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The utilization of multi-omics research has gained popularity in clinical investigations. However, effectively managing and merging extensive and diverse datasets presents a challenge due to its intricacy. This research introduces a Multi-Omics Analysis Sandbox Toolkit, an online platform designed to facilitate the exploration, integration, and visualization of datasets ranging from single-omics to multi-omics. This platform establishes connections between clinical data and omics information, allowing for versatile analysis and storage of both single and multi-omics data. Additionally, users can repeatedly utilize and exchange their findings within the platform. This toolkit offers diverse alternatives for data selection and gene set analysis. It also presents visualization outputs, potential candidates, and annotations. Furthermore, this platform empowers users to collaborate by sharing their datasets, analyses, and conclusions with others, thus enhancing its utility as a collaborative research tool. This Multi-Omics Analysis Sandbox Toolkit stands as a valuable asset in comprehensively grasping the influence of diverse factors in diseases and pinpointing potential biomarkers. [BMB Reports 2024; 57(12): 521-526].
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http://dx.doi.org/10.5483/BMBRep.2023-0155 | DOI Listing |
Ecotoxicol Environ Saf
September 2025
Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, 107 Wenhua West Road, Jinan, Shandong 250012, China; Shandong Key Laboratory of Reproductive Health and Birth Defects Prevention and Control, China. Electronic address:
Di-isobutyl phthalate (DiBP), a member of the phthalate esters, is frequently used in manufacturing consumer and industrial products as plasticizer to improve durability and flexibility. Despite much research, little is known about the direct mechanisms by which DiBP harms the male reproductive system. In the present study, a male ICR mice model was developed to investigate the reproductive effect and mechanism of DiBP exposure, followed by transcriptomics, non-targeted metabolome, and 16S rDNA sequencing accordingly.
View Article and Find Full Text PDFRedox Biol
September 2025
Multi-Omics Platform, Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto, Japan; Human Biology Microbiome Quantum Research Center, Keio University School of Medicine, Tokyo, Japan. Electronic address:
Ferroptosis, an iron-dependent cell death mechanism characterized by excessive lipid peroxidation, has been implicated in numerous human diseases and organ pathologies. However, current detection methods necessitate invasive tissue sampling to assess lipid peroxidation, making noninvasive detection of ferroptosis in human subjects extremely challenging. In this study, we employed oxidative volatolomics to comprehensively characterize the volatile oxidized lipids (VOLs) produced during ferroptosis.
View Article and Find Full Text PDFBrief Bioinform
August 2025
School of Computer Science, Xi'an Polytechnic University, 710048, Xi'an, China.
Cancer, with its inherent heterogeneity, is commonly categorized into distinct subtypes based on unique traits, cellular origins, and molecular markers specific to each type. However, current studies primarily rely on complete multi-omics datasets for predicting cancer subtypes, often overlooking predictive performance in cases where some omics data may be missing and neglecting implicit relationships across multiple layers of omics data integration. This paper introduces Multi-Layer Matrix Factorization (MLMF), a novel approach for cancer subtyping that employs multi-omics data clustering.
View Article and Find Full Text PDFZool Res
September 2025
Department of Urology & Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China. E-mail:
Chromatin remodeling and transcriptional reprogramming play critical roles during mammalian meiotic prophase I; however, the precise mechanisms regulating these processes remain poorly understood. Our previous work demonstrated that deletion of heat shock factor 5 (HSF5), a member of the heat shock factor family, induces meiotic arrest and male infertility. However, the molecular pathways through which HSF5 governs meiotic progression have not yet been fully elucidated.
View Article and Find Full Text PDFPhysiol Plant
September 2025
School of Forestry and Grassland Science, Ningxia University, Yinchuan, China.
Using high- and low-surface flatness fruits of Ziziphus jujuba Mill. cv. "Lingwuchangzao" at different developmental stages as test materials, this study examined the mechanisms underlying variations in fruit appearance and internal quality.
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