Tools and Resources

A Tools and Resources article allows authors to publish the details of new experimental techniques, datasets, software tools, and other resources.

Latest articles

    1. Genetics and Genomics

    Specific modulation of CRISPR transcriptional activators through RNA-sensing guide RNAs in mammalian cells and zebrafish embryos

    Oana Pelea, Sarah Mayes ... Tatjana Sauka-Spengler
    RNA-sensing guide RNAs provide a programmable platform for conditional, sequence-specific activation of CRISPR-Cas9 upon RNA detection in diverse biological contexts.
    1. Neuroscience

    A computational pipeline to track chromatophores and analyze their dynamics

    Johann Ukrow, Mathieu DM Renard ... Gilles Laurent
    Computer code is provided to track the size and shape of deformable pigment cells in the skin of cephalopods from high-resolution video images.
    1. Computational and Systems Biology
    2. Neuroscience

    A SMARTTR workflow for multi-ensemble atlas mapping and brain-wide network analysis

    Michelle Jin, Simon O Ogundare ... Christine Ann Denny
    A new scalable workflow for analyzing multiple ensemble datasets incorporates SMARTTR, an R package supporting network analysis, visualization, and the import of external datasets.
    1. Neuroscience

    Social rank-order stability of mice revealed by a novel food competition paradigm in combination with available space competition paradigms

    Meiqiu Liu, Yue Chen, Rongqing Chen
    Social status of mice in an established colony is stably expressed in several types of competition paradigms, including food and space competitions.
    1. Genetics and Genomics
    2. Neuroscience

    Rapid and inducible mislocalization of endogenous TDP43 in a novel human model of amyotrophic lateral sclerosis

    Johanna Ganssauge, Sophie Hawkins ... Akshay Bhinge
    A novel human iPSC-derived model induces mislocalization of endogenous TDP-43 without mutations or stress, recapitulating key ALS features including deficits in neuronal loss and morphology, splicing errors, and microRNA dysregulation.
    1. Biochemistry and Chemical Biology
    2. Cell Biology

    Decoding protein phosphorylation during oocyte meiotic divisions using phosphoproteomics

    Leonid Peshkin, Enrico maria Daldello ... Catherine Jessus
    A comprehensive resource describes protein abundance and phosphorylation dynamics during Xenopus oocyte maturation, serving as an essential tool for investigating the molecular mechanisms driving meiotic progression.
    1. Neuroscience

    Heron, a Knowledge Graph editor for intuitive implementation of Python-based experimental pipelines

    George Dimitriadis, Ella Svahn ... Athena Akrami
    A Python-based, open source, GUI application for straightforward development and execution of scientific experiments over multiple machines.
    1. Neuroscience

    Inference technique for the synaptic conductances in rhythmically active networks and application to respiratory central pattern generation circuits

    Yaroslav Molkov, Anke Borgmann ... Jeffrey Smith
    A robust method to infer excitatory and inhibitory synaptic conductances from neuronal recordings reveals functional circuit organization in rhythmic networks.
    1. Cell Biology
    2. Neuroscience

    CellSeg3D, Self-supervised 3D cell segmentation for fluorescence microscopy

    Cyril Achard, Timokleia Kousi ... Mackenzie Weygandt Mathis
    Self-supervised deep learning models can accurately perform 3D segmentation of cell nuclei in complex biological tissues, enabling scalable analysis in settings with limited or no ground truth annotations.
    1. Computational and Systems Biology

    Artificial intelligence driven tumor risk stratification from single-cell transcriptomics using phenotype algebra

    Namrata Bhattacharya, Anja Rockstroh ... Debarka Sengupta
    SCellBOW is a language model-based scRNA-seq analysis method that identifies malignant cell subpopulations and infers marker-free survival risks using transfer learning.