Gokcumen Lab

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

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

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

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/gbe/article/...
🦷🦷 #TEETH 🥛🥛 #MILK 💧💧 #SALIVA❗️

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...

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...

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

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-...

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.

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

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-...

✨ 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

Such a great talk this morning on primate amylase evolution by @evobioclio.bsky.social #ESEB2025

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: https://atillalab.org/ #postdoc

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 ...

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...

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 ...

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...

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...

❗️❗️❗️👄👄 #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

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...

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.

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.

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...

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...

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...

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/...

👇🏽

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.

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...

New manuscript from the Gokcumen Lab! @gokcumenlab.bsky.social

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...

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!