1,487 results found
    1. Neuroscience

    Stability of neocortical synapses across sleep and wake states during the critical period in rats

    Brian A Cary, Gina G Turrigiano
    Sleep and wake states are not sufficient to drive changes in neocortical synaptic strengths.
    1. Computational and Systems Biology
    2. Chromosomes and Gene Expression

    NF-κB oscillations translate into functionally related patterns of gene expression

    Samuel Zambrano, Ilario De Toma ... Alessandra Agresti
    NF-κB oscillations synchronize to external perturbations as a damped oscillator, producing different transcription dynamics.
    1. Cancer Biology
    2. Computational and Systems Biology

    Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data

    Aurélie Anne-Gaëlle Gabriel, Julien Racle ... David Gfeller
    EPIC-ATAC accurately quantifies cell-type heterogeneity in tumor bulk ATAC-Seq samples using reliable cell-type specific chromatin accessibility markers for the major cell types found in tumor microenvironments.
    1. Neuroscience

    Interactions between circuit architecture and plasticity in a closed-loop cerebellar system

    Hannah L Payne, Jennifer L Raymond, Mark S Goldman
    A comprehensive modeling approach reconciles experimental observations with classic plasticity mechanisms in the cerebellar cortex, demonstrating how learning-related changes in neural activity can appear to contradict the sign of the underlying plasticity when feedback is present.
    1. Computational and Systems Biology
    2. Physics of Living Systems

    Combining mutation and recombination statistics to infer clonal families in antibody repertoires

    Natanael Spisak, Gabriel Athènes ... Aleksandra M Walczak
    HILARy is a new algorithm for grouping B-cell receptor sequences into distinct lineages, a crucial task to analyze immune response and memory through repertoire sequencing.
    1. Computational and Systems Biology

    Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species

    Arnaud Belcour, Clémence Frioux ... Anne Siegel
    Computational models and software connect metagenomics to metabolic network reconstruction, assess metabolic complementarity between species, and identify critical species associated to functions of interest.
    1. Cell Biology
    2. Structural Biology and Molecular Biophysics

    Molecular determinants of large cargo transport into the nucleus

    Giulia Paci, Tiantian Zheng ... Edward A Lemke
    Efficient nuclear transport of very large biomolecules, relevant for viral transport, scales non-linearly with size and its kinetics can be explained by a simple two-parameter energetic model.
    1. Chromosomes and Gene Expression

    Nup98-dependent transcriptional memory is established independently of transcription

    Pau Pascual-Garcia, Shawn C Little, Maya Capelson
    Transcription and epigenetic memory of transcription are two co-occurring independent pathways, governed by different rate constants and unique parameters.
    1. Cell Biology
    2. Physics of Living Systems

    Bridging the gap between single-cell migration and collective dynamics

    Florian Thüroff, Andriy Goychuk ... Erwin Frey
    A computational model, based on single-cell features like contractility and polarizability, quantitatively describes cellular dynamics from the single cell level up to small cohorts and confluent tissues.
    1. Computational and Systems Biology
    2. Evolutionary Biology

    Quantifying microbial fitness in high-throughput experiments

    Justus Wilhelm Fink, Michael Manhart
    Not revised
    Reviewed Preprint v1
    • Important
    • Solid

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