TaRTLEt: Transcriptionally-active Riboswitch Tracer Leveraging Edge deTection by Sachit Kshatriya, Sarah C. Bagby

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Unravelling NK cell subset dynamics and specific gene signatures post-ibrutinib therapy in chronic lymphocytic leukaemia via single-cell transcriptomics by Chunlan Liu, Tianjian Ding, Rong Zou, Aili Zhang, Zhengzhuo Zhi, Sili Wang

“…The CNI, derived from its key genes, holds promise as a predictor of immune therapeutic responses, highlighting the significance of CLL_NK subset dynamics and their genetic underpinnings in CLL management.…”
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Hypoxia reconstructed colorectal tumor microenvironment weakening anti-tumor immunity: construction of a new prognosis predicting model through transcriptome analysis by Ruizhi Zhang, Yisong Gao, Chong Li, Ruikang Tao, Gan Mao, Tianyu Song, Wenxiang Nie, Suao Liu, Kaixiong Tao, Wei Li

“…This study aims to develop a novel hypoxia-related prognostic score (HPS) based on hypoxia-associated genes to improve CRC prognostication and inform treatment strategies.MethodsTranscriptomic data from CRC patients were analyzed using Lasso regression to identify hypoxia-associated genes with the strongest prognostic significance. …”
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A hybrid 1DCNN-GRU deep learning framework for classifying caprine granulosa cell fertility potential using single-cell transcriptomics by Thanida Sananmuang, Denis Puthier, Kaj Chokeshaiusaha

“…However, the lack of a standardized, quantifiable method to assess GC quality using transcriptomic data has limited the translation of such findings into reproductive applications. …”
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Transcriptomic analysis of human primary T cells after short-term leucine-deprivation and evaluation of kinase GCN2's role in regulating differential gene expression. by Aurore Dougé, Gwendal Cueff, Céline Keime, Valérie Carraro, Céline Jousse, Paul Rouzaire, Alain Bruhat

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Identification of programmed cell death-related genes and construction of a prognostic model in oral squamous cell carcinoma using single-cell and transcriptome analysis by Yongheng Li, Yang Yu, Shaonan Hu, Simin Li

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Targeted transcriptomic analysis of well-differentiated and dedifferentiated liposarcoma reveals multiple dysregulated pathways including glucose metabolism, TGF-β, and HIF-1 signa... by Ashley Patton, Natalie Horn, Puja Upadhaya, Patricia Sarchet, Raphael E. Pollock, Raphael E. Pollock, Steve Oghumu, Obiajulu Hans Iwenofu, Obiajulu Hans Iwenofu

“…The future of targeted therapy for WD/DDLPS is promising with the intention to spare multi-visceral removal due to radical surgical resection. …”
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Transcriptomics of tissue exosomes to investigate miR-195-5p’s amelioration of endometrial fibrosis via the YAP-Smad7 pathway: an animal study by Jia-ming Chen, Qiao-yi Huang, Wei-hong Chen, Jin-xiang Wu, Ling-tao Zheng, Hui-jie You, Yan-chuan Shi, Shu Lin, Qi-rong Shi

“…Methods Exosomes from rat uterine tissue with intrauterine adhesions were analyzed via transcriptomics to identify downstream target genes of miR-195-5p, cross-referencing with the human endometrial transcriptomics database GSE224093. …”
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Deciphering the role of SEMA4A/MAPK signaling in sepsis: insights from Mendelian randomization, transcriptomic, single-cell sequencing analyses, and vitro experiments by Meng-Qin Pei, Yan-Ling Lin, Li-Ming Xu, Yu-Shen Yang, Zhen-Dong Sun, Ya-Fen Zeng, Gui-Dan Wang, He-Fan He, Li-Ying Yu, Li-Ying Yu

“…This study aims to uncover new therapeutic targets for sepsisMethodsThree independent transcriptomic datasets from sepsis patients in the GEO database were utilized. …”
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The PRMT5-splicing axis is a critical oncogenic vulnerability that regulates detained intron splicing by Colin E. Fowler, Natalie A. O’Hearn, Griffin J. Salus, Arundeep Singh, Paul L. Boutz, Jacqueline A. Lees

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Nitroxoline evidence amoebicidal activity against Acanthamoeba castellanii through DNA damage and the stress response pathways by Lijun Chen, Wei Han, Wenwen Jing, Meng Feng, Qingtong Zhou, Xunjia Cheng

“…Nitroxoline, a quinoline derivative with well-established antibacterial, antifungal, and antiviral properties, is a promising therapeutic candidate. This study aimed to elucidate cellular signalling events that counteract the effects of nitroxoline. …”
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The Effects of FR and UVA Irradiation Timing on Multi-Omics of Purple Lettuce in Plant Factories by Yubin Zhang, Zhaoxin Li, Ning Zhang, Xiujuan Chai

“…The synergistic application of far-red (FR) and ultraviolet A (UVA) irradiation presents a promising approach for enhancing growth and the enrichment of secondary metabolites in plants. …”
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Integration of Transcriptomics and Proteomics to Elucidate Inhibitory Effect and Mechanism of Antifungalmycin B from Marine <i>Streptomyces hiroshimensis</i> in Treating <i>Talarom... by Qiqi Li, Zhou Wang, Cuiping Jiang, Jianglin Yin, Yonghong Liu, Xinjian Qu, Xiangxi Yi, Chenghai Gao

“…In this study, we employed a mouse model in conjunction with transcriptomic and proteomic approaches to explore the antifungal activity of ANB against <i>T. marneffei</i>. …”
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Genome-Wide Association Integrating a Transcriptomic Meta-Analysis Suggests That Genes Related to Fat Deposition and Muscle Development Are Closely Associated with Growth in Huaxi... by Cheng-Li Liu, Tao Ren, Peng-Cheng Ruan, Yong-Fu Huang, Simone Ceccobelli, De-Jun Huang, Lu-Pei Zhang, Guang-Xin E

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Comprehensive transcriptome analysis reveals MSTRG.19853.1/ssc-miR-361-3p/NPPA axis is related to hypoxic adaptation in Tibetan pigs by Pan Li, Wei Cheng, Zhandui Pubu, Peng Shang, Hao Zhang, Bo Zhang

“…The MSTRG.19853.1/ssc-miR-361-3p/NPPA axis represents a promising candidate for regulating cardiac adaptation under hypoxia, pending in vivo validation. …”
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Meta-analysis of multi-center transcriptomic profiles and machine learning reveal phospholipase Cβ4 as a Wnt/Ca²+ signaling mediator in glioblastoma immunotherapy by Zhaoming Song, Fei Wang, Chen Yang, Yanao Guo, Jinfeng Li, Run Huang, Hongyi Ling, Guosheng Cheng, Zhouqing Chen, Zhanchi Zhu, Zhong Wang

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An integrated machine learning model of transcriptomic genes in multi-center chronic obstructive pulmonary disease reveals the causal role of TIMP4 in airway epithelial cell by Erkang Yi, Haiqing Li, Yu Liu, Qingyang Li, Chengshu Xie, Ruining Sun, Fan Wu, Zhishan Deng, Kunning Zhou, Hairong Wang, Xinru Ran, Yumin Zhou, Pixin Ran

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InSituCor: exploring spatially correlated genes conditional on the cell type landscape by Patrick Danaher, Dan McGuire, Lidan Wu, Michael Patrick, David Kroeppler, Haiyan Zhai, Deniz G. Olgun, Dennis Gong, Jingyi Cao, William L. Hwang, Joachim Schmid, Joseph M. Beechem

“…Abstract In spatial transcriptomics data, spatially correlated genes promise to reveal high-interest phenomena like cell–cell interactions and latent variables. …”
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Integrated RNA Sequencing Analysis Revealed Early Gene Expression Shifts Associated with Cancer Progression in MCF-7 Breast Cancer Cells Cocultured with Adipose-Derived Stem Cells by Minh Ngoc Vu, Hoang Duc Le, Thi Tien Vu, Trung Nam Nguyen, Hoang Ha Chu, Van Ngoc Bui

“…We performed an RNA-seq analysis to identify significant transcriptomic changes in cocultured MCF-7 cells and carried out functional enrichment analyses to uncover key biological pathways influenced by ADSCs. …”
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Identification of key genes involved in collagen hydrogel-induced chondrogenic differentiation of mesenchymal stem cells through transcriptome analysis: the role of m6A modificatio... by Chaotao Chen, Kai Xiong, Kanglu Li, Bo Zhou, Jianwen Cheng, Bo Zhu, Li Zheng, Jinmin Zhao

“…Abstract Collagen hydrogel has been shown promise as an inducer for chondrogenic differentiation of bone marrow mesenchymal stem cells (BMSCs), contributing to the repair of cartilage defects. …”
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