Browse our Tools and Resources

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    1. Cell Biology
    2. Developmental Biology

    An efficient and scalable pipeline for epitope tagging in mammalian stem cells using Cas9 ribonucleoprotein

    Pooran Singh Dewari, Benjamin Southgate ... Steven M Pollard
    Biochemical tags can be easily knocked into endogenous genes in mammalian stem cells using optimised and scalable protocols that will enable annotation of protein levels, localisation and interaction partners.
    1. Developmental Biology

    Multi-view light-sheet imaging and tracking with the MaMuT software reveals the cell lineage of a direct developing arthropod limb

    Carsten Wolff, Jean-Yves Tinevez ... Anastasios Pavlopoulos
    Quantitative analyses of multi-dimensional microscopy datasets with a new Fiji/ImageJ plugin for cell tracking reveal the lineage restrictions and morphogenetic cellular behaviors underlying embryonic limb outgrowth in the direct developing crustacean Parhyale hawaiensis.
    1. Stem Cells and Regenerative Medicine

    Live cell-lineage tracing and machine learning reveal patterns of organ regeneration

    Oriol Viader-Llargués, Valerio Lupperger ... Hernán López-Schier
    A combination of live cell tracking, cell-lineage tracing and machine learning shows that injured sensory organs repair accurately regardless of the extent of damage.
    1. Chromosomes and Gene Expression

    A gene-specific T2A-GAL4 library for Drosophila

    Pei-Tseng Lee, Jonathan Zirin ... Hugo J Bellen
    A library of a thousand gene-specific intronic GAL4 insertions was generated, which caused a severe loss of function, permitted the assessing of gene expression, allowed the rescue of mutated gene with UAS-cDNA constructs, and provided a tool for the reversion of mutant phenotypes in specific cells or tissues.
    1. Developmental Biology
    2. Neuroscience

    Evolution and cell-type specificity of human-specific genes preferentially expressed in progenitors of fetal neocortex

    Marta Florio, Michael Heide ... Michael Hiller
    Transcriptomic and genomic analysis provides a resource of 50 primate-specific genes preferentially expressed in neural progenitors of fetal human neocortex, 15 of which are specific to humans.
    1. Neuroscience

    A spike sorting toolbox for up to thousands of electrodes validated with ground truth recordings in vitro and in vivo

    Pierre Yger, Giulia LB Spampinato ... Olivier Marre
    A spike sorting toolbox to quickly and reliably access the activity of thousands of neurons recorded with dense extracellular probes.
    1. Computational and Systems Biology
    2. Immunology and Inflammation

    Method for identification of condition-associated public antigen receptor sequences

    Mikhail V Pogorelyy, Anastasia A Minervina ... Aleksandra M Walczak
    Without using control cohorts, a statistical method identifies candidates for immune receptors associated with diseases from repertoire sequencing datasets.
    1. Neuroscience

    Efficient and accurate extraction of in vivo calcium signals from microendoscopic video data

    Pengcheng Zhou, Shanna L Resendez ... Liam Paninski
    A new open-source computational toolbox for processing in vivo microendoscopic calcium imaging data performs signal demixing and denoising much more accurately than previously available methods, significantly improving the utility of this imaging modality.
    1. Cell Biology

    Single-cell RNA-seq reveals hidden transcriptional variation in malaria parasites

    Adam J Reid, Arthur M Talman ... Mara KN Lawniczak
    Plasmodium parasite transcription shifts dramatically along asexual development, and transmission stages variably express important immune evasion genes, suggesting much interesting biology has until now been hidden by bulk analyses.
    1. Computational and Systems Biology
    2. Neuroscience

    Automated analysis of long-term grooming behavior in Drosophila using a k-nearest neighbors classifier

    Bing Qiao, Chiyuan Li ... Sheyum Syed
    Drosophila grooming is driven by two internal programs.