Browse our Tools and Resources

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    1. Computational and Systems Biology
    2. Stem Cells and Regenerative Medicine

    Self-assembling manifolds in single-cell RNA sequencing data

    Alexander J Tarashansky, Yuan Xue ... Bo Wang
    An iterative self-assembling algorithm identifies the intrinsic structures in single-cell transcriptomic data and helps to discover new cell populations that are undetectable by existing methods.
    1. Cell Biology
    2. Neuroscience

    Implementation of an antibody characterization procedure and application to the major ALS/FTD disease gene C9ORF72

    Carl Laflamme, Paul M McKeever ... Peter S McPherson
    An easy-to-implement antibody validation pipeline addresses the reproducibility crisis resulting from the use of non-specific antibodies.
    1. Plant Biology

    Proximity labeling of protein complexes and cell-type-specific organellar proteomes in Arabidopsis enabled by TurboID

    Andrea Mair, Shou-Ling Xu ... Dominique C Bergmann
    Proximity-labeling using engineered biotin ligases TurboID and miniTurbo enables detection of cell-type-specific and low abundance protein complexes and subcellular proteomes in Arabidopsis and other plants.
    1. Microbiology and Infectious Disease

    Transcriptome dynamics of the Myxococcus xanthus multicellular developmental program

    José Muñoz-Dorado, Aurelio Moraleda-Muñoz ... Juana Pérez
    Investigation of global gene expression profiles during formation of the Myxococcus xanthus specialized biofilm reveals a genetic regulatory network that coordinates cell motility, differentiation, and secondary metabolite production.
    1. Neuroscience

    Brian 2, an intuitive and efficient neural simulator

    Marcel Stimberg, Romain Brette, Dan FM Goodman
    Brian 2 is a software package for neural simulations that makes it both easy and computationally efficient to define original models for computational experiment.
    1. Neuroscience

    A toolbox of nanobodies developed and validated for use as intrabodies and nanoscale immunolabels in mammalian brain neurons

    Jie-Xian Dong, Yongam Lee ... James S Trimmer
    Nanobodies are developed that target neuronal proteins with restricted subcellular distributions and used as intrabodies to deliver cargo to specific sites within neurons and nanoscale immunolabels for improved imaging resolution.
    1. Neuroscience

    An arbitrary-spectrum spatial visual stimulator for vision research

    Katrin Franke, André Maia Chagas ... Thomas Euler
    Towards a community effort, we here present a flexible yet standardised visual stimulator design based on open hardware and software.
    1. Genetics and Genomics
    2. Neuroscience

    A scalable platform for the development of cell-type-specific viral drivers

    Sinisa Hrvatin, Christopher P Tzeng ... Michael E Greenberg
    Highly paralleled functional evaluation of enhancer activity in single cells generates new cell-type-specific tools with broad medical and scientific applications.
    1. Neuroscience

    Long-term adult human brain slice cultures as a model system to study human CNS circuitry and disease

    Niklas Schwarz, Betül Uysal ... Henner Koch
    Viral transduction and gene manipulation of adult human brain slices will be of great value allowing investigations including therapeutic screening, electrophysiological and structural studies of properties of human CNS circuitry.
    1. Computational and Systems Biology
    2. Immunology and Inflammation

    Deep generative models for T cell receptor protein sequences

    Kristian Davidsen, Branden J Olson ... Frederick A Matsen IV
    Deep learning improves estimation of T cell receptor cohort frequencies and learns the rules of VDJ recombination, potentially making it helpful for vaccine design.