Tools and Resources

A Tools and Resources article allows authors to publish the details of new experimental techniques, datasets, software tools, and other resources.

Latest articles

    1. Computational and Systems Biology

    Genome-scale annotation of protein binding sites via language model and geometric deep learning

    Qianmu Yuan, Chong Tian, Yuedong Yang
    Integration of language model and geometric deep learning enables accurate and efficient genome-scale annotation of comprehensive protein-ligand binding sites.
    1. Neuroscience

    Transcriptomic atlas of midbrain dopamine neurons uncovers differential vulnerability in a Parkinsonism lesion model

    Behzad Yaghmaeian Salmani, Laura Lahti ... Thomas Perlmann
    Single nuclei RNA sequencing unmasks 16 variants of midbrain dopamine neurons within a continuum of their gene expression landscape and resolves their differential vulnerability.
    1. Genetics and Genomics

    Expanding the Drosophila toolkit for dual control of gene expression

    Jonathan Zirin, Barbara Jusiak ... Norbert Perrimon
    A CRISPR knock-in approach enables the efficient generation of tissue-specific LexA and QF driver lines which can simultaneously control gene expression in multiple tissues.
    1. Chromosomes and Gene Expression
    2. Computational and Systems Biology

    voyAGEr, a free web interface for the analysis of age-related gene expression alterations in human tissues

    Arthur L Schneider, Rita Martins-Silva ... Nuno L Barbosa-Morais
    voyAGEr is an online platform that facilitates the exploration of age-related gene expression dynamics in human tissues, allowing users to analyse tissue- and sex-specific changes alongside donor medical histories.
    1. Neuroscience

    Establishment of transgenic fluorescent mice for labeling synapses and screening synaptogenic adhesion molecules

    Lei Yang, Jingtao Zhang ... Chen Zhang
    A Syt1-tdTomato transgenic mice with normal synaptic transmission is established to label synapse in situ and screen synaptogenic adhesion molecules.
    1. Computational and Systems Biology
    2. Immunology and Inflammation

    Transformer-based spatial–temporal detection of apoptotic cell death in live-cell imaging

    Alain Pulfer, Diego Ulisse Pizzagalli ... Santiago Fernandez Gonzalez
    ADeS, a novel deep learning approach for apoptosis detection, achieves 98% accuracy in vitro and in vivo while providing unprecedented insights into the spatial–temporal foundation of cell death.
    1. Cell Biology

    A novel imaging method (FIM-ID) reveals that myofibrillogenesis plays a major role in the mechanically induced growth of skeletal muscle

    Kent W Jorgenson, Jamie E Hibbert ... Troy A Hornberger
    A novel imaging method for measuring myofibril size/number reveals that the radial growth of muscle fibers that occurs in response to increased mechanical loading is largely mediated by myofibrillogenesis.
    1. Computational and Systems Biology
    2. Immunology and Inflammation

    Enhancing TCR specificity predictions by combined pan- and peptide-specific training, loss-scaling, and sequence similarity integration

    Mathias Fynbo Jensen, Morten Nielsen
    NetTCR 2.2 demonstrates advances in predicting MHC-peptide-TCR interactions through integration of pan- and peptide-specific training strategies, loss-scaling and sequence similarity scoring.
    1. Cell Biology

    An open-source, high-resolution, automated fluorescence microscope

    Ando Christian Zehrer, Ana Martin-Villalba ... Helge Ewers
    High-quality fluorescence live-cell and single molecule imaging via computer-controlled, user-assembled microscope that fits in incubator, can in large parts be 3D printed and employs open source software and electronics.
    1. Computational and Systems Biology
    2. Neuroscience

    Dissecting muscle synergies in the task space

    David O'Reilly, Ioannis Delis
    A novel network information framework quantifies muscle interactions, characterises their task-relevance, and identifies networks of muscles with similar and complementary functional roles.