I’m very proud to announce my first publication. Featured on the cover of G3 Genes | Genomes | Genetics. The haplotype-resolved genome of European hazelnut will be a valuable resource for the plant breeding program here at Oregon State University. academic.oup.com/g3journal/a…

The AI models will not be able to predict true biology. The data is too poor. Too many assumptions using tools for which it doesn’t have the context or understand the limitations. Accurate and cheap promoter & UTR identification assays in non model species seems far away.

Interesting that it performs well on protein and chemical reasoning and then all models fail to integrate those datasets via phylogeny.

A Nanopore ultralong run we just did for Hop! Nearly 110Gb off a single flow cell with the true N50 probably >70Kb. Very excited for this one 🚀🧬 #ONT

Finally using pixi to write up all code for a project. Multiple sub environments, with underlying tasks and scripts singularity container calls within. Excited to just include the .toml .lock with publication and be done with it. Should have done this months ago!

It’s a great tune. But I might be biased🧬

Can we make it easier to submit gff files to genbank? It is so convoluted and time consuming compared to a genome upload. I’m still seeing papers say “check figshare” tempting me to do the same.

Pleased to share this free link to our new review of genome annotation in @NatureRevGenet, which just appeared today. Co-authored with Hyunjoo (Hayden) Ji and Mihaela Pertea @elapertea. We focus particularly on human annotation: rdcu.be/e4mI1

Preparing a 20min talk for a broad audience interested in AI and GPUs. Three case studies: metagenome assembly binning (LORBIN), gene prediction model generation (Tiberius) and pangenome variant calling (DeepVariant). Yes, I will be speaking fast. 1 slide for installs though!

Excited about this tool! The upcoming trio feature is particularly important for these complex regions

The complete genome of a songbird. #ReferenceGEnome #SongbirdGenome #ZebraFinchGenome #T2T #LongRead #Sequencing @biorxiv_genomic biorxiv.org/content/10.1101/…

~25% of human candidate cis-regulatory elements (cCREs) are derived from transposable elements, further shaping gene regulation, TF binding, and GWAS variant enrichment. Uncover the science behind it: biorxiv.org/content/10.1101/…

The growing library of vertebrate genomes is already transforming scientific exploration and enabling research that would have been impossible just six years ago. We look forward to more collaborative insights from this stellar team as they continue generating reference genomes for species with backbones! Across the globe, EBP groups are sequencing vertebrate genomes — both locally and globally — to contribute to the growing database of high-quality reference genomes! 🧬🌍 The Vertebrate Genomes Project, an EBP genomic powerhouse, collaborates with other EBP initiatives, including the B10K project at BGI Group (10,000 Bird Genomes), the Amphibian Genomics Project, the Tree of Life Programme, DAISEA AfricaBP, the Cetacean Genomes Project (whales and dolphins), and many more. Together, these projects show how global collaboration can overcome challenges, sequence rare or hard-to-find species, and develop shared methods that benefit researchers worldwide. @genomeark | @DAISEA_AfricaBP | @erga_biodiv European Reference Genome Atlas | @PEPR_ATLASea : atlas of marine genomes | @sangerinstitute | @BioplatformsAus Australia | Wise Ancestors | and many more groups! Several EBP groups are now on BlueSky, please find us there to follow updates: linktr.ee/earthbiogenomeproj…

This morning Mark Blaxter, Head of the Tree of Life Programme, was on BBC Radio 4 Today discussing the importance of sequencing all life, including those in our oceans 🌊 Catch up here (starting at 2hrs 26 mins) ⤵️ bbc.co.uk/sounds/play/m002hb…

Pangenome-guided sequence assembly via binary optimisation. #GenomeAssembly #PangenomeGuiedeAssembly @biorxiv_genomic biorxiv.org/content/10.1101/…

New preprint shows that DALI, TM-align and Foldseek overestimate protein structure alignment significance by 5-6 orders of magnitude biorxiv.org/content/10.1101/…](biorxiv.org/content/10.1101/…

Evaluation of sequencing reads at scale using rdeval. #SequencingData #ReadsSummary #Bioinformatics academic.oup.com/bioinformat…

A really nice paper. Still a lot of work to do for plant scientists looking to take their annotations to the next level and make use of next-gen protein prediction and binding algorithms. Thanks to the Maize folks for this solid work!!

🌍 Hear from Erich Jarvis, chair of the EBP-affiliated Vertebrate Genomes Project at the Rockefeller University, as he explains why high-quality reference genomes across the Tree of Life are essential for conservation. 🦜🐋🐒 🧬He also shares how the VGP is helping to coordinate a nationwide platform to ensure the continued generation of reference genomes across the United States. 👉 bit.ly/401IbWl @genomeark @RockefellerUniv @erichjarvis #Conservation #Genomics #DNA #scienceinnovation #fundingnews #sciencenews

Slides from my talk (with Kamil Jaron) on an history of k-mers in bioinformatics: rayan.chikhi.name/pdf/2025-k…