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Volume 55 Issue 5, May 2023

Aberrant splicing prediction

Genetic variants can lead to aberrant splicing whereby exons are skipped or incorrectly included in a transcript, which may cause disease. This is depicted by the odd presence of a red segment (‘wrong exon’) in a rope. AbSplice is a model that predicts the effect of DNA variation on tissue-specific RNA splicing.

See Wagner, Çelik et al.

Image: Getty Images. Cover Design: Tulsi Voralia.

Editorial

  • As computational analysis becomes ever-more ubiquitous for researchers, the deposition of the underlying code is now an expected part of publication. Shortcomings in code sharing can lead to delays in peer review and publication, as well as reproducibility issues that are easily avoided with author preparation.

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  • Reconstructing phylogenetic trees from large collections of genome sequences is a computationally challenging task. We developed MAPLE, a method for performing phylogenetic inference on large numbers of closely related genomes, which might be useful when studying the evolution and spread of SARS-CoV-2 and of infectious pathogens in future pandemics.

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  • We developed a machine learning model to quantify cardiac fibrosis (which is associated with cardiovascular disease) using cardiac MRI data from 41,505 UK Biobank participants. In the subsequent large-scale GWAS of cardiac fibrosis, we identified 11 independent genomic loci, 9 of which were implicated in in vitro cardiac fibroblast activation.

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  • Liability scores for chronic obstructive pulmonary disease obtained from our deep learning model improve genetic association discovery and risk prediction. We trained our model using full spirograms and noisy medical record labels obtained from self-reporting and hospital diagnostic codes, and demonstrated that the machine-learning-based phenotyping approach can be generalized to diseases that lack expert-defined annotations.

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  • We introduce scEC&T-seq, a new single-cell sequencing method that enables parallel profiling of extrachromosomal circular DNA and mRNAs in single cells. Using scEC&T-seq, we characterized all types of circular DNA elements in single human cancer cells and profiled the intercellular heterogeneity and structural dynamics of cancer-specific extrachromosomal DNA.

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  • Single-cell RNA-sequencing analysis combined with host genetic data for a Japanese population reveals the dysfunction of innate immune cells, particularly non-classical monocytes, in individuals with severe COVID-19, as well as enrichment of host genetic risk factors for severe COVID-19 in monocytes and dendritic cells.

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  • Genome assembly of nine wild species and two domesticated accessions of tomato generated a super-pangenome for the tomato clade. Comparative analyses revealed the landscape of structural variations in wild and cultivated tomatoes and led to the discovery of a wild tomato gene that has the potential for yield increase in modern breeding.

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