Herald:The Biostar Herald for Monday, December 04, 2023

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The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here.

This edition of the Herald was brought to you by contribution from Mensur Dlakic, Istvan Albert, and was edited by Istvan Albert,

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Comparing methods for constructing and representing human pangenome graphs | Genome Biology | Full Text (genomebiology.biomedcentral.com)

In this work, we collect all publicly available high-quality human haplotypes and construct the largest human pangenome graphs to date, incorporating 52 individuals in addition to two synthetic references (CHM13 and GRCh38). We build variation graphs and de Bruijn graphs of this collection using five of the state-of-the-art tools: Bifrost, mdbg, Minigraph, Minigraph-Cactus and pggb. We examine differences in the way each of these tools represents variations between input sequences, both in terms of overall graph structure and representation of specific genetic loci.

submitted by: Istvan Albert

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Current approaches to genomic deep learning struggle to fully capture human genetic variation | Nature Genetics (www.nature.com)

Recent studies show that current state-of-the-art models struggle to accurately characterize expression variation from personal genomes, limiting their usefulness in personalized medicine.

submitted by: Istvan Albert

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Benchmarking of deep neural networks for predicting personal gene expression from DNA sequence highlights shortcomings | Nature Genetics (www.nature.com)

Our approach identifies a limitation of current methods to correctly predict the direction of variant effects.

submitted by: Istvan Albert

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Personal transcriptome variation is poorly explained by current genomic deep learning models | Nature Genetics (www.nature.com)

Here, we evaluate four state-of-the-art models on paired personal genome and transcriptome data and find limited performance when explaining variation in expression across individuals.

submitted by: Istvan Albert

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@mike_schatz is genomics data astronomical, or is astronomy data genomical? https://t.co/dyqPB6U0ya

— 𝕐 (@[e-mail]) (@nomad421) November 29, 2023

submitted by: Istvan Albert

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Accurate prediction of protein–nucleic acid complexes using RoseTTAFoldNA | Nature Methods (www.nature.com)

Accurate prediction of protein–nucleic acid complexes using RoseTTAFoldNA

submitted by: Mensur Dlakic

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