Browse our latest Computational and Systems Biology articles

Page 14 of 121
    1. Chromosomes and Gene Expression
    2. Computational and Systems Biology

    DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci

    Yuzhen Liu, Christopher D McGann ... Devin K Schweppe
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Solid
    • Incomplete
    1. Chromosomes and Gene Expression
    2. Computational and Systems Biology

    Large-scale analysis of the integration of enhancer-enhancer signals by promoters

    Miguel Martinez-Ara, Federico Comoglio, Bas van Steensel
    A high-throughput enhancer-enhancer-promoter reporter assay indicates that pairs of enhancers generally activate promoters in a near-additive manner, and that promoters transform their collective effect non-linearly.
    1. Computational and Systems Biology
    2. Genetics and Genomics

    DGRPool, a web tool leveraging harmonized Drosophila Genetic Reference Panel phenotyping data for the study of complex traits

    Vincent Gardeux, Roel PJ Bevers ... Bart Deplancke
    The DGRPool web tool aggregates phenotyping data from the Drosophila Genetic Reference Panel, streamlining genetic association studies and offering new insights into genetic and phenotypic variation in complex traits.
    1. Computational and Systems Biology
    2. Genetics and Genomics

    A metabolic modeling-based framework for predicting trophic dependencies in native rhizobiomes of crop plants

    Alon Avraham Ginatt, Maria Berihu ... Shiri Freilich
    Understanding metabolic interactions and successive cross-feeding in native microbiomes illuminates the mechanisms behind plant disease promotion and suppression, enhancing our ability to manipulate microbiomes toward specific functions of interest.
    1. Computational and Systems Biology
    2. Neuroscience

    White matter structural bases for phase accuracy during tapping synchronization

    Pamela Garcia-Saldivar, Cynthia de León ... Hugo Merchant
    Comparison between tapping performance of humans during a synchronization task and new metrics that characterize the U-fiber system of white matter revealed large intersubject correlations between phase accuracy at specific tempos and the strength of connectivity in their audiomotor system.
    1. Computational and Systems Biology
    2. Neuroscience

    Supercomputer framework for reverse engineering firing patterns of neuron populations to identify their synaptic inputs

    Matthieu K Chardon, Y Curtis Wang ... Charles J Heckman
    Estimating the organization of supraspinal input to motoneurons in humans is not currently possible, but a promising reverse engineering technique has been developed using large-scale supercomputing and computational neuroscience.
    1. Computational and Systems Biology
    2. Physics of Living Systems

    Light-driven synchronization of optogenetic clocks

    Maria Cristina Cannarsa, Filippo Liguori ... Roberto Di Leonardo
    Introducing the optorepressilator, a synthetic genetic oscillator that can be synchronized, entrained, and detuned by green light to precisely control periodic gene expression in single cells or entire bacterial populations.
    1. Computational and Systems Biology
    2. Cancer Biology

    Is tumor mutational burden predictive of response to immunotherapy?

    Carino Gurjao, Dina Tsukrov ... Leonid A Mirny
    Revised
    Reviewed Preprint v2
    Updated
    • Useful
    • Solid
    1. Computational and Systems Biology

    Systems analysis of miR-199a/b-5p and multiple miR-199a/b-5p targets during chondrogenesis

    Krutik Patel, Matt Barter ... Daryl P Shanley
    A multi-disciplined approach uncovered microRNA-199a/b-5p as important regulators of chondrogenesis, which negatively regulate mRNAs such as FZD6, ITGA3, and CAV1 for protective purposes during chondrogenesis.
    1. Computational and Systems Biology
    2. Microbiology and Infectious Disease

    Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data

    Michael B Hall, Ryan R Wick ... Lachlan Coin
    Nanopore sequencing effectively resolves key challenges in bacterial small variant detection, providing a more accurate alternative to traditional sequencing methods.