Computational biology and bioinformatics articles within Nature Communications

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  • Article
    | Open Access

    Nanoparticles are a promising approach to increase immunogenicity of protein antigens for vaccines. Here, Brouwer et al. design self-assembling, two-component protein NPs that present native-like SOSIP trimers of HIV envelope protein and determine immunogenicity in a small animal model.

    • Philip J. M. Brouwer
    • , Aleksandar Antanasijevic
    •  & Rogier W. Sanders

  • Article
    | Open Access

    Invasive non-typhoidal Salmonella (iNTS) infections are dominated by antibiotic resistant isolates of the sequence type (ST) 313. Here, the authors identify the ST313 sublineage II.1 in the Democratic Republic of the Congo exhibiting extensive drug resistance and genetic signatures potentially associated with host adaptation.

    • Sandra Van Puyvelde
    • , Derek Pickard
    •  & Stijn Deborggraeve

  • Article
    | Open Access

    HiChIP/PLAC-seq assay is popular for profiling 3D genome interactions among regulatory elements at kilobase resolution. Here the authors describe FitHiChIP an empirical null-based, flexible computational method for statistical significance estimation and loop calling from HiChIP data.

    • Sourya Bhattacharyya
    • , Vivek Chandra
    •  & Ferhat Ay

  • Article
    | Open Access

    Epistasis underlies the complexity of genotype-phenotype maps. Here, the authors analyze 8,192 mutants that link two phenotypically distinct variants of the Entacmaea quadricolor fluorescent protein, and show the existence, but also the sparsity, of high-order epistatic interactions.

    • Frank J. Poelwijk
    • , Michael Socolich
    •  & Rama Ranganathan

  • Article
    | Open Access

    TDP43 aggregates are a hallmark of amyotrophic lateral sclerosis. By using deep mutagenesis to measure the toxicity of more than 50,000 mutations in the prion domain of TDP43, the authors conclude that mutations that increase toxicity promote formation of liquid-like condensates, while aggregation of TDP43 is protective for the cell.

    • Benedetta Bolognesi
    • , Andre J. Faure
    •  & Ben Lehner

  • Article
    | Open Access

    UPF1 mediates the decay of target mRNA in a 3′ untranslated region (UTR)-length-dependent manner. Here the authors reveal that the 3′UTR-length-dependent regulation of UPF1-dependent mRNA decay occurs through EJC-independent but miRNA-dependent regulation.

    • Jungyun Park
    • , Jwa-Won Seo
    •  & Jin-Wu Nam

  • Article
    | Open Access

    Recent studies have identified a large, phylogenetically distinct clade of bacteria, the candidate phyla radiation (CPR). Here, Méheust and colleagues analyze almost 3600 genomes to characterize the protein family content of CPR versus other bacteria and archaea.

    • Raphaël Méheust
    • , David Burstein
    •  & Jillian F. Banfield

  • Article
    | Open Access

    Identifying ligands which activate the specific effectors driving particular in vivo drug effects remains challenging. Here, the authors apply unsupervised clustering of pharmacodynamic parameters to classify GPCR ligands into different categories with similar signaling profiles and shared frequency of report of side effects.

    • Besma Benredjem
    • , Jonathan Gallion
    •  & Graciela Pineyro

  • Article
    | Open Access

    We currently lack generic methods to map RNA modifications across the entire transcriptome. Here, the authors demonstrate that m6A RNA modifications can be detected with high accuracy using nanopore direct RNA sequencing.

    • Huanle Liu
    • , Oguzhan Begik
    •  & Eva Maria Novoa

  • Article
    | Open Access

    While many pleiotropic genetic loci have been identified, how they contribute to phenotypes across traits and diseases is unclear. Here, the authors propose decomposition of genetic associations (DeGAs), which uses singular value decomposition, to characterize the underlying latent structure of genetic associations of 2,138 phenotypes.

    • Yosuke Tanigawa
    • , Jiehan Li
    •  & Manuel A. Rivas

  • Article
    | Open Access

    HIV-1 usually targets active genes and integrates near the nuclear pore compartment. Here the authors show that recurrently targeted genes are proximal to super-enhancer genomic elements, which cluster in specific spatial compartments of the T cell nucleus, suggesting a role for nuclear organisation in viral infection.

    • Bojana Lucic
    • , Heng-Chang Chen
    •  & Marina Lusic

  • Article
    | Open Access

    Light intensity on the retina can fluctuate rapidly during natural vision, posing a challenge for encoding visual information. Here, the authors report that mechanisms of sensitization/facilitation maintain the sensitivity of the numerically dominant neural pathway in the primate retina during dynamic vision.

    • Todd R. Appleby
    •  & Michael B. Manookin

  • Article
    | Open Access

    Archaea and bacteria often have gene pairs with overlapping stop and start codons, suggesting translational coupling. Here, Huber et al. analyse overlapping gene pairs from 720 genomes, and validate translational coupling via termination-reinitiation for 14 gene pairs in Haloferax volcanii and Escherichia coli.

    • Madeleine Huber
    • , Guilhem Faure
    •  & Jörg Soppa

  • Article
    | Open Access

    Prediction of protein structures on the scale of genomes remains a challenge. Here the authors introduce a protein structure prediction method that uses deep learning to predict inter-atomic distances, torsion angles and hydrogen bonds, and apply it to predict the structures of 1475 Pfam domains.

    • Joe G. Greener
    • , Shaun M. Kandathil
    •  & David T. Jones

  • Comment
    | Open Access

    Forecasting is beginning to be integrated into decision-making processes for infectious disease outbreak response. We discuss how technologies could accelerate the adoption of forecasting among public health practitioners, improve epidemic management, save lives, and reduce the economic impact of outbreaks.

    • Dylan B. George
    • , Wendy Taylor
    •  & Nicholas G. Reich

  • Article
    | Open Access

    The effect of spontaneous variations in prestimulus neural activity on subsequent perception is incompletely understood. Here, using MEG, the authors identify two distinct neural processes that can influence object recognition in different ways.

    • Ella Podvalny
    • , Matthew W. Flounders
    •  & Biyu J. He

  • Article
    | Open Access

    Non-additive genetic interactions are plastic and can complicate genetic prediction. Here, using deep mutagenesis of the lambda repressor, Li et al. reveal that changes in gene expression can alter the strength and direction of genetic interactions between mutations in many genes and develop mathematical models for predicting them.

    • Xianghua Li
    • , Jasna Lalić
    •  & Ben Lehner

  • Article
    | Open Access

    PrediXcan is a widely used gene expression imputation method that links genetic variants to gene expression. Here, the authors develop EpiXcan which leverages epigenetic annotations to inform transcriptomic imputation and further use the obtained gene-trait associations for computational drug repurposing.

    • Wen Zhang
    • , Georgios Voloudakis
    •  & Panos Roussos

  • Article
    | Open Access

    Multi-omic profiling is a powerful approach to dissecting molecular mechanisms in disease. Here the authors generate whole proteome, phosphoproteome and transcriptome profiles from two mouse models of high-grade glioma driven by different oncogenes, and validate identified master regulators with a CRISPR screen.

    • Hong Wang
    • , Alexander K. Diaz
    •  & Junmin Peng

  • Article
    | Open Access

    The advent of single-cell RNA sequencing has revealed significant transcriptional heterogeneity in cancer, but its relationship to genomic heterogeneity remains unclear. Focusing on acute myeloid leukemia samples, the authors describe a general approach for linking mutation-containing cells to their transcriptional phenotypes using single-cell RNA sequencing data.

    • Allegra A. Petti
    • , Stephen R. Williams
    •  & Timothy J. Ley

  • Article
    | Open Access

    Gene activation requires an increase of successful initiation events. Here, by employing a genome-wide kinetic analysis of transcription, the authors showed that gene activation generally requires a decrease in RNA Polymerase II (Pol II) promoter-proximal pausing while transcription of enhancer elements is not limited by Pol II pausing.

    • Saskia Gressel
    • , Björn Schwalb
    •  & Patrick Cramer

  • Article
    | Open Access

    Efficient sampling of rare events in all-atom molecular dynamics simulations remains a challenge. Here, the authors adapt the Predictive Information Bottleneck framework to sample biomolecular structure and dynamics through iterative rounds of biased simulations and deep learning.

    • Yihang Wang
    • , João Marcelo Lamim Ribeiro
    •  & Pratyush Tiwary

  • Article
    | Open Access

    Squamous cell lung cancer has dismal prognosis due to the dearth of effective treatments. Here, the authors perform an integrated proteogenomic analysis of the disease, revealing three proteomics-based subtypes and suggesting potential therapeutic opportunities.

    • Paul A. Stewart
    • , Eric A. Welsh
    •  & Eric B. Haura

  • Article
    | Open Access

    Interpreting genetic variation in the noncoding genome remains challenging, with functional effects difficult to predict. Here, the authors perform saturation mutagenesis combined with massively parallel reporter assays for 20 disease-associated regulatory elements, quantifying the effects of over 30,000 variants.

    • Martin Kircher
    • , Chenling Xiong
    •  & Nadav Ahituv

  • Article
    | Open Access

    Increasing amount of public omics data are important and valuable resources for the research community. Here, the authors develop a set of metrics to quantify the attention and impact of biomedical datasets and integrate them into the framework of Omics Discovery Index (OmicsDI).

    • Yasset Perez-Riverol
    • , Andrey Zorin
    •  & Henning Hermjakob

  • Article
    | Open Access

    Oct4, along with Sox2 and Klf4 can induce pluripotency, but structurally similar factors like Oct6 cannot. Here, using pluripotency competent and incompetent factors, the authors show that Sox2 plays a dominant role in facilitating chromatin opening at Oct4 bound DNA early during reprogramming to pluripotency.

    • Vikas Malik
    • , Laura V. Glaser
    •  & Ralf Jauch

  • Article
    | Open Access

    Compared to bulk data, cell-type-specific DNA methylation data provide higher resolution of epigenetic variation. Here, the authors introduce Tensor Composition Analysis, a novel computational approach for learning cell-type-specific DNA methylation from tissue-level bulk data, and show its application in epigenome-wide association studies.

    • Elior Rahmani
    • , Regev Schweiger
    •  & Eran Halperin

  • Article
    | Open Access

    The position, shape and number of transcription start sites (TSS) regulate gene expression. Here authors present MAPCap, a method for high-resolution detection and differential expression analysis of TSS, and apply MAPCap to early fly development, detecting stage and sex-specific promoter and enhancer activity.

    • Vivek Bhardwaj
    • , Giuseppe Semplicio
    •  & Asifa Akhtar

  • Article
    | Open Access

    Polymorphisms in the avian influenza A virus (IAV) polymerase restrict its host range during transmission from birds to mammals. Here, the authors investigate differences in the host chromatin regulator ANP32A regarding IAV polymerase adaptation, and profile ANP32A splicing to predict avian species associated with pre-adaptive human-signatures in the virus.

    • Patricia Domingues
    • , Davide Eletto
    •  & Benjamin G. Hale

  • Article
    | Open Access

    Finding driver genes sheds lights on the biological mechanisms propelling the development of a tumour, and can suggest therapeutic strategies. Here, the authors develop driverMAPS, a model-based approach to identify driver genes, and apply it to TCGA datasets.

    • Siming Zhao
    • , Jun Liu
    •  & Xin He

  • Article
    | Open Access

    Most databases of genotype-phenotype associations are manually curated. Here, Kuleshov et al. describe a machine curation system that extracts such relationships from the GWAS literature and synthesizes them into a structured knowledge base called GWASkb that can complement manually curated databases.

    • Volodymyr Kuleshov
    • , Jialin Ding
    •  & Michael Snyder

  • Article
    | Open Access

    Serum-resistant bacteria can escape complement killing in the bloodstream. Here, using metabolomics and metabolite perturbations, the authors describe an altered metabolic state in serum-resistant Escherichia coli and show that exogenous glycine potentiates elimination of pathogenic bacteria in vivo.

    • Zhi-xue Cheng
    • , Chang Guo
    •  & Xuan-xian Peng

  • Article
    | Open Access

    Many genetic variants identified in genome-wide association studies are associated with gene expression. Here, Porcu et al. propose a transcriptome-wide summary statistics-based Mendelian randomization approach (TWMR) that, applied to 43 human traits, uncovers hundreds of previously unreported gene–trait associations.

    • Eleonora Porcu
    • , Sina Rüeger
    •  & Zoltán Kutalik

  • Review Article
    | Open Access

    Glycomics is gaining momentum in basic, translational and clinical research. Here, the authors review current reporting standards and analysis tools for mass-spectrometry-based glycomics, and propose an e-infrastructure for standardized reporting and online deposition of glycomics data.

    • Miguel A. Rojas-Macias
    • , Julien Mariethoz
    •  & Niclas G. Karlsson

  • Article
    | Open Access

    The fraction of protein-protein interactions (PPIs) that can be disrupted without fitness effect is unknown. Here, the authors model how disease-causing mutations and common mutations carried by healthy people perturb the interactome, and estimate that <20% of human PPIs are completely dispensable.

    • Mohamed Ghadie
    •  & Yu Xia

  • Article
    | Open Access

    A number of computational methods have been developed for calling structural variants (SVs) using short read sequencing data. Here, the authors perform a comprehensive benchmarking analysis comparing 10 general-purpose callers and provide recommendations for both users and methods developers.

    • Daniel L. Cameron
    • , Leon Di Stefano
    •  & Anthony T. Papenfuss

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