Articles in 2024

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  • We present a method to alleviate re-identification risks behind sharing haplotype reference panels for imputation. In an anonymized reference panel, one might try to infer the genomes’ phenotypes to re-identify their owner. Our method protects against such attack by shuffling the reference panels genomes while maintaining imputation accuracy.

    Research Briefing
  • MISATO, a dataset for structure-based drug discovery combines quantum mechanics property data and molecular dynamics simulations on ~20,000 protein–ligand structures, substantially extends the amount of data available to the community and holds potential for advancing work in drug discovery.

    • Matthew Holcomb
    • Stefano Forli
    News & Views
  • The authors develop the tool RESHAPE to share reference panels in a safer way. The genome–phenome links in reference panels can generate re-identification threats and RESHAPE breaks these links by shuffling haplotypes while preserving imputation accuracy.

    • Théo Cavinato
    • Simone Rubinacci
    • Olivier Delaneau
    ArticleOpen Access
  • Multicellular modeling is increasingly being used to understand biological systems. SimuCell3D is a tool that allows mechanically realistic simulations, using the deformable cell model, to be developed and run.

    • Domenic P. J. Germano
    • James M. Osborne
    News & Views
  • We highlight the vibrant discussions on quantum computing and quantum algorithms that took place at the 2024 American Physical Society March Meeting and invite submissions that notably drive the field of quantum information science forward.

    Editorial
  • Cooperation is crucial for human prosperity, and population structure fosters it through pairwise interactions and coordinated behavior in larger groups. A recent study explores the evolution of behavioral strategies in higher-order population structures, including pairwise and multi-way interactions to reveal that higher-order interactions promote cooperation across networks, especially when they are formed by conjoined communities.

    • Valerio Capraro
    • Matjaž Perc
    News & Views
  • SANGO efficiently removed batch effects between the query and reference single-cell ATAC signals through the underlying genome sequences, to enable cell type assignment according to the reference data. The method achieved superior performance on diverse datasets and could detect unknown tumor cells, providing valuable functional biological signals.

    Research Briefing
  • Approaches are needed to accelerate the discovery of transition metal complexes (TMCs), which is challenging owing to their vast chemical space. A large dataset of diverse ligands is now introduced and leveraged in a multiobjective genetic algorithm that enables the efficient optimization of TMCs in chemical spaces containing billions of them.

    Research Briefing
  • Cooperation is not merely a dyadic phenomenon, it also includes multi-way social interactions. A mathematical framework is developed to study how the structure of higher-order interactions influences cooperative behavior.

    • Anzhi Sheng
    • Qi Su
    • Joshua B. Plotkin
    Article
  • Wildfires have increased in frequency and intensity due to climate change and have had severe impacts on the built environment worldwide. Moving forward, models should take inspiration from epidemic network modeling to predict damage to individual buildings and understand the impact of different mitigations on the community vulnerability in a network setting.

    • Hussam Mahmoud
    Comment
  • This study introduces SANGO, a method for accurate single-cell annotation leveraging genomic sequences around accessibility peaks within single-cell ATAC sequencing data. SANGO consistently outperforms existing methods across diverse datasets for identification of cell type and detection of unknown tumor cells. SANGO enables the discovery of cell-type-specific functional insights through expression enrichment, cis-regulatory chromatin interactions and motif enrichment analyses.

    • Yuansong Zeng
    • Mai Luo
    • Yuedong Yang
    Article
  • A fast and versatile three-dimensional cell-based model, called SimuCell3D, is developed for high-resolution simulations of large and complex biological tissues. SimuCell3D natively integrates intra- and extracellular entities, including extracellular matrix, nuclei and polarized cell surfaces.

    • Steve Runser
    • Roman Vetter
    • Dagmar Iber
    ResourceOpen Access