Dr. Arun Sethuraman

Recently we're working with SNPs from whole genome assemblies to estimate ARGs. It's a pain to go from alignment files to vcf, keeping track of masked and invariant sites. So we wrote a snakemake/SLURM pipeline. Hope it's useful to others, and don't hesitate to post issues if there are problems!

Incorporating polygenic risk scores and social determinants of health across populations: Considerations and best practices in research Despite increasing focus on the intersection of genetic and social risk factors on health, heterogeneity in how these factors are measured, distributed, and analyzed across populations and datasets co...

🧬 New Review from Cromer et al!
📄 Incorporating polygenic risk scores and social determinants of health across populations: Considerations and best practices in research
#PRS #SDoH

Large genome model: Open source AI trained on trillions of bases System can identify genes, regulatory sequences, splice sites, and more.

Evo 2 is here, and the scale is wild. It’s trained on nearly 9 trillion bases across all domains of life, picking out regulatory DNA and splice sites that often trip humans up. It’s fully open-source and already identifying critical BRCA2 mutations with impressive accuracy.
🧬💻

A digital CAPTCHA verification window titled "Select all squares with PIPES" against a plain white background. The window contains a 3×3 grid of numbered squares, mixing literal hardware, smoking pipes, and programming syntax.

These captchas just keep getting harder #rstats

That's a good name for software:

MKado: a toolkit for McDonald-Kreitman tests of natural selection

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

Good morning ❤️

Population genomics using ancient DNA data 21th-25th September 2026

🚨 Registrations are now open for the 4th edition of the course Population Genomics Using Ancient DNA with @arunsethuraman.bsky.social & @cegamorim.bsky.social 🧬

Learn to analyse aDNA data, from data QC to population structure & demographic inference.

www.physalia-courses.org/courses-work...

I think Calvin doesn’t think my breakfast looks very appetizing - where’s the tuna, human?!

On the expansion and evolution of a master’s project Academics often lament that hardly any master’s projects – even the best ones – get published. The student moves on. Other research takes priority. No one has time to do the final analyses. Here I tel...

Academics often lament that hardly any master’s projects get published. The student moves on. Other research takes priority. No one has time to do the final analyses. Here I tell how one master’s project was, through persistent teamwork, finally carried over the finish line: go.nature.com/4aKs7N3

Pic from my tenure + NSF CAREER award celebration party back in 2023 at Jody’s! ❤️

I miss my Hey Lab peeps, but more importantly, I miss collaborating on all this fun science. Congrats to Alex & @sarahtishkoff.bsky.social on this new paper! I remember discussing ghost introgression with them back in 2013/14. So happy to see it come to fruition. www.science.org/doi/10.1126/...

I had fun writing this N&Vs on two fascinating new papers on centromere evolution in yeast. If you’re interested in how centromeres adapt yet stay functional, here’s my take. rdcu.be/e6DD0 @nature.com @gautamdey.bsky.social @gsherloc.bsky.social @helsenjana.bsky.social @maxhaase.bsky.social

The core-pivotal index: a geometry-first approach to academic impact The defining goal of the academic endeavor is to establish a single perfect value that completely summarizes entire careers’ achievements. Such an index wo

@russcd.bsky.social ushers in a new era of academic metrics with the core-pivotal author index, which assigns all credit to authors that occupy the exact center of the author list, while non-central peripheral authors receive no credit whatsoever.

🔗 doi.org/10.1093/molbev/msag026

#evobio #molbio

Awww! Thank you - this just made my day! ❤️ Hail our beautiful spider bebes!

Postdoctoral Researcher - Evolutionary Genomics and Population Genetics Position Title: Postdoctoral Researcher - Evolutionary Genomics and Population Genetics Appointment Type: Post Doc/Trainee Job Description: Summary of Duties and Responsibilities: We are seeking a Pos...

Postdoc in evolutionary genetics with @mbhufford.bsky.social isu.wd1.myworkdayjobs.com/IowaStateJob...

Integrating the Microbiome Into Infection Ecology and Evolution in Wild Animals Parasites are a ubiquitous force in nature threatening wildlife populations and ecosystems. Interactions between hosts and their parasites are impacted by host-associated microbiomes, which are essen...

A nice collaboration from post-docs in my lab 😊 onlinelibrary.wiley.com/doi/full/10.... @jingdi.bsky.social @luismsilva.bsky.social @paradyseb.bsky.social @molecularecolup.bsky.social

We are very excited to share a new resource from our team: spatial subcellular proteome maps in plants! We developed an MS-based method that registers localizations of about 8000 proteins in Arabidopsis roots in a single experiment.

(1/9)
www.biorxiv.org/cgi/content/...

The distribution of fitness effects of new mutations in regulatory regions of the D. melanogaster genome https://www.biorxiv.org/content/10.64898/2026.03.01.708907v1

Detecting and Quantifying Networks of Biological Kinship via Exponential Family Random Graph Models Abstract. Genetic relatedness between ancient humans can help to identify close and distant connections between groups and populations, uncovering signatur

Excited to share our study in GENETICS on exploring biological kinship in ancient DNA data sets (doi.org/10.1093/gene...).

Using ERGMs to find variables that correlate with relatedness, and applied to 6th-9th century Avar, we find evidence for female exogamy and the existence of an elite class.

Was seed color in early crops really chosen for aesthetics?
White seeds evolved repeatedly-not because humans preferred them, but because losing pigmentation reduced seed dormancy. Ecology, not intention, may have driven domestication. www.biorxiv.org/content/10.6...
#PlantScience #Domestication

TLDR? Here, lemme be your AI chatbot and summarize it for you. 1) Don’t, 2) Absolutely not, 3) Nope, 4) No no no, and 5) Go see your real physician.

Researchers in the US might be having feelings about writing grants atm-I know I am!

We still need to write them. In this Evolution Exchange, I again chat with Sam Scheiner, who summarizes how to write a competitive proposal.

His advice is gold, and helpful regardless of funder. Pls RT!

We have a new preprint! - "Ancient Pathogen Genomics in Africa – Current Evidence and Future Directions"

A review of current evidence, challenges, and opportunities for studying past epidemics and host–pathogen evolution using ancient DNA from African contexts.

www.preprints.org/manuscript/2...

Had my folks send me some golden oldies for my upcoming keynote lecture. Here’s my mom running a teacher workshop in the early 90s, and my dad presenting his carburetor innovations to then Indian Prime Minister, Rajiv Gandhi in the mid 80s. ❤️

Annotating genomes at increased scale and resolution - Nature Reviews Genetics In this Review, Ji et al. overview how rapidly advancing experimental and computational methods are enabling improved and automated annotation of gene structure and function, providing researchers wit...

The growing number of sequenced #genomes provides a positive feedback loop, in which database searches become more effective and shared sequence patterns emerge more clearly www.nature.com/articles/s41... #biodiversity #genomics

rambaut/figtree Automatically exported from code.google.com/p/figtree - rambaut/figtree

The first version of FigTree was released nearly 20 years ago and it is still widely used (including by me). But there are currently 85 issues on the GitHub repo (github.com/rambaut/figt...) and some of them I don’t really like the look of.

😹😹😹😹😹

Please make it stop. Ugh. This is worse than Googling symptoms.

So proud of students from my lab who presented at the @sandiegostate.bsky.social Student Symposium (S3) today! Also, if you’re in town, I am SDSU’s keynote speaker at the S3 Awards Ceremony, happening next Friday (3/6) at 8.30 am, Montezuma Hall @ The Student Union. See y’all there!

Stanford researchers help trace ancestry for African Americans A group of Stanford researchers is offering a mathematical model to help link family connections up to 410 years ago.

Excited that our work was featured on the local (Bay Area) news for their Black History month series. Interview with Noah and clips from my interview with @dornsife.usc.edu and CGSI talk in the article below

www.nbcbayarea.com/discover-bla...