Sulfated dietary fiber protects gut microbiota from antibiotics by Fuqing Wu, Xiaoqian Annie Yu, David Angeles-Albores, Susan E. Erdman, Eric J. Alm

“…This protective effect is dependent on the structural integrity, molecular weight, and sulfur content of the polysaccharide. Transcriptomic analysis showed that while fucoidan had minimal impact on baseline gene expression, it counteracted about 60% of the genes induced by kanamycin, suggesting a potential inhibition of kanamycin. …”
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Urinary Immune Complexes Reflect Renal Pathology in Lupus Nephritis by Chenling Tang, Aygun Teymur, Tianfu Wu

“…Background/Objectives: Lupus nephritis (LN) is a serious complication of systemic lupus erythematosus (SLE), involving immune complex deposition in the kidneys. While renal biopsy is the diagnostic gold standard, its invasiveness limits frequent use, driving the need for non-invasive urinary biomarkers to monitor disease progression and response to treatment. …”
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Cardiovascular diseases in the elderly: possibilities for modulating autophagy using non-coding RNAs by Silvia Scalabrin, Stefano Cagnin, Stefano Cagnin

“…Finally, we conducted a comprehensive meta-analysis of transcriptomic data to underscore the paramount importance of autophagy while demonstrating it as a process that is frequently dysregulated in both cardiac and vascular cells under pathological conditions. …”
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E2F1 suppresses Epstein-Barr virus lytic reactivation through cellular and viral transcriptional networks. by Joyanta Biswas, Sk Asif Ali, Samaresh Malik, Subhadeep Nag, Piyali Mukherjee, Abhik Saha

“…While ectopic E2F1 expression suppresses lytic replication, E2F1 depletion markedly accelerates this process. …”
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Multivariate stochastic modeling for transcriptional dynamics with cell-specific latent time using SDEvelo by Xu Liao, Lican Kang, Yihao Peng, Xiaoran Chai, Peng Xie, Chengqi Lin, Hongkai Ji, Yuling Jiao, Jin Liu

“…Using both simulated and four scRNA-seq and spatial transcriptomics datasets, we show that SDEvelo can model the random dynamic patterns of mature-state cells while accurately detecting carcinogenesis. …”
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TREM1 is essential for maintaining stemness of liver cancer stem-like cells in hepatocellular carcinoma by Arsha Sreekumar, Ashwin Ajith, Kenza Mamouni, Daniel D. Horuzsko, Anatolij Horuzsko

“…IntroductionHepatocellular carcinoma (HCC) is the most common primary liver cancer and a leading cause of cancer-related mortality worldwide. While the Triggering Receptor Expressed on Myeloid Cells 1 (TREM1) is well-known for its role in amplifying inflammation within the tumor microenvironment (TME), its tumor-intrinsic role remains poorly defined. …”
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Progression of Ankle Osteoarthritis Is Associated with Distinct Synovial Phenotypes by Julia Matthias MD, Michael A. David PhD, Sara E. Buckley DO, Nathaniel Zona BA, Michael Zuscik PhD, Kenneth Hunt MD

“…Thus, this study aimed to characterize ankle synovium's transcriptomic and histological landscape with progression of ankle OA. …”
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The Genome Assembly of Vitis vinifera cv. Shiraz by Cristobal A. Onetto, Christopher M. Ward, Anthony R. Borneman

“…The availability of a reference genome for Shiraz expands the pool of genomes available for wine grapes while providing a foundation resource for whole-genome studies involving this iconic cultivar, including intracultivar variant identification and transcriptomic studies using a matching reference genome.…”
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A R1-type MYB CmREVEILLE2 regulates light-mediated chlorophyll biosynthesis and green color formation in chrysanthemum flowers by Jingjie Fang, Sitong Liu, Sijia Chen, Huijie Deng, Linxia Zhao, Xinwei Liang, Ziqiang Chen, Xiaoqin Zhang, Songwen Xu, Caiyun Wang, Jing Luo

“…CmRVE2 expression was significantly upregulated under HL conditions, while its expression was lower under LL compared to ML. …”
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Beyond the nuclear border: single-cell analysis of in situ sequenced human brain tissue using cellular features by Janssen M. Kotah, Thomas Rust, Hilmar R. J. van Weering, Janneke Bosma, Amber L. Woudstra, Susanne M. Kooistra, Bart J. L. Eggen

“…Abstract Spatial transcriptomics has advanced our understanding of cellular heterogeneity at single-cell resolution. …”
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Dual role of Eisenia fetida and its excreta in boosting tomato biomass and defense against Botrytis cinerea by Maryan Chelkha, Rubén Blanco-Pérez, Jorge Dueñas-Hernani, Ignacio Vicente-Díez, Victoria Pastor, Raquel Campos-Herrera

“…Earthworms (EWs) enhance soil and indirectly affect plant growth, while their cutaneous excreta (CEx) contain bioactive compounds capable of eliciting plant responses. …”
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Fungus-mediated plant-pollinator mutualism in Monoon laui (Annonaceae): functional differentiation of stigmatic exudate and petal nectar by Yanwen Chen, Bine Xue, Juan Diego Gaitán-Espitia, Richard M. K. Saunders

“…Transcriptomic and proteomic comparisons between the two organs and their exudates corroborate the nutritional profiles, with a stronger immune response on stigmas. …”
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Interpretable and integrative analysis of single-cell multiomics with scMKL by Samuel D. Kupp, Ian A. VanGordon, Mehmet Gönen, Sadık Esener, Sebnem Ece Eksi, Çiğdem Ak

“…It outperforms existing methods while delivering interpretable results that identify key transcriptomic and epigenetic features, as well as multimodal pathways– that existing methods have failed to achieve, in breast, lymphatic, prostate, and lung cancers. …”
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Baseline cell cycle and immune profiles indicate CDK4/6 inhibitor response in metastatic HR + /HER2- breast cancer by Stephanie L. Tzetzo, Emily Schultz, Jianxin Wang, Hanna R. Rosenheck, Sidney Mahan, Erik S. Knudsen, Agnieszka K. Witkiewicz

“…Abstract While CDK4/6 inhibitors (CDK4/6i) and endocrine therapy are standard-of-care for metastatic HR + /HER2- breast cancer, patient selection for durable efficacy remains undefined. …”
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Expression Profiling of a Heterogeneous Population of ncRNAs Employing a Mixed DNA/LNA Microarray by Konstantinia Skreka, Marek Zywicki, Michael Karbiener, Alexander Hüttenhofer, Marcel Scheideler, Mathieu Rederstorff

“…Mammalian transcriptomes mainly consist of non protein coding RNAs. …”
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Comparison of baseline global gene expression profiles of prostate cancer cell lines LNCaP and DU145 by Khalid Ahmed, Zhannur Omarova, Alisalman Sheikh, Gulzhan Abuova, Kulsoom Ghias, Syed Hani Abidi

“…Characterizing their baseline transcriptomics profiles (without any intervention) can offer insights into baseline genetic features and oncogenic pathways that should be considered while interpreting findings after various experimental interventions such as exogenous gene transfection or drug treatment. …”
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FPR3 orchestrates macrophage polarization in breast cancer: multi-omics dissection of prognostic relevance and therapeutic targeting by Ying Chen, Xin Tang, Liran Zhu, Yi Wang, Gaopeng Li, Wulin Yang

“…Methods A comprehensive analysis integrating bulk RNA-seq transcriptomics, methylomics, single-cell transcriptomics, and spatial single-cell transcriptomics data was conducted to elucidate the distinctive characteristics of FPRs in breast cancer. …”
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Machine Learning Inference of Gene Regulatory Networks in Developing <i>Mimulus</i> Seeds by Albert Tucci, Miguel A. Flores-Vergara, Robert G. Franks

“…We deployed two GRN inference algorithms—RTP-STAR and KBoost—on three different subsets of our transcriptomic dataset. While the two algorithms yielded GRNs with different regulations and topologies when working with the same data subset, there was still significant overlap in the specific gene regulations they inferred, and they both identified potential novel regulatory mechanisms that warrant further investigation.…”
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The conserved wobble uridine tRNA thiolase Ctu1 is required for angiogenesis and embryonic development. by Yangziwei Yu, Chuqiao Wang, Yan Wang, Heng Shi, Huiyuan Hu, Yibin Du, Zhaoli Zhou

“…Elongator mutant animals exhibit severe phenotypes, while the biological function of Ctu1 in vertebrate animal models remains poorly characterized. …”
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Identification of a PANoptosis-related gene signature reveals therapeutic potential of SFRP2 in pulmonary arterial hypertension by Li Li, Mukamengjiang Juaiti

“…Gene expression was further validated using a rat PAH model and pulmonary artery fibroblasts (PAAFs), while hub gene functions were investigated at the cellular level through Western blot, CCK-8, and flow cytometry assays.ResultsThrough integrated transcriptomic analysis, SFRP2 was identified as a feature gene related to PAH and PANoptosis. …”
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