Identification and Cross-Platform Validation of Sparse Molecular Classifiers for Antibody-Mediated and T-Cell–Mediated Rejection After Kidney Transplantation by Jasper Callemeyn, Josué Manik Nava-Sedeño, Dany Anglicheau, Jack Beadle, Jan Hinrich Bräsen, Marian C. Clahsen-van Groningen, Iacopo Cristoferi, Henriette de Loor, Andreas Deutsch, Marie Essig, Wilfried Gwinner, Philip F. Halloran, Dennis A. Hesselink, Priyanka Koshy, Dirk Kuypers, Evelyne Lerut, Pierre Marquet, Robert C. Minnee, Candice Roufosse, Ben Sprangers, Amaryllis H. Van Craenenbroeck, Haralampos Hatzikirou, Maarten Naesens

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mNSF: multi-sample non-negative spatial factorization by Yi Wang, Kyla Woyshner, Chaichontat Sriworarat, Genevieve Stein-O’Brien, Loyal A. Goff, Kasper D. Hansen

“…Through simulations and real data analysis, we demonstrate mNSF’s efficacy in identifying true factors, shared anatomical regions, and region-specific biological functions. mNSF’s performance is comparable to alignment-based methods when alignment is feasible, while enabling analysis in scenarios where spatial alignment is unfeasible. mNSF shows promise as a robust method for analyzing spatially resolved transcriptomics data across multiple samples.…”
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Revealing the dynamic changes of metabolites and molecular mechanisms of chlorogenic acid accumulation during the leaf development of Vaccinium dunalianum based on multi-omic analy... by Anmian Zhang, Jiaxin Liu, Weicheng Li, Lihong Yang, Wenjin Duan, Ping Zhao, Zhiyu Pu, Yong Ding

“…Additionally, this study also reveals V. dunalianum holds promise as a natural antioxidant source for functional foods, providing data support for network pharmacology.…”
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Virtual Screening and Meta-Analysis Approach Identifies Factors for Inversion Stimulation (Fis) and Other Genes Responsible for Biofilm Production in <i>Pseudomonas aeruginosa</i>:... by Promise M. Emeka, Lorina I. Badger-Emeka, Krishnaraj Thirugnanasambantham

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Advancing precision antibody-drug conjugate therapy: unique proteogenomic profiles of tumor subsets in non-small cell lung cancer by Edwin Lin, Ying-Chun Lo, Vivek Subbiah, Rajat Thawani, Aakash Desai

“…Abstract Antibody-drug conjugates (ADCs) represent a promising therapeutic strategy for non-small cell lung cancer (NSCLC), targeting tumor-specific antigens with precision. …”
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Targeting PDCD4 in cancer and atrial fibrillation: mechanistic insights from integrated multi-omics and single-cell analysis by Juledezi Hailati, Zhiqiang Liu, Lei Zhang, Muhuyati Wulasihan

“…Drug prediction analyses revealed sirtinol and trichostatin as promising therapeutic drugs for targeting Atad5 and Sirt1, respectively, with good molecular docking scores (&lt; -5 kcal/mol). …”
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Overexpression of Lol-miR11467 negatively affects osmotic resistance in Larix kaempferi 3 × L. gmelinii 9 by Sufang Zhang, Shanshan Yan, Li Zhang, Pingyu Yan, Hanguo Zhang, Lei Zhang

“…Molecular breeding offers a promising approach to shorten the breeding cycle and achieve genetic improvements more efficiently. …”
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Causal Correlations Between Plasma Metabolites, Inflammatory Proteins, and Chronic Obstructive Pulmonary Disease: A Mendelian Randomization and Bioinformatics-Based Investigation by Cao S, Gu Y, Lu G, Zhu L, Feng S, Bian T

“…These findings offer novel insights into metabolism-inflammation-COPD mechanisms, suggesting that interventions targeting metabolic processes may represent a promising strategy for preventing the onset or progression of COPD.Keywords: Mendelian randomization, chronic obstructive pulmonary disease, inflammation, metabolism, single-cell RNA-seq, transcriptomics…”
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Identifying acute myeloid leukemia subtypes based on pathway enrichment by Ling Zhong, Ling Zhong, Ling Zhong, Ling Zhong, Jiangti Luo, Jiangti Luo, Jiangti Luo, Jiangti Luo, Junze Dong, Xiang Yang, Xiaosheng Wang, Xiaosheng Wang, Xiaosheng Wang, Xiaosheng Wang

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Downregulation of PGK1 promotes lipid peroxidation and suppresses proliferation in cervical cancer revealed by liquid-liquid phase separation-related gene signature by Beilei Zhang, Zhanghang Li, Zhaojie Yang, Yidan Yin, Mingke Duan, Lei Wang, Qirui Zhan, Fu Wang, Ruifang An

“…This study leverages single-cell sequencing and transcriptome analysis to identify LLPS-linked therapeutic targets in cervical cancer. …”
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Multi-strain probiotics attenuate carbohydrate-lipid metabolic dysregulation in type 2 diabetic rats via gut-liver axis modulation by Yecheng Gao, Yanfang Liu, Zelong Li, Liyi Lu, Yajuan Guo, Dun Su, Heping Zhang

“…Exogenous probiotics have the potential to serve as a promising therapeutic strategy to improve diabetes-related symptoms. …”
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Alkannin Induces G2/M-Phase Arrest, Apoptosis, and Inhibition of Invasion by Targeting GSK3&beta; in Esophageal Squamous Cell Carcinoma by Ma H, Xu P, Jia Y, Zhou Y, Li X, Wang Y, Ma K

“…Consistently, in vivo administration of Alkannin significantly reduced the growth of ESCC tumors in nude mice.Conclusion: This study is the first to demonstrate that Alkannin, by targeting GSK3β, induces G2/M-phase arrest in ESCC cells, thereby inhibiting migration, invasion, and inducing apoptosis, suggesting that Alkannin may be a promising antitumor agent for treating ESCC. Keywords: esophageal squamous cell carcinoma, Alkannin, network pharmacology, transcriptomics, Glycogen Synthase Kinase 3&#x03B2…”
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The role of cytokine licensing in shaping the therapeutic potential of wharton’s jelly MSCs: metabolic shift towards immunomodulation at the expense of differentiation by Olena Rogulska, Eliska Vavrinova, Irena Vackova, Jarmila Havelkova, Klara Gotvaldova, Pavel Abaffy, Sarka Kubinova, Michal Sima, Pavel Rossner, Lucie Bacakova, Pavla Jendelova, Katarina Smolkova, Yuriy Petrenko

“…In this study, we evaluated the transcriptomic, metabolomic, and functional changes induced by short-term TNF-α/IFN-γ priming of Wharton’s jelly-derived MSCs (WJ-MSCs). …”
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Drug Repurposing to Inhibit Oncostatin M in Crohn’s Disease by Faranak Bahramimehr, Axel Guthart, Stefanie Kurz, Yuanping Hai, Mona Dawood, Rümeysa Yücer, Nasim Shahhamzehei, Ralf Weiskirchen, Wilfried Roth, Wolfgang Stremmel, Gerhard Bringmann, Thomas Efferth

“…In conclusion, we have identified oncostatin M as a promising new drug target for Crohn’s disease through transcriptomics and ecamsule as a potential new drug candidate for Crohn’s disease through a drug-repurposing approach both in silico and in vitro.…”
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Deciphering Immunometabolic Landscape in Rheumatoid Arthritis: Integrative Multiomics, Explainable Machine Learning and Experimental Validation by Dong Q, Wu J, Zhang H, Chen X, Xu X, Chen J, Shi C, Luo L, Zhang D

“…CMAP, molecular docking, and PheWAS analysis further highlighted vismodegib as a promising therapeutic candidate.Conclusion: This study clarifies the key immunometabolic mechanisms in RA, pinpointing promising paths for better prevention, diagnosis, and treatment.Keywords: rheumatoid arthritis, dendritic cells, single-cell sequencing, bulk transcriptome, explainable machine learning, drug repositioning…”
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Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data by Marco Stock, Corinna Losert, Matteo Zambon, Niclas Popp, Gabriele Lubatti, Eva Hörmanseder, Matthias Heinig, Antonio Scialdone

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Integrating brain proteomes and genetics to identify novel risk genes in chronic widespread musculoskeletal pain by Zhisen Dai, Yanlin Wu, Huaqing Huang, Huizhe Zheng

“…These genes represent promising targets for future research and therapeutic intervention development.…”
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2-Nonanol produced by Bacillus velezensis EM-1: a new biocontrol agent against tobacco brown spot by Xiaona Sui, Xiaobin Han, Xianbo Wang, Jun Wan, Mingxia Wen, Donglin Zhao, Yanfen Zheng, Chengsheng Zhang, Chuantao Xu, Youqiang Wang

“…These findings suggest that 2-nonanol holds potential as a biocontrol agent for managing tobacco brown spot disease, underscoring the promising role of volatile organic compounds (VOCs) in the development of environmentally friendly biocontrol products.…”
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Novel machine‐learning bioinformatics reveal distinct metabolic alterations for enhanced colorectal cancer diagnosis and monitoring by Rui Xu, Hyein Jung, Fouad Choueiry, Shiqi Zhang, Rachel Pearlman, Heather Hampel, Ning Jin, Jieli Li, Jiangjiang Zhu

“…Meanwhile, complementary transcriptomic data were also analyzed and integrated to further understand CRC metabolic dysregulations. …”
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Torreya grandis nut peptides regulate lipid-II inhibitors in high-fat diet-fed mice by Rabia Durrani, Sun Yutian, Hou Bowen, Hammad Ullah, Erwann Durand, Yang Meiyun, Long Yiyang, André Delavault, Muhammad Yasir, Huan Weiwei, Gao Fei, Song Lili

“…These findings suggested T. grandis as a promising supplement in food and a key nut for nutraceutical purposes.…”
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