Application of artificial intelligence large language models in drug target discovery by Xinyu Liu, Jia Zhang, Xiaoran Wang, Maoda Teng, Guoying Wang, Xiaoming Zhou, Xiaoming Zhou

“…These technological advancements provide multi-dimensional biological evidence supporting drug target discovery and contribute to a more efficient screening process for candidate targets. …”
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Genome-wide association study of common bean (Phaseolus vulgaris L.) unveils novel loci governing root-to-seed zinc allocation by Muhammad Tanveer Altaf, Muhammad Azhar Nadeem, Sefa Ayten, Emre Aksoy, Sheikh Mansoor, E. M. B. M. Karunathilake, Yong Suk Chung, Faheem Shehzad Baloch

“…Candidate genes, Vacuolar Iron Transporter 1 (VIT1) and Wall-Associated Kinase-Like 4 (WAKL4), were implicated in Zn homeostasis and distribution. In silico transcriptomics analysis further validated the role of these genes under Zn-deficient conditions in Arabidopsis. …”
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Single-nucleus RNA sequencing reveals distinct pathophysiological trophoblast signatures in spontaneous preterm birth subtypes by Cherilyn Uhm, Jianlei Gu, Weina Ju, Stephanie Pizzella, Hande Oktay, Joyce Yao-Chun Peng, Sararose Guariglia, Yong Liu, Hongyu Zhao, Yong Wang, Ramkumar Menon, Nanbert Zhong

“…Using single-nucleus RNA sequencing, we investigated transcriptomic and cellular differences at the maternal–fetal interface in pPROM and sPTL placentas. …”
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Mitochondrial respiration atlas reveals differential changes in mitochondrial function across sex and age by Dylan C Sarver, Muzna Saqib, Fangluo Chen, G William Wong

“…Organ function declines with age, and large-scale transcriptomic analyses have highlighted differential aging trajectories across tissues. …”
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Genome-Wide Identification and Characterization of the Polygalacturonase Gene Family in Common Vetch (<i>Vicia sativa</i>) by Xiaobing Yang, Tianmiao Liu, Zhongfu Yang, Zhou Li, Xuechun Zhao, Jihui Chen, Xinyao Gu, Jin He, Chao Chen, Rui Dong

“…The VsPG promoters were enriched with elements responsive to abscisic acid, low temperatures, and aluminum stress. Transcriptomic and qPCR analyses revealed tissue-specific and stress-responsive expression patterns of the <i>VsPGs</i>. …”
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Genome-Wide Identification and Expression Analysis of the G-Protein Gene Family in Barley Under Abiotic Stresses by Ailing Han, Zhengyuan Xu, Zhenyu Cai, Yuling Zheng, Mingjiong Chen, Liyuan Wu, Qiufang Shen

“…The expression patterns of G-protein genes were further validated using a quantitative real-time PCR (qRT-PCR) technique, indicating the reliability of transcriptomic data, as well as special responses to salt, drought, and waterlogging stresses. …”
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Prognostic risk modeling of endometrial cancer using programmed cell death-related genes: a comprehensive machine learning approach by Tianshu Chen, Yuhan Yang, Zhizhong Huang, Feng Pan, Zhendi Xiao, Kunxue Gong, Wenguang Huang, Liu Xu, Xueqin Liu, Caiyun Fang

“…Methods Utilizing transcriptomic data from TCGA-UCEC and GSE119041 datasets, we employed a comprehensive approach involving 117 machine learning algorithms. …”
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Deciphering the role of MFGE8 in lactation using CRISPR-CAS9 based gene editing in Buffalo mammary epithelial cells by Preeti Vats, Rohit Kumar, Raghvendra Kumar, Jai K. Kaushik, Ashok K. Mohanty, Sudarshan Kumar

“…To the best of our knowledge, this is the first study which provides a comprehensive proteome profile of MFGE8 knockout BuMEC and explores downstream effects of disruption of MFGE8 gene.…”
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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

“…Gene duplication analysis identified 21 tandem and 66 segmental duplication events across chromosomes. Transcriptomic data from autumn leaves of different colours and under low-temperature stress were analyzed for ArUGT expression patterns. …”
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A meta-analysis of gene expression signatures of blood pressure and hypertension. by Tianxiao Huan, Tõnu Esko, Marjolein J Peters, Luke C Pilling, Katharina Schramm, Claudia Schurmann, Brian H Chen, Chunyu Liu, Roby Joehanes, Andrew D Johnson, Chen Yao, Sai-Xia Ying, Paul Courchesne, Lili Milani, Nalini Raghavachari, Richard Wang, Poching Liu, Eva Reinmaa, Abbas Dehghan, Albert Hofman, André G Uitterlinden, Dena G Hernandez, Stefania Bandinelli, Andrew Singleton, David Melzer, Andres Metspalu, Maren Carstensen, Harald Grallert, Christian Herder, Thomas Meitinger, Annette Peters, Michael Roden, Melanie Waldenberger, Marcus Dörr, Stephan B Felix, Tanja Zeller, International Consortium for Blood Pressure GWAS (ICBP), Ramachandran Vasan, Christopher J O'Donnell, Peter J Munson, Xia Yang, Holger Prokisch, Uwe Völker, Joyce B J van Meurs, Luigi Ferrucci, Daniel Levy

“…Gene set enrichment analysis suggested that the BP-related global gene expression changes include genes involved in inflammatory response and apoptosis pathways. Our study provides new insights into molecular mechanisms underlying BP regulation, and suggests novel transcriptomic markers for the treatment and prevention of hypertension.…”
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Polycystic ovary syndrome and epithelial-mesenchymal transition: Mendelian randomization and single-cell analysis insights by Dong Liu, Dan Liu, Kunyan Zhou

“…Objective This study aimed to explore key genes associated with EMT in PCOS and their potential molecular regulatory mechanisms, exclusively from the perspective of transcriptomics and single-cell RNA sequencing (scRNA-seq), combined with Mendelian Randomization (MR) analysis. …”
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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

“…These findings offer new insights into the molecular mechanisms of CRC and provide a potential theoretical basis for targeting VSIG4 in immunotherapy.…”
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Monoclonal antibody therapy demonstrates increased virulence of a lineage VII strain of Lassa virus in nonhuman primates by Courtney Woolsey, Robert W. Cross, Abhishek N. Prasad, Krystle N. Agans, Viktoriya Borisevich, Daniel J. Deer, Natalie S. Dobias, Alyssa C. Fears, Mack B. Harrison, Megan L. Heinrich, Karla A. Fenton, Robert F. Garry, Luis M. Branco, Thomas W. Geisbert

“…This data causes concern regarding the ability of heterologous vaccines and treatments to provide cross protection against lineage VII LASV isolates.…”
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Oxygen Glucose Deprivation-Induced Lactylation of H3K9 Contributes to M1 Polarization and Inflammation of Microglia Through TNF Pathway by Lu He, Rui Yin, Weijian Hang, Jinli Han, Juan Chen, Bin Wen, Ling Chen

“…Inhibiting P300 or reducing lactate dehydrogenase A expression decreased H3K9 lactylation, suppressing M1 polarization. Transcriptomic analysis indicated that H3K9 lactylation regulated M1 polarization via the TNF signaling pathway. …”
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PPDPF promotes the progression of esophageal squamous cell carcinoma via c-Myc/CD24 axis by Ning Ma, Wei Chen, Yu Chen, Xiang Wang, Bing Zhu, Kai Ding, Lin Qiu, Jing-jing Li, Jing-Yi Huang, Xin Liang, Yan-Jun Xiang, Qian-Zhi Ni, Zhi-Chao Liu, Qian-Wen Zheng, Yi-Kang Wang, Hui-Jun Cao, Ji Xia, Sheng Xu, Xiao-Song Qiu, Xi-Ran Zhang, Lingyun Long, Zhi-Gang Li, Fan Yao

“…RNA sequencing was performed to profile transcriptomic changes upon PPDPF deficiency. Fluorescence microscopy-based phagocytosis assay and flow cytometry were employed to analyze macrophage phagocytosis. …”
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GLP-1R/GCGR dual agonism dissipates hepatic steatosis to restore insulin sensitivity and rescue pancreatic β-cell function in obese male mice by Rhianna C. Laker, Shaun Egolf, Sarah Will, Louise Lantier, Owen P. McGuinness, Charles Brown, Nicholas Bhagroo, Stephanie Oldham, Kyle Kuszpit, Alex Alfaro, Xidan Li, Taewook Kang, Giovanni Pellegrini, Anne-Christine Andréasson, Sarina Kajani, Sadichha Sitaula, Martin R. Larsen, Christopher J. Rhodes

“…BAT from cotadutide-treated mice have induction of UCP-1 protein, increased mitochondrial area and a transcriptomic profile of increased fat oxidation and mitochondrial activity. …”
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CYP1B1-AS1 regulates CYP1B1 to promote Coxiella burnetii pathogenesis by inhibiting ROS and host cell death by Aryashree Arunima, Seyednami Niyakan, Samantha M. Butler, Sabrina D. Clark, Anna Pinson, Doyoung Kwak, Elizabeth Di Russo Case, Xiaoning Qian, Paul de Figueiredo, Erin J. van Schaik, James E. Samuel

“…Our results highlight the critical roles of lncRNAs in immune regulation and provide a valuable resource for future lncRNA research.…”
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LOX-1 rewires glutamine ammonia metabolism to drive liver fibrosis by Ruihua Huang, Hanyu Cui, Mohammed Abdulaziz Yahya Ali Alshami, Chuankui Fu, Wei Jiang, Mingyuan Cai, Shuhan Zhou, Xiaoyun Zhu, Changping Hu

“…LOX-1 knockout rats were subjected to CCl4 or methionine and choline-deficient diet (MCD) to induce liver fibrosis. Transcriptomic and metabolomics analysis were used to investigate the involvement and mechanism of LOX-1 on liver fibrosis. …”
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Genome-Wide Identification of Superoxide Dismutase (<i>SOD</i>) Gene Family in <i>Cymbidium</i> Species and Functional Analysis of <i>CsSOD</i>s Under Salt Stress in <i>Cymbidium s... by Ruyi Li, Songkun Lin, Yin Yan, Yuming Chen, Linying Wang, Yuzhen Zhou, Shuling Tang, Ning Liu

“…These findings all highlight the crucial role of <i>CsSOD</i>s in the salt stress response and provide valuable insights for further breeding salt-tolerance varieties of <i>C. sinense</i>.…”
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Co-Cultivation with Azolla Affects the Metabolome of Whole Rice Plant Beyond Canonical Inorganic Nitrogen Fertilization by Elena Consorti, Alma Costarelli, Sara Cannavò, Martina Cerri, Maria Cristina Valeri, Lara Reale, Antonietta Saccomanno, Chiara Paleni, Veronica Gregis, Martin M. Kater, Federico Brilli, Francesco Paolocci, Andrea Ghirardo

“…Overall, our study provides new insights into Azolla’s beneficial and growth-promoting effects on rice. …”
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