Computational models articles within Nature Communications

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  • Article
    | Open Access

    Integrated analyses of multiple large-scale screenings can be complicated by batch effects and technical artefacts. McFarland et al. introduce DEMETER2, a hierarchical model coupled with model-based normalization, which allows the assessment of differential dependencies across genes and cell lines.

    • James M. McFarland
    • , Zandra V. Ho
    •  & Aviad Tsherniak

  • Article
    | Open Access

    The decision when to stop an intervention is a critical component of parasite elimination programmes, but reliance on surveillance data alone can be inaccurate. Here, Michael et al. combine parasite transmission model predictions with disease survey data to more reliably determine when interventions can be stopped.

    • Edwin Michael
    • , Morgan E. Smith
    •  & Frank O. Richards

  • Article
    | Open Access

    How heterogeneities arise in stem cell populations remains unclear. Here, Glen et al. find that in ESC colonies cell cycle asynchronies modulate gap junctions, causing variation in intracellular signalling molecule diffusion between cells, and ultimately in spatial heterogeneity in differentiation.

    • Chad M. Glen
    • , Todd C. McDevitt
    •  & Melissa L. Kemp

  • Article
    | Open Access

    Generation and iterative optimization of designed enzymes can provide valuable insights for a more efficient catalysis. Here the authors have followed the iterative improvement of a designed Kemp eliminase and show that remote point mutations could remodel the designed active site via substantial conformational reorganization.

    • Nan-Sook Hong
    • , Dušan Petrović
    •  & Colin J. Jackson

  • Article
    | Open Access

    Inference and representation of differentiation trajectories from single cell RNA-seq data remains a challenge. Here, the authors offer a visualization approach that captures both continuous differentiation trajectories and discrete clusters representing metastable states along the trajectories.

    • Fabrizio Costa
    • , Dominic Grün
    •  & Rolf Backofen

  • Article
    | Open Access

    AGO-PAR-CLIP is widely used for high-throughput miRNA target characterization. Here, the authors show that the previously neglected non-T-to-C clusters denote functional miRNA binding events, and develop microCLIP, a super learning framework that accurately detects miRNA interactions.

    • Maria D. Paraskevopoulou
    • , Dimitra Karagkouni
    •  & Artemis G. Hatzigeorgiou

  • Article
    | Open Access

    How reproducible evolutionary processes are remains an important question in evolutionary biology. Here, the authors compile a compendium of more than 15,000 mutation events for Escherichia coli under 178 distinct environmental settings, and develop an ensemble of predictors to predict evolution at a gene level.

    • Xiaokang Wang
    • , Violeta Zorraquino
    •  & Ilias Tagkopoulos

  • Article
    | Open Access

    While drugs can interact in both target and off-target cell types, more favorable interaction in the target cell may nevertheless allow for a therapeutic window. Here, the authors show, using two yeast species as a model, that differential drug interactions indeed adjust the selective window.

    • Zohar B. Weinstein
    • , Nurdan Kuru
    •  & Murat Cokol

  • Article
    | Open Access

    Technical noise in experiments is unavoidable, but it introduces inaccuracies into the biological networks we infer from the data. Here, the authors introduce a diffusion-based method for denoising undirected, weighted networks, and show that it improves the performances of downstream analyses.

    • Bo Wang
    • , Armin Pourshafeie
    •  & Jure Leskovec

  • Article
    | Open Access

    Cell arrangement in the plane of epithelia is well studied, but its three-dimensional packing is largely unknown. Here the authors model curved epithelia and predict that cells adopt a geometrical shape they call “scutoid”, resulting in different apical and basal neighbours, and confirm the presence of scutoids in curved tissues.

    • Pedro Gómez-Gálvez
    • , Pablo Vicente-Munuera
    •  & Luis M. Escudero

  • Article
    | Open Access

    Community detection allows one to decompose a network into its building blocks. While communities can be identified with a variety of methods, their relative importance can’t be easily derived. Here the authors introduce an algorithm to identify modules which are most promising for further analysis.

    • Marinka Zitnik
    • , Rok Sosič
    •  & Jure Leskovec

  • Article
    | Open Access

    MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression but many quantitative aspects of miRNA biology remain to be elucidated. Based on a library of miRNA sensors, the authors quantify miRNA regulation at single cell level and develop a model to predict miRNA target interactions.

    • Jeremy J. Gam
    • , Jonathan Babb
    •  & Ron Weiss

  • Article
    | Open Access

    How transcription factors find their targets in vivo is still poorly understood. Here the authors use molecular dynamics simulations to investigate how transcription factors diffuse on chromatin, providing a theoretical framework for understanding the key role of genome conformation in this process.

    • Ruggero Cortini
    •  & Guillaume J. Filion

  • Article
    | Open Access

    Main-chain tracing remains a time-consuming task for medium resolution cryo-EM maps. Here the authors describe MAINMAST, a computational approach for building main-chain structure models of proteins from EM maps of 4-5 Å resolution that builds main-chain models of the protein by tracing local dense points in the density distribution.

    • Genki Terashi
    •  & Daisuke Kihara

  • Article
    | Open Access

    Many genes of functional and clinical significance are highly polymorphic and experience structural alterations. Here, Numanagić et al. develop Aldy, a computational tool for resolving the copy number and the sequence content of each copy of a gene by analyzing whole or targeted genome sequencing data.

    • Ibrahim Numanagić
    • , Salem Malikić
    •  & S. Cenk Sahinalp

  • Article
    | Open Access

    Despite its popularity for measuring the spatial organization of mammalian genomes, the resolution of most Hi-C datasets is coarse due to sequencing cost. Here, Zhang et al. develop HiCPlus, a computational approach based on deep convolutional neural network, to infer high-resolution Hi-C interaction matrices from low-resolution Hi-C data.

    • Yan Zhang
    • , Lin An
    •  & Feng Yue

  • Article
    | Open Access

    It is not known whether the shape of a cell can regulate cellular phenotype independently. Here, the authors show that culturing kidney podocytes or smooth muscle cells on 3-D biomimetic surfaces results in phenotypic changes and that cell shape is sensed by integrin β3 in a tension-independent manner.

    • Amit Ron
    • , Evren U. Azeloglu
    •  & Ravi Iyengar

  • Article
    | Open Access

    Tip-growing cells can find their growing path toward the source of attractive signals. Here, using experimental data and mathematical modeling, Luo et al. demonstrate that tip-localized exocytosis can integrate guidance cues with Rho GTPase signaling to control cell wall mechanics and direct tip growth in Arabidopsis pollen tubes.

    • Nan Luo
    • , An Yan
    •  & Zhenbiao Yang

  • Article
    | Open Access

    The NMR chemical shifts of a substance in urine strongly depend on the composition of the mixture itself, and this makes automatic assignment for quantification very difficult. Here the authors show the chemical shifts of signals and the concentration of NMR-invisible inorganic ions in urine, are predictable.

    • Panteleimon G. Takis
    • , Hartmut Schäfer
    •  & Claudio Luchinat

  • Article
    | Open Access

    Artemether lumefantrine is widely used for the treatment of uncomplicated malaria. The impact of imperfect patient adherence to the six-dose regimen is hard to assess. Using adherence data for unsupervised patients, the authors model how suboptimal adherence affects treatment outcomes.

    • Joseph D. Challenger
    • , Katia Bruxvoort
    •  & Lucy C. Okell

  • Article
    | Open Access

    Microbes live in communities and exchange metabolites, but the resulting dynamics are poorly understood. Here, the authors study the interplay between metabolite production strategies and population dynamics, and find that complex and unexpected dynamics emerge even in simple microbial economies.

    • Yoav Kallus
    • , John H. Miller
    •  & Eric Libby

  • Article
    | Open Access

    Existing transcriptional regulatory networks models fall short of deciphering the cooperation between multiple transcription factors on dynamic gene expression. Here the authors develop an integrative method that combines gene expression and transcription factor-DNA binding data to decode transcription regulatory logics.

    • Bin Yan
    • , Daogang Guan
    •  & Hailong Zhu

  • Article
    | Open Access

    Tree branches follow allometric scalings between length, thickness and dry mass. Here, Eloy and colleagues develop a functional-structural model that shows how such allometries in tree architecture can emerge through evolution as a result of competition for light, wind biomechanics, and wind sensing.

    • Christophe Eloy
    • , Meriem Fournier
    •  & Bruno Moulia

  • Article
    | Open Access

    The structure and dynamics of microbial communities reflect trade-offs in the ability to use different resources. Here, Josephides and Swain incorporate metabolic trade-offs into an eco-evolutionary model to predict networks of mutational paths and the evolutionary outcomes for microbial communities.

    • Christos Josephides
    •  & Peter S. Swain

  • Article
    | Open Access

    The RNA Recognition Motif (RRM) is the most ubiquitous RNA binding domain. Here the authors combined NMR and molecular dynamics simulations and show that the RRM RNA binding surface exists in different states and that a conformational switch of aromatic side-chains fine-tunes sequence specific binding affinities.

    • Nana Diarra dit Konté
    • , Miroslav Krepl
    •  & Frédéric H.-T. Allain

  • Article
    | Open Access

    The pancreas arises from a small population of cells but how individual cells contribute to organ formation is unclear. Here, the authors deconstruct pancreas organogenesis into clonal units, showing that single progenitors give rise to heterogeneous multi-lineage and endocrinogenic single-lineage clones.

    • Hjalte List Larsen
    • , Laura Martín-Coll
    •  & Anne Grapin-Botton

  • Article
    | Open Access

    Early molecules of life likely served both as templates and catalysts, raising the question of how functionally distinct genomes and enzymes arose. Here, the authors show that conflict between evolution at the molecular and cellular levels can drive functional differentiation of the two strands of self-replicating molecules and lead to copy number differences between the two.

    • Nobuto Takeuchi
    • , Paulien Hogeweg
    •  & Kunihiko Kaneko

  • Article
    | Open Access

    Deregulation of E2F family transcription factors is associated with cancer progression and metastasis. Here, the authors construct a map of the regulatory network around the E2F family, and using gene expression profiles, identify tumour type-specific regulatory cores and receptor expression signatures associated with epithelial-mesenchymal transition in bladder and breast cancer.

    • Faiz M. Khan
    • , Stephan Marquardt
    •  & Brigitte M. Pützer

  • Article
    | Open Access

    Cells in the connective tissue are surrounded by a heterogeneous network of biopolymers. Here, the authors investigate how such heterogeneity affects cellular mechanosensing by simulating the deformation response of experimental and modelled biopolymer networks to locally applied forces.

    • Farzan Beroz
    • , Louise M. Jawerth
    •  & Ned S. Wingreen

  • Article
    | Open Access

    Parasitemia has been considered the main determinant of visceral leishmaniasis transmission. By combining imaging, qPCR and experimental xenodiagnoses with mathematical models, Doehl et al. argue that the patchy landscape of parasites in the skin is necessary to explain infectiousness.

    • Johannes S. P. Doehl
    • , Zoe Bright
    •  & Paul M. Kaye

  • Article
    | Open Access

    There are few methods available that can quantify relationships between cell types in tissue images. Here the authors present a quantitative method to evaluate cellular organization, validated in the mouse thymus and spinal cord, called Multitaper Circularly Averaged Spectral Analysis (MiCASA).

    • Andrew Sornborger
    • , Jie Li
    •  & Nancy R. Manley

  • Article
    | Open Access

    The three-dimensional architecture of genome-reduced bacteria is poorly understood. Here the authors combine Hi-C with super-resolution microscopy inMycoplasma pneumoniaeand provide evidence of how supercoiling and local organization influences gene regulation.

    • Marie Trussart
    • , Eva Yus
    •  & Luís Serrano

  • Article
    | Open Access

    Embryonic development is a complex process where genetic and biochemical information direct morphogenesis. Here the authors describe MecaGen, an agent-based model and simulation platform of multicellular development designed to allow a quantitative comparison between simulations and real biological data.

    • Julien Delile
    • , Matthieu Herrmann
    •  & René Doursat

  • Article
    | Open Access

    The cornea is formed of cells that originate from the outer circle of stem cells and that move towards its centre. Here, the authors show that the movement pattern is self-organised, requiring no cues, and that stem cell leakage may account for the presence of stem cells at the centre of the cornea.

    • Erwin P. Lobo
    • , Naomi C. Delic
    •  & J. Guy Lyons

  • Article
    | Open Access

    The prolactin receptor consists of a folded extracellular domain, a transmembrane domain and an intracellular intrinsically disordered domain. Here the authors use a combined experimental and computational approach to obtain a structure of a class I cytokine receptor, the human prolactin receptor.

    • Katrine Bugge
    • , Elena Papaleo
    •  & Birthe B. Kragelund

  • Article
    | Open Access

    Sudden arrhythmic death is a leading cause of mortality, however approaches to identify at-risk patients are of low sensitivity and specificity. Here, the authors develop a personalized approach to assess arrhythmia risk in post-infarction patients based on cardiac imaging and computational modelling that significantly outperforms existing clinical metrics.

    • Hermenegild J. Arevalo
    • , Fijoy Vadakkumpadan
    •  & Natalia A. Trayanova

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