KAT2B regulates estradiol synthesis via H3K27ac/PPARα in granulosa cells of PCOS patients by Ao Wang, Xiao-Fei Zhang, Cong-Jian Luo, Yu-Dong Liu, Pei-Ru Chen, An-Lan Wang, Jun Zhang, Song-Yu Huang, Xin-Yi Huang, Shi-Ling Chen, Xing-Yu Zhou

“…While KAT2B has been documented to participate in various biological processes, its specific role and mechanism in the pathogenesis of PCOS remain largely unknown. …”
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Impact of β-defensin 103 (DEFB103) copy number variation on bull sperm parameters and post-insemination uterine gene expression. by Ozge Sidekli, Edward J Hollox, Sean Fair, Kieran G Meade

“…As genetic diversity of DEFB103 CN was only apparent in the LF group, three bulls per CNV class (low, intermediate and high CN) were chosen for more detailed comparative functional analysis. Sperm from low CN bulls exhibited higher binding to the oviductal epithelium, while high CN increased sperm membrane fluidity in vitro (p < 0.05). …”
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A multi-omics technology to the study of lactic acid bacteria responses to environmental stress: the past, current and future trends by Yaqi Liu, Jingxian Sun, Xiaowen Liu, Mingpeng Zheng, Wen Ma, Gang Jin

“…While several studies have been carried out in the past by using single-omics techniques to investigate their response to environmental stress, most researchers are now using a multi-omics approach to explore more detail in the biological regulatory networks and molecular mechanisms of lactic acid bacteria in response to environmental stress, thereby overcoming the limitations of single- omics analysis. …”
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Monkeyflower (Mimulus) uncovers the evolutionary basis of the eukaryote telomere sequence variation. by Surbhi Kumawat, Askhan Shametov, Liia R Valeeva, Yoonha Ju, Irene Martinez, Dhenugen Logeswaran, Hongfei Chen, Jenn M Coughlan, Julian J-L Chen, Yao-Wu Yuan, James M Sobel, Dal-Hoe Koo, Eugene V Shakirov, Jae Young Choi

“…We conducted de novo transcriptomics and genome analysis of 18 species, and discovered Mimulus has evolved at least three different telomere sequences: (AAACCCT)n, (AAACCCG)n, and (AAACCG)n. …”
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An in-silico pan-cancer bulk and single-cell profiling of transcription factors in protein autoubiquitination by Angela Dong, Ayana Rasteh, Panpan Wang, Hengrui Liu

“…Additionally, single-cell transcriptomic analysis uncovered cancer-type-specific functional states. …”
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Pyroptosis-related lncRNAs are potential biomarkers for predicting prognoses and immune landscapes in patients with gastric adenocarcinoma by Haidu Hong, Yuancheng Huang, Zehong Yang, Xiaotao Jiang, Hong Liu

“…Based on correlation analysis and univariate Cox regression, prognostic PRlncRNA were identified. …”
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Neural representation of cytokines by vagal sensory neurons by Tomás S. Huerta, Adrian C. Chen, Saher Chaudhry, Aisling Tynan, Timothy Morgan, Kicheon Park, Richard Adamovich-Zeitlin, Bilal Haider, Jian Hua Li, Mitali Nagpal, Stavros Zanos, Valentin A. Pavlov, Michael Brines, Theodoros P. Zanos, Sangeeta S. Chavan, Kevin J. Tracey, Eric H. Chang

“…In male mice with induced colitis, inflammation increased the baseline activity of these neurons but decreased responsiveness to specific cytokines, reflecting altered neural excitability. Transcriptomic analysis of vagal ganglia from colitis mice revealed downregulation of cytokine signaling pathways, while neuronal activity pathways were upregulated. …”
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An immune-focused supplemental alignment pipeline captures information missed from dominant single-cell RNA-seq analyses, including allele-specific MHC-I regulation by Sebastian Benjamin, GW McElfresh, Maanasa Kaza, Gregory J. Boggy, Benjamin Varco-Merth, Benjamin Varco-Merth, Sohita Ojha, Shana Feltham, William Goodwin, William Goodwin, Candice Nkoy, Candice Nkoy, Derick Duell, Derick Duell, Andrea Selseth, Tyler Bennett, Aaron Barber-Axthelm, Nicole N. Haese, Nicole N. Haese, Helen Wu, Courtney Waytashek, Carla Boyle, Jeremy V. Smedley, Jeremy V. Smedley, Caralyn S. Labriola, Caralyn S. Labriola, Michael K. Axthelm, Michael K. Axthelm, R. Keith Reeves, R. Keith Reeves, Daniel N. Streblow, Daniel N. Streblow, Jonah B. Sacha, Jonah B. Sacha, Afam A. Okoye, Afam A. Okoye, Scott G. Hansen, Scott G. Hansen, Louis J. Picker, Louis J. Picker, Benjamin N. Bimber, Benjamin N. Bimber

“…IntroductionRNA sequencing (RNA-seq) can measure whole transcriptome gene expression from tissues or even individual cells, providing a powerful tool to study the immune response. …”
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The immunosuppressive role of VSIG4 in colorectal cancer and its interaction with the tumor microenvironment by H. G. Zhang, W. R. Yao, Z. Y. Zhou, L. Liu

“…The Seurat package was employed for clustering single-cell data, while the “Monocle2” algorithm was used to perform pseudo-time analysis on the differentiation trajectory of macrophages. …”
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Hypoxia-induced RHCG as a key regulator in psoriasis and its modulation by secukinumab by Shun Guo, Qian Zhang, Yuan-jie Liu, Yun-yao Hu, Cong Liu, Hui Shen, Jia Liu

“…We employed bioinformatics approaches, including spatial transcriptomics analysis, single-cell transcriptomics analysis, and bulk data analysis, to elucidate the biological functions of RHCG. …”
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CCDC138 overexpression predicts poor prognosis and highlights ciliopathy-linked mechanisms in uterine corpus endometrial carcinoma by Aiping Wang, Fang Yang, Chunhua Zhang, Shi Li, Han Fu

“…IntroductionUterine corpus endometrial carcinoma (UCEC) is a prevalent malignancy of the female reproductive system with increasing incidence, necessitating the identification of molecular mechanisms and biomarkers. While coiled-coil domain-containing protein 138 (CCDC138) is implicated in ciliopathies and cancer, its role in UCEC remains underexplored.MethodsWe integrated transcriptomic and proteomic data from the Cancer Genome Atlas (TCGA), Clinical Proteomic Tumor Analysis Consortium (CPTAC), and Genotype-Tissue Expression (GTEx). …”
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TREM1 is essential for maintaining stemness of liver cancer stem-like cells in hepatocellular carcinoma by Arsha Sreekumar, Ashwin Ajith, Kenza Mamouni, Daniel D. Horuzsko, Anatolij Horuzsko

“…In CDX models, TREM1-deficient LCSLCs exhibited markedly reduced tumorigenicity. Transcriptomic analysis revealed distinct, context-dependent gene expression changes in nuclear and extracellular signaling pathways following TREM1 loss. …”
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Comparison of baseline global gene expression profiles of prostate cancer cell lines LNCaP and DU145 by Khalid Ahmed, Zhannur Omarova, Alisalman Sheikh, Gulzhan Abuova, Kulsoom Ghias, Syed Hani Abidi

“…Characterizing their baseline transcriptomics profiles (without any intervention) can offer insights into baseline genetic features and oncogenic pathways that should be considered while interpreting findings after various experimental interventions such as exogenous gene transfection or drug treatment. …”
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Multi-Omics Profiling Reveals Glycerolipid Metabolism-Associated Molecular Subtypes and Identifies ALDH2 as a Prognostic Biomarker in Pancreatic Cancer by Jifeng Liu, Shurong Ma, Dawei Deng, Yao Yang, Junchen Li, Yunshu Zhang, Peiyuan Yin, Dong Shang

“…<b>Results</b>: Pan-cancer analysis identified molecular features of GMRGs in cancers, while scRNA-seq, spatial transcriptomics, and lipidomics highlighted GLM heterogeneity in PC. …”
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Machine Learning Inference of Gene Regulatory Networks in Developing <i>Mimulus</i> Seeds by Albert Tucci, Miguel A. Flores-Vergara, Robert G. Franks

“…We deployed two GRN inference algorithms—RTP-STAR and KBoost—on three different subsets of our transcriptomic dataset. While the two algorithms yielded GRNs with different regulations and topologies when working with the same data subset, there was still significant overlap in the specific gene regulations they inferred, and they both identified potential novel regulatory mechanisms that warrant further investigation.…”
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The conserved wobble uridine tRNA thiolase Ctu1 is required for angiogenesis and embryonic development. by Yangziwei Yu, Chuqiao Wang, Yan Wang, Heng Shi, Huiyuan Hu, Yibin Du, Zhaoli Zhou

“…Elongator mutant animals exhibit severe phenotypes, while the biological function of Ctu1 in vertebrate animal models remains poorly characterized. …”
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Loss of function of MusaPUB genes in banana can provide enhanced resistance to bacterial wilt disease by Leena Tripathi, Valentine Otang Ntui, Samwel Muiruri, Trushar Shah, Jaindra Nath Tripathi

“…The gene targets used in this study, MusaPUB22 and MusaPUB23, were identified through prior comparative transcriptomics analysis, which revealed their upregulation in susceptible versus resistant genotypes during early infection with Xvm. …”
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Effects of Liquid Bio-Fertilizer on Plant Growth, Antioxidant Activity, and Soil Bacterial Community During Cultivation of Chinese Cabbage (<i>Brassica rapa</i> L. ssp. <i>pekinens... by Tran Yen Linh Le, Junkyung Lee, Su-Yeon Shim, Jiwon Jung, Soo-Ryang Kim, Sung-Ha Hong, Myung-Gyu Lee, Sun-Goo Hwang

“…Transcriptomic analysis identified 445 differentially expressed genes with upregulation in the metabolism and photosynthesis-related pathways, suggesting improved nutrient assimilation and energy production. …”
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Site-2 protease Sll0528 interacts with RbcR to regulate carbon/nitrogen homeostasis in the cyanobacterium Synechocystis sp. PCC 6803 by Shiqi Lin, Taotao Zheng, Yongyi Mo, Ge Zhang, Gu Chen

“…Transcriptomic analysis showed that the knockout of sll0528 led to a significant downregulation of the RbcR regulon, including the ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) operon rbcLXS. …”
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The Immune‐Related Gene CD48 Is a Prognostic Biomarker Associated With the Breast Cancer Tumor Microenvironment by Yi Zhao, Hengheng Zhang, Wenwen Wang, Guoshuang Shen, Miaozhou Wang, Zhen Liu, Jiuda Zhao, Jinming Li

“…ABSTRACT Background While tumor cells can affect the biological behavior of malignant tumors, the tumor microenvironment (TME) also plays an important role in the occurrence, development, and metastasis of tumors. …”
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