For the past 30 years, “whole-genome sequencing” has been a misnomer. Today the T2T Consortium publishes a dozen papers heralding a future of truly complete genomes for humans and nearly any vertebrate 👨‍🔬🐒🐦🐀🦒🐎🫏🐹🐟 (sorry, no salamanders): www.cell.com/consortium/t... 🧵[1/15]

Finding this quite hard to stomach from a country that is bombing the shit out of other countries…

JOB ALERT! I'm hiring two postdocs in Computational Genomics to join our lab in beautiful Gothenburg, Sweden. Please share and repost! CGRLab.github.io/research/

At the end of the term I asked my college creative wriing students to submit anonymous thoughts on AI. No real surprises: Mood ranges from resignation to despair, capitulation from embittered erosion of standards to total, feelings of betrayal from deep to furious. 1/

🚨 🚨 🚨 NEW: A shocking @USCIS memo seems to declare that hundreds of thousands of immigrants living in this country and applying for green cards must instead apply for visas abroad; which could MASSIVELY disrupt lives. 🧵 on what we know, and what we don’t.

Congratulations, @vikramshivakumar.bsky.social!

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...

🚨🚨🚨 "At least 63 times since 2007, data from some of the 28 human genomic repositories that the N.I.H. controls was improperly released to researchers, used for unapproved purposes or made vulnerable to theft..." (Gift Link) www.nytimes.com/2026/01/24/u...

Genetic Data From Over 20,000 U.S. Children Misused for ‘Race Science’

nytimes.com

Pregnancy loss is common in humans, and chromosomal abnormalities are the leading cause. Using genetic data from ~140,000 IVF embryos, we show that maternal variation in meiosis genes influences recombination and aneuploidy risk. First authors: @saracarioscia.bsky.social & @aabiddanda.github.io

Common variation in meiosis genes shapes human recombination and aneuploidy - Nature

Analysis of data from pre-implantation genetic testing sheds light on the genetic basis of meiotic-origin aneuploidy, the leading cause of human pregnancy loss, identifying common genetic variants ass...

nature.com

Appalling. This whole situation has been handled so poorly, without any care for the community at Brown, the community and people that live in and around the university, and the larger Providence community.

Peter Baker@peterbakernyt.bsky.social · 9mo ago

Authorities release the man detained after the Brown University shooting spree, meaning the killer is still at large. www.nytimes.com/live/2025/12...

Just awful, awful news. Sending all my love and thoughts to those affected, and to the many on campus who never should have had to experience this.

The Associated Press@apnews.com · 9mo ago

BREAKING: Police say there are multiple victims who have been shot after an active shooter was reported at Brown University.

Hey folks, as news of Watson's demise spreads, please don't set aside his weighty legacy of misogyny and racism. He was truly among the worst of us. www.vox.com/2019/1/15/18...

DNA scientist James Watson has a remarkably long history of sexist, racist public comments

“People say it would be terrible if we made all girls pretty,” he said in 2003. “I think it would be great.”

vox.com

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:

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.

cs.jhu.edu

Fantastic talk by @vikramshivakumar.bsky.social Mumemto—Scalable multi-MUM finding for pangenomes Papers biorxiv.org/content/10.1101/2025.05.20.654611 & doi.org/10.1186/s13059-025-03644-0 Code: github.com/vikshiv/mume... Very efficient pangenome visualization tool, revealing synteny and variations!

Today, for no particular reason at all, it is worth sharing this, as a reminder of what one man's lies can do. Taken from this resource from my alma mater: costsofwar.watson.brown.edu (Specific page is: costsofwar.watson.brown.edu/costs/human/...)

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]

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 ...

biorxiv.org

Small victories, but this doesn’t seem to apply to those currently on an H-1B visa. Wish it was made clear in the initial “proclamation”, before we spent the entire day panicking while trying to figure out a way to get a friend back to the US before midnight.

Arun Das@arun-das.bsky.social · 12mo ago

This is catastrophic. So, so many people I know and love are going to find it impossible to stay and work in the US, and it makes it almost impossible for people like me to stay and work here in the longer term, no matter how qualified we are.

This is catastrophic. So, so many people I know and love are going to find it impossible to stay and work in the US, and it makes it almost impossible for people like me to stay and work here in the longer term, no matter how qualified we are.

New blog post – A quick look at Roche's SBX lh3.github.io/2025/09/11/a...

Extremely disappointed in my alma mater, who have chosen to fold without a fight and endanger the most vulnerable members of our community instead of standing up for them. Spineless and shameful.

The New York Times@nytimes.com · last yr.

Breaking News: Brown University was said to have reached a deal with the Trump administration to restore federal funding. nyti.ms/459nQzY

Getting into computational biology this summer? 🏖️ 📖 Check out “Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References” by @arun-das.bsky.social‬, @mikeschatz.bsky.social, and more for a great introduction to the field:

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

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...

biorxiv.org

Easily the most important thing happening next week. Come and watch my friend Sara defend her PhD!

Sara Carioscia@saracarioscia.bsky.social · last yr.

I'm defending my PhD next Friday, May 23!(!!!!). I'll be highlighting our work looking at aneuploidy in early human development. If you're interested I'd love to have you join via Zoom (DM me for info) or on the Homewood campus!

Really cool work from @arun-das.bsky.social on recovering sequence from unmapped reads (even with T2T reference or HPRC pangenomes!). Can recover a decent amount of sequence per individual using these approaches. Check it out!

Arun Das@arun-das.bsky.social · last yr.

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:

@arun-das.bsky.social's thesis research demonstrates that short-read mapping-based approaches, even using complete linear (T2T-CHM13) and pangenome (HPRC) references, miss a lot of variation that can be recovered from unmapped reads.

Arun Das@arun-das.bsky.social · last yr.

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:

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:

bioRxiv Genomics@biorxiv-genomic.bsky.social · last yr.

Assembling unmapped reads reveals hidden variation in South Asian genomes https://www.biorxiv.org/content/10.1101/2025.05.14.653340v1

Happening at 2pm in Biondi - come and check out Vikram’s great work!

Vikram Shivakumar@vikramshivakumar.bsky.social · last yr.

Excited to share our latest work on comparing and visualizing multiple genome assemblies to identify conservation and structural variation in pangenomes with Mumemto! Check out poster 250 at #bog25 if you are here. New preprint coming very soon 👀

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 😃

JHU Computer Science@jhucompsci.bsky.social · last yr.

Congratulations, @arun-das.bsky.social!

Hello Bluesky 👋🏾 I’m going to be defending my thesis on Wednesday, so I thought this was as good a time as any to introduce myself and my work. I’m Arun Das, I’m a PhD student in Schatz Lab @ JHU, and my work broadly focuses on algorithms to improve accessibility and representation in genomics.