Sign in

alex ioannidis

@alexgioannidis.bsky.social
169 followers 90 following 74 posts

computational genomics, ML & AI in health, professing, kitesurfing, sailing καὶ γνώσεσθε τὴν ἀλήθειαν, καὶ ἡ ἀλήθεια ἐλευθερώσει ὑμᾶς

PostsRepliesMedia
alex ioannidis @alexgioannidis.bsky.social · 17/09/2026
Fst is a key genetic differentiation metric, but it emphasizes common variants over rare. In IEEE ICASSP out now lab member Margarita Geleta introduces Fq, which can be tuned across the allele freq spectrum. Fst & Shannon differentiation fall out of it as special cases. arxiv.org/abs/2511.03063
1114
alex ioannidis @alexgioannidis.bsky.social · 03/09/2026
ARGformer is out in Bioinformatics! doi.org/10.1093/bioi... Just as PCA reduces dimensionality from genotypes, ARGformer can do this now for ARGs...yielding a representation that comes directly from inferred genealogical topologies & at a haplotype level across each individual genome.
doi.org
ARGformer: learning on ancestral recombination graphs with transformers
AbstractMotivation. Recent advances in inference of the ancestral recombination graph (ARG), which describes how segments of chromosomes trace back through
11910
alex ioannidis @alexgioannidis.bsky.social · 01/09/2026
Gnomix is published! www.nature.com/articles/s41... Still the most accurate & fastest local ancestry inference (LAI) method, bests Flare and others (RecombMix & Orchestra) released since our preprint. Easy to use, github.com/AI-sandbox/g... Use it with our toolkit, snputils.org
nature.com
Scalable high resolution ancestry deconvolution for genomic data - Nature Communications
The authors present Gnomix, a local ancestry framework that delivers leading accuracy across diverse admixed datasets on both whole-genome and array data with high efficiency, together with Gnofix, it...
22614
Reposted by alex ioannidis
Stephan Schiffels @stschiff.bsky.social · 12/08/2026
If you are interested in learning computational population genetics and ancient genomics, I have curated my list of workshops and online tutorials (and will continue to do so) indicating suitability for self-learners and status. You find the list [here](www.stephanschiffels.de/resources.html).
16039
alex ioannidis @alexgioannidis.bsky.social · 30/07/2026
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.
1113
alex ioannidis @alexgioannidis.bsky.social · 22/07/2026
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...
161
alex ioannidis @alexgioannidis.bsky.social · 16/07/2026
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...
doi.org
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
1137
alex ioannidis @alexgioannidis.bsky.social · 12/07/2026
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...
1113
Reposted by alex ioannidis
New York Times Opinion @nytopinion.nytimes.com · 06/07/2026
The University of California should bring back a standardized test admissions requirement, the editorial board writes.
nyti.ms
Opinion | Bring Back the SAT, California
Under the test-blind policy, more students are thrown into classes for which they are unprepared.
032
alex ioannidis @alexgioannidis.bsky.social · 07/07/2026
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!
130
alex ioannidis @alexgioannidis.bsky.social · 24/06/2026
Who wants free coffee?! Join our lab!
000
alex ioannidis @alexgioannidis.bsky.social · 12/06/2026
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.
biorxiv.org
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...
160
Reposted by alex ioannidis
Human Pangenome Reference Consortium @humanpangenome.bsky.social · 24/04/2026
Scenes from the HUGO workshop in Athens, Greece 🇬🇷 HPRC collaboration in action, advancing pangenomics both stateside and abroad.
011
Reposted by alex ioannidis
Mayor Zohran Kwame Mamdani @mayor.nyc.gov · 24/04/2026
Today marks the 111th anniversary of the Armenian Genocide. As we honor the 1.5 million Armenians murdered by the Ottoman Empire across modern-day Turkey, Syria, and Armenia, we must refuse to let history repeat itself.
In 2020, the military forces of Azerbaijan and Turkey attacked the Armenian population in Nagorno-Karabakh. In 2023, Azerbaijan expelled over 100,000 Armenians from Nagorno-Karabakh, continuing the genocidal campaign that had begun over 100 years prior.
On this day of remembrance, we reaffirm the right of the Armenian people - and all people — to freedom, safety, and self-determination.
8193481745
Reposted by alex ioannidis
April Wei @aprilwei.bsky.social · 12/04/2026
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
24618
Reposted by alex ioannidis
Cecilia Padilla-Iglesias @ceciliapad.bsky.social · 28/03/2026
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
072
Reposted by alex ioannidis
The New York Times @nytimes.com · 12/03/2026
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
115932
Reposted by alex ioannidis
Financial Times @financialtimes.com · 01/02/2026
China’s genius plan ft.trib.al/YYI7wOj
ft.trib.al
China’s genius plan
A network of ultra-competitive high-school talent streams has been turning out the leading lights of science and tech
5127
alex ioannidis @alexgioannidis.bsky.social · 20/12/2025
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.
020
Reposted by alex ioannidis
Oded Rechavi @odedrechavi.bsky.social · 16/12/2025
Life is what happens when you’re busy trying to get your paper published
1707
Reposted by alex ioannidis
Foundation for Individual Rights and Expression @thefireorg.bsky.social · 12/09/2025
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.
3127
Reposted by alex ioannidis
Foundation for Individual Rights and Expression @thefireorg.bsky.social · 16/09/2025
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."
0145
alex ioannidis @alexgioannidis.bsky.social · 23/08/2025
010
alex ioannidis @alexgioannidis.bsky.social · 28/07/2025
"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...
npr.org
Tom Lehrer, influential musical satirist, dies at 97
The songwriter and math professor found a following with his satirical political songs.
110
alex ioannidis @alexgioannidis.bsky.social · 05/07/2025
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?
321
Reposted by alex ioannidis
Nature @nature.com · 30/06/2025
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 go.nature.com/40wPxkB
go.nature.com
’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.
07932
Reposted by alex ioannidis
pacsym.bio @pacsym.bio · 14/06/2025
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.
1189
alex ioannidis @alexgioannidis.bsky.social · 11/06/2025
Sad.
110
Reposted by alex ioannidis
Jonathan Pritchard @jkpritch.bsky.social · 01/06/2025
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.
384108
Reposted by alex ioannidis
Nature @nature.com · 29/05/2025
Most proteins are left-handed, but scientists have found an ancient molecule that works in both mirror-image forms go.nature.com/4mCImRm
go.nature.com
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.
04912
alex ioannidis @alexgioannidis.bsky.social · 29/03/2025
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...
thecrimson.com
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...
120
Reposted by alex ioannidis
Joshua J. Friedman @joshuajfriedman.com · 24/03/2025
Imagine getting this text
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?"
523741
Reposted by alex ioannidis
Charles Ornstein @charlesornstein.bsky.social · 16/03/2025
We Were Badly Misled About the Event That Changed Our Lives @zey.bsky.social
nytimes.com
Opinion | We Were Badly Misled About Covid
The same dangerous mistakes. The same lack of candor.
1258
alex ioannidis @alexgioannidis.bsky.social · 08/03/2025
"The secret history of Syria’s new leader, Ahmed al-Sharaa" Financial Times on.ft.com/3FepkzK The new jihadist leader of Syria went to fight for Saddam Hussein & fought for al-Baghdadi of ISIS, but now being a religious minority resisting him makes you bad (Assad remnant) according to NYT (below).
140
Reposted by alex ioannidis
Somewhere In ATX @somewhereinatx.bsky.social · 04/03/2025
If you live in San Francisco, you should punish whoever is behind your city suing the EPA.
031
Reposted by alex ioannidis
The New York Times @nytimes.com · 25/01/2025
The CIA has said for years that it did not have enough information to conclude how the Covid pandemic originated. The agency has issued a new assessment this week, with analysts saying they now favor the theory that it emerged from an accidental leak at a research lab in Wuhan, China.
nyti.ms
C.I.A. Now Favors Lab Leak Theory to Explain Covid’s Origins
A new analysis that began under the Biden administration is released by the C.I.A.’s new director, John Ratcliffe, who wants the agency to get “off the sidelines” in the debate.
361464109
Reposted by alex ioannidis
The New York Times @nytimes.com · 29/01/2025
More U.S. eighth graders are getting low scores on a federal reading test now than at any time in the exam’s three-decade history, according to the latest test scores.
nytimes.com
American Children’s Reading Skills Reach New Lows
With little post-pandemic recovery, experts wonder if screen time and school absence are among the causes.
5518239
Reposted by alex ioannidis
Nicholas A. Christakis @nachristakis.bsky.social · 26/01/2025
Researchers paid $9 billion over 5 years for their findings to be freely accessible. This is based on a study of the global expenditure on article processing charges (APCs) paid to six publishers for open access between 2019 and 2023. arxiv.org/abs/2407.16551
arxiv.org
Estimating global article processing charges paid to six publishers for open access between 2019 and 2023
This study presents estimates of the global expenditure on article processing charges (APCs) paid to six publishers for open access between 2019 and 2023. APCs are fees charged for publishing in some ...
28452
Reposted by alex ioannidis
Francisco De La Vega @ribozyme.bsky.social · 06/01/2025
It’s a wrap! Another successful @pacsym.bio session on “Overcoming health disparities.” Great papers and panel/discussion session. Thanks to authors and co-organizers.
011
Reposted by alex ioannidis
April Wei @aprilwei.bsky.social · 05/12/2024
Our work w/ two co-first authors Drew DeHaas and Ziqing Pan is now published. GRG allows large amounts of WGS polymorphism data to be analyzed in RAM via graph traversal & algebra operations & has some intrinsic connection w/ popgen data generating process & is different from ARG
12211
Reposted by alex ioannidis
UC Santa Cruz Genomics Institute @ucscgenomics.bsky.social · 30/04/2024
A new era of genomics is here 🧬 Complete human genome sequences have filled gaps in genomes, while pangenomes capture genetic diversity across populations. Check out "Beyond the Human Genome Project" review: www.annualreviews.org/content/jour... @khmiga.bsky.social @benedictpaten.bsky.social
annualreviews.org
Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References | Annual Reviews
The Human Genome Project was an enormous accomplishment, providing a foundation for countless explorations into the genetics and genomics of the human species. Yet for many years, the human genome ref...
012