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...

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...

1/ Excited to share my first first-author preprint from my PhD!

We introduce Perseus, a lineage-aware confidence estimation framework for taxonomic classification in long-read metagenomics.

Preprint: www.biorxiv.org/content/10.6...
Code: github.com/matnguyen/Pe...

Time for a thread on our Christmas preprint “Origin and evolution of acrocentric chromosomes in human and great apes”. I had so much fun with this project and paper. It will be hard to summarize in a thread, but I’ll try www.biorxiv.org/content/10.6... [1/21]

Legal disclaimer: We are in no way affiliated with Auntie Anne’s or any other pretzel-based entity 🥨

Johns Hopkins researchers to present at Genome Informatics 2025 Students from the Department of Computer Science will give talks and present posters on their research in genome informatics.

Check out the cool work being presented by our students at Genome Informatics! This year’s event was co-organized by @benlangmead.bsky.social, & features talks from @vikramshivakumar.bsky.social & more, plus posters from @alexsweeten.bsky.social, @maojanlin.bsky.social, & @sinamajidian.bsky.social:

A complete diploid human genome benchmark for personalized genomics Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...

Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]

Congratulations @benlangmead.bsky.social!

Congrats to @dantipov.bsky.social et al. on the publication of Verkko2! The team put a ton of work into this making it the first assembler that deals with the complexity of human acrocentric chromosomes. Lots of interesting discoveries to come! genome.cshlp.org/content/earl...

Partitioned Multi-MUM finding for scalable pangenomics Pangenome collections are growing to hundreds of high-quality genomes. This necessitates scalable methods for constructing pangenome alignments that can incorporate newly-sequenced assemblies. We prev...

Excited to share a new update to Mumemto, scaling MUM and conserved element finding to any size pangenome! Preprint out now w/ @benlangmead.bsky.social.
Mumemto scales to the new HPRC v2 release and beyond, and can merge in future assemblies without any recomputation! 1/n

Our pre-print on investigating variation in South Asian genomes is now out!

Thank you to @mikeschatz.bsky.social, @rajivmccoy.bsky.social and @aabiddanda.bsky.social for all their work on this.

🧵 A thread on the key results and takeaways from our work:

NIH is allowing us to recruit postbacs and postdocs again. Please reach out if you are interested in working with us! Ad: genomeinformatics.github.io/jobs2025/

Thank you to everyone who attended, and thank you to everyone who got me to this point - I appreciate you all.

I'm on the job market this summer, so please send any interesting opportunities my way 😃

@alexsweeten.bsky.social (John Hopkins) closes the session with improvements in annotation of satellite DNA in human assemblies

Glad my pun was appreciated 😂

A phylogeny of the 7 ape genomes that have now been completed from "T2T", with Homer Simpson representing mankind.

A project five years in the making, we've now published complete "T2T" genomes for six additional ape species! It turns out that finishing (and analyzing) six genomes is slightly more work than one... doi.org/10.1038/s415...

We ran Mumemto on 474 human assemblies from @humanpangenome.bsky.social to find syntenic regions using MUMs. Mumemto scales remarkably well to large pangenomes thanks to compressed-space algos! It took under 2 days across 7 nodes (each using ~500 GB memory).

k-mers have been hit by a smooth criminal 😎

ModDotPlot session is happening now:
www.youtube.com/watch?v=fkkJ...
You can learn how to visualizate tandem repeats.
academic.oup.com/bioinformati...
@thebgacademy.bsky.social @alexsweeten.bsky.social

Animated GIF - Find & Share on GIPHY Discover & share this Animated GIF with everyone you know. GIPHY is how you search, share, discover, and create GIFs.

ModDotPlot preprint is now out! Winner of best poster at RECOMB 2023, it can generate either static or interactive dotplots in minutes using hierarchical modimizers. With @alexsweeten.bsky.social and @mikeschatz.bsky.social
Preprint: www.biorxiv.org/content/10.1...
Code: github.com/marbl/ModDot...