Browse our Tools and Resources

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    1. Computational and Systems Biology
    2. Developmental Biology

    Constructing and optimizing 3D atlases from 2D data with application to the developing mouse brain

    David M Young, Siavash Fazel Darbandi ... Stephan J Sanders
    A computational tool developed to construct three-dimensional anatomical atlases from two-dimensional data generates volumetrically complete and aligned atlases for all stages of development in the Allen Developing Mouse Brain Atlas.
    1. Neuroscience

    Exposing distinct subcortical components of the auditory brainstem response evoked by continuous naturalistic speech

    Melissa J Polonenko, Ross K Maddox
    The response from discrete stages of the early auditory pathway can be measured by subtle manipulations to long-form natural speech stimuli paired with deconvolution analysis of electroencephalography data.
    1. Cell Biology

    One-shot analysis of translated mammalian lncRNAs with AHARIBO

    Luca Minati, Claudia Firrito ... Massimiliano Clamer
    Detection of translated lncRNAs through selective isolation of active ribosomes, ribosome-associated RNAs and corresponding de novo synthesised peptides.
    1. Developmental Biology
    2. Genetics and Genomics

    Precise base editing for the in vivo study of developmental signaling and human pathologies in zebrafish

    Marion Rosello, Juliette Vougny ... Filippo Del Bene
    Base editors, with improved specificity and expanded PAM sequence recognition, can be used in zebrafish for the rapid and efficient introduction of single base pair mutations.
    1. Cancer Biology
    2. Computational and Systems Biology

    shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data

    Kenichi Shimada, John A Bachman ... Timothy J Mitchison
    shinyDepMap helps users explore the essentiality, selectivity, and function of the genes across hundreds of cancer cell lines and identify cancer drug targets.
    1. Physics of Living Systems
    2. Stem Cells and Regenerative Medicine

    Global and local tension measurements in biomimetic skeletal muscle tissues reveals early mechanical homeostasis

    Arne D Hofemeier, Tamara Limon ... Timo Betz
    Combining global and local force measurements of reconstituted muscle tissue using a new chamber system that is compatible with high-resolution microscopy shows mechanical homeostasis already within a week.
    1. Biochemistry and Chemical Biology

    Identification of host proteins differentially associated with HIV-1 RNA splice variants

    Rachel Knoener, Edward Evans III ... Lloyd M Smith
    The distinct protein-RNA interactomes of HIV-1 RNA splice forms are revealed using a powerful multiplex strategy for RNA capture and mass spectrometric analysis.
    1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    A nuclease- and bisulfite-based strategy captures strand-specific R-loops genome-wide

    Phillip Wulfridge, Kavitha Sarma
    BisMapR reveals strand-specific R-loops with high resolution at small-scale genomic features including bidirectionally transcribed promoters and enhancers.
    1. Cell Biology

    In vivo proteomic mapping through GFP-directed proximity-dependent biotin labelling in zebrafish

    Zherui Xiong, Harriet P Lo ... Thomas E Hall
    BLITZ system enables proximity-dependent biotin labelling in live zebrafish embryos with cell and tissue specificity, providing a versatile and valuable tool for proteomic discovery using the zebrafish model.
    1. Ecology

    A remote sensing derived data set of 100 million individual tree crowns for the National Ecological Observatory Network

    Ben G Weinstein, Sergio Marconi ... Ethan P White
    A first continental data set of tree crown predictions is derived across the United States for the National Ecological Observatory Network.