Jack Kosmicki

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 😂

a cartoon of a man giving an ok sign with the word perfection below him ALT: a cartoon of a man giving an ok sign with the word perfection below him

I'm 100% serious - these are eye-opening results!

The idea that the PPP captures environment is horrendously under-appreciated and your paper very convincingly demonstrates this. Showing stratification based on HOW LONG since quit smoking is both insane, but also such a chef's kiss moment!!

4) >50% of proteins predictive of disease also predict smoking (this does vary significantly by disease).

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

2) proteomics stratifies smokers, prior smokers, & non smokers (Fig. 4a)
3) proteomics even stratifies how LONG it has been since you quit smoking (Fig. 4b)🤯

Kristin Tsuo, @genetisaur.bsky.social, & Mark Daly just wrote the best proteomics paper I've read.

They convincingly show how smoking and alcohol (aka, the environment) dramatically influences proteomics data.

Some 🤯 results
1) proteomics predicts frequency (5a) & quanity (5b) of alcohol consumed

I will be recruiting two PhDs for my ERC Project HERDPATH - let's discover out how livestock and pathogens evolved together using #aDNA. Projects will be animal or pathogen focused but will be in dialogue.

Details at my quaint website below. Deadline 3rd October.

kevingdaly.github.io

🎉🎉🎉Congratulations Kevin!!!!! Very well-deserved!!!!!!

Second craziest thing you'll read today: from 2026 I will be leading an @erc.europa.eu Starter Grant project. HERDPATH will explore how livestock and their pathogens co-evolved during the last 10,000 years. PhD advertisements to come!

Press release below with one of the few good photos of me.

a close up of a pokemon card with foreign writing ALT: a close up of a pokemon card with foreign writing

😂 A WashU professor embezzled $412k and used the money to buy . . . *checks notes* . . . collectible trading cards

www.justice.gov/usao-edmo/pr...

Shameless promotion from #isba11 - I'll be hiring PhDs to start early 2026 (plus postdocs starting later), using #adna to study livestock and pathogen coevolution, particularly looking at inbreeding and immune gene evolution!

Contact me at kevin[at]palaeome.org, full ad to come. Please share!

As for other fields, like human genetics and neuroimaging, it is clear that small, under-powered studies (often with uncorrected stats and no replication sample) JUST GENERATE NOISE.

COMMERCIAL | Ancestry Confirmed as Wrexham AFC Official Club Partner Wrexham AFC are pleased to announce Ancestry as our new official family history partner, with the company’s brand to feature on the front of our new 2025/26 training wear – as worn for the first time ...

A tale of two DTC DNA companies.

While 23andMe is dealing with the bankruptcy fallout, Ancestry is sponsoring Ryan Reynolds' and Rob McElhenney's Welsh football club, Wrexham AFC.

PS: I loved watching Welcome to Wrexham ❤️
www.wrexhamafc.co.uk/news/2025/ju...