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Gokcumen Lab

@gokcumenlab.bsky.social
233 followers 411 following 8 posts

Investigating the evolutionary history of genetic variations to explain biological diversity and disease in modern and ancient human populations.

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Charikleia Karageorgiou (Clio) @evobioclio.bsky.social · 26/08/2026
New @heredityjournal.bsky.social podcast about structural variation and our recent Heredity special issue, "Functional and Adaptive Effects of Genomic Structural Variation"
shows.acast.com
Special Issue on Structural Variation | Heredity Podcast
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American Society of Human Genetics (ASHG) @geneticssociety.bsky.social · 06/08/2026
False positives abound in trans-eQTL discovery. The authors of @ajhgnews.bsky.social's latest article develop a method to identify the mapping artifacts that produce spurious results: www.cell.com/ajhg/abstract/S0002-92… #ASHG @gokcumenlab.bsky.social #HumanGenetics
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Gokcumen Lab @gokcumenlab.bsky.social · 30/07/2026
Typeset version of new paper out in @genomebiolevol.bsky.social. Link: academic.oup.com/gbe/article/... We identified segmental duplications in genomes from 117 vertebrate species (thanks to @vertebrategenomes.bsky.social ). We describe the properties and evolution of segmental duplications.
academic.oup.com
Genomes From 117 Vertebrate Species Reveal Rapidly Evolving Segmental-Duplication Landscapes
Abstract. Segmental duplications are major drivers of evolutionary innovation; yet, their dynamics across vertebrates remain poorly understood. Here, we id
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Genome Biology and Evolution @genomebiolevol.bsky.social · 30/07/2026
@alberaqil.bsky.social et al. identify segmental duplications from genomes of 117 vertebrates, finding that the genomic architecture underlying segmental duplications is highly dynamic, uniquely shaping each lineage's potential to adapt 🔗 doi.org/10.1093/gbe/evag043 #societyjournal #evolution
doi.org
Genomes From 117 Vertebrate Species Reveal Rapidly Evolving Segmental-Duplication Landscapes
Abstract. Segmental duplications are major drivers of evolutionary innovation; yet, their dynamics across vertebrates remain poorly understood. Here, we id
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Gokcumen Lab @gokcumenlab.bsky.social · 29/07/2026
New paper with @rajivmccoy.bsky.social @ajhgnews.bsky.social. Bottom line: Polymorphic gene duplications absent in the reference genome can produce spurious trans-eQTLs, and we propose a method to identify these false positives. authors.elsevier.com/c/1nWChgeXHnOF
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The American Journal of Human Genetics @ajhgnews.bsky.social · 28/07/2026
🧬 New from Aqil et al! 📄 Mismapping of sequencing reads from polymorphic duplications generates spurious trans-eQTLs
cell.com
Mismapping of sequencing reads from polymorphic duplications generates spurious trans-eQTLs
Polymorphic gene duplications absent from the reference genome can generate spurious trans-eQTLs. Specifically, variants tagging the polymorphic duplicate may masquerade as trans-eQTLs regulating the ...
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Charikleia Karageorgiou (Clio) @evobioclio.bsky.social · 21/07/2026
Only 3 days left to submit an abstract for the Great Lakes Annual Meeting of Evolutionary Genomics! The abstract submission deadline is July 24; registration will remain open until August 10. GLAM will be held on August 15, at the University at Buffalo. The participation is capped at 100 people.
forms.gle
GLAM-Evogen 2026 Registration and Abstract Submission Portal
GLAM-Evogen will be held on August 15, 2026 at University at Buffalo, NY. We aim to bring together faculty and trainees from a range of backgrounds with a particular focus on work at the interface bet...
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Luane Landau @lulandau.bsky.social · 23/06/2026
Come to my talk today at 2:30 PM in the Expression/Transcriptomics session #Evol2026 I’ll talk about how gene duplication and regulatory architecture drive the evolution of new traits in salivary glands, and hopefully convince you that this is a cool system for studying the evol of gene expression!
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Charikleia Karageorgiou (Clio) @evobioclio.bsky.social · 19/06/2026
We are excited to announce that the 2026 Great Lakes Annual Meeting of Evolutionary Genomics (GLAM-EvoGen) will take place on Saturday, August 15, 2026 at the University at Buffalo. More information is available on our website: gokcumenlab.org/glam2026/ @gokcumenlab.bsky.social
gokcumenlab.org
GLAM2026 – Gokcumen Lab
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Adam Phillippy @aphillippy.bsky.social · 08/06/2026
T2T assemblies for nearly all major Y chromosome haplogroups courtesy of a collab between @humanpangenome.bsky.social and HGSVC! What was once the hardest human chromosome to finish can now be routinely assembled thanks to ONT + Verkko www.biorxiv.org/content/10.6...
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Charikleia Karageorgiou (Clio) @evobioclio.bsky.social · 26/05/2026
Our paper on recurrent independent duplications in the primate amylase locus is now out in Cell Reports! Huge thanks to @petarpajic, @spit-lab.bsky.social and @gokcumenlab.bsky.social for their support. More about the work in the thread below from when we first shared the preprint last August.
cell.com
Convergent evolution through independent rearrangements in the primate amylase locus
Structurally complex loci can repeatedly generate similar traits; Karageorgiou et al. established primate amylase locus as a structural variation hotspot, potentially seeded by transposable elements. ...
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Luane Landau @lulandau.bsky.social · 05/05/2026
1/ New paper out in Nature Communications! We studied the salivary amylase gene, AMY1, in Indigenous Andean populations and found evidence that high AMY1 copy number rapidly increased in frequency, likely through recent positive selection. doi.org/10.1038/s414...
doi.org
Rapid adaptive increase of amylase gene copy number in Indigenous Andeans - Nature Communications
The salivary amylase gene exhibits copy-number variation linked to dietary shifts. Here, the authors describe an adaptive expansion of the amylase gene in Indigenous Andean populations coinciding with...
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Charikleia Karageorgiou (Clio) @evobioclio.bsky.social · 28/03/2026
The special issue Functional and Adaptive Effects of Genomic Structural Variation is now out in Heredity. Many thanks to all contributors for their submissions, to the editorial team at @heredityjournal.bsky.social and to @ellenleffler.bsky.social, @mydennis.bsky.social & @gokcumenlab.bsky.social!
nature.com
Special Issue: Functional and Adaptive Effects of Genomic Structural Variation
See more information on the new Heredity special issue on functional and adaptive effects of genomic structural variation.
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Christian Landry @christianlandry.bsky.social · 24/03/2026
Nice surprise this morning! A Dispatch on our paper on paralog interference now out in Current Biology! By Krishna Swamy and Jun-Yi Leu. www.cell.com/current-biol...
cell.com
Evolution: Paralog interference stabilizes gene duplicates
Gene duplicates are traditionally viewed as evolutionarily unstable, as one copy can freely accumulate deleterious mutations and be lost. A new study reveals that paralog interference exposes certain ...
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bioRxivpreprint @biorxivpreprint.bsky.social · 20/03/2026
Gene Expansion and Regulatory Rewiring Shape Sex-Biased Evolution of the Mouse Submandibular Gland Secretome www.biorxiv.org/content/10.64898/20…
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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 20/03/2026
Gene Expansion and Regulatory Rewiring Shape Sex-Biased Evolution of the Mouse Submandibular Gland Secretome www.biorxiv.org/content/10.64898/20…
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Genome Biology and Evolution @genomebiolevol.bsky.social · 20/01/2026
Pajic & @gokcumenlab.bsky.social synthesize the evolution of VNTRs in mammals, including mutational mechanisms and selective forces driving their evolution, and propose a theoretical framework for their persistence through evolutionary tradeoffs. 🔗 doi.org/10.1093/gbe/evaf250 #genome #evolution
doi.org
Evolutionary Balancing of Genetic Consequence and Innovation in Mammals Through Variable Number Tandem Repeats
Abstract. Understanding genomic function has historically relied on sequence conservation across evolutionary time. However, advances in genomics have reve
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Charikleia Karageorgiou (Clio) @evobioclio.bsky.social · 08/01/2026
New review from @gokcumenlab.bsky.social led by Petar Pajic on VNTRs. If you’re interested in VNTRs, this is a very nice synthesis. academic.oup.com/gbe/article/...
academic.oup.com
Evolutionary Balancing of Genetic Consequence and Innovation in Mammals Through Variable Number Tandem Repeats
Abstract. Understanding genomic function has historically relied on sequence conservation across evolutionary time. However, advances in genomics have reve
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Stefan Ruhl 🦷💧🦠 @spit-lab.bsky.social · 12/10/2025
academic.oup.com/gbe/article/... 🦷🦷 #TEETH 🥛🥛 #MILK 💧💧 #SALIVA❗️
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Gokcumen Lab @gokcumenlab.bsky.social · 10/10/2025
Our preprint, "Read mismapping from segmental duplications drives spurious trans associations," is out! We argue that both RNA and DNA read mismapping can lead to false signals in QTLs, Hi-C, GWAS, and gene co-expression. And there is a way to identify them! Link: www.biorxiv.org/content/10.1...
biorxiv.org
Read mismapping from segmental duplications drives spurious trans associations
Heritable variation in gene regulation shapes both disease risk and evolution. Trans -acting quantitative trait loci ( trans -QTLs) are the primary source of this variation within species, yet they re...
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Stefan Ruhl 🦷💧🦠 @spit-lab.bsky.social · 27/09/2025
What have 🦷🦷 #TEETH 🦷🦷, 🥛 #MILK 🥛, and💧💧 #SALIVA 💧💧to do with each other? Ask PetarPajic, Luane Landau, and Omer Gokcumen @gokcumenlab.bsky.social ❗️ academic.oup.com/gbe/article-...
academic.oup.com
Saliva Protein Genes in Humans were Shaped During Primate Evolution
Abstract. Genes within the secretory calcium-binding phosphoprotein locus diversified along with the formation of a calcified skeleton in vertebrates, the
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Genome Biology and Evolution @genomebiolevol.bsky.social · 24/09/2025
Pajic, @gokcumenlab.bsky.social @spit-lab.bsky.social et al. explored the evolution of saliva-related SCPP genes, observing extensive diversification of SCPP genes within mammals, driven by gene duplications and losses. 🔗 doi.org/10.1093/gbe/evaf165 #genome #evolution #primates
SCPP gene presence/absence phylogeny. Blocks represent genes within the SCPP locus, color-coded by functional relevance: enamel (purple), milk (blue), saliva (yellow), and genes implicated in all three functions (red). The animal phylogeny is shown on the left with species silhouettes. Two primate species (baboon and green monkey) are depicted placing blocks representing saliva-related genes at the points in evolution where these genes emerged. Imagine designed in BioRender.
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Gokcumen Lab @gokcumenlab.bsky.social · 25/08/2025
New paper with @spit-lab.bsky.social @genomebiolevol.bsky.social - Bottom-line: genes that encode secreted saliva genes evolve pretty fast and gene duplications/deletions are mostly the culprit. academic.oup.com/gbe/advance-...
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Gokcumen Lab @gokcumenlab.bsky.social · 20/08/2025
✨ 1 of the proudest achievements of the lab. the sex- and diet-dependent effects of an ancient deletion (>Neanderthal–human divergence) in the 3rd conserved exon of GHR (GHRd3). growth, resistance to hunger, and metabolism. www.science.org/doi/10.1126/... #BioRenderForGrants #ScienceAdvances
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Alexa Sadier @aigverte.bsky.social · 19/08/2025
Such a great talk this morning on primate amylase evolution by @evobioclio.bsky.social #ESEB2025
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EvolDir @evoldir.bsky.social · 06/08/2025
Postdoctoral Research Associate sought for lipid biology and evolutionary genomics project. Ideal candidates in cell biology or bioinformatics; must be eager to learn interdisciplinary skills. Contact Dr. Ekin Atilla-Gokcumen: ekinatil@buffalo.edu. More info: atillalab.org #postdoc
atillalab.org
Atilla Lab – at the University at Buffalo
Atilla Lab – at the University at Buffalo
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Charikleia Karageorgiou (Clio) @evobioclio.bsky.social · 15/08/2025
Our latest preprint explores the evolution of the primate amylase locus, uncovering structural innovations, regulatory shifts and molecular convergence. www.biorxiv.org/content/10.1...
biorxiv.org
Convergent evolution through independent rearrangements in the primate amylase locus
Structurally complex regions of the genome are increasingly recognized as engines of evolutionary convergence due to their propensity to generate recurrent gene duplications that give rise to similar ...
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Cedric Boeckx @cedricboeckx.bsky.social · 15/08/2025
Very nice comparative study led @evobioclio.bsky.social from @gokcumenlab.bsky.social, using the the primate amylase locus to reveal how structural and regulatory modularity in complex genomic regions drives evolutionary innovation and molecular convergence 🧪🧬 www.biorxiv.org/content/10.1...
biorxiv.org
Convergent evolution through independent rearrangements in the primate amylase locus
Structurally complex regions of the genome are increasingly recognized as engines of evolutionary convergence due to their propensity to generate recurrent gene duplications that give rise to similar ...
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Stefan Ruhl 🦷💧🦠 @spit-lab.bsky.social · 03/08/2025
❗️❗️❗️👄👄 #MOUTH 👄👄 🦷🦷 #TEETH 🦷🦷 💧💧 #SALIVA 💧💧🦠🦠 #MICROBIOME🦠🦠 🍭🍭 #glycotime 🍭🍭 ❗️❗️❗️ ❗️We are hiring❗️Check out this full-time tenure track academic faculty position in the #UBSDM's Department of Oral Biology. ms.spr.ly/6045sKrT9
ubjobs.buffalo.edu
Assistant Professor/Associate Professor, Oral Biology
The University at Buffalo School of Dental Medicine (SDM) invites applications from qualified early- to mid-career oral health scientists and/or clinician-scientists for a full-time tenure track acade...
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Megan Dennis @mydennis.bsky.social · 21/07/2025
Check out our latest work co-led by @dcsoto.bsky.social and @jmuribescr.bsky.social identifying hundreds of human duplicated gene families using the new T2T-CHM13 assembly, with a focus on those potentially contributing to brain evolution 🧪: authors.elsevier.com/a/1lTQtL7PXu...
authors.elsevier.com
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Charikleia Karageorgiou (Clio) @evobioclio.bsky.social · 28/07/2025
Outreach volunteers sought! @imprintedgene.bsky.social and I will host “Breaking Bread: Exploring the Evolution of Amylase in humans” at Festa Major de Gràcia, Barcelona (16 Aug, 19:00). We need 1-2 volunteers (ES/EN) for visitor guidance and on-site translation. Please DM or email me if interested.
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Gokcumen Lab @gokcumenlab.bsky.social · 15/07/2025
Great write-up by Technology Networks on our recent work on switch-like gene expression in humans. It is short, clear, and just a 4-min read. If transcriptomic variation interests you, please give it a look! Write-up: www.technologynetworks.com/genomics/new... Paper: www.nature.com/articles/s41...
technologynetworks.com
Hundreds of Human Genes Show “Switch-Like” Behavior
University of Buffalo researchers conducted a systematic analysis of switch-like genes by analyzing genomes, transcriptomes and methylomes from 943 individuals and 27 different tissues.
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Gokcumen Lab @gokcumenlab.bsky.social · 02/07/2025
University press release for our recent study, "Switch-like gene expression modulates disease risk," published in Nature Communications. Link to paper: www.nature.com/articles/s41...
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Dilek Koptekin @dilekopter.bsky.social · 26/06/2025
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/... 👇🏽
science.org
Out-of-Anatolia: Cultural and genetic interactions during the Neolithic expansion in the Aegean
West 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...
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Charikleia Karageorgiou (Clio) @evobioclio.bsky.social · 25/06/2025
Excited to share that I’ve been selected as a Spring 2025 recipient of the DeLill Nasser Award for Professional Development in Genetics! Very grateful to the Genetics Society of America @genetics-gsa.bsky.social for their support.
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Charikleia Karageorgiou (Clio) @evobioclio.bsky.social · 22/06/2025
New manuscript from the Gokcumen Lab! @gokcumenlab.bsky.social
nature.com
Switch-like gene expression modulates disease risk - Nature Communications
While switch-like expression (“on” in some individuals and “off” in others) has been linked to biological variation and disease susceptibility, a systematic analysis across tissues is lacking. Here, w...
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Charikleia Karageorgiou (Clio) @evobioclio.bsky.social · 19/06/2025
Made it to Athens, GA for #Evol2025! Very excited to be attending my first in-person Evolution meeting. I'll be giving a talk on the evolution of the primate amylase locus and presenting a poster on our recent paper about the human amylase locus this Sunday. DM me if you want to catch up!
doi.org
Reconstruction of the human amylase locus reveals ancient duplications seeding modern-day variation
Previous studies suggested that the copy number of the human salivary amylase gene, AMY1, correlates with starch-rich diets. However, evolutionary analyses are hampered by the absence of accurate, seq...
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