New Perspective: "Are cereal grasses a single genetic system?" rdcu.be/dErWS 30 years of genetic and genomic research in cereal crops. Genome sequences have revealed common evolutionary patterns and differences between species and will support applications in breeding.

Comprehensive genome analysis and variant detection at scale using DRAGEN. #GenomeAnalysis #VariantCalling #Bioinformatics Illumina #Dragen Nature Biotechnology nature.com/articles/s4158…

CRAG very first nanopore run was on #wheat CWR Aegilops COUSIN project! 🌱🌱 You can see by the faces that we’re pretty happy with the first result :) Joint effort with Llorenç Rovirosa and Raúl Castanera to set everything up.

Last week our #AGenT Postdoc Fellow Yuxi Hu at CRAG traveled to Canada 🍁 to carry out her secondment at U Calgary with #DrMarcusSamuel to work on the two #Pisum CWR assemblies in the framework of COUSIN project 🫛🫛 Best of Luck Yuxi, and lots of progress!

We build a pangenome reference to study genetic basis of agronomic traits and to establish GS models for grapevine breeding doi.org/10.1038/s41588… Nature Portfolio Nature Genetics International Viticulture and Enology Society VitisGen3 Horticulture Research ASHS ASPB Plant Editors Global Plant Council National Grape Research Alliance

sTELLeR: Detecting transposable elements in long read genomes academic.oup.com/bioinformatics…

Release of DeepVariant 1.8. Large speed improvement (~67% faster) via small model for easy sites. New Pangenome-aware option. Reduces error by ~30% for vg-mapped WGS ~10% for BWA WGS ~5% BWA exome. New config for custom model users, see release notes 1/3 github.com/google/deepvar…

gaftools: a toolkit for analyzing and manipulating pangenome alignments biorxiv.org/content/10.110… 🧬🖥️🧪 Source (MIT): github.com/marschall-lab/… Docs: gaftools.readthedocs.io/en/latest/

I'm very happy to announce that the MCHelper (tool for the curation of transposable element libraries) paper has finally been published in Genome Research! I will be happy to receive your feedback! genome.cshlp.org/content/early/…

Our hitchhiking paper is out at genomebiology.biomedcentral.com/articles/10.11… - a great collaborative effort with Prasadms Josipa Lipovac, FilipTomas13 JJ Liu. Briefly, Oxford Nanopore is enough for high-quality human genomes. Recently, HERRO showed that even UL is sufficient. 1/3

Verkko2: Integrating proximity ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding biorxiv.org/content/10.110… 🧬🖥️🧪 github.com/marbl/verkko

The 1001G+ project: A curated collection of Arabidopsis thaliana long-read genome assemblies to advance plant research biorxiv.org/cgi/content/sh… #biorxiv_genomic

Super proud - our new work about two troublesome TEs spreading into several Droso species in just a few decades; it was so much fun to work with the amazing Riccardo Pianezza Almorò Dr. Sarah Signor rdcu.be/d5G1M

🚨New paper, now published in nature! Using pan-genetics across the Solanum genus🍅🥔🍆we reveal why gene duplications🧬are major contingencies in crop engineering. My postdoc work in the Lippman lab Cold Spring Harbor Laboratory, in collab. with Michael Schatz and many others! nature.com/articles/s4158…

geneviewer - Gene Cluster Visualizations in R. Imports data from GenBank, FASTA, and GFF files, performs BlastP and MUMmer alignments, and displays results on gene arrow maps. github.com/nvelden/genevi… #Rstats

Grateful to share that our study on "The genetic architecture of cell type–specific cis regulation in maize" is now published in Science Magazine! Huge thank you to all co-authors and the 4 tough, but fair, reviewers who helped to improve the study 🌽🧬 science.org/doi/10.1126/sc…

Telomere-to-telomere de novo assembly from standard ONT reads (LSK114, Simplex). A really exciting advance—makes high-quality assembly practical for population-scale sequencing! Preprint from Haoyu Cheng, Heng Li and colleagues biorxiv.org/content/10.110…

PanTE: A Comprehensive Framework for Transposable Element Discovery in Graph-based Pangenomes： researchsquare.com/article/rs-586… International congress on transposable elements

Glad to see this out! The ability to map protein footprints with high resolution has been missing in the field, but no longer. Finally some definitive answers on the regulatory potential of maize transposons. Fantastic work by Josh Cuperus and co. nature.com/articles/s4147…

"A new simulation pipeline enhances benchmarking of transposon polymorphism detection tools" - a new PCI Genomics recommendation from Raúl Castanera: tinyurl.com/mr2ac84m