Onur Özer

onur-ozer.shinyapps.ioHLA PCA Viewer (1000 Genomes + Your Genotype)

17 June 2025

Have you recently registered as a blood marrow donor and got your HLA genotyped? Why don’t you try this little app I built? HLA PCA Viewer is a Shiny app that plots your HLA genotype onto a PCA space derived from the 1000 Genomes Project. onur-ozer.shinyapps.io/hla-pca/ github.com/onur-ozer/HL...

the-scientist.comHLA Defense: A Survival Game Exploring Host-Pathogen Interactions | The ScientistA video game invites players to strategize and adapt to ride out the relentless battle between pathogens and immune defenses. It’s game on!

My little side project made it to the news! HLA Defense, the survival game I built, was featured in The Scientist! www.the-scientist.com/hla-defense-... Here is the link to the game if you want to give it a try: onur-ozer.github.io/immune-defen...

Onur Özer reposted

Max Reuter

@maxreuter.bsky.social

21 Jan

A new preprint from the lab, with postdoc @deboraycb.bsky.social and collaborators @aidaandres.bsky.social and Tim Connallon: “Characterising the detectable and invisible fractions of genomic loci under balancing selection” www.biorxiv.org/content/10.6...

biorxiv.orgbiorxiv.org

Onur Özer reposted

Darren Dahly

@statsepi.bsky.social

They hounded Aaron Swartz to death for downloading papers from jstor but society is now supposed to just accept mass theft because this thing can write that TPS report *for* you. en.wikipedia.org/wiki/Aaron_S...

en.wikipedia.orgAaron Swartz - Wikipedia

John Scalzi@scalzi.com

This is your occasional reminder that generative "AI" in particular could have been developed on public domain materials and/or licensed and compensated works but the major players intentionally, methodically and systemically chose to steal labor from working creative folks instead

doi.orgAncient genomics study reveals low HLA diversity in eastern hunter-gatherers - Genome BiologyBackground Eastern hunter-gatherers (EHG) contributed varying proportions of genetic ancestry to many modern Europeans. However, how this contribution shaped the human leukocyte antigen (HLA) gene diversity remains unexplored. Sakhtysh in western Russia comprises one of the largest EHG-affiliated burial complexes. The site's continuous use offers a rare opportunity to investigate the genetic history, immune-gene diversity, and pathogen exposure within a hunter-gatherer population. Results Genome-wide data from 36 individuals (spanning Lyalovo–Volosovo traditions, 6800–4800 cal BP) place the Sakhtysh population within the EHG cluster, with high genetic affinity to contemporaneous groups across northwestern Russia and the eastern Baltic. This genetic composition remained stable for over two millennia and there is no evidence of admixture with neighboring western hunter-gatherer or farmer groups. We report HLA genotypes for 27 Sakhtysh individuals, representing the first true HLA calls from ancient hunter-gatherers. HLA diversity is low in the Sakhtysh population, likely due to their small population size. Specific alleles like B*27:05 are observed at high frequencies (~ 50%), despite being relatively rare in modern populations, suggesting shifts in selective pressures. Pathogen screening identified a restricted spectrum of causal agents including possible zoonoses with Erysipelothrix rhusiopathiae and chronic infections with hepatitis B virus and parvovirus B19. Conclusions The Sakhtysh community shows genetic continuity across cultural transitions. This population exhibits limited HLA diversity and unexpectedly high frequency of certain alleles. These patterns were likely influenced by low pathogen diversity and possible adaptation to specific environmental factors.

Paper alert for both #HLA and #ancientDNA enthusiasts! Our new paper is out in Genome Biology! doi.org/10.1186/s130... We analyzed genome-wide and HLA data from individuals buried at Sakhtysh. Here are a few highlights from the paper: #aDNA #paleogenomics #immunogenomics #immunology

Two other alleles DRB1*14:01 and DRB1*14:02 also hint at a very interesting story starting from ancient north eurasians (ANE) and extending to native Americans. But this deserves its own post in the future.

Huge thanks to all co-authors and everyone involved in fieldwork, lab work, and analysis on this project.

While this is somewhat consistent with a small effective population size of EHG, some alleles were very common. An example is B*27:05 that reached ~50% frequency and a positive trend in the Ewens-Watterson test hints this may reflect selection rather than drift / demography alone.

The DRB1*08:01~DQB1*04:02 haplotype is also very common in Sakhtysh. This is an interesting haplotype because in European farmers, it only appears after admixture with WHG. This suggests it was already common in WHG, and pointing again to that deep shared ancestry between WHG and EHG.

Genome-wide analysis places all Sakhtysh individuals within the eastern hunter-gatherer (EHG) cluster with genetic continuity spanning cultural traditions. We also detect a WHG-related component, likely a remnant of the shared Paleolithic ancestry between EHG and WHG rather than later gene flow.

Using targeted enrichment, we managed to genotype 27 of these individuals at classical HLA loci. This allows us to have a first glimpse into the HLA diversity in ancient hunter-gatherers... which turned out to be strikingly low.

7 Mar

Last week I attended the 18th East-West Immunogenetics Conference in Zagreb, where I presented on insights from ancient DNA regarding HLA evolution. I would like to thank Renata Zunec and Zorana Grubic for the great organization and their kind invitation to speak. #immunology #HLA #MHC #ancientDNA

7 Mar

I am pleased to see the continuing interest in ancient DNA research within the transplant community. The conference theme emphasized "Building the Future" and I believe that this requires a firm understanding of our evolutionary foundations.

@chrislintott.bsky.social

7 Mar

It was a pleasure to become more acquainted with many of the familiar names in the transplantation field, and I already look forward to future meetings. #immunogenetics #EWIC2026

Onur Özer reposted

Diyar H. (He/Him)

@diyarhamidi.bsky.social

23 Feb

Dear all, The deadline has been extended to 27 February! We will host the 29th DZG Graduate Meeting in Evolutionary Biology! Don’t miss this great opportunity to share your research, exchange ideas, and connect with other researchers in evolutionary biology. Scan the QR for details👇

Onur Özer reposted

Chris Lintott

28 Jan

We’re getting so many journal submissions from people who think ‘it kinda works’ is the standard to aim for.

Carl T. Bergstrom@carlbergstrom.com

1. The thing about science that these jokers don't understand is that science cannot be vibe-coded. Whatever its flaws, the point with vibe coding is that you're trying to quickly make something that sorta works, where you can immediately sorta see if it sorta works and then sorta use it.

25 Dec 2025

I started working on a project in January 2024 and submitted the manuscript in October 2024. Now, after 15 months and a single round of revision, we are still waiting for the editorial decision. My new year resolution might be to withdraw this manuscript and submit somewhere else.

25 Dec 2025

That might have been a reasonable timeline after several rounds of revision with 3+ reviewers, but that's not even the case. Comments received in mid-June and we resubmitted in August. I can even see that both reviewers sent further comments in September but total crickets since then.

academic.oup.comThe current landscape of adaptive immune receptor genomic and repertoire data: OGRDB and VDJbaseAbstract. Accurate characterization of adaptive immune receptor repertoires through high-throughput sequencing is critical for understanding immune respons

25 Dec 2025

I wish I had done this at the beginning (lessons learned) but I am wondering if I can upload this manuscript as a preprint at this stage, given the need to show that I actually did some work...

Onur Özer reposted

Diyar H. (He/Him)

@diyarhamidi.bsky.social

11 Dec 2025

We are very excited to be organising this symposium at SMBE @official-smbe.bsky.social next year! We look forward to your abstracts and to being in Copenhagen!

Society for Molecular Biology and Evolution@official-smbe.bsky.social

Onur Özer reposted

ayeletperes.bsky.social

@ayeletperes.bsky.social

7 Nov 2025

New manuscript out in NAR! tinyurl.com/4rrbuesn 🧬 VDJbase and OGRDB now support 3000+ IG/TR samples across human and rhesus macaque with curated AIRR-seq and long-read genomic data. From population analysis to precision annotation. @guryaari.bsky.social @cdubsig.bsky.social @williamlees.bsky.social

genomemedicine.biomedcentral.comHLA-DRB1*15:01 is associated with a reduced likelihood of longevity in northern European men - Genome MedicineBackground Prior research on the genetics of human longevity has identified only a few robust associations. While these studies highlight the importance of metabolic processes for longevity, the contr...

27 Oct 2025

A new paper about #longevity and #HLA: Men with HLA-DRB1*15:01 might be among the unlucky ones... “HLA-DRB1*15:01 is associated with a reduced likelihood of longevity in northern European men” It was great to work with Nicolas on that paper! genomemedicine.biomedcentral.com/articles/10....

Onur Özer reposted

Jamie Winternitz

@jcwinternitz.bsky.social

13 Oct 2025

Join Our Citizen Science Project! We are mapping the house mouse hybrid zone in Schleswig-Holstein, DE, and you can help. Visit our House Mouse Hybrid Zone Project website to learn more jwinternitz.github.io/mouse-hybrid.... Funded by @dfg.de at @uni-hamburg.de #DFG #musmusculus #wildmice

Onur Özer reposted

Shai Carmi

@shaicarmi.bsky.social

11 Sept 2025

Brilliant paper by Visscher et al. Populations differ in traits/disease burden. Are these differences due to genetics? Comparing single variants or polygenic scores between populations is biased due to environmental confounders correlated with the variants. 1/3 www.medrxiv.org/content/10.1...

medrxiv.orgDirect effect of genetic ancestry on complex traits in a Mexican populationHuman populations differ in disease prevalences and in average values of phenotypes, but the extent to which differences are caused by genetic or environmental factors is unknown for most complex trai...

science.orgOut-of-Anatolia: Cultural and genetic interactions during the Neolithic expansion in the AegeanWest Anatolia has been a crucial yet elusive element in the Neolithic expansion from the Fertile Crescent to Europe. In this work, we describe the changing genetic and cultural landscapes of early Hol...

29 June 2025

I remember back when I was learning Python, a computer engineer mentioned objects and I asked "What is an object?" The answer was: "What do you mean? Everything is an object in Python!" and he continued without expanding. I wish more explanations like this were available back then...

Ming Tommy Tang@tommytang.bsky.social

1/ What the heck is an "object" (like a Seurat object) in programming? If you're in bioinformatics, this term shows up a lot. Let’s break it down with examples that actually make sense 🧵

Onur Özer reposted

Dilek Koptekin

@dilekopter.bsky.social

26 June 2025

Happy to share our new study from my PhD on the spread of farming across Anatolia and into the Aegean and then into Europe. @compevohumang.bsky.social www.science.org/doi/10.1126/... 👇🏽

Onur Özer reposted

LBV Magazine

@labrujulaverde.bsky.social

27 June 2025

A Matriarchal Society Existed in Çatalhöyük During the Neolithic More Than 10,000 Years Ago, Researchers Find www.labrujulaverde.com/en/2025/06/a...

labrujulaverde.comA Matriarchal Society Existed in Çatalhöyük During the Neolithic More Than 10,000 Years Ago, Researchers FindOn the Anatolian plains, more than ten thousand years ago, one of humanity’s first major farming communities flourished, burying its dead beneath the floors of its homes. Now, two recently published s...

9 June 2025

I am honored and humbled to receive the Jon van Rood Award for Best Abstract at EFI 2025! My first EFI was amazing and I am looking forward to many more ahead! #EFI2025 #immunogenetics

14 May 2025

#EFI2025 is about to kick off in beautiful Prague! 🇨🇿 I’ll be presenting in the Best Abstracts session on Saturday, sharing our work on ancient HLA diversity in Europe. Super excited for a week of science, new connections, and fresh ideas! #HLA #AncientDNA #Immunogenetics #MHC

I have always been proud of my university ODTÜ in Turkey, not only for its academic success but also for the political stance of students. Right now, this is the treatment faced by students who stand up for democracy. (photo credit unknown for now)

Resistance against the current regime is nothing new. I began my bachelor's in 2010, and my entire university life was marked by pepper spray, batons, water cannons, and plastic bullets. Yet, at the time, the regime was being praised in Europe for its supposed "democratic" values.

Anyway, I will cut it short. The people of Turkey are suffering under a crushing economic decline, political oppression, censorship, a degrading quality of education and a collapsed electoral system. We are digging under the rubble with the hope of seeing the light.

Syria was handed over to an ISIS commander with a million-dollar reward on his head just a few months ago. Taliban leaders are quietly being removed from terrorist lists. The rabid far-right government of Israel gets unconditional support for its massacre of Palestinians.

Sadly, all of this was not only supported by the usual suspects of the far-right, but also by liberals, greens, social democrats, etc. Anyone can be accommodated, even praised, as long as they are useful. This has been the case for the regime in Turkey for a long time.

Anybody who dares to speak up against the party-state feels "the Iron Heel". Hundreds of citizens -students, journalists, politicians- are under arrest, websites are blocked, TV channels are getting broadcast bans. All to ensure the continuation of a corrupt regime.

kulturkampftr.substack.comTurkey ResistsBy arresting İmamoğlu, Erdoğan banks on public apathy. He's getting the opposite.

Authoritarianism is on the rise across the globe, paving the way for extremist governments. In our interconnected world, ignoring the suffering of ordinary people is no longer an option. Unfortunately, the Western world has recently failed many tests in this regard.

This is not an isolated case, of course. If you have been following the news, you are likely aware of the ongoing political crackdown in Turkey. Here is a summary of the situation (from 5 days ago). Since then, the crackdown only escalated. kulturkampftr.substack.com/p/turkey-res...

doi.orgAdmixture as a source for HLA variation in Neolithic European farming communities - Genome BiologyBackground The northern European Neolithic is characterized by two major demographic events: immigration of early farmers from Anatolia at 7500 years before present, and their admixture with local wes...

Hello Blue world! I recently migrated from the old Twitter as I got tired of the continuous bombardment of far-right propaganda. I intend to use this account mainly for scientific exchange with a pinch of politics. So, why not start with a summary of our recent paper? doi.org/10.1186/s130...

More importantly, we don't know if that haplotype was already common in WHG or not. Having some frequency data would allow us to estimate expected frequencies after the admixture and test whether the observed frequency can be explained solely by admixture or not.

I will present some results of this study together with our other projects on ancient #HLA diversity in Europe at the 38th European Immunogenetics & Histocompatibility Conference #EFI2025 #MHC #immunogenomics #ancientDNA

Combining targeted HLA genotyping with the genomewide data, we found that LF individuals carrying DRB1*08:01-DQB1*04:02 haplotype had an excess of WHG ancestry across the MHC region, suggesting that this haplotype introgressed from the hunter-gatherers.

What could be the reason for this excess WHG ancestry across the MHC region? Our pathogen screening did not provide any obvious target. There are some associations between DRB1*08:01-DQB1*04:02 alleles and some pathogens, notably the hepatitis-B virus. But was it enough to drive such a signal?

We next moved to the part that I personally feel closer to: the HLA analysis. Using capture-based sequencing and a stringent genotyping approach, we managed to obtain HLA genotypes of 135 individuals (EF = 45, LF = 90). Overall, the Neolithic HLA diversity was lower than modern populations.

We also observed an increased diversity from EF to LF. We hypothesized that this could result from the admixture between EF and WHG. Using a local ancestry inference method called RFMix and we found that across the MHC region, the WHG ancestry was much higher than the genomewide average.

We analyzed the genetic data of 125 individuals, 49 early farmers (EF) and 76 late farmers (LF). Remains of these individuals were recovered from seven sites within modern central and southern Germany. Right away, we observe an increase in WHG ancestry in the LF group, compared to EF.

We observed that the WHG ancestry in LF exceeded what we expected from other contemporaneous farmers around Europe. This highlights the regional variation in cultural practices and interactions between communities. Furthermore, the WHG admixture appears to be male-biased.

This picture has changed in the following millennia as we observe more and more WHG-related ancestry in farming societies. The evolutionary dynamics behind this admixture are still a matter of research, and some interesting questions remain open.