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More articles from Resources

  • Cross-comparison of strains used for mitochondrial imaging in <em>Caenorhabditis elegans</em> during aging
    Open Access
    Cross-comparison of strains used for mitochondrial imaging in Caenorhabditis elegans during aging

    Juri Kim, Naibedya Dutta, Matthew Vega, Andrew Bong, Maxim Averbukh, Rebecca Aviles Barahona, Athena Alcala, Jacob T Holmes, Gilberto Garcia, Ryo Higuchi-Sanabria

    Juri Kim ... Ryo Higuchi-Sanabria

    Published 3 June 2025

    This study evaluates mitochondrial imaging in C. elegans during aging, comparing various transgenic constructs for tissue-specific mitochondrial visualization. The findings highlight technical considerations, imaging method standardization, and the utility of C. elegans as a robust model for studying mitochondrial dynamics.

  • Cytokine storm and vascular leakage in severe dengue: insights from single-cell RNA profiling
    Open Access
    Cytokine storm and vascular leakage in severe dengue: insights from single-cell RNA profiling

    Mohamad Al Kadi, Maika Yamashita, Masayuki Shimojima, Tomoki Yoshikawa, Hideki Ebihara, Daisuke Okuzaki, Takeshi Kurosu

    Mohamad Al Kadi ... Takeshi Kurosu

    Published 24 March 2025

    Fixed single-cell RNA profiling identified IL-17A/F-producing γδ T cells, ILC3s, and Th17 cells, cooperative roles of M1- and M2-like macrophages, and dual roles of neutrophils during severe dengue.

  • Gastric cancer genomics study using reference human pangenomes
    Open Access
    Gastric cancer genomics study using reference human pangenomes

    Du Jiao, Xiaorui Dong, Shiyu Fan, Xinyi Liu, Yingyan Yu, Chaochun Wei

    Du Jiao ... Chaochun Wei

    Published 27 January 2025

    Using a concept called graph pangenome for many individual genomes as the baseline can improve the identification and characterization of large-sized genomic variations for disease genomics study.

  • Systematic assessment of structural variant annotation tools for genomic interpretation
    Open Access
    Systematic assessment of structural variant annotation tools for genomic interpretation

    Xuanshi Liu, Lei Gu, Chanjuan Hao, Wenjian Xu, Fei Leng, Peng Zhang, Wei Li

    Xuanshi Liu ... Wei Li

    Published 10 December 2024

    This study benchmarks eight structural variant prioritization tools, highlighting their comparable effectiveness in predicting pathogenicity and providing insights for improved genomic research.

  • Mass spectrometry–based proteomic exploration of diverse murine macrophage cellular models
    Open Access
    Mass spectrometry–based proteomic exploration of diverse murine macrophage cellular models

    Jack Gudgeon, Abeer Dannoura, Ritika Chatterjee, Frances Sidgwick, Benjamin BA Raymond, Andrew M Frey, José Luis Marin-Rubio, Matthias Trost

    Jack Gudgeon ... Matthias Trost

    Published 7 November 2024

    In this article, we characterised multiple murine macrophage cell models by proteomics and identified significant differences compared with bone marrow–derived macrophages.

  • Clonal landscape of autoantibody-secreting plasmablasts in COVID-19 patients
    Open Access
    Clonal landscape of autoantibody-secreting plasmablasts in COVID-19 patients

    Shuhei Sakakibara, Yu-Chen Liu, Masakazu Ishikawa, Ryuya Edahiro, Yuya Shirai, Soichiro Haruna, Marwa Ali El Hussien, Zichang Xu, Songling Li, Yuta Yamaguchi, Teruaki Murakami, Takayoshi Morita, Yasuhiro Kato, Haruhiko Hirata, Yoshito Takeda, Fuminori Sugihara, Yoko Naito, Daisuke Motooka, Chao-Yuan Tsai, Chikako Ono, Yoshiharu Matsuura, James B Wing, Hisatake Matsumoto, Hiroshi Ogura, Masato Okada, Atsushi Kumanogoh, Yukinari Okada, Daron M Standley, Hitoshi Kikutani, Daisuke Okuzaki

    Shuhei Sakakibara ... Daisuke Okuzaki

    Published 17 September 2024

    This study identifies a public autoantibody clonotype that sheds light on the development of COVID-19–associated autoantibodies through single-cell immunoglobulin repertoire analysis of plasmablasts.

  • Quantitative assessment of the nanoanatomy of the contractile vacuole complex in <em>Trypanosoma cruzi</em>
    Open Access
    Quantitative assessment of the nanoanatomy of the contractile vacuole complex in Trypanosoma cruzi

    Ingrid Augusto, Wendell Girard-Dias, Alejandra Schoijet, Guillermo Daniel Alonso, Rodrigo V Portugal, Wanderley de Souza, Veronica Jimenez, Kildare Miranda

    Ingrid Augusto ... Kildare Miranda

    Published 29 July 2024

    Electron microscopy analysis of the osmoregulatory system in T. cruzi cell lines subjected to cryopreparation methods revealed dynamic changes in the contractile vacuole complex (CVC) and the structure of the adhesion plaque domain during the CVC pulsation cycle.

  • Gene expression and chromatin conformation of microglia in virally suppressed people with HIV
    Open Access
    Gene expression and chromatin conformation of microglia in virally suppressed people with HIV

    Johannes CM Schlachetzki, Sara Gianella, Zhengyu Ouyang, Addison J Lana, Xiaoxu Yang, Sydney O’Brien, Jean F Challacombe, Peter J Gaskill, Kelly L Jordan-Sciutto, Antoine Chaillon, David Moore, Cristian L Achim, Ronald J Ellis, Davey M Smith, Christopher K Glass

    Johannes CM Schlachetzki ... Christopher K Glass

    Published 26 July 2024

    Leveraging our rapid autopsy “Last Gift” cohort at UCSD, we identified distinct microglial gene expression profiles despite ART.

  • A large-scale cancer-specific protein–DNA interaction network
    Open Access
    A large-scale cancer-specific protein–DNA interaction network

    Yunwei Lu, Anna Berenson, Ryan Lane, Isabelle Guelin, Zhaorong Li, Yilin Chen, Sakshi Shah, Meimei Yin, Luis Fernando Soto-Ugaldi, Ana Fiszbein, Juan Ignacio Fuxman Bass

    Yunwei Lu ... Juan Ignacio Fuxman Bass

    Published 16 July 2024

    This study delineates a large-scale cancer gene TF-DNA interaction network, highlighting potential oncogene-targeted therapeutics and complex TF roles in gene regulation. This study also offers a valuable resource for future research in cancer gene regulation and for therapeutic development.

  • Transient chromatin decompaction at the start of <em>D. melanogaster</em> male embryonic germline development
    Open Access
    Transient chromatin decompaction at the start of D. melanogaster male embryonic germline development

    Yi-Ru Li, Li Bin Ling, Angel Chao, Sebastian D Fugmann, Shu Yuan Yang

    Yi-Ru Li ... Shu Yuan Yang

    Published 11 July 2024

    Our genomics profiling of the earliest fruit fly germline revealed a brief window of major chromatin remodeling in the male germline right after zygotic activation and suggests reprogramming in the early stages of germline to be an evolutionarily conserved phenomenon.

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