zheng Liang

“…Bulk and single-cell transcriptomics and proteomics data were analyzed. Cell passage effects on aging and the impact of PIK3CB modulation on YAP1 were evaluated. …”
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Effect of age and sex differences on the abundances of neuronal, glial, and endothelial cells in non-diseased brain tissue. by Arttu Autio-Kimura, Tapio Nevalainen, Mikko Hurme

“…Advances in sequencing technology have enabled large-scale transcriptomic studies, such as the Genotype-Tissue Expression (GTEx) project, providing valuable resources for investigating the cellular landscape of the human brain. …”
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The mechanism of maternal inheritance of glycolipid metabolism disorder in a zebrafish model of type 2 diabetes by Fuqi Yang, Ying Zhang, Panyu Ju, Leyu Li, Yu Gong, Qian Zhang, Jiaolong Huang, Peng Duan, Xingjian Zhou

“…This study emphasised the impacts of maternal preconception zebrafish hyperglycaemia on glycolipid metabolism in the offspring, transferring the maternal origin of the disease to the preconception stage and providing a reference for further research on the aetiology of glycolipid metabolism disorders.…”
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Integrative multi-omic analysis of NLRP3 inflammasome dysregulation and subtyping for personalized treatment in acute myeloid leukemia by Hong Zhang, Linlin Yang, Yukexin Liu, Dongju Wang, Liming Shi, Changyu Tian

“…In this study, we analyzed genomic, bulk-, and single-cell transcriptomic data to assess the contribution of NLRP3 inflammasome genes to AML. …”
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BFGF mitigates CTX-induced ovarian cytotoxicity via SERPINE1/HIF-1 and Nrf-2/HO-1 signaling pathways by Yao Li, Lin Zhang, Hongqing Lv, Chenxuan Mei, Min Hu

“…BFGF treatment significantly enhanced cell viability, reduced apoptosis, and restored mitochondrial membrane potential in CTX-treated ovarian cells. Transcriptomic analysis revealed that BFGF activated the SERPINE1/HIF-1 signaling pathway, promoting angiogenesis, reducing apoptotic signaling, and enhancing cell cycle progression by upregulating Cyclin D1 and CDK4. …”
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Light-dependent variations in fatty acid profiles and gene expression in Antarctic microalgal cultures. by Jacqui Stuart, Kirsty F Smith, Matt Miller, John K Pearman, Natalie Robinson, Lesley Rhodes, Lucy Thompson, Sarah Challenger, Nicole Parnell, Ken G Ryan

“…This and the FA composition changes show the variability of acclimation strategies for different taxonomic groups, providing insights into the responses of microalgae to light stress. …”
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Analysis of immune cell infiltration in the tumor microenvironment of cervical cancer and its impact on immunotherapy by Fei Qin, Lu Huan, Xia Shi, Yuanyuan Hua, Yi Wu

“…This study aimed to identify novel prognostic biomarkers and therapeutic targets through a multi-omics approach, providing insights into the tumor immune microenvironment.MethodsWe integrated transcriptomic, mutational, and clinical data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) to construct a prognostic model. …”
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Long-term adaptation following influenza A virus host shifts results in increased within-host viral fitness due to higher replication rates, broader dissemination within the respir... by Julien A R Amat, Veronica Patton, Caroline Chauché, Daniel Goldfarb, Joanna Crispell, Quan Gu, Alice M Coburn, Gaelle Gonzalez, Daniel Mair, Lily Tong, Luis Martinez-Sobrido, John F Marshall, Francesco Marchesi, Pablo R Murcia

“…Our results reveal previously unknown links between virus genotype and the host response to infection, providing new insights on the relationship between virus evolution and fitness.…”
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Genome-wide identification and expression profiling of the bZIP gene family in Chrysanthemum indicum and the functional analysis of CibZIP29 under cadmium stress by Shengyan Chen, Yin Zhang, Kaiyuan Zhang, Shuguang Liu, Yujia Yang, Xingnong Xu

“…Overexpression of CibZIP29 in transgenic Arabidopsis enhanced Cd tolerance, providing new insights into the molecular mechanisms underlying Cd stress response in C. indicum. …”
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Algorithms and tools for data-driven omics integration to achieve multilayer biological insights: a narrative review by Aurelia Morabito, Giulia De Simone, Roberta Pastorelli, Laura Brunelli, Manuela Ferrario

“…In the present review, we focus on strategies that have been applied in literature to integrate genomics, transcriptomics, proteomics, and metabolomics in the year range 2018–2024. …”
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FPR3 orchestrates macrophage polarization in breast cancer: multi-omics dissection of prognostic relevance and therapeutic targeting by Ying Chen, Xin Tang, Liran Zhu, Yi Wang, Gaopeng Li, Wulin Yang

“…Methods A comprehensive analysis integrating bulk RNA-seq transcriptomics, methylomics, single-cell transcriptomics, and spatial single-cell transcriptomics data was conducted to elucidate the distinctive characteristics of FPRs in breast cancer. …”
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Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses by Sarah Buddle, Leysa Forrest, Naomi Akinsuyi, Luz Marina Martin Bernal, Tony Brooks, Cristina Venturini, Charles Miller, Julianne R. Brown, Nathaniel Storey, Laura Atkinson, Timothy Best, Sunando Roy, Sian Goldsworthy, Sergi Castellano, Peter Simmonds, Heli Harvala, Tanya Golubchik, Rachel Williams, Judith Breuer, Sofia Morfopoulou, Oscar Enrique Torres Montaguth

“…Protocols were designed to retain the host transcriptome, since this could help confirm the absence of infectious agents. …”
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A companion to the preclinical common data elements for proteomics, lipidomics, and metabolomics data in rodent epilepsy models. A report of the TASK3‐WG4 omics working group of th... by Laura Bindila, Tore Eid, James D. Mills, Michael S. Hildebrand, Gary P. Brennan, Susan A. Masino, Vicky Whittemore, Piero Perucca, Christopher A. Reid, Manisha Patel, Kevin K. Wang, Erwin A. vanVliet

“…We discuss the important elements that need to be considered for the proteomics, lipidomics, and metabolomics methodologies, providing a rationale for the parameters that should be documented.…”
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An integrated investigation of mitochondrial genes in COPD reveals the causal effect of NDUFS2 by regulating pulmonary macrophages by Xiaoli Zou, Qiqing Huang, Tutu Kang, Shaoran Shen, Chenxi Cao, Jianqing Wu

“…Results Differential expression genes (DEGs) from six publicly available bulk human lung tissue transcriptomic datasets of COPD patients were intersected with the known mitochondria-related genes from MitoCarta3.0 to obtain mitochondria-related DEGs associated with COPD (MitoDEGs). …”
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Identification of heat shock transcription factor gene families in sunflower and their expression profiles under abiotic stress(向日葵热激转录因子基因家族鉴定及其在非生物胁迫下的表达分析)... by 宋慧芳(SONG Huifang), 薛宏宇(XUE Hongyu), 王茜(WANG Xi), 卢俊洁(LU Junjie), 李晨雨(LI Chenyu), 刘阿克(LIU Ake)

“…A systematic study of HSF gene family in sunflower could provide an important reference for functional studies of HSF family and molecular breeding of sunflower. . …”
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