Phytochemical characterization and bioinformatics guided evaluation of antioxidant and cytotoxic effects of Psoralea bituminosa by Nour H. Aboalhaija, Rima Hajjo, Fatma Afifi, Heba Syaj, Rana Abu-Dahab

“…Cheminformatics clustering supported these findings, identifying distinct structural groups with differing drug-likeness scores. Bioinformatics analysis further identified transcriptomic signatures enriched in oxidative phosphorylation and key cancer-related pathways (e.g., TP53, PI3K, NRF2, and MYC), offering mechanistic insight. …”
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Antifungal and antibiofilm activities of flavonoids against Candida albicans: Focus on 3,2′-dihydroxyflavone as a potential therapeutic agent by Jin-Hyung Lee, Yong-Guy Kim, Inji Park, Jintae Lee

“…In addition, 3,2′-DHF dramatically inhibited cell aggregation and germ tube/hyphae formation. Transcriptomic analyses revealed that flavone and 3,2′-DHF behaved differently, as 3,2′-DHF downregulated the expressions of germ tube/hyphae-forming and biofilm-related genes (ECE1, HWP1, TEC1, and UME6) but upregulated the biofilm/hyphal regulators (CHK1, IFD6, UCF1, and YWP1). …”
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An insulin-like peptide specific for a cockroach male reproductive gland. by Viviana Pagone, David Pujal, José Luis Maestro

“…A comparison of the transcriptomes of control and BgILP8-depleted glands revealed only small differences. …”
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Age-related cerebral amyloid angiopathy accumulation in the APPSw mouse model is associated with perivascular inflammation and brain-wide vascular and inflammatory gene and protein... by Katelynn E. Krick, Erica M. Weekman, Sherika N. Johnson, Tiffany L. Sudduth, Colin B. Rogers, Emma J. Nicolayson, Maureen T. Kleinhenz, Donna M. Wilcock

“…Further, we identified differences in abundance of proteins (CD45, GFAP, CD31) based on presence of CAA positive vessels within a brain region. …”
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Harnessing the diversity of a lettuce wild relative to identify anthocyanin-related genes transcriptionally responsive to drought stress by Inés Medina-Lozano, Inés Medina-Lozano, Jérôme Grimplet, Jérôme Grimplet, Aurora Díaz, Aurora Díaz

“…Lettuce is a crop particularly vulnerable to drought. A transcriptomic study in the variety ‘Romired’ and the wild relative Lactuca homblei was conducted to understand the increase in anthocyanins (only significant in L. homblei) in response to drought previously observed. …”
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Identification of progression related LncRNAs in colorectal cancer aggressiveness by Wei Xi, Xinxin Sun, Mingwei Wang, Xizi Wang, Kun Li, Runze Jiang, Xiaodong Jia, Wenxiao Wang

“…In this study, we identified key progression-related lncRNAs in CRC by integrating transcriptomic data from TCGA and single-cell RNA sequencing (scRNA-seq). …”
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ATR Deficiency Impairs DNA Damage Repair and Accelerates Cellular Senescence in Bovine Mammary Epithelial Cells, Leading to Lactation Dysfunction by Qijun Zhou, Zijian Geng, Shuai Lian, Jianfa Wang, Rui Wu

“…Our findings indicated differences in relevant pathways, including DNA damage repair and apoptosis, which are influenced by increasing parity. …”
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The therapeutic potential of pegylated arginase I treatment in glioblastoma by Marcus Kwong Lam Fung, Shing Chan, Stella Sun, Ping De Zhang, Gilberto Ka Kit Leung, Godfrey Chi Fung Chan

“…BCT-100 inhibited growth and induced cell death in four GBM cell lines in vitro. Transcriptomics of U87 and U373 treated with BCT-100 responded differently. …”
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Identification of macrophage-associated diagnostic biomarkers and molecular subtypes in gestational diabetes mellitus based on machine learning by Kai Wei, Liyun Yuan, Yongsheng Ge, Han Yu, Guoping Zhao, Guoqing Zhang, Guohua Liu

“…A diagnostic model for GDM derived from endothelial cell transcriptomes was constructed by employing a variety of machine learning ensemble algorithms, achieving an AUC of 0.887. …”
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Biomarkers and therapeutic strategies targeting microglia in neurodegenerative diseases: current status and future directions by Min-Young Noh, Hyuk Sung  Kwon, Min-Soo Kwon, Minyeop Nahm, Hee Kyung Jin, Jae-sung Bae, Seung Hyun Kim

“…Despite notable progress, many of these biomarkers remain restricted to preclinical studies and face translational challenges due to species-specific differences, lack of standardization, and clinical heterogeneity. …”
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Comprehensive Characterization of Mesenchymal Stem Cells from Human Placenta and Fetal Membrane and Their Response to Osteoactivin Stimulation by C. M. Raynaud, M. Maleki, R. Lis, B. Ahmed, I. Al-Azwani, J. Malek, F. F. Safadi, A. Rafii

“…These MSCs could be differentiated into mesodermal cells expressing cell markers and cytologic staining consistent with mature osteoblasts and adipocytes. Transcriptomic analysis and cytokine arrays demonstrated broad similarity between placenta- and membrane-derived MSCs and only discrete differences with BM-MSCs with enrichment of networks involved in bone differentiation. …”
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Synergistic effects of ectoine and biostimulants combinations on tomato seedling growth and heat stress resilience by Yanyan Chen, Weimin Xu, Chuankun Han, Miao Zhang, Ying Chen, Yujia Ma, Xinjun Zhang, Huhu Liu, Wenna Zhang

“…Among the treatments, HCE (HRW + CSL + E) exhibited the most pronounced effects on root growth, increasing root length, volume, and surface area, while E and HE (HRW + E) demonstrated the highest phenotypic index and stress resilience under heat stress conditions. Transcriptomic analysis revealed significant differences in differentially expressed genes (DEGs) among treatments. …”
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Epigenomic and 3D genomic mapping reveals developmental dynamics and subgenomic asymmetry of transcriptional regulatory architecture in allotetraploid cotton by Xianhui Huang, Yuejin Wang, Sainan Zhang, Liuling Pei, Jiaqi You, Yuexuan Long, Jianying Li, Xianlong Zhang, Longfu Zhu, Maojun Wang

“…A comparison among subgenomes in the 12 tissues reveals widespread differences in the reorganization of 3D genome structures, with the Dt subgenome exhibiting a higher extent of dynamic chromatin status than the At subgenome. …”
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Multi‐omics analyses reveal the interaction between colonic microbiota and host in Min and Yorkshire pigs by Xiaoyu Huang, Huihui Li, Feng Cheng, Ligang Wang, Guoqing Cao, Lixian Wang, Lijun Shi

“…Through the correlation analysis of colonic microbiota with metabolomics of colonic content or transcriptomics of colonic tissues, we provided direct and indirect relationships of microorganisms and hosts. …”
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Comparative analysis of library preparation approaches for FFPE gene expression profiling and related recommendations by Sara Pignatta, Marcella Tazzari, Valentina Indio, Maria Maddalena Tumedei, Francesco Limarzi, Francesca Tauceri, Michela Tebaldi, Dalila Fanelli, Jenny Bulgarelli

“…Abstract Next-Generation Sequencing (NGS) has transformed cancer research and clinical practice, with Whole Exome Sequencing (WES) driving advances in mutational profiling and personalized oncology. Yet, transcriptomic signatures remain essential for understanding disease mechanisms, including therapy resistance pathways. …”
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Targeting myeloid cells in pancreatic ductal adenocarcinoma: from primary tumors to liver metastasis by Ruining Gong, Ying Chen, Chang Li, Huan Zhang, Zimin Liu, Qian Yu

“…Advancements in single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics have provided deeper insights into the molecular intricacies and diversity of PDAC, revealing potential therapeutic targets. …”
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Integrative analysis of epigenetic and transcriptional interrelations identifies histotype-specific biomarkers in early-stage ovarian carcinoma by Hugo Swenson, Ella Ittner, Lucas Werner, Elisabeth Werner Rönnerman, Claudia Mateoiu, Anikó Kovács, Pernilla Dahm-Kähler, Ghassan M. Saed, Szilárd Nemes, Per Karlsson, Toshima Z. Parris, Khalil Helou

“…Gene expression for the candidate biomarkers was found to be reproducible across external cohorts, with histotype-specific differences remaining homogenous. Conclusions This study identified promising histotype-specific biomarkers for EOC using integrative transcriptomic and epigenomic analysis. …”
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Low level of tonic interferon signalling is associated with enhanced susceptibility to SARS-CoV-2 variants of concern in human lung organoids by Meaghan Flagg, Kerry Goldin, Lizzette Pérez-Pérez, Manmeet Singh, Brandi N. Williamson, Nathanael Pruett, Chuong D. Hoang, Emmie de Wit

“…Transcriptomic analysis revealed that increased susceptibility to SARS-CoV-2 infection in these hLOs was associated with reduced tonic interferon signaling activity at baseline. …”
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Molecular Mechanism of Body Color Change in the Ecological Seedling Breeding Model of <i>Apostichopus japonicus</i> by Lingshu Han, Pengfei Hao, Haoran Xiao, Weiyan Li, Yichen Fan, Wanrong Tian, Ye Tian, Luo Wang, Yaqing Chang, Jun Ding

“…To investigate the molecular and genetic basis of this novel red coloration, we compared the growth conditions of red sea cucumbers and green sea cucumbers, as well as the differences in the pigment composition, gene expression and metabolites of their body walls. …”
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Chronic toxicity mechanisms of 6PPD and 6PPD-Quinone in zebrafish by Fang Jiao, Yang Zhao, Qiang Yue, Qi Wang, Zhongzhi Li, Wanjing Lin, Lingxi Han, Liangfu Wei

“…Exposure to both compounds impaired zebrafish growth, induced hepatic damage, and disrupted locomotor behavior. Transcriptomic analysis of liver tissue revealed disturbances in lipid and carbohydrate metabolic pathways in both treatment groups, with distinct differences in gene expression patterns and biochemical responses between 6PPD and 6PPDQ. …”
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