Research articles

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  • Seqwalk is a scalable method for designing orthogonal DNA barcode libraries, producing one million barcodes in 20 s on a standard laptop.

    • Gokul Gowri
    • Kuanwei Sheng
    • Peng Yin
    Brief CommunicationOpen Access
  • 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
  • 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
  • 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
  • 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
  • An optimization algorithm is used to discover guest molecules based on knowing only the structure of the host. The molecules are represented as 3D volumes, optimized to improve host–guest interaction and converted into SMILES using a transformer model.

    • Juan M. Parrilla-Gutiérrez
    • Jarosław M. Granda
    • Leroy Cronin
    ArticleOpen Access
  • Automated algorithm discovery has been difficult for artificial intelligence given the immense search space of possible functions. Here explainable neural networks are used to discover algorithms that outperform those designed by humans.

    • Paul J. Blazek
    • Kesavan Venkatesh
    • Milo M. Lin
  • The authors introduce two cellular barcoding tools: CellBarcode, for extracting and filtering diverse DNA barcodes from bulk and single-cell sequencing data; and CellBarcodeSim, for simulating barcoding experiments, thus enabling the investigation of the impact of biological and technical factors on barcode detection.

    • Wenjie Sun
    • Meghan Perkins
    • Anne-Marie Lyne
    ResourceOpen Access
  • The authors develop a general method that combines machine learning and physics to construct macroscopic dynamics directly from microscopic observations, leading to an intuitive understanding of polymer stretching in elongational flow.

    • Xiaoli Chen
    • Beatrice W. Soh
    • Qianxiao Li
    ArticleOpen Access
  • A mathematical framework that allows computing the input–output function of neurons with active dendrites reveals how dendrites readily and potently control the response variability, a result that is experimentally confirmed.

    • Zachary Friedenberger
    • Richard Naud
    Brief Communication