Browse our Tools and Resources

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    1. Epidemiology and Global Health

    Using step selection functions to analyse human mobility using telemetry data in infectious disease epidemiology: a case study of leptospirosis

    Pablo Ruiz Cuenca, Fábio N Souza ... Emanuele Giorgi
    Step selection functions are a useful tool for analysing fine-scale human movements to understand environmental interactions in the context of infectious disease epidemiology.
    1. Neuroscience

    Hierarchical Bayesian modeling of multiregion brain cell count data

    Sydney Dimmock, Benjamin MS Exley ... Cian O'Donnell
    Bayesian hierarchical models offer powerful statistical tools for neuroscientists to analyze whole-brain cell count data, as demonstrated here using two example datasets from different laboratories.
    1. Computational and Systems Biology

    Martinize2 and Vermouth provide a unified framework for molecular topology generation

    Peter C Kroon, Fabian Grünewald ... Siewert J Marrink
    Enabling high-throughput simulations of proteins within the Martini framework.
    1. Neuroscience

    A deep learning approach for the analysis of birdsong

    Therese MI Koch, Ethan S Marks, Todd F Roberts
    An open-source deep learning toolkit performs accurate annotation and similarity scoring of zebra finch song, along with comprehensive feature extraction, enabling consistent, interpretable comparisons of vocal phenotypes across research groups.
    1. Computational and Systems Biology

    OpenSpliceAI provides an efficient modular implementation of SpliceAI enabling easy retraining across nonhuman species

    Kuan-Hao Chao, Alan Mao ... Mihaela Pertea
    OpenSpliceAI is an open, retrainable framework for splice site prediction that enables rapid, memory-efficient, cross-species analyses at scale with accuracy comparable to SpliceAI.
    1. Neuroscience

    Longitudinal assessment of DREADD expression and efficacy in the monkey brain

    Yuji Nagai, Yukiko Hori ... Takafumi Minamimoto
    Designer Receptors Exclusively Activated by Designer Drug (DREADD) expression in macaque brains peaks around 2 months after adeno-associated virus injection and remains stable for over a year before gradually declining.
    1. Neuroscience

    Exploring neurodevelopment via spatiotemporal collation of anatomical networks with NeuroSC

    Noelle L Koonce, Sarah E Emerson ... Daniel A Colón-Ramos
    NeuroSC provides an open-source framework for comparative connectomics, integrating neuronal morphologies, contacts, and synapses across developmental stages and datasets.
    1. Neuroscience

    Remote automated delivery of mechanical stimuli coupled to brain recordings in behaving mice

    Justin Burdge, Anissa Jhumka ... Ishmail Abdus-Saboor
    Development of robotic device for pain and somatosensory assays in rodents allows remote, quantitative, and reproducible delivery of mechanical stimuli.
    1. Cancer Biology
    2. Computational and Systems Biology

    BEHAV3D Tumor Profiler to map heterogeneous cancer cell behavior in the tumor microenvironment

    Emilio Rios-Jimenez, Anoek Zomer ... Maria Alieva
    BEHAV3D Tumor Profiler enables researchers without computational expertise to uncover heterogeneous cell behaviors and explore their relationships with microenvironmental features in intravital microscopy data.
    1. Plant Biology

    Structure-guided secretome analysis of gall-forming microbes offers insights into effector diversity and evolution

    Soham Mukhopadhyay, Muhammad Asim Javed ... Edel Perez-Lopez
    Comparative structural genomics identifies unique effector architectures and ankyrin-mediated host targeting, revealing central and conserved strategies that underpin the pathogenicity of diverse gall-forming microbial species across evolutionary lineages.