Browse our Tools and Resources

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    1. Computational and Systems Biology
    2. Ecology

    A rapid phylogeny-based method for accurate community profiling of large-scale metabarcoding datasets

    Lenore Pipes, Rasmus Nielsen
    Tronko provides a scalable solution for accurate taxonomic assignment for large-scale metabarcoding datasets by overcoming the speed and memory limitations of previous phylogenetic placement methods.
    1. Biochemistry and Chemical Biology

    Quantitative mapping of proteasome interactomes and substrates using ProteasomeID

    Aleksandar Bartolome, Julia C Heiby ... Alessandro Ori
    Proximity labeling combined with mass spectrometry enables to map the proteasome proximal proteome in cells and mouse tissues.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Genetic code expansion, click chemistry, and light-activated PI3K reveal details of membrane protein trafficking downstream of receptor tyrosine kinases

    Duk-Su Koh, Anastasiia Stratiievska ... Sharona E Gordon
    The generation of phosphoinositide 3,4,5-trisphosphate causes an increase in the number of TRPV1 ion channels and insulin receptors in the plasma membrane.
    1. Neuroscience

    A dynamic generative model can extract interpretable oscillatory components from multichannel neurophysiological recordings

    Proloy Das, Mingjian He, Patrick L Purdon
    Oscillation component analysis enables cognitive neuroscientists to summarize millisecond-precision high-dimensional neurophysiological recordings into a smaller set of oscillatory components through biophysically inspired generative modeling of neural oscillations.
    1. Biochemistry and Chemical Biology

    Probing PAC1 receptor activation across species with an engineered sensor

    Reto B Cola, Salome N Niethammer ... Tommaso Patriarchi
    A new genetically encoded sensor robustly detects exogenously applied PAC1R ligands in vitro, ex vivo, and in vivo (in zebrafishes and mice) serving as a useful resource for probing PAC1R functions.
    1. Cell Biology
    2. Neuroscience

    Combining array tomography with electron tomography provides insights into leakiness of the blood-brain barrier in mouse cortex

    Georg Kislinger, Gunar Fabig ... Martina Schifferer
    An array tomography and electron tomography hybrid approach based on coated plastic tape as support advances ultrastructural analysis of biological phenomena that require cell- and tissue-level contextualization of the finest subcellular textures.
    1. Neuroscience

    MotorNet, a Python toolbox for controlling differentiable biomechanical effectors with artificial neural networks

    Olivier Codol, Jonathan A Michaels ... Paul L Gribble
    MotorNet is a Python toolbox for training artificial neural networks to control arbitrarily complex, differentiable, and biomechanically realistic musculo-skeletal effectors on user-defined sensorimotor tasks.
    1. Medicine

    An atlas of brain-bone sympathetic neural circuits in mice

    Vitaly Ryu, Anisa Azatovna Gumerova ... Mone Zaidi
    Central SNS outflow sites originating from 87 brain nuclei and sub-nuclei in six brain divisions innervate bone.
    1. Neuroscience

    Multi-day neuron tracking in high-density electrophysiology recordings using earth mover’s distance

    Augustine Xiaoran Yuan, Jennifer Colonell ... Timothy D Harris
    Neurons can be tracked in mice implanted with Neuropixels 2.0 probes for up to 8 weeks using visual receptive fields to score tracking in the absence of reference data.
    1. Neuroscience

    Machine learning of dissection photographs and surface scanning for quantitative 3D neuropathology

    Harshvardhan Gazula, Henry FJ Tregidgo ... Juan E Iglesias
    New open-source software enables, for the first time, extraction of quantitative information from brain dissection photographs that are routinely taken at brain banks for archiving purposes but otherwise not exploited.