Jack Kosmicki

It's mostly an interactive way to engage with the complete scope of the paper (main text, supplemental text/tables, and any code/data). Also being able to generate a slide deck that summarizes the entire interactive session is 🔥 [just make sure you install document and pptx skills]!

vibe reading papers with Claude is a game changer #vibereading

😂 I like blue too!!

But in all seriousness, hope you all recover quickly!

Ancient bone found in Spain could be from Hannibal's war elephants It would be the first hard evidence that elephants were used in battle by General Hannibal.

I found @gingerhowley.bsky.social's next aDNA project ;)

www.bbc.com/news/article...

The No ICE in Minnesota is a fantastic deal. Lots of good video games and lots of physical games (TTRPG, etc) too! itch.io/b/3484/no-ic...

🎉Congratulations Caleb! Such a creative and beautiful study and to top it off, so elegantly written.

Population-scale sequencing resolves determinants of persistent EBV DNA - Nature Population-scale WGS reveals genetic determinants of persistent EBV DNA, linking immune regulation—especially antigen processing and MHC class II variation—to EBV persistence and heterogeneous di...

Today in @nature.com, we describe how discarded reads in biobank-scale WGS can help resolve the genetic predictors and consequences of Epstein-Barr Virus (EBV) infection.

Wonderful working with @ryandhindsa.bsky.social @sherrynyeo.bsky.social @erinmayc.bsky.social

www.nature.com/articles/s41...

A new preprint from Peter Mchale and Michael Goldberg in my group on the latent biases inherent to current models of non-coding constraint.

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

It's truly a sad state of affairs when it takes longer to pull GWAS sumstats out of the AllofUs research platform than it takes to generate them.

Really nice work by @nbaya.bsky.social and co. showing that, as expected, individuals whose observed phenotype deviates from their genetically predicted trait are enriched for rare damaging variants in associated genes with said trait.

Now to see if embryo selection companies pick up on this 😉

Embryo selection company Herasight goes all in on eugenics ...

I wrote about the bizarre case of Herasight, the embryo selection company going all in on eugenics.

Get notifications on desktop and mobile from long-running jobs in your terminal sessions If you’re like me, you get tired of waiting for long-running jobs in the terminal. You run a new command, and you don’t really know how long it should take to finish. Will it be done in 30 seconds? 5 ...

You run a new command in #rlang #python #bash, and you don’t really know how long it should take.

Will it be done in 30 seconds? 5 minutes? 45 minutes? Longer? 😫

An automatic notification might help to stay focused on #programming

Let me introduce you to ntfy.sh

slowkow.com/notes/ntfy/

Genetic analysis of 7,000 year old preserved goat leather from Cueva de los Murciélagos (Albuñol, Spain). Advances in ancient DNA research have expanded the range of materials from which genetic information can be recovered, enabling the analysis of atypical materials. These often preserve both host and e...

Another #aDNA preprint! We recovered DNA from 7,000 year old (!) goat leather from Cueva de los Murciélagos - and see a genetic link with Bermeya goats today!

Credit to Francisco Martínez-Sevilla for seeing me on Youtube(?!) + reaching out to collaborate - there's still value in the internet.

Excited to share our new FinnGen single-nucleus multiome preprint! 🧬

We profiled ~10M PBMCs (snRNA-seq + snATAC-seq) from 1,108 Finnish donors to map how genetic variants drive complex disease through chromatin and gene regulation 🧵👇
🔗 Link: www.medrxiv.org/content/10.1...

Massive single-cell study by Kanai et al (www.medrxiv.org/content/10.1...):
- Once statistical power is high, constrained genes have more (though weaker) eQTLs.
- Chromatin-QTLs near constrained genes have "normal" effect sizes, colocalize more with disease, but exhibit attenuated peak-gene effects.

Sumstats are currently available upon request: forms.office.com/r/qipvY8nNTK

🚨Nearly all GWAS is done in adults - making inferences about genetic effects in children or child-specific traits/diseases impossible to know.

A huge study of 80.6k Japanese children covering 1.1k GWASes (many for the first time) by is now out www.medrxiv.org/content/10.1...

Great use of AI 🙄

www.nature.com/articles/s41...

Boston’s first-ever Michelin Guide revealed: See which restaurants made it The Michelin Guide has officially revealed which restaurants in Boston are worthy of its prestigious honor.

Yes, Boston's food scene is . . . underwhelming at best. The only restaurant to receive a ⭐️ was 311 Omakase - not the local favorites - Sarma, Oleana, Mooncusser, Nightshade Noodle Bar (which frankly are all massively overrated).
www.masslive.com/boston/2025/...

Inferring Domestic Goat Demographic History Through Ancient Genome Imputation Abstract. Goats were among the earliest managed animals, making them a natural model to explore the genetic consequences of domestication. However, a chall

Our paper on imputation of ancient goat genomes is now available at GBE - congratulations to @jolijnerven.bsky.social #aDNA

🚨I did my PhD at Harvard and it fundamentally shaped who I am today. It's extremely sad to see their PhD admission cuts for the next 2 years.
- Science ⬇️75%
- Arts & Humanities ⬇️60%
- Social Sciences ⬇️50–70%
- History ⬇️60%
- Org. & Evo. Bio. ⬇️75%
- German ⬇️100%

www.thecrimson.com/article/2025...

FinnGen public release October 14: The first set of clinical laboratory value GWAS results. FinnGen logo and a black-and-white abstract genetic data pattern at the bottom. Graphics credits: Aalto University, Visual Communication Design Team.

Just in time for #ASHG2025, a new FinnGen public data release is live!
This release features the first clinical laboratory value association results. Analyses cover 383 lab measurements (OMOPIDs) with data from ≥1,000 participants each.
Access the results here: www.finngen.fi/en/access_re...

Meet FinnGen at the ASHG 2025! | FinnGen Results based on the FinnGen data are presented in almost 40 talks or posters during the 2025 Annual Meeting of the American Society of Human Genetics (ASHG) in Boston, October 14-18. We also have a b...

We’re getting ready for an exciting week at #ASHG2025 in Boston! Come meet the FinnGen team at booth 147 - we’ll be sharing updates and showcasing new public resources and tools. Plus, don’t miss the various presentations featuring FinnGen results across the program!
www.finngen.fi/en/meet-finn...

Improved allele frequencies in gnomAD through local ancestry inference - Nature Communications This study incorporates local ancestry into the Genome Aggregation Database (gnomAD) to improve allele frequency estimates for admixed populations, enhancing variant interpretation and enabling more accurate and equitable genomic research and clinical care.

📃 We’re excited to share our latest work, now published in Nature Communications — a major update to the Genome Aggregation Database (gnomAD) that improves allele frequency resolution for two gnomAD-defined genetic ancestry groups using local ancestry inference (LAI).

😬😬😬😬

Old Goats: 3,000 years of genetic connectivity of the domestic goat in Ireland The domestic goat likely first arrived to the island of Ireland as part of the introduction of agriculture approximately 5,900 years ago, and remains a part of the island's biocultural heritage. Howev...

Very happy to see our pre-print on ancient Irish goat genetics on bioRxiv #aDNA #spiergorm

I want to acknowledge this was only possible through the work of the late Dr. Judith Findlater, along with Prof. Eileen Murphy at @qubelfastofficial.bsky.social.

Interested in goats 🐐? Read our pre-print on ancient Irish goats and their connection to the Old Irish goat breed

Just look at this dashing individual, courtesy of the Old Irish Goat society

Overview of a research study about COVID-19. The study includes three cohorts: (1) 351 acute COVID-19 patients across 5 severity levels and 3 time points profiled by multiple modalities, (2) 4 acute COVID-19 patients treated with tocilizumab, (3) 73 patients, 43 of whom were previously infected with SARS-CoV-2 3 months ago. The overview shows the general study design and visualizations of the single-cell RNA sequencing data analyzed in this study.

I'd like to announce the medRxiv preprint of our latest work:

A multimodal atlas of COVID-19 severity identifies hallmarks of dysregulated immunity.

www.medrxiv.org/content/10.1...

Until I saw this was related to #TraitorsIRL, I thought this was a joke related to an entirely other event 😂