Joint fluid multi-omics improves diagnostic confidence during evaluation of children with presumed septic arthritis by Yolanda Peña-López, Naureen G. Tareen, Bo Zhang, Indu Raman, Carlos A. Arana, Chengsong Zhu, Yang Liu, Pratibha Selvakumar, Nicolai S. C. van Oers, Simrat Morris, Lora V. Hooper, Lawson A. B. Copley, Prithvi Raj

“…Methods Twelve children with suspected septic arthritis were prospectively enrolled to compare standard of care tests with a rapid multi-omics approach. The multi-omics combined bacterial 16S rRNA metagenomics, single cell transcriptomics, and proteomics on knee joint fluid specimens. …”
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Support Vector Machine – Recursive Feature Elimination for Feature Selection on Multi-omics Lung Cancer Data by Nuraina Syaza Azman, Azurah A Samah, Ji Tong Lin, Hairudin Abdul Majid, Zuraini Ali Shah, Nies Hui Wen, Chan Weng Howe

“…The cleaned LUSC datasets are then integrated to form a multi-omics dataset. Feature selection was performed on the LUSC multi-omics data using SVM-RFE to select several optimal feature subsets. …”
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Multi-omics analysis of hexaploid triticale that show molecular responses to salt stress during seed germination by Dongxia Wang, Jiedong Li, Shiming Li, Jiongjie Fu, Baolong Liu, Baolong Liu, Baolong Liu, Dong Cao, Dong Cao, Dong Cao

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Multi-omic and single-cell profiling of chromothriptic medulloblastoma reveals genomic and transcriptomic consequences of genome instability by Petr Smirnov, Moritz J. Przybilla, Milena Simovic-Lorenz, R. Gonzalo Parra, Hana Susak, Manasi Ratnaparkhe, John KL. Wong, Verena Körber, Jan-Philipp Mallm, George Philippos, Martin Sill, Thorsten Kolb, Rithu Kumar, Nicola Casiraghi, Konstantin Okonechnikov, David R. Ghasemi, Kendra Korinna Maaß, Kristian W. Pajtler, Anna Jauch, Andrey Korshunov, Thomas Höfer, Marc Zapatka, Stefan M. Pfister, Wolfgang Huber, Oliver Stegle, Aurélie Ernst

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Machine learning‐based multi‐omics models for diagnostic classification and risk stratification in diabetic kidney disease by Xian Shao, Suhua Gao, Pufei Bai, Qian Yang, Yao Lin, Mingzhen Pang, Weixi Wu, Lihua Wang, Ying Li, Saijun Zhou, Hongyan Liu, Pei Yu

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Real world perspectives on endometriosis disease phenotyping through surgery, omics, health data, and artificial intelligence by Camran R. Nezhat, Tomiko T. Oskotsky, Joshua F. Robinson, Susan J. Fisher, Angie Tsuei, Binya Liu, Juan C. Irwin, Brice Gaudilliere, Marina Sirota, David K. Stevenson, Linda C. Giudice

“…Integrating single-cell and other omic disease data with clinical and surgical metadata can identify multiple disease subtypes with translation to novel diagnostics and therapeutics. …”
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Multi‐omics graph convolutional networks for digestive system tumour classification and early‐late stage diagnosis by Lin Zhou, Zhengzhi Zhu, Hongbo Gao, Chunyu Wang, Muhammad Attique Khan, Mati Ullah, Siffat Ullah Khan

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Unveiling the mechanism of micro-and-nano plastic phytotoxicity on terrestrial plants: A comprehensive review of omics approaches by Asad Jamil, Ambreen Ahmad, Muhammad Moeen-ud-din, Yihao Zhang, Yuxuan Zhao, Xiaochen Chen, Xiaoyu Cui, Yindong Tong, Xianhua Liu

“…Recent advancements in omics technologies such as proteomics, metabolomics, transcriptomics, and microbiomics, coupled with emerging technologies like 4D omics, phenomics, spatial transcriptomics, and single-cell omics, offer unprecedented insight into the physiological, molecular, and cellular responses of terrestrial plants to MNPs exposure. …”
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Multi-omics approaches for understanding gene-environment interactions in noncommunicable diseases: techniques, translation, and equity issues by Robel Alemu, Nigussie T. Sharew, Yodit Y. Arsano, Muktar Ahmed, Fasil Tekola-Ayele, Tesfaye B. Mersha, Azmeraw T. Amare

“…This scoping review evaluates the global landscape of multi-omics data related to NCDs from 2000 to 2024, focusing on recent advancements in multi-omics data integration, translational applications, and equity considerations. …”
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Editorial: New techniques in microbiome research - volume II: Host-microbiome interactions using ‘meta-omics’ techniques by Tao Lin

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Uncovering the molecular mechanisms behind Alzheimer’s and Parkinson’s disease through multi-omics: an interview with Bruno A. Benitez by Bruno A. Benitez

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Multi-omics analysis reveals distinct gene regulatory mechanisms between primary and organoid-derived human hepatocytes by Haoyu Wu, Annie S. P. Yang, Suzan Stelloo, Floris J. M. Roos, René H. M. te Morsche, Anne H. Verkerk, Maria V. Luna-Velez, Laura Wingens, Johannes H. W. de Wilt, Robert W. Sauerwein, Klaas W. Mulder, Simon J. van Heeringen, Monique M. A. Verstegen, Luc J. W. van der Laan, Hendrik Marks, Richárd Bártfai

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Author Correction: Synthetic augmentation of cancer cell line multi-omic datasets using unsupervised deep learning by Zhaoxiang Cai, Sofia Apolinário, Ana R. Baião, Clare Pacini, Miguel D. Sousa, Susana Vinga, Roger R. Reddel, Phillip J. Robinson, Mathew J. Garnett, Qing Zhong, Emanuel Gonçalves

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Multi-omics analyses identify gut microbiota-fecal metabolites-brain-cognition pathways in the Alzheimer’s disease continuum by Han Zhao, Xia Zhou, Yu Song, Wenming Zhao, Zhongwu Sun, Jiajia Zhu, Yongqiang Yu

“…Furthermore, we assessed the associations between these multi-omics changes using correlation and mediation analyses. …”
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MONet: cancer driver gene identification algorithm based on integrated analysis of multi-omics data and network models by Yingzan Ren, Tiantian Zhang, Jian Liu, Fubin Ma, Jiaxin Chen, Ponian Li, Guodong Xiao, Chuanqi Sun, Yusen Zhang

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Omics-Based Interaction Analysis Reveals Interplay of Chemical Pollutant (Ozone) and Photoradiation (UVSSR) Stressors in Skin Damage by Hong Zhang, Yiying Dong, Xue Xiao, Xiao Cui, Xuelan Gu

Subjects: “…omics-based interaction effect…”
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Multi-omic and machine learning analysis of mitochondrial RNA modification genes in lung adenocarcinoma for prognostic and therapeutic implications by Xiao Zhang, Jiatao Liu, Yaolin Cao, Wei Wang, Haoran Lin, Yue Yu

“…Recognizing the pivotal role of mitochondrial RNA modifications (MRM) in cancer progression, this study aims to provide a comprehensive analysis of MRM-related genes and their clinical relevance in lung adenocarcinoma (LUAD). Integrating multi-omic datasets, we systematically explored the molecular features of MRM-related genes across various cancers and identified distinct expression patterns and prognostic associations. …”
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Integrated electronic nose and multi-omics reveal changes in flavour characterization of cashmere goats and tan sheep meat by Ju Zhang, Shuang Pang, Ge Yan, Lulu Wang, Yuan Xu, Yuheng Bai, Ran Li, Xihong Wang, Yu Jiang

“…This study aimed to employ a multi-omics method to identify key compounds contributing to the sensory flavour of mutton and to investigate the internal correlation between volatile metabolites and lipids in Cashmere goats and Tan sheep. …”
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Comprehensive multi-omics, behavioral and morphological analysis of the hazards of nano-plastics in mice with internal carotid artery occlusion by Lu Wang, Jia-Qi Ma, Li-Jia Song, Xiao-Peng Qu, Yue Zhang, Hai-Ming Fan, Chao Wang, Long-Long Zheng, Guo-Dong Gao, Yan Qu, Liang-Liang Shen, Bei Liu

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HighDimMixedModels.jl: Robust high-dimensional mixed-effects models across omics data. by Evan Gorstein, Rosa Aghdam, Claudia Solís-Lemus

“…Our simulations provide new insights into the algorithm's behavior in these settings, and, comparing the performance of two popular penalties, we demonstrate that the smoothly clipped absolute deviation (SCAD) penalty consistently outperforms the least absolute shrinkage and selection operator (LASSO) penalty in terms of both variable selection and estimation accuracy across omics data. To empower researchers in biology and other fields to fit models with the SCAD penalty, we implement the algorithm in a Julia package, HighDimMixedModels.jl.…”
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