707 results found
    1. Computational and Systems Biology

    Sensitive remote homology search by local alignment of small positional embeddings from protein language models

    Sean R Johnson, Meghana Peshwa, Zhiyi Sun
    Protein language deep learning models can quickly and accurately translate amino acid sequences into profile hidden Markov models or a structure alphabet, dramatically improving remote homology search sensitivity without compromising space or time efficiency.
    1. Neuroscience

    anTraX, a software package for high-throughput video tracking of color-tagged insects

    Asaf Gal, Jonathan Saragosti, Daniel JC Kronauer
    anTraX is an algorithm and software package that facilitates automated analyses of insect social behavior in species and experimental settings that are not accessible with currently existing technology.
    1. Computational and Systems Biology
    2. Neuroscience

    Graphical-model framework for automated annotation of cell identities in dense cellular images

    Shivesh Chaudhary, Sol Ah Lee ... Hang Lu
    Unbiased and automatic annotation using structured prediction framework with efficiently built data-driven atlases is more accurate than registration-based methods for cell identifications in dense images and enables fast whole-brain analysis.
    1. Neuroscience

    Spinal premotor interneurons controlling antagonistic muscles are spatially intermingled

    Remi Ronzano, Sophie Skarlatou ... Marco Beato
    Multiple trans-synaptic tracing methods reveal that there is no spatial segregation between flexor and extensor premotor interneurons in the lumbar spinal cord.
    1. Developmental Biology
    2. Stem Cells and Regenerative Medicine

    Epithelial geometry regulates spindle orientation and progenitor fate during formation of the mammalian epidermis

    Kimberly Box, Bradley W Joyce, Danelle Devenport
    Early in mammalian epidermal development, basal epidermal progenitor cells utilize packing and three-dimensional geometry, rather than cortical polarity cues, to inform division orientation and progenitor cell fate.
    1. Microbiology and Infectious Disease
    2. Physics of Living Systems

    High-throughput imaging and quantitative analysis uncovers the nature of plasmid positioning by ParABS

    Robin Köhler, Eugen Kaganovitch, Seán M Murray
    The ParABS system positions plasmids precisely within the cell but just below the threshold for oscillatory dynamics.
    1. Computational and Systems Biology
    2. Ecology

    TRex, a fast multi-animal tracking system with markerless identification, and 2D estimation of posture and visual fields

    Tristan Walter, Iain D Couzin
    Being fast, memory efficient, easy to use, and with powerful integrated tools, TRex will lower barriers of entry into, and enable more ambitious approaches to, the quantitative study of behavior.
    1. Developmental Biology

    Multi-view light-sheet imaging and tracking with the MaMuT software reveals the cell lineage of a direct developing arthropod limb

    Carsten Wolff, Jean-Yves Tinevez ... Anastasios Pavlopoulos
    Quantitative analyses of multi-dimensional microscopy datasets with a new Fiji/ImageJ plugin for cell tracking reveal the lineage restrictions and morphogenetic cellular behaviors underlying embryonic limb outgrowth in the direct developing crustacean Parhyale hawaiensis.
    1. Neuroscience

    Visual pursuit behavior in mice maintains the pursued prey on the retinal region with least optic flow

    Carl D Holmgren, Paul Stahr ... Jason ND Kerr
    Digital reconstruction of environment combined with eye and head-tracking enabled the process of prey-detection and capture to be seen from the freely moving mouse’s point-of-view and shows the exact visual-field and retinal location mice use when chasing prey and the advantage.
    1. Neuroscience
    2. Physics of Living Systems

    Fast deep neural correspondence for tracking and identifying neurons in C. elegans using semi-synthetic training

    Xinwei Yu, Matthew S Creamer ... Andrew M Leifer
    A deep neural network trained on semi-synthetic data learns to quickly track and identify neurons in Caenorhabditis elegans.

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