Pan-cancer characterization of m6A-mediated regulation of T cell exhaustion dynamics and clinical relevancies in human cancers by Weiping Ji, Ye Fang, Liwei Chen, Yitong Zheng, Yifei Pei, Changqiu Mei, Meng Zhou

“…Here, we conducted a pan-cancer analysis integrating multi-omics data from cell lines, single-cell RNA sequencing, and pan-cancer and immunotherapy datasets to explore the dynamic interplay between m6A modification and TEX. …”
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MKRN1 promotes colorectal cancer metastasis by activating the TGF-β signalling pathway through SNIP1 protein degradation by Yi Zhang, Qin-shan Li, Hong-lin Liu, Hong-ting Tang, Han-lin Yang, Dao-qiu Wu, Yu-ying Huang, Li-cheng Li, Li-hong Liu, Meng-xing Li

“…A combination of MKRN1 quantitative proteomics, ubiquitination modification omics analysis, and a string of in vitro and in vivo experiments revealed the potential mechanisms by which MKRN1 regulates CRC metastasis. …”
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Mechanistic evaluation of enhanced graphene toxicity to Bacillus induced by humic acid adsorption by Xuejiao Zhang, Jin Zeng, Jason C. White, Fangbai Li, Zhiqiang Xiong, Siyu Zhang, Yuze Xu, Jingjing Yang, Weihao Tang, Qing Zhao, Fengchang Wu, Baoshan Xing

“…Contrary to previous data, GNSs-HA exhibits greater toxicity compared to GNSs. Multi-omics combined with sensitive bioassays and electrochemical methods reveals GNSs disrupt oxidative phosphorylation by causing physical membrane damage. …”
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Global trends and research frontiers on machine learning in sustainable animal production in times of climate change: Bibliometric analysis aimed at insights and orientations for t... by Robson Mateus Freitas Silveira, Concepta Mcmanus, Iran José Oliveira da Siva

“…The main insights generated in the bibliometric analysis were (i) sustainable animal production changed from unidisciplinary science to multidisciplinary science linked to agricultural, environmental and engineering sciences, mainly to genetics and computing; (ii) the concept of sustainable animal production emerged from animal welfare and climate change concepts found in UN's 2030 Agenda; (iii) omics sciences, greenhouse gases, energy efficiency and animal welfare are the main keywords for bibliometric analyses in future studies related to sustainable animal production in the coming centuries; (iii) prediction and classification analyses, i.e., supervised machine learning models used as main tools in animal production; (iv) residual feed intake applied to measure sustainable feed efficiency in animal farming in the past and nowadays; and (v) The United States, China, Brazil and Australia are the main countries publishing studies on sustainability in animal production, but only China has been gaining prominence in publications in this field, in recent years, and it will turn this country into an emerging leader in future publications on this topic. …”
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Comprehensive pan-cancer analysis reveals NTN1 as an immune infiltrate risk factor and its potential prognostic value in SKCM by Fuxiang Luan, Yuying Cui, Ruizhe Huang, Zhuojie Yang, Shishi Qiao

“…This study aimed to elucidate the role of NTN1 in pan-cancer using multi-omics data and explore its potential as a prognostic biomarker in SKCM. …”
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Characterizing immune biomarkers and effector CD8+ T-cell exhaustion in pancreatic adenocarcinoma via single-cell RNA sequencing profiling by Rawaa AlChalabi, Raghda Makia, Semaa A. Shaban, Ahmed AbdulJabbar Suleiman

“…Methods: We employed a multi-omics approach, integrating single-cell RNA sequencing data with whole genome sequencing to identify dysregulated exhaustion-related immune markers in CD8+ T-cells in PDAC. …”
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High interstitial fluid pressure enhances USP1-dependent KIF11 protein stability to promote hepatocellular carcinoma progression by Zhengyi Wu, Chao Li, Shouhua Zhang, Liang Sun, Junwen Hu, Bingbing Qiu, Shuiqiu Liu, Yiran Hong, Tianxiang Chen, Kai Wang, Xiangbao Yin, Jinlong Yan

“…Results Results demonstrated that the HIFP environment significantly increased the proliferation, invasion, and metastasis in HCC cells. Omics analysis and subsequent molecular validation revealed that KIF11 protein levels were markedly upregulated under HIFP, despite no significant change in mRNA levels. …”
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Elevated miR-221-3p inhibits epithelial–mesenchymal transition and biochemical recurrence of prostate cancer via targeting KPNA2: an evidence-based and knowledge-guided strategy by Dingchao Li, Jingang Jian, Manhong Shi, Zihao Chen, Anguo Zhao, Xuedong Wei, Yuhua Huang, Yalan Chen, Jianquan Hou, Yuxin Lin

“…Then a knowledge-guided network strategy was applied to prioritize key targets of miR-221-3p in PCa progression based both on topological and functional characterization of genes in multi-omics miRNA-mRNA and protein-protein interaction networks. …”
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Insufficient gene expression and lost gene regulatory network may underlie the mechanism of Hirschsprung Disease in 5p–syndrome by Yizhao Luan, Peng Li, Yuanyuan Luo, Hong Zhang, Xiaochun Zhu, Yan Zhang, Aihua Yin, Qiang Wu, Chengwei Chai

“…On the other hand, integrating gene regulatory relationship estimated from single cell chromatin accessibility omics of enteric neurons, we found that the 5p deletion regions contained key cis-regulatory regions for HSCR-related gene GDNF. …”
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From chaos to order: optimizing fecal microbiota transplantation for enhanced immune checkpoint inhibitors efficacy by Anqi Lin, Aimin Jiang, Lihaoyun Huang, Yu Li, Chunyanx Zhang, Lingxuan Zhu, Weiming Mou, Zaoqu Liu, Jian Zhang, Quan Cheng, Ting Wei, Peng Luo

“…We outline critical research directions, encompassing the need for large-scale, multi-center randomized controlled trials, in-depth microbial ecology studies, and the integration of multi-omics approaches with artificial intelligence. Regulatory and ethical challenges are critically addressed, underscoring the imperative for standardized protocols and rigorous long-term safety assessments. …”
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ITGA4 as a potential prognostic and immunotherapeutic biomarker in human cancer and its clinical significance in gastric cancer: an integrated analysis and validation by Jiaxing Zhang, Jiaxing Zhang, Gang Wang, Jie Liu, Futian Tang, Song Wang, Yumin Li, Yumin Li

“…However, its role across different cancer types is not well understood.MethodsUtilizing multi-omics data, we comprehensively evaluated ITGA4’s expression, clinical relevance, diagnostic and prognostic value, functions, mutations, and methylation status, along with its impact on immunity, mismatch repair (MMR), heterogeneity, stemness, immunotherapy responsiveness, and drug resistance in pan-cancer, with partial validation in gastric cancer (GC) using transcriptomic analysis, single-cell data, western blot (WB), wound-healing assay, flow cytometry and immunohistochemistry (IHC). …”
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Adrenomedullin 2 attenuates anxiety-like behaviors by increasing IGF-II in amygdala and re-establishing blood–brain barrier by Denian Wang, Zhi Yang, Pengfei Wu, Qingyan Li, Chunyan Yu, Ying Yang, Yuefan Du, Mengwei Jiang, Junpeng Ma

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PDZRN3 regulates adipogenesis of mesenchymal progenitors in muscle by Hiroki Iida, Minako Kawai-Takaishi, Yoshihiro Miyagawa, Yasuhiko Takegami, Akiyoshi Uezumi, Takeshi Honda, Shiro Imagama, Tohru Hosoyama

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Single-Cell RNA Sequencing Reveals LEF1-Driven Wnt Pathway Activation as a Shared Oncogenic Program in Hepatoblastoma and Medulloblastoma by Christophe Desterke, Yuanji Fu, Jenny Bonifacio-Mundaca, Claudia Monge, Pascal Pineau, Jorge Mata-Garrido, Raquel Francés

“…Both tumor types can exhibit genetic alterations that affect the β-catenin and Wnt pathways; (2) Materials and Methods: This study used bioinformatics and integrative analysis of multi-omics data at both the tumor and single-cell levels to investigate two distinct pediatric tumors: medulloblastoma and hepatoblastoma; (3) Results: The cross-transcriptome analysis revealed a commonly regulated expression signature between hepatoblastoma and medulloblastoma tumors. …”
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Engineered biomimetic cisplatin-polyphenol nanocomplex for chemo-immunotherapy of glioblastoma by inducing pyroptosis by Xinyan Hao, Yucheng Tang, Wenjie Xu, Ming Wang, Jiayi Liu, Yongjiang Li, Jun He, Yanjin Peng, Pengcheng Sun, Dehua Liao, Xiongbin Hu, Tiantian Tang, Min Zhou, Ruyue Han, Jiemin Wang, João Conde, Daxiong Xiang, Junyong Wu

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Spatially Resolved Multiomics: Data Analysis from Monoomics to Multiomics by Changxiang Huan, Jinze Li, Yingxue Li, Shasha Zhao, Qi Yang, Zhiqi Zhang, Chuanyu Li, Shuli Li, Zhen Guo, Jia Yao, Wei Zhang, Lianqun Zhou

“…Moreover, the spatial resolution, high-throughput detection capability, capture efficiency, and compatibility with various sample types of omics technology have considerably advanced. Despite the technological advances in this field, data analysis frameworks have stagnated. …”
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The effects of Thymus capitatus essential oil topical application on milk quality: a systems biology approach by Ralph Nehme, Chiara Gini, Elise Vanbergue, Sergine Even, Filippo Biscarini, Sonia Andrés, Lucie Rault, Faustine Noel, Valerie Hardit, Said Bouhallab, David M. Pereira, Riadh Ksouri, Philippe Roussel, Secundino López, Paola Cremonesi, Bianca Castiglioni, Donatella Caruso, Fiorenza Faré, Manuela Fontana, Fabrizio Ceciliani, Latifa Abdennebi-Najar

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Comprehensive analysis of the expression and prognostic value of ARMCs in pancreatic adenocarcinoma by Guanxiang Zhuo, Shengzhai Lin, Fei Yuan, Qiaoling Zheng, Yinpin Guo, Zuwei Wang, Jianfei Hu, Meihong Yao, Fuxiu Zhong, Shi Chen, Yanling Chen, Huixing Chen

“…Then, Gene Expression Profiling Interactive Analysis (GEPIA), the cBioPortal database, the Human Protein Atlas (HPA), Kaplan-Meier Plotter, LinkedOmics Database, Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG), Cytoscape and Timer were used to analyze the relationship between ARMCs and PAAD. …”
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Using Quantitative Trait Locus Mapping and Genomic Resources to Improve Breeding Precision in Peaches: Current Insights and Future Prospects by Umar Hayat, Cao Ke, Lirong Wang, Gengrui Zhu, Weichao Fang, Xinwei Wang, Changwen Chen, Yong Li, Jinlong Wu

“…This work shows how combining genome-wide association studies and machine learning can improve the synthesis of multi-omics data and result in faster breeding cycles while preserving genetic diversity. …”
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The Platelet-Specific Gene Signature in the Immunoglobulin G4-Related Disease Transcriptome by Ali Kemal Oguz, Cagdas Sahap Oygur, Bala Gur Dedeoglu, Irem Dogan Turacli, Sibel Serin Kilicoglu, Ihsan Ergun

“…Secondary analysis of omics data sets has great potential to reveal new and valuable information.…”
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