Computational models articles within Nature Communications

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  • Article
    | Open Access

    Interrelating metabolites by their fragmentation spectra is central to metabolomics. Here the authors align fragmentation spectra with both statistical significance and allowance for multiple chemical differences using Significant Interrelation of MS/MS Ions via Laplacian Embedding (SIMILE).

    • Daniel G. C. Treen
    • , Mingxun Wang
    •  & Benjamin P. Bowen

  • Article
    | Open Access

    The app-based COVID Symptom Study was launched in Sweden in April 2020 to contribute to real-time COVID-19 surveillance using daily symptom reports from study participants. Here, the authors show how syndromic surveillance can be used to estimate regional COVID-19 prevalence and to predict later COVID-19 hospital admissions.

    • Beatrice Kennedy
    • , Hugo Fitipaldi
    •  & Tove Fall

  • Article
    | Open Access

    Identifying effective drug combinations to treat cancer is a challenging task, either experimentally or computationally. Here, the authors develop a bipartite network modelling approach to propose drug combination strategies in acute myeloid leukaemia using patient and cell line drug screening data.

    • Mohieddin Jafari
    • , Mehdi Mirzaie
    •  & Jing Tang

  • Article
    | Open Access

    The design of feedback biomolecular controllers is essential to synthetically regulate biological processes in a robust and timely fashion. Here the authors introduce a wide array of biomolecular Proportional-Integral-Derivative (PID) controllers that are capable of enhancing stability and dynamic performance, and also reducing stochastic noise.

    • Maurice Filo
    • , Sant Kumar
    •  & Mustafa Khammash

  • Article
    | Open Access

    While large-scale 3D genome architecture is well studied, the limits of resolution have hindered our understanding on the fine scale. Here the authors mapped 1D epigenomic profiles to fine-scale 3D chromatin structures with their deep learning model CAESAR. The model predicted fine-scale structures, such as short-range chromatin loops and stripes, that Hi-C datasets fail to detect.

    • Fan Feng
    • , Yuan Yao
    •  & Jie Liu

  • Article
    | Open Access

    Here the authors introduce Cellar, an interactive webserver for analyzing single-cell omics data. They show that Cellar supports all aspects of the analysis and modeling process and can be used to integrate different types of single cell omics and spatial data.

    • Euxhen Hasanaj
    • , Jingtao Wang
    •  & Ziv Bar-Joseph

  • Article
    | Open Access

    "Representation learning plays an increasing role in protein sequence analysis. This paper seeks to clarify how to ensure that such representations are meaningful, proposing best practices both for the choice of methods and the subsequence analysis

    • Nicki Skafte Detlefsen
    • , Søren Hauberg
    •  & Wouter Boomsma

  • Article
    | Open Access

    The rapid temperature drop during plunge-freezing affects the structural ensembles obtained by cryo-EM. To quantify the extent of perturbation, Bock and Grubmüller combined continuum calculations, MD simulations, and kinetic models.

    • Lars V. Bock
    •  & Helmut Grubmüller

  • Article
    | Open Access

    Serological classification of influenza infection has classically been based on a four-fold or higher increase in antibody levels, but this approach may not be optimal. Here, the authors develop a Bayesian model to improve identification of infections in serological samples by accounting for individual antibody dynamics.

    • Tim K. Tsang
    • , Ranawaka A. P. M. Perera
    •  & Simon Cauchemez

  • Article
    | Open Access

    Gambiense human African trypanosomiasis (sleeping sickness or gHAT) has been targeted for elimination of transmission by 2030. Here, the authors project impacts of gHAT interventions in the Democratic Republic of the Congo and derive a priority list of health zones requiring enhanced control to achieve this target.

    • Ching-I Huang
    • , Ronald E. Crump
    •  & Kat S. Rock

  • Article
    | Open Access

    The authors use an agent-based model to investigate the potential of reactive vaccination strategies for COVID-19 outbreak mitigation. They find that distributing vaccines in schools and workplaces where cases are detected is more impactful than non-reactive strategies in a wide range of epidemic scenarios.

    • Benjamin Faucher
    • , Rania Assab
    •  & Chiara Poletto

  • Article
    | Open Access

    Cas9 off-target sites can be predicted by many bioinformatics tools. Here the authors present low complexity mechanistic model that characterizes SpCas9 kinetics in free-energy terms, allowing quantitative prediction of off-target activity in bulk-biochemistry, single molecule, and whole-genome profiling experiments.

    • Behrouz Eslami-Mossallam
    • , Misha Klein
    •  & Martin Depken

  • Article
    | Open Access

    Mitochondrial variants are informative endogenous barcodes for clonal substructure. Here, the authors developed a computational method MQuad to effectively detect these clonal informed mtDNA variants from single-cell RNA, DNA or ATAC sequencing data.

    • Aaron Wing Cheung Kwok
    • , Chen Qiao
    •  & Yuanhua Huang

  • Article
    | Open Access

    Morphogen gradients encode positional information during development. Here the authors use theory and simulations to suggest a positional accuracy of single gradients that directly explains the observed precision of progenitor domain boundaries.

    • Roman Vetter
    •  & Dagmar Iber

  • Article
    | Open Access

    Twice weekly mass testing using lateral flow tests has helped to control pupil-to-pupil transmission in English secondary schools. Here, the authors show that repeat testing of contacts alongside mass testing could greatly reduce absences with only a marginal increase in transmission, compared to isolating contacts.

    • Trystan Leng
    • , Edward M. Hill
    •  & Louise Dyson

  • Article
    | Open Access

    Gene fusions are an important class of mutations in tumor genomes. Here, the authors develop a single-cell gene fusion detection method scFusion and demonstrate its applications in cancer single-cell studies.

    • Zijie Jin
    • , Wenjian Huang
    •  & Ruibin Xi

  • Article
    | Open Access

    Randomized clinical trials are often plagued by selection bias, and expert-selected covariates may insufficiently adjust for confounding factors. Here, the authors develop a framework based on natural language processing to uncover interpretable potential confounders from text.

    • Jiaming Zeng
    • , Michael F. Gensheimer
    •  & Ross D. Shachter

  • Article
    | Open Access

    Population density can influence the dynamics of emerging infections, but the specific effects at a local (within-city) level are not well understood. Here, the authors investigate the influence of population density on dynamics of dengue outbreaks in Rio de Janeiro and propose that this variable holds the key to how space should be aggregated.

    • Victoria Romeo-Aznar
    • , Laís Picinini Freitas
    •  & Mercedes Pascual

  • Article
    | Open Access

    The tumour microenvironment counteracts immune therapy in Glioblastomas. Authors show here, using spatially resolved and single cell transcriptomics, that dysfunctional T cells are induced by a myeloid cell subset via Interleukin-10 signalling, and inhibition of the downstream JAK/STAT pathway might restore glioblastoma immune therapy responsiveness.

    • Vidhya M. Ravi
    • , Nicolas Neidert
    •  & Dieter Henrik Heiland

  • Article
    | Open Access

    Metabolically active organelles compete for cytosolic space and resources during metabolism rewiring. Here, the authors develop a computational model of yeast metabolism and resource allocation to predict condition- and compartment-specific proteome constraints that govern metabolic strategies.

    • Ibrahim E. Elsemman
    • , Angelica Rodriguez Prado
    •  & Bas Teusink

  • Article
    | Open Access

    Genetic associations can be biased by conditioning on a phenotype. This study presents ‘Slope-Hunter’, a method which uses model-based clustering to correct this bias, even in the presence of genetic correlation, assuming the class of SNPs affecting only the collider explains more variation in the collider than any other class of SNPs.

    • Osama Mahmoud
    • , Frank Dudbridge
    •  & Kate Tilling

  • Article
    | Open Access

    The sequence determinants governing CRISPR/Cas9 specificity are not fully understood. Here, the authors devise a high-throughput dual-target synthetic system to explore the sequence features associated with CRISPR/Cas9 off-target effect, reveal a set of sequence-dependent rules, and develop an off-target prediction model and a strategy for Cas9-based allele-specific editing.

    • Rongjie Fu
    • , Wei He
    •  & Han Xu

  • Article
    | Open Access

    Reactive school class closures have been widely implemented to mitigate COVID-19 outbreaks. Here, the authors show that, compared to symptom-prompted PCR testing, screening for cases in schools with antigen tests leads to greater reductions in infection rates in both students and the wider community.

    • Quan-Hui Liu
    • , Juanjuan Zhang
    •  & Marco Ajelli

  • Article
    | Open Access

    Understanding the pharmacokinetics of locally-injected drugs could aid in the design of immunotherapies to maximize their therapeutic effect. Here, by evaluating different IL-2 fusion proteins, the authors show that molecular weight and matrix binding affect anti-tumor immune response and report a pharmacokinetic framework to predict response to intratumoral IL-2 therapy.

    • Noor Momin
    • , Joseph R. Palmeri
    •  & K. Dane Wittrup

  • Article
    | Open Access

    Face-selective neurons are observed in the primate visual pathway and are considered as the basis of face detection in the brain. Here, using a hierarchical deep neural network model of the ventral visual stream, the authors suggest that face selectivity arises in the complete absence of training.

    • Seungdae Baek
    • , Min Song
    •  & Se-Bum Paik

  • Article
    | Open Access

    Vaccination campaigns against COVID-19 are allowing the progressive release of physical distancing restrictions in many countries. Here, the authors assess the impact of the vaccination program in Italy and evaluate possible prospects for reopening the society while at the same time keeping COVID-19 under control.

    • Valentina Marziano
    • , Giorgio Guzzetta
    •  & Stefano Merler

  • Article
    | Open Access

    In this study, Tran Kiem et al. examine the contribution of different age groups to COVID-19 transmission. Using data from the French epidemic in summer 2020, they report that while individuals aged 80 years and older are more at risk, pandemic control in the absence of vaccines required measures targeted at all age groups.

    • Cécile Tran Kiem
    • , Paolo Bosetti
    •  & Simon Cauchemez

  • Article
    | Open Access

    Simulation is useful for developing and evaluating computational methods. Here, the authors develop a comprehensive evaluation framework, SimBench, to benchmark Single-cell RNA-seq simulation methods through a diverse collection of experimental datasets.

    • Yue Cao
    • , Pengyi Yang
    •  & Jean Yee Hwa Yang

  • Article
    | Open Access

    One might think that complete extinction of a virulent pathogen is the most effective way of saving a population. For a bacteria-phage system, Skanata and Kussell show that sustaining a minimum pathogen level is actually favorable to prevent a complete loss of immunity in the long run.

    • Antun Skanata
    •  & Edo Kussell

  • Article
    | Open Access

    Associations have been established between brain folding and white matter connectivity. Here the authors show that axon elongation, in response to mechanical stresses during cortical expansion and folding, may be sufficient to induce tissue remodeling consistent with white matter organization.

    • Kara E. Garcia
    • , Xiaojie Wang
    •  & Christopher D. Kroenke

  • Article
    | Open Access

    Bacterial biofilms exhibit complex spatiotemporal pattern formation. Here the authors report a collective cell reorientation cascade in growing Vibrio cholerae biofilms that leads to a differentially ordered, spatiotemporally coupled core-rim structure.

    • Japinder Nijjer
    • , Changhao Li
    •  & Jing Yan

  • Article
    | Open Access

    Nanopore sequencing allows users to identify nucleotide sequence from ionic currents. Here, the authors use deep learning to facilitate the de novo identification of modified nucleotides, particularly methylated cytosine and guanine, from the measured ionic currents without the need for controls.

    • Hongxu Ding
    • , Ioannis Anastopoulos
    •  & Benedict Paten

  • Article
    | Open Access

    Despite the clear causal relationship between genotype and phenotype in rare diseases, identifying the pathobiological mechanisms at various levels of biological organization remains a practical and conceptual challenge. Here, the authors introduce a network approach for evaluating the impact of rare gene defects across biological scales.

    • Pisanu Buphamalai
    • , Tomislav Kokotovic
    •  & Jörg Menche

  • Article
    | Open Access

    The ChAdOx1 nCoV-19 vaccine requires two doses, but under limited supply single dose regimens have also been considered. Here, the authors show using static transmission modelling that under certain conditions it is optimal to more expediently administer a single dose to a larger proportion of the population.

    • Ricardo Aguas
    • , Anouska Bharath
    •  & Rima Shretta

  • Article
    | Open Access

    Generative models have become increasingly popular in protein design, yet rigorous metrics that allow the comparison of these models are lacking. Here, the authors propose a set of such metrics and use them to compare three popular models.

    • Francisco McGee
    • , Sandro Hauri
    •  & Allan Haldane

  • Article
    | Open Access

    The timely hepatitis B birth dose vaccination is recommended for all new-borns by the WHO, but coverage is inconsistent. Here, the authors model the impact of scaling-up coverage in 110 low and middle income countries and assess how it may be affected by delays for example caused by the COVID-19 pandemic.

    • Margaret J. de Villiers
    • , Shevanthi Nayagam
    •  & Timothy B. Hallett

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