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. Structural Biology and Molecular Biophysics

    PPIscreenML is a method for structure-based screening of protein-protein interactions using AlphaFold

    Victoria Mischley, Johannes Maier ... John Karanicolas
    PPIscreenML is a rigorously benchmarked method that uses AlphaFold2 to screen for interacting protein pairs, and it provides superior performance to other available methods.
    1. Developmental Biology
    2. Genetics and Genomics

    The robust, high-throughput, and temporally regulated roxCre and loxCre reporting systems for genetic modifications in vivo

    Mengyang Shi, Jie Li ... Bin Zhou
    New mouse genetic tools, roxCre and loxCre, facilitate the study of gene function in cells of interest, allowing for simultaneous and efficient gene knockout and precise lineage tracing in vivo.
    1. Ecology
    2. Neuroscience

    New idtracker.ai rethinks multi-animal tracking as a representation learning problem to increase accuracy and reduce tracking time

    Jordi Torrents, Tiago Costa, Gonzalo de Polavieja
    Identification of each animal in a collective becomes possible even when individuals are never all visible simultaneously, enabling faster and more accurate analysis of collective behavior.
    1. Cell Biology

    Probing metazoan polyphosphate biology using Drosophila reveals novel and conserved polyP functions

    Sunayana Sarkar, Harsha Sharma ... Manish Jaiswal
    A genetic toolkit establishes Drosophila as a tractable metazoan system for systematic interrogation of conserved biological functions of the ancient polymer polyphosphate.
    1. Chromosomes and Gene Expression
    2. Computational and Systems Biology

    DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci

    Yuzhen Liu, Christopher D McGann ... Devin K Schweppe
    DNA O-MAP enables proximity labeling at specific genomic loci in fixed cells using programmable oligonucleotides, revealing locus-proximal proteomes and chromatin interactions without genetic modification.
    1. Medicine

    Single transcript level atlas of oxytocin and the oxytocin receptor in the mouse brain

    Vitaly Ryu, Anisa Azatovna Gumerova ... Mone Zaidi
    The compendium of oxytocin and its receptor in the brain could provide further insights into the peripheral and central effects of oxytocin in health and disease.
    1. Neuroscience

    Precision cutaneous stimulation in freely moving mice

    Isobel Parkes, Ara Schorscher-Petcu ... Liam E Browne
    A closed-loop system delivers cutaneous optical stimulation during movement in freely behaving mice, enabling controlled somatosensory input in naturalistic settings.
    1. Developmental Biology
    2. Genetics and Genomics

    A genome-wide MAGIC kit for recombinase-independent mosaic analysis in Drosophila

    Yifan Shen, Ann T Yeung ... Chun Han
    A comprehensive toolkit enables genome-wide, recombinase-independent mosaic analysis in Drosophila, permitting clonal analysis of pericentromeric genes, deficiency chromosomes, and interspecific hybrids previously inaccessible to standard methods.
    1. Neuroscience

    Resolving synaptic events using subsynaptically targeted GCaMP8 variants

    Jiawen Chen, Junhao Lin ... Dion K Dickman
    New synaptically targeted GCaMP8 sensors and analysis tools capture calcium dynamics with the speed and sensitivity previously achievable only through electrophysiology and chemical dyes.
    1. Chromosomes and Gene Expression
    2. Developmental Biology

    Massively parallel reporter assay for mapping gene-specific regulatory regions at single-nucleotide resolution

    Alastair J Tulloch, Ryan Nicholas Delgado ... Constance L Cepko
    Integrated locus-specific and mutational MPRAs reveal regulatory modules and nucleotide determinants governing cell type-specific gene expression, providing a scalable framework for mapping cis-regulatory architecture.