alex ioannidis
@alexgioannidis.bsky.social
computational genomics, ML & AI in health, professing, kitesurfing, sailing καὶ γνώσεσθε τὴν ἀλήθειαν, καὶ ἡ ἀλήθεια ἐλευθερώσει ὑμᾶς https://ioannidislab.ai
Just got our @genomeresearch.bsky.social article by Margarita Geleta. 📬 I love hard copies...still here's a link genome.cshlp.org/content/36/2... Rita's article was a tour de force of genomic uses for the autoencoder architecture: compression, dim reduction, ancestry, synthetic genomes.
Some data isn't fit for LLMs, esp. many biomedical datasets & anything with spreadsheets. Large Tabular Models (LTMs) are the way to go! Our LTM (iLTM accepted #KDD2026) is now in the dictionary! Thanks @spectrum.ieee.org and @merriamwebster.bsky.social! www.merriam-webster.com/dictionary/t...
Scaling genetic clustering (ADMIXTURE/STRUCTURE-style unsupervised clustering) is now easy. Out in Bioinformatics, our ADAMIXTURE method clusters all of UK Biobank (500k genomes) in just over a hour with likelihoods as good as ADMIXTURE, which would take weeks. doi.org/10.1093/bioi...
ADAMIXTURE: adaptive first-order optimization for biobank-scale genetic clustering
AbstractMotivation. Estimating genetic clusters from sequencing data is a fundamental task in population and medical genetics, enabling demographic inferen
doi.org
Proud of @carbarjon.bsky.social who just earned her PhD after getting the cover of Nature Medicine earlier this spring! In her study we show clinically relevant allele frequencies can vary regionally across Mexico by more than even between many global populations. www.nature.com/articles/s41...
The University of California should bring back a standardized test admissions requirement, the editorial board writes.
Opinion | Bring Back the SAT, California
Under the test-blind policy, more students are thrown into classes for which they are unprepared.
nyti.ms
How better to celebrate Independence and Freedom than the free launching of fireworks all across east Oakland? While we in Academia argue about the abstract, life is happening here, and I love it!
We are presenting ARGformer tonight at #PEQG26! We released ARGformer this winter (www.biorxiv.org/content/10.6...) bc ARGs are huge & hard to use. ARGformer turns local genealogical paths into tokens & learns dense embeddings, similar to language embeddings, to visualize, clustering, and query.
ARGformer: learning on ancestral recombination graphs with transformers
Recent advances in inference of the ancestral recombination graph (ARG), which describes how segments of chromosomes trace back through recombination and shared lineages, have made it possible to reco...
biorxiv.org
Scenes from the HUGO workshop in Athens, Greece 🇬🇷 HPRC collaboration in action, advancing pangenomics both stateside and abroad.
Very proud to share our new work on General, orders-of-magnitude faster whole-genome analysis with genotype representation graphs (GRG). We topped ourselves in this one 🚀 and made GRG a practical foundation for biobank-scale population and statistical genetics. www.biorxiv.org/content/10.6...
biorxiv.org
www.biorxiv.org/content/10.6... thoughtful new local ancestry method by Rita Geleta, @alexgioannidis.bsky.social & others. Really looking forward to using it! 🧬
biorxiv.org
The Israeli bombardment in Lebanon has killed more than 680 people and displaced over 800,000, according to Lebanese officials. Follow live Middle East updates. nyti.ms/4b6i7iH
This matches my experience. The implementation of this system has increased inequality in some cases. Underrepresented groups are underrepresented in getting extra exam time in my classes, imposing an additional burden on those groups, as others shift their exam times forward, chasing the curve.
Financial Times@financialtimes.com · 8mo agoHow redefining special needs rocked education on.ft.com/4iRbp22 | opinion
Life is what happens when you’re busy trying to get your paper published
Student acceptance of violence to silence speakers is at a record high. In 2020, 1 in 5 students said violence was acceptable to stop a speaker. In 2025, that number is 1 in 3. That’s a 79% increase in just five years. And it’s chilling.
The attorney general would be wise to read the words of the Supreme Court, which has repeatedly held that the "proudest boast" of America's free speech tradition is "freedom for the thought that we hate."
"He retired from public performances in the 1970s and focused on teaching. He taught for many years at the University of California, Santa Cruz, splitting his time between there and Cambridge." Tom Lehrer had it all figured out. RIP to one of my heroes. www.npr.org/2025/07/27/8...
Tom Lehrer, influential musical satirist, dies at 97
The songwriter and math professor found a following with his satirical political songs.
npr.org
I'm disturbed by tenured faculty on here behaving like high school bullies. I ask them to look up ad hominem and recognize that what Mamdani did was atrocious and newsworthy. Why are we defending an uber-privileged applicant whose father was faculty at the Ivy League university he was applying to?
After a quarter of a century, the UCSC Genome Browser remains an essential tool for navigating the genome and understanding its structure, function and clinical impact https://go.nature.com/40wPxkB
’We couldn’t live without it’: the UCSC Genome Browser turns 25
After a quarter of a century, the website remains an essential tool for navigating the genome and understanding its structure, function and clinical impact.
go.nature.com
It is with great sadness that we mourn the loss of our friend and colleague Dr. Atul Butte. A hui hou Atul. We will miss you.
I have an opportunity to hire a staff scientist for my lab. Looking for someone with outstanding skillset in ML/statistics, genomics applications; interest in mentoring, strong publication record, PD experience required. Email CV to me+cc my assistant (see 'contact' on my website). Ad to follow.
Most proteins are left-handed, but scientists have found an ancient molecule that works in both mirror-image forms https://go.nature.com/4mCImRm
Rare ‘ambidextrous’ protein breaks rules of handedness
Most proteins are left-handed, but scientists have found an ancient molecule that works in both mirror-image forms.
go.nature.com
Very sad to see this. Cemal Kafadar is a deep, evenhanded scholar, and had a formative influence on my understanding of Ottoman history as an undergraduate. www.thecrimson.com/article/2025...
Harvard Dismisses Leaders of Center for Middle Eastern Studies | News | The Harvard Crimson
Interim Harvard Dean of Social Science David M. Cutler ’87 dismissed the director of the Center for Middle Eastern Studies, professor of Turkish Studies Cemal Kafadar, and its associate director, Hist...
thecrimson.com
We Were Badly Misled About the Event That Changed Our Lives @zey.bsky.social
Opinion | We Were Badly Misled About Covid
The same dangerous mistakes. The same lack of candor.
nytimes.com
![Nearly simultaneously, at approximately 7:02 p.m., Ms. Chung received a text
message from a number previously unknown to her, saying: "Hi, Yunseo. This is Audrey from the
police. My job is to reach out to you and see if you have any questions about your recent arrest
and the process going forward. When are [sic] available for a phone call?"](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:qrllvid7s54k4hnwtqxwetrf/bafkreih4efjchfebza6qjktkedhrsponybzoedwx4xvajvhvb4onu6q5jy)