Browse our Tools and Resources

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    1. Computational and Systems Biology
    2. Ecology

    TRex, a fast multi-animal tracking system with markerless identification, and 2D estimation of posture and visual fields

    Tristan Walter, Iain D Couzin
    Being fast, memory efficient, easy to use, and with powerful integrated tools, TRex will lower barriers of entry into, and enable more ambitious approaches to, the quantitative study of behavior.
    1. Computational and Systems Biology
    2. Microbiology and Infectious Disease

    Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

    Francesco Beghini, Lauren J McIver ... Nicola Segata
    The bioBakery 3 platform enables improved, integrated, and strain-level analysis of microbial communities from large-scale meta-omic data.
    1. Neuroscience

    Visualizing anatomically registered data with brainrender

    Federico Claudi, Adam L Tyson ... Tiago Branco
    Brainrender is an open-source and user-friendly software for combining any type of anatomically registered data into custom interactive 3D renderings.
    1. Neuroscience

    An open-source device for measuring food intake and operant behavior in rodent home-cages

    Bridget A Matikainen-Ankney, Thomas Earnest ... Alexxai V Kravitz
    An open-source behavioral platform allows for operant, feeding, and circadian experiments in rodent home-cages.
    1. Developmental Biology
    2. Neuroscience

    Transcriptional profiling of mouse peripheral nerves to the single-cell level to build a sciatic nerve ATlas (SNAT)

    Daniel Gerber, Jorge A Pereira ... Ueli Suter
    Establishing transcriptional profiles of nerve-inhabitant cells as resource to foster the fundamental understanding of peripheral nerves.
    1. Neuroscience

    Relationship between simultaneously recorded spiking activity and fluorescence signal in GCaMP6 transgenic mice

    Lawrence Huang, Peter Ledochowitsch ... Lu Li
    Simultaneous calcium imaging and cell-attached recording in GCaMP6 transgenic mice in vivo reveals spiking-fluorescence relationship that supports more refined inference of neuronal activities from calcium imaging data.
    1. Immunology and Inflammation
    2. Neuroscience

    Development and characterization of a chronic implant mouse model for vagus nerve stimulation

    Ibrahim T Mughrabi, Jordan Hickman ... Stavros Zanos
    Long-term, dose-controlled vagus nerve stimulation (VNS) is feasible in mice using a multi-lab validated implantation procedure, allowing therapeutic testing of VNS in many disease models.
    1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    An atlas of the binding specificities of transcription factors in Pseudomonas aeruginosa directs prediction of novel regulators in virulence

    Tingting Wang, Wenju Sun ... Jian Yan
    The transcription factor (TF)-binding specificities of Pseudomonas aeruginosa allow us to predict virulence-associated TFs and their target genes, which will facilitate to find effective treatment and prevention for its associated diseases.
    1. Developmental Biology

    In vivo proximity labeling identifies cardiomyocyte protein networks during zebrafish heart regeneration

    Mira I Pronobis, Susan Zheng ... Kenneth D Poss
    Proximity labeling-based proteomic strategies applied in zebrafish identify new insights into protein network changes in heart muscle cells during regeneration and implicate Rho A as a target of ErbB2 signaling during zebrafish heart regeneration.
    1. Genetics and Genomics
    2. Immunology and Inflammation

    Simultaneous trimodal single-cell measurement of transcripts, epitopes, and chromatin accessibility using TEA-seq

    Elliott Swanson, Cara Lord ... Peter J Skene
    Simultaneous multimodal measurement of chromatin accessibility, gene expression, and protein expression provides a unified view of the molecular underpinnings of immune cell state in health and disease.