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Page 3 of 277
    1. Computational and Systems Biology
    2. Chromosomes and Gene Expression

    Stochastic modelling, Bayesian inference, and new in vivo measurements elucidate the debated mtDNA bottleneck mechanism

    Iain G Johnston, Joerg P Burgstaller ... Nick S Jones
    New modelling, statistics, and experiments show that cellular populations of mitochondrial DNA (mtDNA) evolve during development according to solvable stochastic dynamics involving binomial partitioning and random turnover, facilitating a predictive and quantitative theory of the mtDNA bottleneck.
    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. Epidemiology and Global Health

    Collider bias and the apparent protective effect of glucose-6-phosphate dehydrogenase deficiency on cerebral malaria

    James A Watson, Stije J Leopold ... Nicholas J White
    Selection bias, also known as collider bias, likely explains the apparent protective effect of G6PD deficiency against cerebral falciparum malaria.
    1. Neuroscience

    Towards biologically plausible phosphene simulation for the differentiable optimization of visual cortical prostheses

    Maureen van der Grinten, Jaap de Ruyter van Steveninck ... Yağmur Güçlütürk
    The provided framework based on biological models and clinical literature can aid in the optimization of visual cortical prostheses through computational or behavioral simulation experiments, serving as a flexible tool for computational, clinical, and behavioral neuroscientists working on visual neuroprosthetics.
    1. Evolutionary Biology
    2. Genetics and Genomics

    Mutation saturation for fitness effects at human CpG sites

    Ipsita Agarwal, Molly Przeworski
    Methylated CpG sites are saturated for T mutations in a sample of 390K human exomes, providing a test case for inferences about fitness effects in human genes, and insight into the interpretation of mutations as pathogenic using reference datasets.
    1. Physics of Living Systems

    How enzymatic activity is involved in chromatin organization

    Rakesh Das, Takahiro Sakaue ... Tetsuya Hiraiwa
    Computer simulations considering actions of the intranuclear enzyme, Topoisomerase-II, in a mechanistic scheme elucidated a capability of enzymes to contribute to controlling chromatin spatial organizations and discovered new characteristic features in eu- and heterochromatin organization caused by the enzymatic activity.
    1. Computational and Systems Biology
    2. Genetics and Genomics

    Spotless, a reproducible pipeline for benchmarking cell type deconvolution in spatial transcriptomics

    Chananchida Sang-aram, Robin Browaeys ... Yvan Saeys
    Estimating cell type composition from a gene expression mixture remains a challenging task, as evidenced by how a simple regression model outperforms many state-of-the-art spatial deconvolution methods.
    1. Microbiology and Infectious Disease
    2. Physics of Living Systems

    Spatial modulation of individual behaviors enables an ordered structure of diverse phenotypes during bacterial group migration

    Yang Bai, Caiyun He ... Xiongfei Fu
    Bacterial population can coordinate individuals of different phenotypes by spatial modulation of their run-and-tumble behaviors, resulting in collective group migration with an ordered structure of phenotypes.
    1. Neuroscience

    A unified internal model theory to resolve the paradox of active versus passive self-motion sensation

    Jean Laurens, Dora E Angelaki
    Central vestibular regions in the brainstem and cerebellum perform dynamic Bayesian inference to combine motor commands and sensory signals into an optimal estimate of self-motion.
    1. Computational and Systems Biology
    2. Neuroscience

    Interrogating theoretical models of neural computation with emergent property inference

    Sean R Bittner, Agostina Palmigiano ... John Cunningham
    Emergent property inference, a novel machine learning methodology, learns distributions of neural circuit model parameters that produce computational properties and provides novel scientific insight through the quantification of the rich parametric structure it captures.