Portable-CELLxGENE: standalone executables of CELLxGENE for easy installation by George T. Hall

“… Biologists who want to analyse their single-cell transcriptomics dataset must install and use specialist software via the command line. …”
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Developments in Toxicity Testing with Duckweeds by Paul Ziegler

“…Biomarkers of toxic effect have long been determined concomitantly with testing for toxicity itself, and their potential for the assessment of toxicity has recently been greatly expanded by transcriptomic, proteomic and metabolomic techniques complemented by FITR spectroscopy, transformation and genotoxicity and timescale toxicity testing. …”
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Applications and advances of multi-omics technologies in gastrointestinal tumors by Yuqing Liu, Feng Gao, Yang Cheng, Liang Qi, Haining Yu

“…Genomics reveals genetic characteristics and heterogeneity of tumors; transcriptomics helps identify molecular subtypes and potential therapeutic targets; proteomics provides important information on core proteins and the immune microenvironment; and metabolomics offers promising biomarkers for early diagnosis. …”
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LCN2-mediated ferroptosis resistance in tissue homeostasis and early-stage tumorigenesis of the fallopian tube epithelium by Keiyo Imaeda, Tomohiro Tamura, Shimpei Nagai, Eiji Sugihara, Juntaro Yamasaki, Yuji Otsuki, Kohei Nakamura, Takashi Takeda, Kanako Nakamura, Yuya Nogami, Kosuke Tsuji, Tatsuyuki Chiyoda, Iori Kisu, Yusuke Kobayashi, Kouji Banno, Rui Yamaguchi, Kazuhiro Sakurada, Hideyuki Saya, Daisuke Aoki, Ahmed Ashour Ahmed, Osamu Nagano, Kenta Masuda, Wataru Yamagami

“…We also analyzed two single-cell transcriptomic data to trace the differentiation trajectory in human FTE, and found that the gene LCN2 serves as a marker gene of early stage of the trajectory. …”
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Early precursor-derived pituitary gland tissue-resident macrophages play a pivotal role in modulating hormonal balance by Henna Lehtonen, Heli Jokela, Julian Hofmann, Lauriina Tola, Arfa Mehmood, Florent Ginhoux, Burkhard Becher, Melanie Greter, Gennady G. Yegutkin, Marko Salmi, Heidi Gerke, Pia Rantakari

“…Using single-cell transcriptomics, fate mapping, and imaging, we characterize pituitary-resident macrophages (pitMØs), revealing their heterogeneity and spatial specialization. …”
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Latent infection of Caenorhabditis elegans by Orsay virus induces age-dependent immunity and cross-protection by Victoria G. Castiglioni, Ana Villena-Giménez, Dominik Herek, Antonio González-Sánchez, Christina Toft, Gustavo G. Gómez, Santiago F. Elena

“…Abstract The C. elegans-Orsay virus pathosystem provides a powerful model for investigating the mechanisms that govern viral infection and immunity. …”
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Biomedical informatics analysis has revealed a novel hub gene of the HBx in the pathogenesis and progression of DLBCL by Ying Zhang, Wei Guo, Haotian Wang, Zhumei Zhan, Rui Xing, Ou Bai

“…HBx enhanced cell proliferation, migration, and invasion in vitro and altered cell cycle progression. Transcriptomic analysis of tumor tissues revealed distinct gene expression profiles. …”
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Dual regulation of Atf3 and Lonp1 as therapeutic targets in cerebral ischaemia-reperfusion injury by Bo Yu, Lin Zhou, Min Zhou, Weijian Fan, Jindong Tong, Jinyun Tan, Weihao Shi

“…Understanding the molecular mechanisms underlying CIRI is crucial for developing effective therapeutic strategies.Objective This study aims to investigate the roles of activating transcription factor 3 (Atf3) and lon protease homolog 1 (Lonp1) in CIRI, particularly focusing on how Atf3 regulates Lonp1 expression and its effects on mitochondrial function.Methods Single-cell transcriptomics and proteomic analyses were employed to explore Atf3's influence on Lonp1 and its subsequent impact on neuronal survival and apoptosis.Results The findings indicate that Atf3 plays a crucial role in modulating Lonp1 expression, which in turn affects mitochondrial function, neuronal survival, and apoptotic pathways.Conclusion This study provides new insights into the regulatory mechanisms of Atf3 and Lonp1 in CIRI, identifying potential therapeutic targets for managing ischemic brain injury and neurodegenerative diseases.…”
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Multiomics and cellular senescence profiling of aging human skeletal muscle uncovers Maraviroc as a senotherapeutic approach for sarcopenia by Yang Li, Chuhan Li, Qin Zhou, Xingyuan Liu, Yulong Qiao, Ting Xie, Hao Sun, Michael Tim-Yun Ong, Huating Wang

“…Here we leverage single nucleus multiomics to profile senescence in mononucleated cells of human skeletal muscle and provide the first senescence atlas. We demonstrate the intra- and inter-populational transcriptomic and epigenomic heterogeneity and dynamics of cellular senescence. …”
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Role of artificial intelligence in digital pathology for gynecological cancers by Ya-Li Wang, Song Gao, Qian Xiao, Chen Li, Marcin Grzegorzek, Ying-Ying Zhang, Xiao-Han Li, Ye Kang, Fang-Hua Liu, Dong-Hui Huang, Ting-Ting Gong, Qi-Jun Wu

“…Furthermore, the integration with transcriptomics, proteomics, and other multi-omics techniques can provide valuable insights into the molecular features of diseases. …”
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Unveiling molecular mechanisms of strobilurin resistance in the cacao pathogen Moniliophthora perniciosa by Paula F.V. Prado, Caio V.C. Mendes, Bárbara A. Pires, Gabriel L. Fiorin, Piotr Mieczkowski, Gonçalo A.G. Pereira, Paulo J.P.L. Teixeira, Daniela P.T. Thomazella

“…Remarkably, long-term exposure to azoxystrobin led to the emergence of a resistant mutant harboring mutations in two putative growth and transcriptional regulators. This work provides new insights into the molecular basis of strobilurin resistance and informs strategies for more effective fungicide deployment in agriculture.…”
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Machine learning uncovers the transcriptional regulatory network for the production host Streptomyces albidoflavus by Mathias Jönsson, Renata Sigrist, Tetiana Gren, Mykhaylo Semenov Petrov, Nils Emil Junge Marcussen, Anna Svetlova, Pep Charusanti, Peter Gockel, Bernhard O. Palsson, Lei Yang, Emre Özdemir

“…Here, we characterize the TRN using independent component analysis on 218 RNA sequencing (RNA-seq) transcriptomes across 88 unique growth conditions. We identify 78 independently modulated sets of genes (iModulons) that quantitatively describe the TRN across diverse conditions. …”
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Advances in the application of multi-omics analysis in skin aging by Boquan Long, Boquan Long, Weitian Pan, Shuozhong Wu, Qianye Nong, Wenhui Li, Siqi Chen, Siqi Chen, Hongwei Guo

“…This review provides an overview of advancements in skin aging research using multi-omics technologies, aiming to foster innovation in research methodologies related to skin aging.…”
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Mitochondrial dysfunction drives a neuronal exhaustion phenotype in methylmalonic aciduria by Matthew C. S. Denley, Monique S. Straub, Giulio Marcionelli, Miriam A. Güra, David Penton, Igor Delvendahl, Martin Poms, Beata Vekeriotaite, Sarah Cherkaoui, Federica Conte, Ferdinand von Meyenn, D. Sean Froese, Matthias R. Baumgartner

“…Our work provides first evidence of mitochondrial driven neuronal dysfunction in MMA, which through our comprehensive characterisation of this paradigmatic model, enables first steps to identifying effective therapies.…”
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Multi-omics dataset of individual variations in growth performance of large yellow croaker by Hao Huang, Zhenheng Cheng, Yabing Wang, Guangde Qiao, Xiaoshan Wang, Yanfeng Yue, Quanxin Gao, Shiming Peng

“…Our findings offer critical insights into the molecular mechanisms underlying growth variations in L. crocea and provide valuable data for the selective breeding of improved strains.…”
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Astrocyte heterogeneity in ischemic stroke: Molecular mechanisms and therapeutic targets by Daxing Li, Xinchen Huo, Ling Shen, Minjie Qian, Jindou Wang, Shijie Mao, Wenjing Chen, Runheng Li, Tianhao Zhu, Beicheng Zhang, Kunxuan Liu, Feifei Wu, Ying Bai

“…However, the relationship between stroke and reactive astrocyte heterogeneity has not been fully elucidated, and regulating the heterogeneity of astrocytes to play a neuroprotective role may provide a new perspective for the treatment of stroke. …”
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Integrated multi-omics profiling characterizes the crucial role of human dental epithelium during tooth development by Ran Zhang, Zongshan Shen, Zhenni Zhao, Xiuge Gu, Tianxing Yan, Wei Wei, Chuan Wu, Jinxuan Xia, Yuanyuan Zhang, Suwen Chen, Linsha Ma, Dong Zhang, Xiaoshan Wu, Paul T. Sharpe, Songlin Wang

“…Here, we linked single-cell RNA sequencing, spatial transcriptomics, and secretome analysis to characterize human fetal tooth development over time. …”
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Early embryonic development in the tick Ixodes scapularis suggests syncytial organization and cellularization before blastoderm formation by Isaac A. Hinne, Hailee R. Ciccotti, Jakub Wudarski, Michael N. Pham, Arvind Sharma, Molly M. McVicar, Benjamin Faustino, Andrew B. Nuss, Prashant P. Sharma, Monika Gulia-Nuss

“…In recent years, many advances have been made in building the toolkit for I. scapularis research, including genomic resources, transcriptomes, and forward and reverse genetics techniques. …”
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TrimNN: characterizing cellular community motifs for studying multicellular topological organization in complex tissues by Yang Yu, Shuang Wang, Jinpu Li, Meichen Yu, Kyle McCrocklin, Jing-Qiong Kang, Anjun Ma, Qin Ma, Dong Xu, Juexin Wang

“…By uncovering CC motifs, TrimNN reveals key associations between spatially distributed cell-type patterns and diverse phenotypes. These insights provide a foundation for understanding biological and disease mechanisms and offer potential biomarkers for diagnosis and therapeutic interventions.…”
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Effects of methyl jasmonate and salicylhydroxamic acid on the biosynthesis of flavonoids in Glycyrrhiza glabra L. hairy roots by Huan-huan Zhao, Ran Du, Ya-lei Han, Zhao-hui Yang, Xiang Qiu, Yu-qi Li, Jian-guo Zhang, Zhi-wei Cheng

“…These findings highlight the divergent role of jasmonate signaling in flavonoid biosynthesis and provide insights for targeted metabolic engineering in G. glabra.…”
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