Genome-wide identification of the UGT genes family in Acer rubrum and role of ArUGT52 in anthocyanin biosynthesis under cold stress by Khan Arif Kamal, Faheem Afzal Shah, Yue Zhao, Zhu Chen, Songling Fu, Zhiyong Zhu, Jie Ren, Hua Liu

“…Conserved motif analysis demonstrated structural similarities within subgroups. …”
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Selective metabolic regulations by p53 mutant variants in pancreatic cancer by Sabrina Caporali, Alessio Butera, Alessia Ruzza, Carlotta Zampieri, Marina Bantula’, Sandra Scharsich, Anna-Katerina Ückert, Ivana Celardo, Ian U. Kouzel, Luigi Leanza, Andreas Gruber, Joan Montero, Angelo D’Alessandro, Thomas Brunner, Marcel Leist, Ivano Amelio

“…This included integrating global metabolomic analysis with epigenomic and transcriptomic profiling in mouse pancreatic cancer cells. …”
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Distinct expression profile reveals glia involvement in the trigeminal system attributing to post-traumatic headache by Gurueswar Nagarajan, Yumin Zhang

“…Furthermore, immunohistochemical study revealed a close interaction between activated microglia and reactive astrocytes correlating with increased calretinin interneurons in the Sp5C. Conclusions Transcriptomics analysis indicated that non-neuronal cells in peripheral TG and successive in situ assays revealed that glia in the central Sp5C are crucial in modulating headache-like symptoms. …”
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A pluripotent stem cell atlas of multilineage differentiation by Sophie Shen, Tessa Werner, Han Sheng Chiu, Xiaoli Chen, Quan Nguyen, Nathan J. Palpant

“…Genome-wide and single-cell transcriptomics technologies likewise offer high-throughput analysis of heterogeneous cell differentiation states. …”
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Smooth muscle cells and fibroblasts in the ascending aorta exhibit minor differences between embryonic origins in angiotensin II-driven transcriptional alterations by Sohei Ito, David B. Graf, Yuriko Katsumata, Jessica J. Moorleghen, Chen Zhang, Yanming Li, Scott A. LeMaire, Ying H. Shen, Hong S. Lu, Alan Daugherty, Hisashi Sawada

“…Cells were sorted based on their embryonic origins and single-cell RNA sequencing was performed. Transcriptomic analysis revealed significant changes in both SHF- and nSHF-derived SMCs following short-term AngII infusion, although differences between the origins were modest. …”
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Exploring the additive antibacterial potential of Cinnamomum cassia volatile oil and imipenem against Acinetobacter baumannii: a multi-omics investigation by Youyuan Lu, Youyuan Lu, Wanlin Xu, Jiahui Xue, Mingxia Xie, Haotian Liu, Ruilin Wang, Gang Li, Hanqing Wang, Hanqing Wang

“…CBV and IPM also induced significant changes at both the transcriptomic and proteomic levels in A. baumannii. Functional analysis revealed that the differentially expressed genes (DEGs) and proteins (DEPs) were involved in multiple pathways. …”
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Genome wide identification of LcC2DPs gene family in Lotus corniculatus provides insights into regulatory network in response to abiotic stresses by Guangfen Yang, Yujie Liu, Zouxian Gong, Siya Chen, Juanying Wang, Li Song, Shihui Liu

“…Transcriptomic analysis links 78 genes to environmental response and stress growth, with 10 validated by qRT-PCR after treatment with 100 μM ABA and IAA, 20% PEG6000, and 4 °C. …”
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Id2 levels determine the development of effector vs. exhausted tissue-resident memory CD8+ T cells during CNS chronic infection by Aboubacar Sidiki K. Coulibaly, Lucie Nozeran, Céline Thomann, Marine Alis, Emilie Bassot, Ali Hassan, Rémi Porte, Marcy Belloy, Nicolas Blanchard, Frederick Masson

“…To investigate this, we performed single-cell transcriptomic analysis of brain CD8+ T cells from mice chronically infected with Toxoplasma gondii. …”
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Shared and distinct peripheral blood immune cell landscape in MCTD, SLE, and pSS by Yanling Cui, Huina Zhang, Yaxuan Deng, Orion Fan, Junbang Wang, Zhonggang Xing, Jianping Tang, Wenmin Zhu, Bangdong Gong, Yi Eve Sun

“…Furthermore, we offer insights into the transcriptomic similarities and heterogeneity across different autoimmune diseases, while highlighting prospective therapeutic targets.…”
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A LINC00472-encoded polypeptide impedes migration and proliferation through modulation of the HDAC2/SP1 axis in non-small cell lung cancer cells by Lei Xu, Haoyong Kuang, Haodong Peng, Sen Wu, Yu Bai, Xiangbo Jia, Wenjian Yao

“…Methods Through integration of ribosome profiling, transcriptomics, and co-expression analysis, we systematically identified lncRNA-encoded polypeptides in NSCLC. …”
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Integrated machine learning and single-cell RNA sequencing reveal COL4A2 and CXCL6 as oxidative stress-associated biomarkers in periodontitis by Siyu Sun, Siyu Sun, Jing Ren, Jing Ren, Xiujuan Zeng, Yanbin Chen, Qianbing Zhou, Junying Yang, Shan Chen

“…This study aims to explore the association between oxidative stress and periodontitis pathogenesis while identifying potential diagnostic biomarkers and therapeutic targets for this condition.MethodsTranscriptomic data from gingival tissues of periodontitis patients and controls were obtained from the Gene Expression Omnibus (GEO) database. …”
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Multiple Omics Analyses Reveal Activation of Nitrogen Metabolism and Flavonoid Glycosylation in <i>Toxicodendron vernicifluum</i> Under High Temperature by Guoqing Bai, Ruiwen Ding, Qizhen Su, Xiaomin Ge, Shasha Li, Huiying Shang, Aiguo Zhao, Chen Chen

“…Indole-3-acetic acid remained stable while abscisic acid decreased, with increases in jasmonic acid and jasmonoyl-L-isoleucine indicating complex hormonal responses. …”
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Target oxidative stress-induced disulfidptosis: novel therapeutic avenues in Parkinson’s disease by Junshi Zhang, Tingting Liu, Haojie Wu, Jianshe Wei, Qiumin Qu

“…These datasets were subjected to: immune infiltration analysis, gene set enrichment analysis (GSEA), weighted gene co-expression network analysis (WGCNA), intersection analysis of oxidative stress-related genes (ORGs) and disulfidptosis-related genes (DRGs) for functional enrichment annotation. …”
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Haplotype-resolved T2T genome assembly of the pear cultivar ‘Danxiahong’ by Xiangzhan Zhang, Jianxin Bian, Yanan Wang, Lei Wang, Long Wang, Suke Wang, Yanli Su, Hang He, Huabai Xue

“…The haplotype-resolved genome of ‘Danxiahong’ significantly contributes to the investigation of genes and molecular mechanisms related to fruit quality, while also facilitating the Multi-Omics analysis, such as comparative genomics, transcriptomics, proteomics, and allelic expression research.…”
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Machine learning-based diagnostic and prognostic models for breast cancer: a new frontier on the clinical application of natural killer cell-related gene signatures in precision me... by Yutong Fang, Rongji Zheng, Yefeng Xiao, Qunchen Zhang, Junpeng Liu, Jundong Wu

“…Furthermore, drug sensitivity analysis indicated that high-risk patients were more sensitive to Thapsigargin, Docetaxel, AKT inhibitor VIII, Pyrimethamine, and Epothilone B, while showing higher resistance to drugs such as I-BET-762, PHA-665752, and Belinostat.ConclusionThis study provides a comprehensive analysis of NRGs in BC and establishes reliable ML-based diagnostic and prognostic models. …”
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Exploring the Role of Bifenthrin in Recurrent Implantation Failure and Pregnancy Loss Through Network Toxicology and Molecular Docking by Shengyuan Jiang, Yixiao Wang, Haiyan Chen, Yuanyuan Teng, Qiaoying Zhu, Kaipeng Xie

“…The diagnostic model based on these genes exhibited good predictive performance in the RIF cohort and was successfully validated in the RPL cohort. Single-cell transcriptomic analysis revealed a significant increase in the proportion of myeloid cells in RPL patients, while immune infiltration analysis showed a consistent downregulation of M2 macrophages in both RIF and RPL. …”
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Vitamin C potentiates the killing of Mycobacterium tuberculosis by bedaquiline through metabolic disruption by Catherine Vilchèze, Saranathan Rajagopalan, Raja Sab Kalluru, Niaz Banaei, William R. Jacobs

“…This combination also enhanced Mtb killing in infected human macrophages and peripheral blood mononuclear cells. Transcriptomic analysis revealed that the BDQ/vitamin C combination induces widespread metabolic disruption in Mtb, characterized by upregulation of stress response and metal ion homeostasis genes and downregulation of energy metabolism and cell wall biosynthesis genes. …”
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Investigation of granuloma-targeted host-pathogen interactions identify vaccine correlates of immune protection associated with control of M. tuberculosis replication by David Forrest Ackart, Dr. Faye Lanni, Victoria Mitcham, Dr. G. Brooke Anderson, Dr. Michael Lyons, Dr. Marcela Henao-Tamayo, Dr Brendan Podell

“…Introduction: Immune correlates of protection to guide vaccine development for tuberculosis (TB) have remained elusive. While a number of blood transcriptomic signatures have been shown to predict clinical states of TB in human subjects, no correlates exist to indicate immune signatures that control bacterial growth, which would inform improved vaccine design. …”
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Modulation by NPY/NPF-like receptor underlies experience-dependent, sexually dimorphic learning by Sonu Peedikayil-Kurien, Rizwanul Haque, Asaf Gat, Meital Oren-Suissa

“…Transcriptomic and behavioral analysis revealed that the neuropeptide receptor npr-5, an ortholog of the mammalian NPY/NPF-like receptor, regulates male learning by modulating neuronal activity. …”
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Endothelial cell proliferation and extracellular matrix-related pathways regulate pulmonary arterial hypertension in rat models by LU Xiaoxuan, GUO Lina, ZHANG Hong, SONG Wanlu, HU Yufei, YANG Peiran

“…Methods Rat PAH models were established using subcutaneous monocrotaline (MCT) injection and the SU5416/hypoxia (SU/Hx) method. Transcriptomic sequencing of lung tissues was performed to identify gene expression and pathway alterations in PAH rats, followed by a comparative analysis with transcriptomic data of patients with idiopathic pulmonary arterial hypertension (IPAH) in NCBI database. …”
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