Computational biology and bioinformatics articles within Nature Communications

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  • Article
    | Open Access

    Determining the different cell types that contribute to a mixture of DNA is key for research and diagnostic applications. Here, authors comprehensively benchmark DNA methylation-based deconvolution methods, evaluating their performance and robustness to technical bias.

    • Kobe De Ridder
    • , Huiwen Che
    •  & Bernard Thienpont

  • Article
    | Open Access

    Contact patterns influence the spread of infectious diseases, but mathematical models of epidemics typically only account for age differences in contacts. Here, the authors investigate the importance of other sociodemographic characteristics in shaping contact patterns and vaccine uptake using survey data from Hungary.

    • Adriana Manna
    • , Júlia Koltai
    •  & Márton Karsai

  • Article
    | Open Access

    Natal downs adapted for heat conservation transition to juvenile feathers that support simple flight during bird development. Here the authors characterize gene expression networks and epigenetic changes and use functional perturbations to characterize evolutionarily conserved regulatory switches that control this transition in birds.

    • Chih-Kuan Chen
    • , Yao-Ming Chang
    •  & Wen‐Hsiung Li

  • Article
    | Open Access

    Skeletal ryanodine receptor controls calcium mobilization indispensable for muscle contraction. Here, authors combine cryo-EM and molecular dynamics to uncover the structural basis of the intricate regulation of this channel by calcium and magnesium.

    • Ashok R. Nayak
    • , Warin Rangubpit
    •  & Montserrat Samsó

  • Article
    | Open Access

    Intestinal homeostasis is maintained by interactions between the gut-associated lymphoid tissue and the resident flora. Here Montorsi et al use multiplexed single cell omics to describe double negative type 2 B cells and DNASE1L3-expressing dendritic cells that interact and associate with microbiota on the human gut antigenic front line.

    • Lucia Montorsi
    • , Michael J. Pitcher
    •  & Jo Spencer

  • Article
    | Open Access

    The Sargasso Sea is a natural laboratory for understanding future conditions of warmer oceans and associated nutrient limitation. Here, the authors combined short- and long-read sequencing to survey Sargasso Sea viral communities.

    • Joanna Warwick-Dugdale
    • , Funing Tian
    •  & Ben Temperton

  • Article
    | Open Access

    The techniques available for comparing protein structures do not focus directly on the chemical nature of residue environments. Here, authors describe a computational method that can capture both the spatial and chemical dissimilarities of residue surroundings.

    • Zsolt Fazekas
    • , Dóra K. Menyhárd
    •  & András Perczel

  • Article
    | Open Access

    The details of how the protein folding and degradation systems collaborate to combat potentially toxic non-native proteins are unknown. Here the authors perform systematic studies of missense and nonsense variants of the cytosolic aspartoacylase, ASPA, where loss-of-function variants are linked to Canavan disease.

    • Martin Grønbæk-Thygesen
    • , Vasileios Voutsinos
    •  & Rasmus Hartmann-Petersen

  • Article
    | Open Access

    Pentamidine and melarsoprol are drugs used to treat sleeping sickness caused by Trypanosoma brucei. Here, authors present cryo-EM structures of TbAQP2 with molecular dynamic simulations, revealing mechanisms shaping substrate specificity and drug permeation.

    • Wanbiao Chen
    • , Rongfeng Zou
    •  & Chongyuan Wang

  • Article
    | Open Access

    Pesticides safeguard crops against pest infestations and mitigate associated risks. In this work, the authors develop a pesticide targeting AlstR-C of T.pityocampa pests, showing promising results without harming other insects, and advancing the development of GPCR-targeted pesticides for insect control.

    • Kübra Kahveci
    • , Mustafa Barbaros Düzgün
    •  & Necla Birgul Iyison

  • Article
    | Open Access

    In proteomics, identifying differentially expressed proteins (DEPs) is critical for uncovering biomarkers and drug targets. However, constructing optimal workflows to achieve maximal identification of DEPs is challenging. Here, the authors performed 34,576 combinatorial experiments on 24 gold standard spike-in datasets to discern optimal workflows.

    • Hui Peng
    • , He Wang
    •  & Wilson Wen Bin Goh

  • Article
    | Open Access

    Direct oral anticoagulants (DOACs) targeting factor Xa that are used to prevent or treat thromboembolic disorders carry the risk of uncontrolled bleeding. Here, the authors present the computational design and evaluation of factor Xa-variants which can be used to reduce DOAC-associated bleeding.

    • Wojciech Jankowski
    • , Stepan S. Surov
    •  & Zuben E. Sauna

  • Article
    | Open Access

    Aberrant signalling pathway activity is relevant for tumour growth and resistance to therapy, but remains hard to understand and target. Here, the authors develop VESPA, a phosphoproteomics-based machine learning algorithm that can elucidate response and adaptation to drug perturbations in cancer signalling pathways.

    • George Rosenberger
    • , Wenxue Li
    •  & Andrea Califano

  • Article
    | Open Access

    Here, based on a systematic review and meta-analysis, the authors analyze the relationship between vaccine immunogenicity and vaccine protection against mpox and predict the durability of protection after vaccination. This helps inform the optimal vaccine deployment in a health emergency.

    • Matthew T. Berry
    • , Shanchita R. Khan
    •  & David S. Khoury

  • Article
    | Open Access

    This study presents a machine learning model that accurately predicts seasonal antigenic changes of influenza A H3N2 using genetic data. The model’s predictions can aid influenza surveillance, vaccine strain selection, and public health management.

    • Syed Awais W. Shah
    • , Daniel P. Palomar
    •  & Matthew R. McKay

  • Article
    | Open Access

    Liquid Chromatography Mass Spectrometry (LC-MS) is a powerful method for profiling biological samples. Here, the authors have developed a suit of Batch Effect Removal Neural Networks (BERNN) to remove batch effects in large LC-MS experiments to maximize sample classification between conditions.

    • Simon J. Pelletier
    • , Mickaël Leclercq
    •  & Arnaud Droit

  • Article
    | Open Access

    Polypharmacology drugs are compounds designed to inhibit multiple protein targets. Here, authors use recent advances in AI to rapidly generate polypharmacology compounds against any pair of protein targets, experimentally validating numerous compounds targeting MEK1 and mTOR.

    • Brenton P. Munson
    • , Michael Chen
    •  & Trey Ideker

  • Article
    | Open Access

    CAR T cell immunotherapy for paediatric solid and brain tumours is constrained by the availability of targetable antigens. Here, the authors investigate the landscape of cancer-specific exons as potential targets by analysing 1,532 RNAseq datasets from 16 types of paediatric solid and brain tumours.

    • Timothy I. Shaw
    • , Jessica Wagner
    •  & Stephen Gottschalk

  • Article
    | Open Access

    Annotation of cell types and quantification of their relative localization in tissues remain challenging. Here, the authors present AnnoSpat (Annotator and Spatial Pattern Finder), a computational tool that can automatically identify cell types and quantify cell-cell proximity relationships.

    • Aanchal Mongia
    • , Fatema Tuz Zohora
    •  & Robert B. Faryabi

  • Article
    | Open Access

    H9N2 avian influenza is a virus with zoonotic potential that is common in poultry in live bird markets in Asia. In this study, the authors use mathematical modelling to characterise transmission of H9N2 in live bird markets in Bangladesh and assess the effectiveness of potential interventions to reduce its circulation.

    • Francesco Pinotti
    • , Lisa Kohnle
    •  & Guillaume Fournié

  • Article
    | Open Access

    It is known that exercise influences many human traits, but not which tissues and genes are most important. This study connects transcriptome data collected across 15 tissues during exercise training in rats as part of the Molecular Transducers of Physical Activity Consortium with human data to identify traits with similar tissue specific gene expression signatures to exercise.

    • Nikolai G. Vetr
    • , Nicole R. Gay
    •  & Stephen B. Montgomery

  • Article
    | Open Access

    Several bottlenecks exist in metabolomics data analysis. Here, the authors present MetaboAnalystR 4.0 as a unified workflow for LC-MS untargeted metabolomics. It highlights significant improvements in LC-MS2 spectral processing and functional analysis, providing an end-to-end computational pipeline.

    • Zhiqiang Pang
    • , Lei Xu
    •  & Jianguo Xia

  • Article
    | Open Access

    When studying nematic ordering of cells in a monolayer, it is commonly assumed that the principal stress and cell shape axes are tightly coupled. Here, the authors measure cell shape and cell-generated contractile stresses and show that cells in monolayers form correlated, dynamic domains in which the stresses are systematically misaligned with the cell bodies.

    • Mehrana R. Nejad
    • , Liam J. Ruske
    •  & Julia M. Yeomans

  • Article
    | Open Access

    Single-cell RNA sequencing data analysis is limited by noise and high dimensionality. Here, authors present scLENS, a tool that automates accurate signal detection without manual input, particularly in complex datasets.

    • Hyun Kim
    • , Won Chang
    •  & Jae Kyoung Kim

  • Article
    | Open Access

    Genomic analyses have indicated that a small number of virus particles usually found new infections. Here, the authors use a mathematical model to show that this small transmission bottleneck is a result of the physical processes of airborne virus emission, diffusion, and inhalation.

    • Patrick Sinclair
    • , Lei Zhao
    •  & Christopher J. R. Illingworth

  • Article
    | Open Access

    Dengue is a major public health concern in the Americas, and the Caribbean can be a source for reintroduction and spread. Here, the authors use travel surveillance data and genomic epidemiology to reconstruct Dengue epidemic dynamics in the Caribbean from 2009-2022.

    • Emma Taylor-Salmon
    • , Verity Hill
    •  & Nathan D. Grubaugh

  • Article
    | Open Access

    This study explores the variation in gene regulation across plant species and genotypes using interpretable deep learning on DNA sequence and RNA-seq data, demonstrating the models’ utility in functional genomics and phenotypic trait prediction.

    • Fritz Forbang Peleke
    • , Simon Maria Zumkeller
    •  & Jędrzej Szymański

  • Article
    | Open Access

    Identifying active compounds for a target is time- and resource-intensive. Here, the authors show that deep learning models trained on Cell Painting and single-point activity data, can reliably predict compound activity across diverse targets while maintaining high hit rates and scaffold diversity.

    • Johan Fredin Haslum
    • , Charles-Hugues Lardeau
    •  & Erik Müllers

  • Article
    | Open Access

    Here the authors report that enhancers appear more often in late-replicating DNA regions and are enriched for mutations affecting TF binding. This relationship with DNA replication time is seen in species evolution and cancer, suggesting a fundamental principle of genome evolution.

    • Paola Cornejo-Páramo
    • , Veronika Petrova
    •  & Emily S. Wong

  • Article
    | Open Access

    The use of data-driven generative models for drug design is challenging due to the scarcity of data. Here, the authors introduce a “zero-shot" generative deep model to enable the generation of molecules by both structure- and ligand-based drug design and apply it to design PPARγ agonists with desired properties.

    • Kenneth Atz
    • , Leandro Cotos
    •  & Gisbert Schneider

  • Article
    | Open Access

    During organ regeneration, gene expression patterns similar to those in normal development are reestablished. Here, Kawasumi-Kita et al. explore core rebooting factors that operate during Xenopus limb regeneration. Their results indicate that hoxc12 and hoxc13 are critical for reactivating tissue growth.

    • Aiko Kawasumi-Kita
    • , Sang-Woo Lee
    •  & Yoshihiro Morishita

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