Differential Analysis of Early-Onset and Late-Onset Colorectal Cancer Based on Multidimensional Evidence Integration: A Review by Xiaoying Mi MS, Peng Zheng MS, Xiangbai Wu MS

“…Additionally, MSI-H is more prevalent in patients with EO-CRC. Differences in transcriptomics and metabolomics profiles have also been observed between EO-CRC and LO-CRC, which may account for their distinct biological characteristics. …”
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Exploring RNA-Seq Data Analysis Through Visualization Techniques and Tools: A Systematic Review of Opportunities and Limitations for Clinical Applications by Farhana Manzoor, Cyruss A. Tsurgeon, Vibhuti Gupta

“…RNA sequencing (RNA-seq) has emerged as a prominent resource for transcriptomic analysis due to its ability to measure gene expression in a highly sensitive and accurate manner. …”
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Integrative Model of Oxidative Stress Adaptation in the Fungal Pathogen Candida albicans. by Chandrasekaran Komalapriya, Despoina Kaloriti, Anna T Tillmann, Zhikang Yin, Carmen Herrero-de-Dios, Mette D Jacobsen, Rodrigo C Belmonte, Gary Cameron, Ken Haynes, Celso Grebogi, Alessandro P S de Moura, Neil A R Gow, Marco Thiel, Janet Quinn, Alistair J P Brown, M Carmen Romano

“…Our deterministic mathematical model integrates two major oxidative stress signalling pathways (Cap1 and Hog1 pathways) with the three major antioxidant systems (catalase, glutathione and thioredoxin systems) and the pentose phosphate pathway, which provides reducing equivalents required for oxidative stress adaptation. …”
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Ensemble modeling of SARS-CoV-2 immune dynamics in immunologically naïve rhesus macaques predicts that potent, early innate immune responses drive viral elimination by Catherine Byrne, Joshua T. Schiffer

“…A 90% knockdown of the innate response from our validated model resulted in a ~10-fold increase in peak viral load during infection. Our approach provides a novel methodological framework for future analyses of similar complex, non-linear multi-component immunologic data sets.…”
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Developmental estrogen exposure in mice disrupts uterine epithelial cell differentiation and causes adenocarcinoma via Wnt/β-catenin and PI3K/AKT signaling. by Elizabeth Padilla-Banks, Wendy N Jefferson, Brian N Papas, Alisa A Suen, Xin Xu, Diana V Carreon, Cynthia J Willson, Erin M Quist, Carmen J Williams

“…Single-cell RNA sequencing (scRNAseq) and spatial transcriptomics of adult control uteri revealed novel markers of uterine epithelial stem cells (EpSCs), identified distinct luminal and glandular progenitor cell (PC) populations, and defined glandular and luminal epithelium (LE) cell differentiation trajectories. …”
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Bacteroides thetaiotaomicron enhances H2S production in Bilophila wadsworthia by Jade Davies, Melinda J. Mayer, Nathalie Juge, Arjan Narbad, Lizbeth Sayavedra

“…Endometabolomic and transcriptomic analyses revealed decreased production of indole by B. thetaiotaomicron in co-culture with B. wadsworthia due to enhanced tryptophan utilization by B. wadsworthia. …”
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Integrative analysis of ceRNA networks and immune cell infiltration in thyroid cancer for enhanced diagnostic and prognostic insights by Chang Lv, Huazhe Wu, Dejun Yin, Wei Fang, Liming Zhou

“…DUXAP8 was positively correlated with activated mast cells and monocytes, while HCP5 was negatively correlated with resting NK cells. This study provides new insights into thyroid cancer pathogenesis, suggesting potential molecular markers for early diagnosis and personalized treatment. …”
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Evolutionary dynamics of Orchid DL paralogs: gene duplication, functional divergence, and expression patterns across Orchid subfamilies by Francesca Lucibelli, Angela Carfora, Annette Becker, Katrin Ehlers, Serena Aceto

“…Conclusions Our study provides insights into the evolutionary trajectory of DL genes in orchids. …”
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Integrating single-cell RNA-seq and bulk RNA-seq to construct a neutrophil prognostic model for predicting prognosis and immune response in oral squamous cell carcinoma by Jinhang Wang, Zifeng Cui, Qiwen Song, Kaicheng Yang, Yanping Chen, Shixiong Peng

“…The prognostic model provides a novel reference for patient stratification and targeted therapy. …”
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Deletion of Nkx2-5 in trabecular myocardium reveals the developmental origins of pathological heterogeneity associated with ventricular non-compaction cardiomyopathy. by Caroline Choquet, Thi Hong Minh Nguyen, Pierre Sicard, Emeline Buttigieg, Thi Thom Tran, Frank Kober, Isabelle Varlet, Rachel Sturny, Mauro W Costa, Richard P Harvey, Catherine Nguyen, Pascal Rihet, Sylvain Richard, Monique Bernard, Robert G Kelly, Nathalie Lalevée, Lucile Miquerol

“…Our results provide insights into the etiology of LVNC and link its pathogenicity with compromised trabecular development including compaction defects and ventricular conduction system hypoplasia.…”
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Harnessing Artificial Intelligence and Machine Learning for Identifying Quantitative Trait Loci (QTL) Associated with Seed Quality Traits in Crops by My Abdelmajid Kassem

“…I also explored AI-driven integration of multi-omics data—genomics, transcriptomics, metabolomics, and phenomics—to improve resolution in QTL mapping. …”
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Transcriptional progression during meiotic prophase I reveals sex-specific features and X chromosome dynamics in human fetal female germline. by Xueying Fan, Ioannis Moustakas, Vanessa Torrens-Juaneda, Qijing Lei, Geert Hamer, Leoni A Louwe, Gonneke S K Pilgram, Karoly Szuhai, Roberto Matorras, Cristina Eguizabal, Lucette van der Westerlaken, Hailiang Mei, Susana M Chuva de Sousa Lopes

“…Analysis of single-cell transcriptomics data from human fetal germ cells (FGC) allowed us to identify the molecular signatures of female meiotic prophase I stages leptotene, zygotene, pachytene and diplotene. …”
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Cell-in-cell associated lncRNA signature predicts prognosis and immunotherapy response in gastric cancer by Junzuo Lin, Liancheng Wu, Zhengfei Zhao

“…Experimental validation confirmed AP000695.2 promoted proliferation and invasion in GC cells (P <0.01).ConclusionThis study establishes CICRlncRNAs as prognostic biomarkers and provides insights for precision therapy, though clinical applicability requires prospective validation.…”
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Mitochondrial genome and transcription of Shiraia-like species reveal evolutionary aspects in protein-coding genes by Xiao-Ye Shen, Xue-Ting Cao, Xiao-Bo Huang, Lan Zhuo, Hui-Meng Yang, Li Fan, Cheng-Lin Hou

“…These findings would provide new insights into secondary metabolite regulation and ROS resistance. …”
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Ageless harmony: decoding the microbiome–stem cell nexus in aging by Swarup K. Chakrabarti, Dhrubajyoti Chattopadhyay

“…Techniques, such as spatial transcriptomics and single-cell sequencing, provide opportunities to unravel the molecular intricacies underpinning the crosstalk between gut microbes and stem cells within their tissue microenvironments, thereby governing health and longevity. …”
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Identification and expression analysis of myo-inositol oxygenase gene family in Brassica napus L. by CHEN Shubing, XU Zishu, HUANG Qian, ZHANG Hui, ZHANG Kangni, DUAN Yi, SUN Yue’e, ZHOU Weijun, XU Ling

“…The results of the protein interaction network analysis further showed that the BnMIOX interacted with proteins including GLCAK, PIS1, VTC2, VTC4, and PDF2.1, implying that BnMIOX genes play key roles in improving the resistance of B. napus. This study provides an important basis for further investigation of the function of BnMIOX genes.…”
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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

“…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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CXCR2 Activated JAK3/STAT3 Signaling Pathway Exacerbating Hepatotoxicity Associated with Tacrolimus by Chen X, Hu K, Zhang Y, He SM, Wang DD

“…The aim of this study was to investigate the mechanism of tacrolimus-induced hepatotoxicity and provide reference for drug development target.Methods: In this study, biochemical analysis, pathological staining, immunofluorescent staining, immunohistochemical staining, transcriptomic analysis, Western blotting was used to investigate the mechanism of tacrolimus-induced hepatotoxicity in gene knockout mice and Wistar rats.Results: In gene knockout mice, compared to wild-type mice, CXCR2-deficiency alleviated tacrolimus-induced hepatotoxicity (P…”
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Tumor-infiltrating lymphocyte therapy: therapeutic advances and prospects by Sarker Drishty Badhon, Gonzalez Marian M., Martinez Sophia, Sang Qing-Xiang Amy

“…Emerging techniques, including single-cell transcriptomics and biomarker-guided TIL selection (e.g., CD137, CD103 markers), have provided deeper insights into the characteristics correlating with successful outcomes. …”
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Cbf11 and Mga2 function together to activate transcription of lipid metabolism genes and promote mitotic fidelity in fission yeast. by Anna Marešová, Michaela Grulyová, Miluše Hradilová, Viacheslav Zemlianski, Jarmila Princová, Martin Převorovský

“…The fission yeast Schizosaccharomyces pombe provides a powerful platform to study the intricate regulatory mechanisms governing these fundamental processes. …”
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