I am still allowed on campus, so please let me know when you will be in town! Will be great to see you! I owe you some hospitality 😊

Would love to reminisce with you all, but I've been signed up for a mountain of mandatory training and online orientations. You mean to tell me that academia has bureaucracy too?! I've been duped!! 😂

🫶

Likewise Denis! Many thanks for your support!

Would be so great to catch up Duncan!

Friday was my last day at NHGRI. After 10 wonderful years, my lab is headed to Johns Hopkins University
genomeinformatics.github.io/movingday/

Congrats Fran! 🎉

Super happy to share the published version of our study: “Germline sequence variation within the ribosomal DNA is associated with human complex traits” in Cell Genomics www.cell.com/cell-genomic...!

Reference mule "Symphony" pictured here with her mom, courtesy of Doug Antczak & Camille Holmes @ Cornell VetMed. I always love when we get to see pictures of the animal we sequenced, especially when they are cute 🐴🐴

🐴 Happy to announce a new addition to the T2T stable! "Fully Phased Telomere-to-Telomere Assemblies for Thoroughbred Horse and Donkey Haplotypes derived from a Mule Illuminate the Peculiar Evolution of Equid Centromeres"
📄 www.biorxiv.org/content/10.6...

This. A thousand times this.

Meiosis faces a fundamental problem:

It must repair hundreds of DNA double-strand breaks while executing a transcriptional programme essential for gamete development.

But many of these breaks occur in genes.

So how are these two processes reconciled?

www.biorxiv.org/content/10.6...

With this new understanding of short-arm structure, our open-source method provides the first short-read, sequencing-based diagnostic for Robertsonian chromosomes, providing a more affordable and scalable option for ROB screening compared to karyotyping 🙌
💾 github.com/marbl/DJCoun... [8/8]

We also identified rare structural variation on the short arms resulting in duplicated (~9%) and deleted (~3%) distal junction sequences. The DJ has been hypothesized to play a role in nucleolar function, so it will be interesting to further investigate the effects of such variation [7/8]

We used this insight to detect potential ROBs in large-scale sequencing cohorts (including UKBioBank) and identified candidate ROB carriers at a frequency of 0.11–0.12%, roughly matching the expected frequency of 1 per 800 individuals [6/8]

Thus, the most common ROBs (i.e. 13;14 or 14;21) result in the loss of exactly 2 of 10 DJ copies, making them an effective marker that can be copy-number typed via short-read sequencing! An individual with 8 DJ copies very likely carries a ROB [5/8]

Total rDNA copy number is highly variable and cannot be used as a reliable maker for ROBs. However, T2T human genomes have revealed that the palindromic “distal junction” (DJ) sequence immediately upstream of the rDNA is both highly conserved and typically single-copy per chromosome [4/8]

With the Gerton and Garrison labs, we recently discovered that most ROBs fuse at a segmental duplication located between the rDNA array and the centromere, resulting in the loss of 2 of the 10 rDNA arrays from the (diploid) genome [3/8]
📄 www.nature.com/articles/s41...

Robertsonian chromosomes (ROBs) are a fusion between the short arms of two acrocentric chromosomes. ROB carriers are generally healthy, but face an increased risk of miscarriage, children with trisomies, and (maybe) certain types of cancer [2/8]

More acrocentric investigations, this one led by @arhie.bsky.social 🕵🏻‍♀️ “Biobank-scale genotyping of Robertsonian translocations reveals hidden structural variation on the human acrocentric chromosomes” 🧵[1/8]
📄 www.biorxiv.org/content/10.6...

We built the first complete genome for the common marmoset, fully resolving regions that were previously missing: centromeres, acrocentric short arms, and more. A new reference genome for anyone working with marmosets. This was an awesome collaborative effort & I’m grateful to all my co-authors! 🧬

Myloasm, our long-read metagenome assembler, is now published! w/ @mgmarin.bsky.social and @lh3lh3.bsky.social

Very rewarding after > a year of development and countless hours thinking about assembly. Thanks to beta testers, Li lab, and reviewers who gave very helpful feedback.

rdcu.be/famFj

Rapid genome modifications including chromosomal fusions and large-scale inversions are key features in Arctic codfish species - Genome Biology Background Genome evolvability involves activation of transposable elements (TEs) that result in novel genomic rearrangements, including translocations, deletions, duplications, as well as larger stru...

Finally is the paper where we present the unique genomic architectures of the Arctic codfishes out!! Nice work by @gadus-sivus.bsky.social and co-authors …
@biovitenskap.bsky.social
@unioslo-cees.bsky.social

link.springer.com/article/10.1...

TTT is compatible with Verkko assembly outputs, and has allowed us to investigate some interesting tangles that were previously hidden by gaps in the assembly, such as these megabase-scale arrays of PAK3-like genes on the zebrafinch Z chromosome 🐦 Try it out for yourself! (4/4)

The size and identity of the involved repeats can make finding the true reconstruction impossible, but TTT searches for a path that is most concordant with the input sequencing data, yielding a good model of the sequence and its internal structure (3/4)

Despite being proposed ~25 years ago, few sequence assemblers actually solve the Eulerian path problem because assembly graphs tend to be noisy. Dima devised a clever approach to optimize the edge multiplicities of a tangle using MILP so that an Eulerian path is guaranteed (2/4)

Recently amplified gene arrays are a super interesting phenomenon, but many still resist our attempts to assemble them. @dantipov.bsky.social has developed a new method (Trivial Tangle Traverser) that resolves assembly graph tangles caused by such sequences (1/4) www.biorxiv.org/content/10.6...

AlphaFold database has entered the era of complexes. Together with NVIDIA, DeepMind and EBI, we use ColabFold, OpenFold and MMseqs2-GPU to predict ~31 million complexes (homo & hetro-dimers) resulting in 1.8 million high-quality predictions
📄 research.nvidia.com/labs/dbr/ass...
🌐 alphafold.ebi.ac.uk

Trippy Memphis bridge https://pangenome.github.io/MemPanG26/

Level up your #pangenomics game! Workshop, conference & biohackathon in #Memphis, May 11-15, 2026. Join us and get your hands dirty with sequence alignment, explicit and implicit graphs, cutting-edge methods, and AI. Register now! pangenome.github.io/MemPanG26/ #Bioinformatics #MemPanG26

Excited so share our newest study using a single-library HiFi-CiFi approach to generate chromosome-scale diploid assemblies of two vole genomes, identifying putative drivers of divergent pair-bonding behavior, namely a prairie-vole-specific duplication of Avpr1a gene, led by @mabuelanin.bsky.social