Computational models articles within Nature Communications

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  • Article
    | Open Access

    Balancing high resolution and broad genome coverage in single-cell Hi-C approaches remains challenging. Here, the authors describe a computational method for the reconstruction of a large 3D-ensemble of single-cell chromatin conformations from population Hi-C measurements and apply this model to study embryogenesis in Drosophila.

    • Qiu Sun
    • , Alan Perez-Rathke
    •  & Jie Liang

  • Article
    | Open Access

    While temperature impacts the function of all cellular components, it’s hard to rule out how the temperature dependence of cell phenotypes emerged from the dependence of individual components. Here, the authors develop a Bayesian genome scale modelling approach to identify thermal determinants of yeast metabolism.

    • Gang Li
    • , Yating Hu
    •  & Jens Nielsen

  • Article
    | Open Access

    Safely reducing the necessary duration of quarantine for COVID-19 could lessen the economic impacts of the pandemic. Here, the authors demonstrate that testing on exit from quarantine is more effective than testing on entry, and can enable quarantine to be reduced from fourteen to seven days.

    • Chad R. Wells
    • , Jeffrey P. Townsend
    •  & Alison P. Galvani

  • Article
    | Open Access

    Computational approaches to predict water’s role in host-ligand binding attract a great deal of attention. Here the authors use a metadynamics enhanced sampling method and machine learning to compute binding energies for host-guest systems from the SAMPL5 challenge and provide details of water structural changes.

    • Valerio Rizzi
    • , Luigi Bonati
    •  & Michele Parrinello

  • Article
    | Open Access

    RNA-sequencing data from tumours can be used to predict the prognosis of patients. Here, the authors show that a neural network meta-learning approach can be useful for predicting prognosis from a small number of samples.

    • Yeping Lina Qiu
    • , Hong Zheng
    •  & Olivier Gevaert

  • Article
    | Open Access

    High numbers of COVID-19-related deaths have been reported in the United States, but estimation of the true numbers of infections is challenging. Here, the authors estimate that on 1 June 2020, 3.7% of the US population was infected with SARS-CoV-2, and 0.01% was infectious, with wide variation by state.

    • H. Juliette T. Unwin
    • , Swapnil Mishra
    •  & Seth Flaxman

  • Article
    | Open Access

    The intrinsically disordered linker histone H1.0 and prothymosin α form a complex which exhibits slow exchange between bound and unbound populations at low protein concentrations and fast exchange at high concentrations. Here authors explain this observation by the formation of transient ternary complexes favored at high protein concentrations that accelerate the exchange.

    • Andrea Sottini
    • , Alessandro Borgia
    •  & Benjamin Schuler

  • Article
    | Open Access

    There is ongoing debate about the effective combination of strategies for COIVD-19 control. Here, the authors use an agent-based model to quantify and compare several intervention strategies, and identify minimal levels of social distancing compliance required to control the epidemic in Australia.

    • Sheryl L. Chang
    • , Nathan Harding
    •  & Mikhail Prokopenko

  • Article
    | Open Access

    Game theory has contributed much to the understanding of social evolution. In an elegant combination of experimental tests and modelling, this study suggests that when bacteria face intense competition, repeated retaliation outcompetes a single tit-for-tat response to attack.

    • William P. J. Smith
    • , Maj Brodmann
    •  & Kevin R. Foster

  • Article
    | Open Access

    The protein translation machinery is the most expensive cellular subsystem in fast growing bacteria. Providing a detailed mechanistic model for this complex system, the authors show that the translation machinery components are expressed such that their combined cost to the cell is minimal.

    • Xiao-Pan Hu
    • , Hugo Dourado
    •  & Martin J. Lercher

  • Article
    | Open Access

    Allele-specific measurements can reveal differences in DNA methylation between homologous alleles associated with changes in genetic sequence. Here, the authors develop a method for detecting allele specific methylation events within haplotypes of linked SNPs, compare it with existing methods, and show it identifies haplotypes for which the genetic variant carries significant information about the methylation state of the allele of origin.

    • J. Abante
    • , Y. Fang
    •  & J. Goutsias

  • Article
    | Open Access

    Correlation network inference is typically based on the significance of the correlation coefficients, but this procedure is not guaranteed to capture biological mechanisms. Here, the authors develop a cutoff selection algorithm that maximizes the overlap between inferred networks and prior knowledge.

    • Elisa Benedetti
    • , Maja Pučić-Baković
    •  & Jan Krumsiek

  • Article
    | Open Access

    An ongoing global debate concerns effective and sustainable lockdown release strategies in the current pandemic. Here, the authors implement a network model at healthcare-relevant spatial scale to show that coordinated local strategies can be effective in containing further resurgence of the disease.

    • Fabio Della Rossa
    • , Davide Salzano
    •  & Mario di Bernardo

  • Article
    | Open Access

    The cellular basis of islet morphogenesis and fate allocation remain unclear. Here, the authors use a R26-CreER-R26R-Confetti mouse line to follow quantitatively the clonal dynamics of islet formation showing how, during the secondary transition, islet progenitors amplify through rounds of stochastic cell division before becoming restricted to α and β cell sublineages.

    • Magdalena K. Sznurkowska
    • , Edouard Hannezo
    •  & Benjamin D. Simons

  • Article
    | Open Access

    How to design experiments that accelerate knowledge discovery on complex biological landscapes remains a tantalizing question. Here, the authors present OPEX, an optimal experimental design method to identify informative omics experiments for both experimental space exploration and model training.

    • Xiaokang Wang
    • , Navneet Rai
    •  & Ilias Tagkopoulos

  • Article
    | Open Access

    COVID-19-related travel restrictions were imposed in China around the same time as major annual holiday migrations, with unknown combined impacts on mobility patterns. Here, the authors show that restructuring of the travel network in response to restrictions was temporary, whilst holiday-related travel increased pressure on healthcare services with lower capacity.

    • Hamish Gibbs
    • , Yang Liu
    •  & Rosalind M. Eggo

  • Article
    | Open Access

    Early stages of the novel coronavirus disease (COVID-19) have been associated with silent hypoxia and poor oxygenation despite relatively small fractions of afflicted lung. Here, the authors present a mathematical model which reproduces the vascular pulmonary mechanisms observed in patients with early COVID-19.

    • Jacob Herrmann
    • , Vitor Mori
    •  & Béla Suki

  • Article
    | Open Access

    Polycomb (PcG) and Trithorax (TrxG) group regulate several hundred target genes with important roles in development and disease. Here the authors combine experiment and theory to provide evidence that the Polycomb/Trithorax system has the potential for a rich repertoire of regulatory modes beyond simple epigenetic memory.

    • Jeannette Reinig
    • , Frank Ruge
    •  & Leonie Ringrose

  • Article
    | Open Access

    There is a great interest in retrieving functional pathways from cryo-EM single-particle data. Here, the authors present an approach that combines cryo-EM with advanced data-analytical methods and molecular dynamics simulations to reveal the functional pathways traversed on experimentally derived energy landscapes using the ryanodine receptor type 1 as an example.

    • Ali Dashti
    • , Ghoncheh Mashayekhi
    •  & Abbas Ourmazd

  • Article
    | Open Access

    The discovery of interventions that slow aging could be accelerated by employing non-invasive biometrics that predict biological age or life expectancy. Here the authors use longitudinal frailty data from naturally aging mice to develop two such tools, that are responsive to interventions.

    • Michael B. Schultz
    • , Alice E. Kane
    •  & David A. Sinclair

  • Article
    | Open Access

    Currently, the frequencies of drug side effects are determined in randomised controlled clinical trials. Here the authors develop an interpretable machine learning approach to predict the frequencies of unknown side effects for drugs with a small number of determined side effect frequencies.

    • Diego Galeano
    • , Shantao Li
    •  & Alberto Paccanaro

  • Article
    | Open Access

    In rodent models of type 2 diabetes, sustained remission of hyperglycemia can be induced by FGF1 action in the mediobasal hypothalamus. Here, the authors show that FGF1-injection is followed by marked changes in glial cell populations and that the sustained glycemic response is dependent on intact melanocortin signaling.

    • Marie A. Bentsen
    • , Dylan M. Rausch
    •  & Tune H. Pers

  • Article
    | Open Access

    The correct identification of copy-number aberrations (CNAs) in tumours can provide information for diagnosis, prognosis and therapeutic strategies. Here, the authors provide an algorithm, HATCHet, which quantifies CNAs using multiple samples from the same patient, providing more accurate information than studying one sample alone.

    • Simone Zaccaria
    •  & Benjamin J. Raphael

  • Article
    | Open Access

    Metastatic melanoma is associated with a poor prognosis and understanding the genetic features of metastases may enable better treatment strategies. Here, the authors analyse multiple metastases from individual patients finding high levels of heterogeneity in metastases from different organs.

    • Roy Rabbie
    • , Naser Ansari-Pour
    •  & David J. Adams

  • Perspective
    | Open Access

    Scarcity of high-quality annotated data and mismatch between the development dataset and the target environment are two of the main challenges in developing predictive tools from medical imaging. In this Perspective, the authors show how causal reasoning can shed new light on these challenges.

    • Daniel C. Castro
    • , Ian Walker
    •  & Ben Glocker

  • Article
    | Open Access

    Deep learning is becoming a popular approach for understanding biological processes but can be hard to adapt to new questions. Here, the authors develop Janggu, a python library that aims to ease data acquisition and model evaluation and facilitate deep learning applications in genomics.

    • Wolfgang Kopp
    • , Remo Monti
    •  & Altuna Akalin

  • Article
    | Open Access

    Evidence that somatic mutation rates in introns exceed those in exons challenges the molecular evolution tenet that mutation rate and sequence function are independent. Here, authors analyze germline de novo mutations and reveal no evidence for mutation rate differences between exons and introns.

    • Miguel Rodriguez-Galindo
    • , Sònia Casillas
    •  & Antonio Barbadilla

  • Article
    | Open Access

    Single cell RNA-seq is a powerful method to assign cell identity, but the purity of cell clusters arising from this data is not clear. Here the authors present an entropy-based statistic called ROGUE to quantify the purity of cell clusters, and identify subtypes within clusters.

    • Baolin Liu
    • , Chenwei Li
    •  & Zemin Zhang

  • Article
    | Open Access

    Lineage tracing studies combining CRISPR-Cas9 editing and scRNA-seq face several challenges and cannot integrate lineages from multiple individuals. Here the authors show that integration of mutation and expression leads to accurate lineage tree inference and enables the learning of a species-invariant lineage tree.

    • Hamim Zafar
    • , Chieh Lin
    •  & Ziv Bar-Joseph

  • Article
    | Open Access

    Programmed ribosomal frameshifting—the slippage of the ribosome to an alternative frame — is critical for viral replication and cellular processes. Here the authors present an approach that can assess the frameshifting potential of a sequence and elucidate the rules governing ribosomal frameshifting.

    • Martin Mikl
    • , Yitzhak Pilpel
    •  & Eran Segal

  • Article
    | Open Access

    Explicit molecular modelling of biological membrane systems is computationally expensive due to the large number of solvent particles and slow membrane kinetics. Here authors present a framework for integrating coarse-grained membrane models with continuum-based hydrodynamics which facilitates efficient simulation of large biomembrane systems.

    • Mohsen Sadeghi
    •  & Frank Noé

  • Article
    | Open Access

    The association between leguminous plants and rhizobial bacteria is a paradigmatic example of a symbiosis driven by metabolic exchanges. Here, diCenzo et al. report the reconstruction and modelling of a genome-scale metabolic network of the plant Medicago truncatula nodulated by the bacterium Sinorhizobium meliloti.

    • George C. diCenzo
    • , Michelangelo Tesi
    •  & Marco Fondi

  • Article
    | Open Access

    Multicellularity is one of the major transitions in evolution. Here, authors use a model to show that compared to unicellular bacteria, multicellular fungi can more rapidly colonise immobile, nutrient poor resources because exoenzymes provide greater or longer lasting benefits to mycelial organisms.

    • Luke L. M. Heaton
    • , Nick S. Jones
    •  & Mark D. Fricker

  • Article
    | Open Access

    Regulation of chromosome structure plays essential roles in many nuclear processes. Here, the authors present TADdyn, a tool that integrates time-course 3C data, restraint-based modelling, and molecular dynamics to simulate the structural rearrangements of genomic loci and find that during gene activation, transcription starting sites contact with open chromatin regions into active physical domains.

    • Marco Di Stefano
    • , Ralph Stadhouders
    •  & Marc A. Marti-Renom

  • Article
    | Open Access

    Recent research has shown that mutational signatures reflective of the history of a cancer can be detected in a cancer genome. Here, using whole genome sequencing of DNA repair deficient and proficient nematodes exposed to genotoxins, the authors show that these mutational signatures reflect both the initial DNA damage that was inflicted and the repair processes that ensue.

    • Nadezda V. Volkova
    • , Bettina Meier
    •  & Moritz Gerstung

  • Article
    | Open Access

    Dpr (Defective proboscis extension response) and DIP (Dpr Interacting Proteins) are immunoglobulin-like cell-cell adhesion proteins that form highly specific pairwise interactions, which control synaptic connectivity during Drosophila development. Here, the authors combine a computational approach with binding affinity measurements and find that DIP/Dpr binding specificity is controlled by negative constraints that interfere with non-cognate binding.

    • Alina P. Sergeeva
    • , Phinikoula S. Katsamba
    •  & Barry Honig

  • Article
    | Open Access

    The phase separation of two species of associating polymers is suppressed by a magic-number effect for certain combinations of the numbers of binding sites. Here the authors use lattice simulations and analytical calculations to show that this magic-number effect can be greatly enhanced if one component has a rigid shape.

    • Bin Xu
    • , Guanhua He
    •  & Ned S. Wingreen

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