Single-cell transcriptome analysis reveals cellular heterogeneity in the aortas of Takayasu arteritis

Authors: Na Gao, He Tang, Taotao Li, Yi Yang, Honglei Zhao, Longfei Wang, Yanqiu Guo, Bokang Qiao, Lili Pan

Source: Arthritis Research & Therapy, Vol 27, Iss 1, Pp 1-15 (2025)

Subject Terms: Takayasu arteritis, Single-cell RNA sequencing, Bulk RNA sequencing, Cellular heterogeneity, Complement pathway, Diseases of the musculoskeletal system, RC925-935

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Relation: https://doaj.org/toc/1478-6362

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Comprehensive analysis of scRNA-seq and bulk RNA-seq reveals the non-cardiomyocytes heterogeneity and novel cell populations in dilated cardiomyopathy

Authors: Siyu He, Chunyu Li, Mingxin Lu, Fang Lin, Sangyu Hu, Junfang Zhang, Luying Peng, Li Li

Source: Journal of Translational Medicine, Vol 23, Iss 1, Pp 1-22 (2025)

Subject Terms: Dilated cardiomyopathy (DCM), Single-cell RNA sequencing (scRNA-seq), Bulk RNA sequencing (Bulk RNA-seq), Non-cardiomyocytes, Heterogeneity, Medicine

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Relation: https://doaj.org/toc/1479-5876

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Wnt signaling aberrant activation drives ameloblastoma invasion and recurrence: bioinformatics and in vitro insights

Authors: Yemei Qian, Hongrong Zhang, Jingyi Li, Liangchong Huang, Yunfa Qin, Jian Zhang, Weihong Wang

Source: BMC Oral Health, Vol 24, Iss 1, Pp 1-9 (2024)

Subject Terms: Ameloblastoma, Wnt signaling pathway, Invasion and Recurrence, Bulk RNA sequencing, Dentistry, RK1-715

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Relation: https://doaj.org/toc/1472-6831

Access URL: https://doaj.org/article/f00125ede0e64366ad2e6b840cd2b7c3

Multi-Omics Exploration of the Role of PTGS2 as a Hub Gene in Ferroptosis Within the Artery of Takayasu Arteritis

Authors: Gao Q, Gao S, Li H, Chen Z, Zhang R, Li Y, Zhang H

Source: Journal of Inflammation Research, Vol Volume 17, Pp 9135-9146 (2024)

Subject Terms: takayasu arteritis, single-cell rna sequencing, bulk rna sequencing, ferroptosis, ptgs2, Pathology, RB1-214, Therapeutics. Pharmacology, RM1-950

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Relation: https://www.dovepress.com/multi-omics-exploration-of-the-role-of-ptgs2-as-a-hub-gene-in-ferropto-peer-reviewed-fulltext-article-JIR; https://doaj.org/toc/1178-7031

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Mechanisms of Berberine in anti-pancreatic ductal adenocarcinoma revealed by integrated multi-omics profiling

Authors: Jia Yang, Tingting Xu, Hongwei Wang, Lei Wang, Yanmei Cheng

Source: Scientific Reports, Vol 14, Iss 1, Pp 1-15 (2024)

Subject Terms: Berberine, Pancreatic ductal adenocarcinoma, Single-cell RNA sequencing, Bulk RNA sequencing, Multi-omics analysis, Medicine, Science

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Relation: https://doaj.org/toc/2045-2322

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A novel lactylation-related gene signature to predict prognosis and treatment response in lung adenocarcinoma

Authors: Hongyi Zhang, Yihao Liu, Xuanguang Li, Chen Ding, Chunqiu Xia, Hua Huang, Hongyu Liu, Jun Chen

Source: Frontiers in Oncology, Vol 15 (2025)

Subject Terms: lactylation-related genes, lung adenocarcinoma, immune cell infiltration, single-cell RNA sequencing, bulk RNA sequencing, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

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Relation: https://www.frontiersin.org/articles/10.3389/fonc.2025.1549724/full; https://doaj.org/toc/2234-943X

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Liver transcriptome analysis reveals PSC-attributed gene set associated with fibrosis progression

Authors: Alena Laschtowitz, Eric L. Lindberg, Anna-Maria Liebhoff, Laura Anne Liebig, Christian Casar, Silja Steinmann, Adrien Guillot, Jun Xu, Dorothee Schwinge, Michael Trauner, Ansgar Wilhelm Lohse, Stefan Bonn, Norbert Hübner, Christoph Schramm

Source: JHEP Reports, Vol 7, Iss 3, Pp 101267- (2025)

Subject Terms: Primary sclerosing cholangitis, Biliary fibrosis, Bulk RNA-sequencing, Liver transcriptome, Diseases of the digestive system. Gastroenterology, RC799-869

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Relation: http://www.sciencedirect.com/science/article/pii/S2589555924002714; https://doaj.org/toc/2589-5559

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Elevated levels of IRF1 and CASP1 as pyroptosis-related biomarkers for intestinal epithelial cells in Crohn’s disease

Authors: Xiaofang Xu, Xiaodan Lv, Ruizhi Zeng, Zhixi Huang, Ziqian Huang, Bing Han, Guangfu Lin, Jianing Lin, Shiquan Li, Junhua Fan, Xiaoping Lv

Source: Frontiers in Immunology, Vol 16 (2025)

Subject Terms: biomarkers, pyroptosis, intestinal epithelial cells, Crohn’s disease, bulk RNA sequencing, single-cell RNA sequencing, Immunologic diseases. Allergy, RC581-607

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Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2025.1551547/full; https://doaj.org/toc/1664-3224

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Epithelial and immune transcriptomic characteristics and possible regulatory mechanisms in asthma exacerbation: insights from integrated studies

Authors: Ye Liu, Yue Li, Ruhao Wu, Yu Wang, Pengfei Li, Tianci Jiang, Ke Wang, Yize Liu, Zhe Cheng

Source: Frontiers in Immunology, Vol 16 (2025)

Subject Terms: asthma exacerbation, single-cell RNA sequencing, bulk RNA sequencing, epithelial cells, immune cells, key regulatory genes, Immunologic diseases. Allergy, RC581-607

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Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2025.1512053/full; https://doaj.org/toc/1664-3224

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Empowering Precision Oncology: Advancing Cancer Research by Augmenting Single-cell RNA and Bulk RNA Sequencing for Confronting the Heterogeneity in Ovarian Cancer

Authors: Muhammed Ali Siham, A. Ashwin Prabahar

Source: Journal of Mid-Life Health, Vol 15, Iss 3, Pp 194-196 (2024)

Subject Terms: bulk rna sequencing, cellular composition, ovarian cancer, single-cell rna sequencing, tumors, Gynecology and obstetrics, RG1-991, Geriatrics, RC952-954.6

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Relation: https://journals.lww.com/10.4103/jmh.jmh_93_23; https://doaj.org/toc/0976-7800; https://doaj.org/toc/0976-7819

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Comprehensive analysis of scRNA-Seq and bulk RNA-Seq reveals ubiquitin promotes pulmonary fibrosis in chronic pulmonary diseases

Authors: Zhuman Wen, Abduxukur Ablimit

Source: Scientific Reports, Vol 14, Iss 1, Pp 1-18 (2024)

Subject Terms: Chronic pulmonary diseases, Single-cell RNA sequencing, Bulk RNA sequencing, Ubiquitination, Immune infiltration, Medicine, Science

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Relation: https://doaj.org/toc/2045-2322

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Scanning sample-specific miRNA regulation from bulk and single-cell RNA-sequencing data

Authors: Junpeng Zhang, Lin Liu, Xuemei Wei, Chunwen Zhao, Yanbi Luo, Jiuyong Li, Thuc Duy Le

Source: BMC Biology, Vol 22, Iss 1, Pp 1-19 (2024)

Subject Terms: miRNA, mRNA, Single-cell RNA-sequencing, Bulk RNA-sequencing, Sample-specific miRNA regulation, Sample correlation network, Biology (General), QH301-705.5

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Relation: https://doaj.org/toc/1741-7007

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Improving human cardiac organoid design using transcriptomics

Authors: Nathaniel A. Hyams, Charles M. Kerr, Dimitrios C. Arhontoulis, Jean Marie Ruddy, Ying Mei

Source: Scientific Reports, Vol 14, Iss 1, Pp 1-11 (2024)

Subject Terms: Human cardiac organoids, Modeling, Bulk RNA-sequencing, Medicine, Science

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Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/e2212772d7d94f549c79d04420802194

Comprehensive Analysis of Immune Cell Infiltration and M2-Like Macrophage Biomarker Expression Patterns in Atrial Fibrillation

Authors: Yang M, Xu X, Zhao XA, Ge YN, Qin J, Wang XY, Dai HL, Jia J, Tao SM

Source: International Journal of General Medicine, Vol Volume 17, Pp 3147-3169 (2024)

Subject Terms: atrial fibrillation, m2 macrophage, cardiac fibrosis, inflammation, single-cell rna-sequencing, bulk rna-sequencing, Medicine (General), R5-920

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Relation: https://www.dovepress.com/comprehensive-analysis-of-immune-cell-infiltration-and-m2-like-macroph-peer-reviewed-fulltext-article-IJGM; https://doaj.org/toc/1178-7074

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Integrative analysis of bulk and single-cell RNA sequencing reveals the gene expression profile and the critical signaling pathways of type II CPAM

Authors: Fengxia Li, Zheng Tan, Hongyu Chen, Yue Gao, Jie Xia, Ting Huang, Liang Liang, Jian Zhang, Xianghong Zhang, Xucong Shi, Qiang Chen, Qiang Shu, Lan Yu

Source: Cell & Bioscience, Vol 14, Iss 1, Pp 1-17 (2024)

Subject Terms: Congenital pulmonary airway malformation, Bulk RNA sequencing, Single-cell RNA sequencing, Cell communication, Biotechnology, TP248.13-248.65, Biology (General), QH301-705.5, Biochemistry, QD415-436

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Relation: https://doaj.org/toc/2045-3701

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Degenerative and regenerative peripheral processes are associated with persistent painful chemotherapy-induced neuropathies in males and females

Authors: George T. Naratadam, Jennifer Mecklenburg, Sergey A. Shein, Yi Zou, Zhao Lai, Alexei V. Tumanov, Theodore J. Price, Armen N. Akopian

Source: Scientific Reports, Vol 14, Iss 1, Pp 1-16 (2024)

Subject Terms: Persistent chronic pain, Painful neuropathy, Paclitaxel, DRG, Bulk RNA sequencing, Regeneration, Medicine, Science

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Relation: https://doaj.org/toc/2045-2322

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Unveiling the role of ACTL6A in uveal melanoma metastasis and immune microenvironment

Authors: Weiqin, Liu ^{a, b, 1}, Qi, Wan ^{a, b, c, 1}, Lin, Jin ^{a, b, d, 1}, Shuxia, Chen ^{a, d, e}, Chang, Liu ^{a, b, ⁎}

Source: In International Immunopharmacology 6 February 2025 147

Urinary TYROBP and HCK as genetic biomarkers for non-invasive diagnosis and therapeutic targeting in IgA nephropathy

Authors: Boji Xie, Shuting Pang, Yuli Xie, Qiuyan Tan, Shanshan Li, Mujia Jili, Yian Huang, Binran Zhao, Hao Yuan, Junhao Mi, Xuesong Chen, Liangping Ruan, Hong Chen, Xiaolai Li, Boning Hu, Jing Huang, Rirong Yang, Wei Li

Source: Frontiers in Genetics, Vol 15 (2024)

Subject Terms: IgA nephropathy, urine bulk RNA sequencing, non-invasive biomarkers, TYROBP, HCK, molecular docking, Genetics, QH426-470

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Relation: https://www.frontiersin.org/articles/10.3389/fgene.2024.1516513/full; https://doaj.org/toc/1664-8021

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Integrated multiomics characterization reveals cuproptosis-related hub genes for predicting the prognosis and clinical efficacy of ovarian cancer

Authors: Yang Xiaorong, Xu Lu, Xu Fangyue, Xu Chao, Gao Jun, Wen Qiang

Source: Frontiers in Immunology, Vol 15 (2024)

Subject Terms: cuproptosis, RiskScore, ovarian cancer, single-cell sequencing, bulk RNA sequencing, Immunologic diseases. Allergy, RC581-607

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Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2024.1452294/full; https://doaj.org/toc/1664-3224

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PPM1G dephosphorylates α-catenin to maintain the integrity of adherens junctions and regulates apoptosis in Sertoli cells

Authors: Li, Xinyao ^{a, 1}, Liu, Qian ^{b, 1}, Wang, Lingling ^b, Bu, Tiao ^c, Yang, Xiwen ^d, Gao, Sheng ^b, Yun, Damin ^{b, ⁎}, Sun, Fei ^{d, e, ⁎⁎}

Source: In Molecular and Cellular Endocrinology 15 April 2025 600