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Methods & Resources

  • Deep learning models link local cellular features with whole-animal growth dynamics in zebrafish
    Open Access
    Deep learning models link local cellular features with whole-animal growth dynamics in zebrafish

    Shang-Ru Yang, Megan Liaw, An-Chi Wei, Chen-Hui Chen

    Shang-Ru Yang ... Chen-Hui Chen

    Published 21 May 2025

    The study introduces a deep learning-assisted approach for uncovering the intricate, real-time cross-length scale interactions between individual cells and the entire organism in a vertebrate model.

  • A fluorescent sensor for real-time monitoring of DPP8/9 reveals crucial roles in immunity and cancer
    Open Access
    A fluorescent sensor for real-time monitoring of DPP8/9 reveals crucial roles in immunity and cancer

    Konstantin Weiss, Yelizaveta Agarkova, Alexandra Zwosta, Sarah Hoevel, Ann-Kathrin Himmelreich, Magdalena Shumanska, Julia Etich, Gereon Poschmann, Bent Brachvogel, Ivan Bogeski, Dirk Mielenz, Jan Riemer

    Konstantin Weiss ... Jan Riemer

    Published 12 May 2025

    Weiss et al developed a genetically encoded biosensor for real-time monitoring of DPP8/9 activity, an important protease, and revealed roles of DPP8/9 in B-cell maturation and melanoma proliferation.

  • The RBR E3 ubiquitin ligase HOIL-1 can ubiquitinate diverse non-protein substrates in vitro
    Open Access
    The RBR E3 ubiquitin ligase HOIL-1 can ubiquitinate diverse non-protein substrates in vitro

    Xiangyi S Wang, Jenny Jiou, Anthony Cerra, Simon A Cobbold, Marco Jochem, Ka Hin Toby Mak, Leo Corcilius, John Silke, Richard J Payne, Ethan D Goddard-Borger, David Komander, Bernhard C Lechtenberg

    Xiangyi S Wang ... Bernhard C Lechtenberg

    Published 1 April 2025

    The RBR E3 ligase HOIL-1 ubiquitinates Ser/Thr residues and various disaccharides in vitro and can be used to generate ubiquitinated sugars as tools to study non-proteinaceous ubiquitination.

  • Visualisation of <em>Euglena gracilis</em> organelles and cytoskeleton using expansion microscopy
    Open Access
    Visualisation of Euglena gracilis organelles and cytoskeleton using expansion microscopy

    Anežka Konupková, Priscila Peña-Diaz, Vladimír Hampl

    Anežka Konupková ... Vladimír Hampl

    Published 7 February 2025

    We applied expansion microscopy to visualise the cytoskeleton, mitochondria, and chloroplasts of Euglena gracilis, which enabled high-resolution imaging, revealing cellular structures and organelle development, demonstrating expansion microscopy’s utility as a complementary method to electron microscopy for studying this protist.

  • Concatemer-assisted stoichiometry analysis: targeted mass spectrometry for protein quantification
    Open Access
    Concatemer-assisted stoichiometry analysis: targeted mass spectrometry for protein quantification

    Jiaxi Cai, Yun Quan, Cindy Yuxuan Zhang, Ziyi Wang, Stephen M Hinshaw, Huilin Zhou, Raymond T Suhandynata

    Jiaxi Cai ... Raymond T Suhandynata

    Published 31 December 2024

    Concatemer-assisted stoichiometry analysis (CASA) addresses a common challenge in cell biology: absolute quantification of protein subunits in native protein complexes.

  • DICE: fast and accurate distance-based reconstruction of single-cell copy number phylogenies
    Open Access
    DICE: fast and accurate distance-based reconstruction of single-cell copy number phylogenies

    Samson Weiner, Mukul S Bansal

    Samson Weiner ... Mukul S Bansal

    Published 12 December 2024

    This work presents two new computational methods for reconstructing tumor cell lineage trees from single-cell copy number data.

  • FrozONE: quick cell nucleus enrichment for comprehensive proteomics analysis of frozen tissues
    Open Access
    FrozONE: quick cell nucleus enrichment for comprehensive proteomics analysis of frozen tissues

    Lukas A Huschet, Fabian P Kliem, Peter Wienand, Claudia M Wunderlich, Andrea Ribeiro, Isabel Bustos-Martínez, Ángel Barco, F Thomas Wunderlich, Maciej Lech, Maria S Robles

    Lukas A Huschet ... Maria S Robles

    Published 12 December 2024

    The authors establish and benchmark a nuclear proteomics workflow that is faster, simpler, and more scalable than classical protocols, while being as efficient, specific, and reproducible.

  • 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.

  • 4G cloning: rapid gene assembly for expression of multisubunit protein complexes in diverse hosts
    Open Access
    4G cloning: rapid gene assembly for expression of multisubunit protein complexes in diverse hosts

    Michael Taschner, Joe Bradley Dickinson, Florian Roisné-Hamelin, Stephan Gruber

    Michael Taschner ... Stephan Gruber

    Published 2 December 2024

    To streamline expression construct preparation for screening in diverse expression hosts, we present vectors and protocols using Golden Gate ligation to guide one-step Gibson assembly.

  • 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.

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