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Pangenome-aware DeepVariant biorxiv.org/content/10.110… #biorxiv_bioinfo

Predicting gene expression from DNA sequence using deep learning models. #GeneExpression #DNAsequencing #DeepLearning Nature Reviews Genetics nature.com/articles/s4157…

SVbyEye: A visual tool to characterize structural variation among whole-genome assemblies academic.oup.com/bioinformatics… 🧬🖥️🧪 github.com/daewoooo/SVbyE…

Nature research paper: Impacts of climate change on global agriculture accounting for adaptation go.nature.com/3TxaXKy

Mumemto: efficient maximal matching across pangenomes. #Pangenomes #VisualizationTool #PangenomeDiagnostic #Bioinformatics #Genomics Genome Biology genomebiology.biomedcentral.com/articles/10.11…

PanVA: a visual analytics tool for pangenomic variant analysis. #Pangenomes #VariantAnalysis #DataVisualization #Genomics #Bioinformatics bioRxiv Bioinfo biorxiv.org/content/10.110…

Recessive epistasis of a synonymous mutation confers cucumber domestication through epitranscriptomic regulation cell.com/cell/fulltext/…

Gene regulatory networks are crucial for understanding complex gene regulation in plants and could help improve crops for more sustainable and climate-resilient agriculture. Read about it in this Review out now in Nature Biotechnology nature.com/articles/s4158…

I am excited to share #PangenePro, our open-source pipeline for rapid gene family analysis at the pangenome level, which has been published in Bioinformatics Advances. Read more: academic.oup.com/bioadv/article…

🔴AGRI Committee Press starts in 30 minutes to vote on the report: The future of agriculture and the post-2027 common agricultural policy Follow live: bit.ly/44ijesb europarl.europa.eu/committees/en/…

Agptools: a utility suite for editing genome assemblies. #GenomeAssembly #AssemblyEditing #AGPfiles #Genomics #Bioinformatics academic.oup.com/bioinformatics…

Can an AI model predict perfectly and still have a terrible world model? What would that even mean? Our new ICML paper formalizes these questions One result tells the story: A transformer trained on 10M solar systems nails planetary orbits. But it botches gravitational laws 🧵

Enhancing stress tolerance in plants via cis-regulatory element modification using gene targeting Ke et al. 📖 nph.onlinelibrary.wiley.com/share/YM4WH3CI…

Excited to share our new method ClipperQTL published in Genome Biology Built on our p-value-free FDR control framework Clipper, ClipperQTL performs on par with FastQTL and runs up to 500× faster. Big thanks to my former PhD student Heather Zhou! genomebiology.biomedcentral.com/articles/10.11… #eQTL

SVPG: A pangenome-based structural variant detection approach and rapid augmentation of pangenome graphs with new samples biorxiv.org/content/10.110…

Data leakage is a common problem in AI. It is analogous to ‘teaching to the test’ and leads to overestimation of model capabilities. This article reports that leakage affected 294 papers across 17 scientific fields.

Detecting Foldback Artifacts in Long Reads biorxiv.org/content/10.110…

Recruitment, rewiring and deep conservation in flowering plant gene regulation nature.com/articles/s4147…

Happy to share that our work from the Nicholas Mancuso lab is out in Nature Genetics! We developed SuShiE, a multiancestry fine-mapping method for molecular traits. doi.org/10.1038/s41588…

5th Int. Legume Society Conference at Dubrovnik, Croacia 8-12 June 2026 Save the date!