The Application of Single-Cell Technologies for Vaccine Development Against Viral Infections by Hong Nhi Nguyen, Isabel O. Vanderzee, Fei Wen

“…Single-cell technologies have emerged as transformative tools for dissecting this immune heterogeneity, providing comprehensive and granular insights into cellular phenotypes, functional states, and dynamic host–pathogen interactions. …”
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Acetylcholinesterase-like proteins are a major component of reproductive trail mucus in the invasive pest land snail, Theba pisana. by Inaliguyau R T Lutschini, Kate R Ballard, Tianfang Wang, Scott F Cummins

“…Pesticides, often containing organophosphates, have long been used as agents for providing immediate short-term recovery, yet are often broad-spectrum, leading to the development of resistance. …”
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Varying effects of chlorination on microbial functional repertoire and gene expression in contrasting effluents by Mandy Lok Yi Tang, Stanley Chun Kwan Lau

“…Notably, the type and extent of alterations in genomic and transcriptomic profiles under chlorination varied greatly between effluents. …”
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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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Regulation of RNA splicing in endometrial tissue and its association with endometriosis by Fei Yang, Ting Qi, Allan F. McRae, Peter A.W. Rogers, Grant W. Montgomery, Sally Mortlock

“…Overall, this study detected transcript isoform-level and RNA splicing level specific changes, providing insights into the dynamic changes in transcriptomic regulation in endometrium and its association with endometriosis.…”
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Application of metabolomics in quality control of traditional Chinese medicines: a review by Peiran Ji, Peiran Ji, Xinquan Yang, Xiangsheng Zhao

“…Additionally, the current challenges of integrating metabolomics with other omics technologies (transcriptomics, spatial metabolomics, etc.) are discussed. …”
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Nasopharyngeal Local Transcriptional Profile upon SARS-CoV-2 Omicron BA.2.2 Breakthrough Infection by Yi Zhang, Yang Zhou, Yumeng Zhang, Jiazhen Chen, Jing Wu, Peng Cui, Shiyong Wang, Yuanyuan Xu, Zhongliang Shen, Tao Xu, Yang Li, Jingwen Ai, Ning Jiang, Chao Qiu, Wenhong Zhang, Haijuan Wang

“…To better understand the anti-viral effects of vaccination on host-virus interactions during the outbreak of BA.2.2 Omicron, we conducted RNA-seq transcriptome analysis on nasopharyngeal swabs from COVID-19 patients in Shanghai. …”
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Local treatment of HVJ-E with T cell costimulatory molecule stimulation elicits systemic anti-tumor effects by Airi Ishibashi, Yue Li, Yuuta Hisatomi, Noriko Ohta, Yuko Uegaki, Atsushi Tanemura, Riuko Ohashi, Koji Kitamura, Kotaro Saga, Yasuhide Yoshimura, Satoko Inubushi, Kyoso Ishida, Sadahiro Iwabuchi, Shinichi Hashimoto, Eiji Kiyohara, Hideo Yagita, Yasufumi Kaneda, Keisuke Nimura

“…These systemic anti-tumor effects required an association between Nkg2d and Nkg2d ligands. Our findings provide insights into how systemic anti-tumor effects are induced and may help the development of therapeutic strategies for eliciting such effects.…”
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Addressing the tissue specificity of U5 snRNP spliceosomopathies by Rahmat Azhari Kemal, Rahmat Azhari Kemal, Raymond T. O’Keefe

“…Cell and animal models can replicate the human clinical specificity providing explanations for the specificity of the disorders. …”
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Functional characterization of O-methyltransferases involved in biosynthesis of flavonoids in dwarf banana Musella lasiocarpa by Long Huang, Pirui Li, Junzhi Wu, Boya Feng, Mei Tian, Shu Xu, Wei Lyu, Xu Feng, Wanli Zhao, Yu Chen

“…Here, we identified and characterized a new caffeic acid O-methyltransferase (COMT) enzyme, designated Ml05G3914, along with three other OMTs (Ml01G0494, Ml04G2958, and Ml08G0855), through genome and transcriptome association analysis. The potential role of MlOMT was studied by testing the catalytic activity of recombinant protein with numerous possible substrates in vitro. …”
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A novel module of MaMADS31-MaBZR2 confers negative regulation of banana fruit ripening by Chaojie Wu, Wei Wei, Danling Cai, Zengxiang Lin, Yingying Yang, Jia Si, Wei Shan, Jianye Chen, Wangjin Lu, Jianfei Kuang

“…Here, a negative regulator, MaMADS31, was characterized according to the banana fruit ripening transcriptome, which displayed nuclear localization and inhibitory transactivation activity. …”
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Uncovering the epigenetic regulatory clues of PRRT1 in Alzheimer’s disease: a strategy integrating multi-omics analysis with explainable machine learning by Fang Wang, Ying Liang, Qin-Wen Wang

“…Methods Through comprehensive DNA methylation and transcriptomic profiling, we identified distinct epigenetic signatures associated with gene PRRT1 expression in AD patient samples compared to healthy controls. …”
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Elucidating genetic intersections: Co-differentially expressed genes in myasthenia gravis and idiopathic inflammatory myopathies and their role in comorbid pathogenesis by Wenqu Yang, Feng Liang

“…Conclusion: The study identifies key genetic intersections between MG and IIM, providing insights into their shared pathogenesis and highlighting potential diagnostic and therapeutic targets. …”
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Navigating single-cell RNA-sequencing: protocols, tools, databases, and applications by Ankish Arya, Prabhat Tripathi, Nidhi Dubey, Imlimaong Aier, Pritish Kumar Varadwaj

“…Abstract Single-cell RNA-sequencing (scRNA-seq) technology brought about a revolutionary change in the transcriptomic world, paving the way for comprehensive analysis of cellular heterogeneity in complex biological systems. …”
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Enhancing detection and monitoring of circulating tumor cells: Integrative approaches in liquid biopsy advances by Thanmayi Velpula, Viswanath Buddolla

“…Combining genomic, transcriptomic, and proteomic analyses with artificial intelligence (AI) tools has enhanced tumor profiling and supports personalized treatment decisions in precision oncology. …”
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Integration of single-cell sequencing and mendelian randomization reveals novel causal pathways between monocytes and hepatocellular carcinoma by Jiang Yu, Jing Yu, Zhou Kang, Yong Peng

“…Methods This investigation employed single-cell transcriptomic analysis of human hepatic innate lymphoid cells (ILCs) to identify monocyte subpopulations and their cellular markers. …”
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Adventitial fibroblasts direct smooth muscle cell-state transition in pulmonary vascular disease by Slaven Crnkovic, Helene Thekkekara Puthenparampil, Shirin Mulch, Valentina Biasin, Nemanja Radic, Jochen Wilhelm, Marek Bartkuhn, Ehsan Bonyadi Rad, Alicja Wawrzen, Ingrid Matzer, Ankita Mitra, Ryan D Leib, Bence Miklos Nagy, Anita Sahu-Osen, Francesco Valzano, Natalie Bordag, Matthias Evermann, Konrad Hoetzenecker, Andrea Olschewski, Senka Ljubojevic-Holzer, Malgorzata Wygrecka, Kurt Stenmark, Leigh M Marsh, Vinicio de Jesus Perez, Grazyna Kwapiszewska

“…Methods: We combined transcriptomic and proteomic profiling with phenotypic characterization of source-matched cells from healthy controls and individuals with idiopathic pulmonary arterial hypertension (IPAH). …”
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Tick HRF-dependent ferroptosis pathway to promote tick acquisition of Babesia microti by Songqin Chen, Shanming Hu, Yongzhi Zhou, Jie Cao, Houshuang Zhang, Yanan Wang, Jinlin Zhou

“…These findings highlight the critical role of tick HRF molecules in regulating ferroptosis and acquisition of B. microti, thereby providing important insights for a deeper understanding of the tick-Babesia interaction.…”
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The Genome Assembly of Vitis vinifera cv. Shiraz by Cristobal A. Onetto, Christopher M. Ward, Anthony R. Borneman

“…The availability of a reference genome for Shiraz expands the pool of genomes available for wine grapes while providing a foundation resource for whole-genome studies involving this iconic cultivar, including intracultivar variant identification and transcriptomic studies using a matching reference genome.…”
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Weighted frequent gene co-expression network mining to identify genes involved in genome stability. by Jie Zhang, Kewei Lu, Yang Xiang, Muhtadi Islam, Shweta Kotian, Zeina Kais, Cindy Lee, Mansi Arora, Hui-Wen Liu, Jeffrey D Parvin, Kun Huang

“…Our results suggest that the commonly recognized characteristics of cancers are supported by highly coordinated transcriptomic activities. This study also demonstrated that the co-expression network directed approach provides a powerful tool for understanding cancer physiology, predicting new gene functions, as well as providing new target candidates for cancer therapeutics.…”
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