Development of the Dutch translational knowledge agenda for inherited metabolic diseases by I. J. Hieltjes, J. H. van derLee, M. C. Groenendijk, G. vanHaaften, P. M. vanHasselt, R. J. Lunsing, G. J. J. vanProoijen, E. M. deRuiter, F. J. vanSpronsen, N. M. Verhoeven‐Duif, A. deVreugd, M. Wagenmakers, H. Zweers, H. Dekker, H. R. Waterham, C. D. vanKarnebeek, R. J. A. Wanders, R. A. Wevers

“…The resulting top 10 research questions cover multiple themes, i.e. prediction of disease progression, development of novel tools, mechanistic insights, improved diagnostics, therapeutic integration of multi‐omics techniques, assessment of impact on daily life, expanding treatment avenues, optimal study designs, effect of lifestyle interventions, and data utilization using FAIR principles. …”
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Resensitizing β‐Lactams by Reprogramming Purine Metabolism in Small Colony Variant for Osteomyelitis Treatment by Tingwang Shi, Qiong Wu, Zesong Ruan, Zhiyuan Luo, Wenbo Wang, Zhao Guo, Yihong Ma, Xin Wang, Guangyu Chu, Han Lin, Min Ge, Yunfeng Chen

“…In this study, phenotypically stable SCV strains are successfully recovered from clinical specimens, characterized by elevated drug resistance and reduced immunogenicity. Multi‐omics analysis revealed that the acquired high drug resistance is associated with altered flux in the purine metabolism pathway, attributable to mutations in the hypoxanthine phosphoribosyltransferase (hpt) gene. …”
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METTL16 is Required for Meiotic Sex Chromosome Inactivation and DSB Formation and Recombination during Male Meiosis by Lisha Yin, Nan Jiang, Wenjing Xiong, Shiyu Yang, Jin Zhang, Mengneng Xiong, Kuan Liu, Yuting Zhang, Xinxin Xiong, Yiqian Gui, Huihui Gao, Tao Li, Yi Li, Xiaoli Wang, Youzhi Zhang, Fengli Wang, Shuiqiao Yuan

“…Mechanistically, in pachytene spermatocytes, METTL16 interacts with MDC1/SCML2 to coordinate DNA damage response (DDR) and XY body epigenetic modifications that establish and maintain MSCI, and in early meiotic prophase I, METTL16 regulates DSB formation and recombination by regulating protein levels of meiosis‐related genes. Furthermore, multi‐omics analyses reveal that METTL16 interacts with translational factors and controls m6A levels in the RNAs of meiosis‐related genes (e.g., Ubr2) to regulate the expression of critical meiotic regulators. …”
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Exploring changes in metabolites and fecal microbiota of advanced gastric cancer based on plasma metabolomics and 16S rDNA sequencing by Xinyi Feng, Yu Zhang, Jun Feng, Zhongjun Li, Zhi Zhang, Lin Zhu, Ruoyu Zhou, Haibo Wang, Xiaojun Dai, Yanqing Liu

“…Currently, there is little research on the omics of gastric cancer and it lacks effective biomarkers. …”
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An early lung cancer diagnosis model for non-smokers incorporating ct imaging analysis and circulating genetically abnormal cells (CACs) by Ran Ni, Yongjie Huang, Lei Wang, Hongjie Chen, Guorui Zhang, Yali Yu, Yinglan Kuang, Yuyan Tang, Xing Lu, Hong Liu

“…The established multi-omics model is a noninvasive prediction tool for non-smoking malignant pulmonary nodule diagnosis. …”
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Fatty acid synthase inhibition improves hypertension-induced erectile dysfunction by suppressing oxidative stress and NLRP3 inflammasome-dependent pyroptosis through activating the... by Jiaochen Luan, Mengchi Yu, Qi Gu, Xuan Zhou, Yunqiang Shao, Tong Chen, Jiayi Zhang, Zheng Zhu, Ninghong Song, Jie Yang

“…Additionally, increased expression of the NLRP3 inflammasome, Caspase-1, GSDMD, and the pro-inflammatory cytokines IL-1β and IL-18 was observed. Multi-omics analysis revealed significant enrichment in lipid metabolic pathways, with Fasn identified as a hub gene. …”
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Artisanal and farmer bread making practices differently shape fungal species community composition in French sourdoughs by Michel, Elisa, Masson, Estelle, Bubbendorf, Sandrine, Lapicque, Léocadie, Nidelet, Thibault, Segond, Diego, Guézenec, Stéphane, Marlin, Thérèse, Devillers, Hugo, Rué, Olivier, Onno, Bernard, Legrand, Judith, Sicard, Delphine

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DNA Methylation and Transcriptome Profiling Reveal the Role of the Antioxidant Pathway and Lipid Metabolism in <i>Plectropomus leopardus</i> Skin Color Formation by Yang Liu, Linna Wang, Zhentong Li, Linlin Li, Tangtang Ding, Shuai Chen, Pengfei Duan, Xinyi Wang, Yishu Qiu, Xiaoyu Ding, Yongsheng Tian

“…Astaxanthin effectively increased the redness value a* and body weight. Multi-omics analyses revealed the crucial roles of pathways related to antioxidants and lipid metabolism, particularly “Tyrosine metabolism”, “Melanogenesis”, “Fatty acid metabolism”, “Fatty acid elongation”, and “Biosynthesis of unsaturated acids”, in red skin coloration. …”
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JUNB O‐GlcNAcylation‐Mediated Promoter Accessibility of Metabolic Genes Modulates Distinct Epithelial Lineage in Pulmonary Fibrosis by Marie‐Therese Bammert, Meshal Ansari, Leoni Haag, Zuhdi Ahmad, Victoria Schröder, Joseph Birch, Diana Santacruz, Werner Rust, Coralie Viollet, Benjamin Strobel, Alec Dick, Florian Gantner, Holger Schlüter, Fidel Ramirez, Muriel Lizé, Matthew J. Thomas, Huy Q. Le

“…Harnessing a 3D patient‐derived organoid model and multi‐omics approach, the first inventory of the connection between metabolic alteration, chromatin accessibility, and transcriptional regulation in IPF aberrant epithelial remodeling is provided. …”
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High expression of SULF1 is associated with adverse prognosis in breast cancer brain metastasis by Yitong Li, Tingting Feng, Qinghong Wang, Yue Wu, Jue Wang, Wenlong Zhang, Qi Kong

“…Thus, expression levels, variations, associations with HER2, biological processes, and pathways involving SULF1 could be analyzed using UALCAN, cBioPortal, GEPIA2, and LinkedOmics databases. Moreover, the sensitivity of SULF1 to existing drugs was explored using drug databases such as RNAactDrug and CADSP. …”
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HIV and the gut microbiome: future research hotspots and trends by Zhen Wu, Zhan-Peng Xie, Xin-Xin Cui, Xiang-Bin Sun, Fang-Yi Zhao, Nuo Wang, Yu Li, Yu Li, Yu Li, Haixia Wang, Haixia Wang, Haixia Wang, Li Zhang, Li Zhang, Li Zhang, Jing Shen, Fulei Chen, Haogang Sun, Jia He, Jia He, Jia He

“…Furthermore, understanding the metabolic mechanisms of short-chain fatty acids in T cells is essential. Additionally, multi-omics analysis holds potential.…”
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Identification of EXPA4 as a key gene in cotton salt stress adaptation through transcriptomic and coexpression network analysis of root tip protoplasts by Qiankun Liu, Pengtao Li, Muhammad Jawad Umer, Mubashir Abbas, Yongqing Zhao, Yu Chen, Yanfang Li, Aiming Zhang, Yuling Liu, Yangyang Wei, Quanwei Lu, Mengying Yang, Yiman Liu, Xiaoyan Cai, Zhongli Zhou, Shuxun Yu, Fang Liu, Renhai Peng

“…Future research should focus on elucidating the precise mechanisms of putative salt tolerance genes like GaEXPA4 and evaluating the potential of signaling pathways, such as MAPK, for engineering enhanced salt resilience in cotton. Integrating multi-omics approaches could further expand the genetic resources available for improving cotton cultivation in saline environments.…”
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Quo vadis autoimmune hepatitis? - Summary of the 5th international autoimmune hepatitis group research workshop 2024Keypoints by Bastian Engel, David N. Assis, Mamatha Bhat, Jan Clusmann, Joost PH. Drenth, Alessio Gerussi, María-Carlota Londoño, Ye Htun Oo, Ida Schregel, Marcial Sebode, Richard Taubert

“…The specific objectives of this year's 5th Workshop were: (1) To further improve diagnostics. (2) Initiate clinical trials including knowledge transfer on drugs from extrahepatic immune-mediated diseases, including B cell-depleting CAR T cells. (3) Utilisation of multi-omics approaches to improve the understanding of disease pathogenesis. (4) Application of machine learning-based approaches established in oncology or transplantation medicine to improve diagnosis and outcome prediction in AIH.…”
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Research Status and Direction of Chronic Obstructive Pulmonary Disease Complicated with Coronary Heart Disease: A Bibliometric Analysis from 2005 to 2024 by Bian H, Zhu S, Xing W, Qi L, Xue J, Peng X, Jin Z, Zhao H

“…To improve the early detection rate of COPD complicated with CHD, the main development direction in the future is to extract computed tomography (CT) features using imaging omics and establish an early prediction model. The results of this study will provide new ideas and directions for subsequent related research.Keywords: chronic obstructive pulmonary disease, COPD, coronary heart disease, CHD, inflammation, bibliometrics, visual analysis…”
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Rap1 and mTOR signaling pathways drive opposing immunotoxic effects of structurally similar aryl-OPFRs, TPHP and TOCP by Bilin Zhao, Shuang Zheng, Gaoxiang Yang, Zhijun He, Jiewei Deng, Lijuan Luo, Xinyan Li, Tiangang Luan

“…This study sought to address the knowledge gap by integrating transcriptomic and metabolomic analyses to elucidate the intricate mechanisms. During individual omics analyses, we unfortunately only obtained highly similar results for both TPHP and TOCP, failing to identify the key reasons for their differences. …”
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From actinic keratosis to cutaneous squamous cell carcinoma: the key pathogenesis and treatments by Zhenlin Li, Zhenlin Li, Zhenlin Li, Zhenlin Li, Fangqi Lu, Fangqi Lu, Fangqi Lu, Fangqi Lu, Fujin Zhou, Fujin Zhou, Fujin Zhou, Dekun Song, Dekun Song, Dekun Song, Lunhui Chang, Lunhui Chang, Lunhui Chang, Lunhui Chang, Weiying Liu, Guorong Yan, Guorong Yan, Guorong Yan, Guolong Zhang, Guolong Zhang, Guolong Zhang, Guolong Zhang

“…Thus, more and more studies are trying to ascertain the potential transformation mechanisms through multi-omics, including genetics, transcriptomics, and epigenetics. …”
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Lachnospiraceae-bacterium alleviates ischemia-reperfusion injury in steatotic donor liver by inhibiting ferroptosis via the Foxo3-Alox15 signaling pathway by Shenghe Deng, Huan Cao, Tongxi Li, Xueling Wang, Junpeng Meng, Teng Zeng, Di Zhang, Shuhua Zhang, Guoliang Wang, Ran Liu, Tianhao Zou, Mao Cai, Ren Lang, Di Lu, Jinyang Gu

“…-treated rats exhibited improved intestinal permeability, reduced IRI severity in both normal and steatotic donor livers, and decreased levels of neutrophil and macrophage infiltration, and inflammatory cytokines. Multi-omics analysis revealed elevated pyruvate levels in transplanted livers after Lachn. treatment, alongside reduced Alox15 and Foxo3 expression. …”
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SNP discovery by exome capture and resequencing in a pea genetic resource collection by Aubert, Grégoire, Kreplak, Jonathan, Leveugle, Magalie, Duborjal, Hervé, Klein, Anthony, Boucherot, Karen, Vieille, Emilie, Chabert-Martinello, Marianne, Cruaud, Corinne, Bourion, Virginie, Lejeune-Hénaut, Isabelle, Pilet-Nayel, Marie-Laure, Bouchenak-Khelladi, Yanis, Francillonne, Nicolas, Tayeh, Nadim, Pichon, Jean-Philippe, Rivière, Nathalie, Burstin, Judith

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Integrating multi-layered biological priors to improve genomic prediction accuracy in beef cattle by Zhida Zhao, Qunhao Niu, Jiayuan Wu, Tianyi Wu, Xueyuan Xie, Zezhao Wang, Lupei Zhang, Huijiang Gao, Xue Gao, Lingyang Xu, Bo Zhu, Junya Li

“…However, the improvement and application of effective strategies for genomic prediction (GP) using multi-omics data remains challenging. Methods We generated 11 feature sets for sequencing variants from genomics, transcriptomics, metabolomics, and epigenetics data in beef cattle, then we assessed the contribution of functional variants using genomic restricted maximum likelihood (GREML). …”
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Prevalence of anaemia and the associated factors among hospitalised people living with HIV receiving antiretroviral therapy in Southwest China: a cross-sectional study by Jie Yuan, Hai Long, Min Liu, Juan He, Jue Liu, Yu Wu, Wenzhan Jing, Min Du, Manna Zhang, Yaping Wang, Su Song, Siqi Liu, Guiying Cao, Yuedong Liang, Xiaoxin Xie, Yanhua Fu

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