Research News
ScienceAdvances publishes new study: A mechanism of gene evolution generating mucin function
Omer Gokcumen, associate professor, Department of Biological Sciences
The interdisciplinary journal, ScienceAdvances, has published a study on mucins. The study demonstrates how a long-time partnership between evolutionary biologists and dental researchers at UB is yielding new insights into genes and proteins that are also important to human health. Senior authors are Omer Gokcumen (UB associate professor of biological sciences) and Stefan Ruhl (interim dean of the UB School of Dental Medicine and a professor of oral biology). The first author is Petar Pajic, UB PhD student in biological sciences. “My team has been studying mucins for many decades, and my collaboration with Dr. Gokcumen has brought this research to a new level by revealing all these exciting novel insights into their evolutionary genetics,” Ruhl says. “At this advanced stage of my career, it is also immensely gratifying to see that the flame of scientific curiosity is being carried on by a new generation of young investigators like Petar Pajic.”
The evolution of mucus: How did we get all this slime?
Petar Pajic, UB PhD student in biological sciences, prepares a saliva sample for separation and analysis. In the new study, the team used a gel electrophoresis technique to separate mucins from other proteins in the saliva of various mammals. Credit: Douglas Levere / University at Buffalo
In mammals, proteins called mucins evolved — again and again — by co-opting non-mucin proteins in a surprising way, study suggests
Release Date: August 26, 2022
BUFFALO, N.Y. — From the slime coating slugs to the saliva in our mouths, many slippery bodily fluids contain mucus. So how did this marvel of biology evolve?
In mammals, the answer is many times, and often in a surprising way, according to a new study on proteins called mucins. These molecules have a variety of functions, but as a family, they are known as components of mucus, where they contribute to the substance's gooey consistency.
Through a comparison of mucin genes in 49 mammal species, scientists identified 15 instances in which new mucins appear to have evolved through an additive process that transformed a non-mucin protein into a mucin.
The scientists propose that each of these “mucinization” events began with a protein that wasn’t a mucin. At some point, evolution tacked a new section onto this non-mucin base: one consisting of a short chain of building blocks called amino acids that are decorated with sugar molecules. Over time, this new region got duplicated, with multiple copies added on to elongate the protein even further, making it a mucin.
From left: The study’s senior authors Omer Gokcumen and Stefan Ruhl, and first author Petar Pajic. Gokcumen is a UB associate professor of biological sciences; Ruhl is interim dean of the UB School of Dental Medicine and a professor of oral biology; and Pajic is a UB PhD student in biological sciences.
The doubled regions, called “repeats,” are key to a mucin’s function, say University at Buffalo researchers Omer Gokcumen and Stefan Ruhl, the senior authors of the study, and Petar Pajic, the first author.
The sugars coating these sections protrude outward like the bristles of a bottle brush, and they bestow mucins with the slimy property that’s vital to many important tasks that these proteins carry out.
The research was published on Aug. 26 in Science Advances.
Petar Pajic, UB PhD student in biological sciences, uses a gel electrophoresis technique to separate mucins from other proteins in a saliva sample. Credit: Douglas Levere / University at Buffalo
“I don’t think it was previously known that protein function can evolve this way, from a protein gaining repeated sequences. A protein that isn’t a mucin becomes a mucin just by gaining repeats. This is an important way that evolution makes slime. It’s an evolutionary trick, and we now document this happening over and over again,” says Gokcumen, PhD, associate professor of biological sciences in the UB College of Arts and Sciences.
“The repeats we see in mucins are called ‘PTS repeats’ for their high content of the amino acids proline, threonine and serine, and they aid mucins in their important biological functions that range from lubricating and protecting tissue surfaces to helping make our food slippery so that we can swallow it,” says Stefan Ruhl, DDS, PhD, interim dean of the UB School of Dental Medicine and professor of oral biology. “Beneficial microbes have evolved to live on mucus-coated surfaces, while mucus can at the same time also act as a protective barrier and defend against disease by shielding us from unwanted pathogenic intruders.”
“Not many people know that the first mucin which had been purified and biochemically characterized came from a salivary gland,” Ruhl adds. “My lab has been studying mucins in saliva for the last 30 years, mostly because they protect teeth from decay and because they help balance the microbiota in the oral cavity.”
The intriguing evolution of an ‘amazing life trait’
Vials of saliva collected from various mammals, including a pig. Credit: Douglas Levere / University at Buffalo
“I think this paper is really interesting,” Gokcumen says. “It’s one of those times where we got lucky. We were studying saliva, and then we found something that’s interesting and cool and decided to look into it.”
While studying saliva, the team noticed that a small salivary mucin in humans called MUC7 was not present in mice. The rodents did, however, have a similarly sized salivary mucin called MUC10. The scientists wanted to know: Were these two proteins related from an evolutionary perspective?
The answer was no. But what the research uncovered next was a surprise. While MUC10 did not appear to be related to MUC7, a protein found in human tears called PROL1 did share a portion of MUC10’s structure. PROL1 looked a lot like MUC10, minus the sugar-coated bottlebrush repeats that make MUC10 a mucin.
“We think that somehow that tear gene ends up repurposed,” Gokcumen says. “It gains the repeats that give it the mucin function, and it’s now abundantly expressed in mouse and rat saliva.”
The scientists wondered whether other mucins might have formed the same way. They began to investigate and discovered multiple examples of the same phenomena. Though many mucins share common ancestry among various groups of mammals, the team documented 15 instances in which evolution appeared to have converted non-mucin proteins into mucins via the addition of PTS repeats.
Petar Pajic, UB PhD student in biological sciences, prepares a saliva sample for separation and analysis. In the new study, the team used a gel electrophoresis technique to separate mucins from other proteins in the saliva of various mammals. Credit: Douglas Levere / University at Buffalo
And this was “with a pretty conservative look,” Gokcumen says, noting that the study focused on one region of the genome in a few dozen mammal species. He calls slime an “amazing life trait,” and he’s curious whether the same evolutionary mechanism might have driven the formation of some mucins in slugs, slime eels and other critters. More research is needed to find an answer.
“How new gene functions evolve is still a question we are asking today,” says Pajic, a UB PhD student in biological sciences. “Thus, we are adding to this discourse by providing evidence of a new mechanism, where gaining repeated sequences within a gene births a novel function.”
“I think this could have even broader implications, both in understanding adaptive evolution and in possibly explaining certain disease-causing variants,” Pajic adds. “If these mucins keep evolving from non-mucins over and over again in different species at different times, it suggests that there is some sort of adaptive pressure that makes it beneficial. And then, at the other end of the spectrum, maybe if this mechanism goes ‘off the rails’ — happening too much, or in the wrong tissue — then maybe it can lead to disease like certain cancers or mucosal illnesses.”
The study on mucins demonstrates how a long-time partnership between evolutionary biologists and dental researchers at UB is yielding new insights into genes and proteins that are also important to human health.
“My team has been studying mucins for many decades, and my collaboration with Dr. Gokcumen has brought this research to a new level by revealing all these exciting novel insights into their evolutionary genetics,” Ruhl says. “At this advanced stage of my career, it is also immensely gratifying to see that the flame of scientific curiosity is being carried on by a new generation of young investigators like Petar Pajic.”
Additional research co-authors include Shichen Shen, PhD, postdoctoral associate, and Jun Qu, PhD, professor, both in the Department of Pharmaceutical Sciences in the UB School of Pharmacy and Pharmaceutical Sciences, and in the UB Center of Excellence in Bioinformatics and Life Sciences; and Alison J. May, PhD, former postdoctoral scholar, and Sarah Knox, PhD, associate professor, both in the Department of Cell and Tissue Biology in the University of California, San Francisco School of Dentistry. May is now an assistant professor at the Icahn School of Medicine at Mount Sinai.
Scientists who conducted the study are supported by the U.S. National Science Foundation, along with the National Institute of Dental and Craniofacial Research and National Cancer Institute, both part of the U.S. National Institutes of Health.
Petar Pajic, UB PhD student in biological sciences, holds a saliva sample from a ferret. The saliva has been combined with a buffer containing a blue dye, which helps scientists track the sample while using a gel electrophoresis technique to separate mucins from other proteins in saliva. Credit: Douglas Levere / University at Buffalo
Media Contact Information
Charlotte Hsu is a former staff writer in University Communications. To contact UB's media relations staff, email ub-news@buffalo.edu or visit our list of current university media contacts.
Faculty Profile
![Omer Gokcumen.]()
Omer Gokcumen
PhD
ProfessorMeyerson Award for Undergraduate Mentoring, 2025Distinguished Postdoc Mentor Award, 2019Research Interests
Human and primate evolution, ancient humans (including Neanderthals and Denisovans), anthropological genomics
Education
- PhD, University of Pennsylvania
- Postdoctoral Research, Harvard Medical School
Research Statement
Omer Gokcumen is an expert in evolutionary anthropology — the study of how humans evolved and how they differ from non-human primates such as gorillas and chimpanzees. His work is tied to human evolution, including evolutionary adaptation and the evolutionary processes that lead to genetic disease.
Gokcumen’s research examines the role that genomic variants, especially deletions and duplications, play in human disease and biology. His laboratory investigates the evolutionary history of genetic variations tied to interesting traits and diseases in modern and ancient human populations.
- 2022 Interview for BBC 4 - Inside Science on our work on evolution of mucus. (here)
- 2022 Interviewed for NPR - RadioLab. “Neanderthals’ revenge” episode on our work on ancient alleles in the human genome. (here)
- 2021 Interviewed for Scientific American on our work on the evolution of human growth hormone receptor. (here)
- 2021 Interviewed for The Scientist on our work on the evolution of human growth hormone receptor. (here)
- 2021 Quoted in How Stuff Works - “How human are humans?” by Joanna Thompson. (here)
- 2020 BBC - Reel
- 2019 Quoted in NYTimes.
- 2022 Pajic et al. A mechanism of gene evolution generating mucin function. Press release. Selected highlights: New Scientist, Yahoo News, BBC, GEN, Inverse.
- 2021 Saitou et al. Sex-specific phenotypic effects and evolutionary history of an ancient polymorphic deletion of the human growth hormone receptor. Press release. Selected highlights: Real Clear Science, The Scientist, Scientific American.
- 2020 Saiotu et al. Functional Specialization of Human Salivary Glands and Origins of Proteins Intrinsic to Human Saliva. Press release. Selected Highlights: Cosmos, CBC- Radio Active.
- 2020 Taskent et al. Analysis of haplotypic variation and deletion polymorphisms point to multiple archaic introgression events, including from Altai Neanderthal lineage. Press release. Selected Highlights: Futurity, Sputnik, Genetic Literacy Project.
Selected Publications
- Veilleux, C.C., Garrett, E.C., Pajic, P.*, Saitou, M.*, Ochieng, J., Dagsaan, L.D., Dominy, N.J., Perry, G.H., Gokcumen, O.*, Melin, A.D. (2023). Veillex Human subsistence and signatures of selection on chemosensory genes. Communications Biology. 6: 683. [co-Corresponding Author].
- Lu, D., Parisi, L.R., Gokcumen, O.*, Attila-Gokcumen, E.A. SREBP activation contributes to fatty acid accumulations in necroptosis. (2023). RSC Chem Biol. 4: 310–322.
- Aqil, A*, Gill, S., Gokcumen, O.*, Malhi, R.S., Reese, E.A., Smith J.L., Heaton, T.T., Lindqvist, C. A paleogenome from a Holocene individual supports genetic continuity in Southeast Alaska (2023). iScience. 26, 106581
- Sun, Y.H., Cui, H., Song, Chi., Shen, J.T., Zhuo, X., Wang, R.H., Yu, X., Ndamba, R., Mu, Q., Gu, H., Wang, D., Murthy, G.G., Li, P., Liang, F., Liu, L., Tao, Q., Wang, Y., Orlowski, S., Xu, Q., Zhou, H., Jagne, J., Gokcumen, O.*, Anthony, N., Zhao, X., Li, X.Z.. Amniotes co-opt intrinsic genetic instability to protect germ-line genome integrity. (2023). Nature Communications. 14:812.
- Dos Santos, A.L.C.*, Sullasi, H.S.L., Gokcumen, O.*, Lindo, J., DeGiorgio, M. Spatiotemporal fluctuations of population structure in the Americas revealed by a meta-analysis of the first decade of archaeogenomes (2022). American Journal of Biological Anthropology. 180: 703-714.
- A Aqil, L Speidel, P Pavlidis, O Gokcumen (2023) Balancing selection on genomic deletion polymorphisms in human. Elife. 12, e79111.
- Nikkanen, J., Leong, W.A., Krause, W.C., Dermadi, D., Maschek, J.A., Van Ry, T., Cox, J.E., Weiss, E.J., Gokcumen, O.*, Chawla, A., Ingraham, H.A. (2022). Trade-Offs Between Hepatic Host Defense and Metabolic Programs Underlie Sex-Biased Diseases. Science. 378: 290-295.
- Dos Santos, A.L.C., Owings, A., Sullasi, H.S.L., Gokcumen, O.*, DeGiorgio, M., Lindo, J. Genomic evidence of ancient migrations along South America's Atlantic coast. (2022). Proceedings of the Royal Society B. 289: 20221078.
- Pajic, P.*, Shen, S., Qu, J., May, A.J., Knox, S., Ruhl, S., Gokcumen, O.* (2022) A mechanism of gene evolution generating mucin function. Science Advances. 8: 34. [Corresponding author].
- Saitou, M.*, Masuda, N., Gokcumen, O.* (2022). Similarity-based analysis of allele frequency distribution among multiple populations identifies adaptive genomic structural variants. Molecular Biology and Evolution. 39: msab313. [Corresponding Author].
- Saitou, M.*, Resendez, S.*, Pradhan, A.J., Wu, F., Lie, N.C., Hall, N.J., Zhu, Q., Reinholdt, L. Satta, Y., Speidel, L., Nakagome, S., Hanchard, N. A., Churchill, G., Lee, C., Atilla-Gokcumen, G. E., Mu, X., Gokcumen, O.* (2021). Sex-specific phenotypic effects and evolutionary history of an ancient polymorphic deletion of the human growth hormone receptor. Sci Adv. 7, eabi4476. [Corresponding Author].
- Starr, I.*, Seiffert-Sinha, K, Sinha, A.A., Gokcumen, O.* (2021). Evolutionary Context of Psoriatic Immune Skin Response. Evolution, Medicine and Public Health. 9: 474-486 [Corresponding Author].
- Pliss, A., Kuzmin, A.N., Lita, A., Kumar, R., Celiku, O., Atilla-Gokcumen G.E., Gokcumen, O.*, Chandra, D., Larion, M., Prasad, P.N. (2021). Single Organelle Optical Omics Platform for Cell Science and Biomarker Discovery. Analytical Chemistry. 93:8281.
- Pradhani et al. (2021). Protein acylation by saturated very long chain fatty acids and endocytosis are involved in necroptosis. Cell Chemical Biology. (In Press)
- Xu, D., Gokcumen, O*., Khurana, E. (2020). Loss-of-function tolerance of enhancers in the human genome. PLoS Genetics. 6:e1008663.
- Eaaswarkhanth, E., dos Santos, A.L.*, Gokcumen, O.*, Al-Mulla, F., Thanaraj, T.A. (2020). Genome-Wide Selection Scan in an Arabian Peninsula Population Identifies a TNKS Haplotype Linked to Metabolic Traits and Hypertension. Genome Biology and Evolution, 12: 77–87 [Highlighted in Human Genetics].
- Gokcumen, O. (2020) Archaic hominin introgression into modern human genomes. Yearbook of Physical Anthropology. 171: 60.
- Saitou, M.* & Gokcumen, O. (2020). An Evolutionary Perspective on the Impact of Genomic Copy Number Variation on Human Health. Journal of Molecular Evolution. 88: 104.
- Thamadilok, S., Choi, K.-S., Ruhl, L., Schulte, F., Kazim, A. L., Hardt, M., Gokcumen, O*., Ruhl, S. (2020).Human and Non-Human Primate Lineage-Specific Footprints in the Salivary Proteome. Molecular Biology and Evolution. 37:39-405.
- O Gokcumen, M Frachetti. The Impact of Ancient Genome Studies in Archaeology. Annual Review of Anthropology. (2020) 49:277–98
- Saitou, M*., Gaylord, E., Xu, D.,Neznanova, L., Nathan, S., Grawe, A., Chang, J., Ryan, William., Ruhl, S., Knox, S.M., and Gokcumen, O*. (2020). Functional Specialization of Human Salivary Glands and Origins of Proteins Intrinsic to Human Saliva. Cell Reports. 33, 108402. [Corresponding Author].
- Ozgur Taskent, Yen Lung Lin, Ioannis Patramanis, Pavlos Pavlidis and Omer Gokcumen, 2020. Analysis of Haplotypic Variation and Deletion Polymorphisms Point to Multiple Archaic Introgression Events, Including from Altai Neanderthal Lineage. https://doi.org/10.1534/genetics.120.303167
- Pradhani et al. (2021). Protein acylation by saturated very long chain fatty acids and endocytosis are involved in necroptosis. Cell Chemical Biology. (In Press)
- Xu, D., Gokcumen, O*., Khurana, E. (2020). Loss-of-function tolerance of enhancers in the human genome. PLoS Genetics. 6:e1008663.
- Eaaswarkhanth, E., dos Santos, A.L.*, Gokcumen, O.*, Al-Mulla, F., Thanaraj, T.A. (2020). Genome-Wide Selection Scan in an Arabian Peninsula Population Identifies a TNKS Haplotype Linked to Metabolic Traits and Hypertension. Genome Biology and Evolution, 12: 77–87 [Highlighted in Human Genetics].
- Gokcumen, O. (2020) Archaic hominin introgression into modern human genomes. Yearbook of Physical Anthropology. 171: 60.
- Saitou, M.* & Gokcumen, O. (2020). An Evolutionary Perspective on the Impact of Genomic Copy Number Variation on Human Health. Journal of Molecular Evolution. 88: 104.
- Thamadilok, S., Choi, K.-S., Ruhl, L., Schulte, F., Kazim, A. L., Hardt, M., Gokcumen, O*., Ruhl, S. (2020).Human and Non-Human Primate Lineage-Specific Footprints in the Salivary Proteome. Molecular Biology and Evolution. 37:39-405.
- O Gokcumen, M Frachetti. The Impact of Ancient Genome Studies in Archaeology. Annual Review of Anthropology. (2020) 49:277–98
- Saitou, M*., Gaylord, E., Xu, D.,Neznanova, L., Nathan, S., Grawe, A., Chang, J., Ryan, William., Ruhl, S., Knox, S.M., and Gokcumen, O*. (2020). Functional Specialization of Human Salivary Glands and Origins of Proteins Intrinsic to Human Saliva. Cell Reports. 33, 108402. [Corresponding Author].
- Ozgur Taskent, Yen Lung Lin, Ioannis Patramanis, Pavlos Pavlidis and Omer Gokcumen, 2020. Analysis of Haplotypic Variation and Deletion Polymorphisms Point to Multiple Archaic Introgression Events, Including from Altai Neanderthal Lineage. https://doi.org/10.1534/genetics.120.303167
- Saito, M., Gokcumen, O. (2019). Resolving the insertion sites of polymorphic duplications reveals a HERC2 haplotype under selection. Genome Biology and Evolution. evz107 [Corresponding Author].
- Pajic, P., Pavlidis, P., Dean, K., Neznanova, L., Daugherity, E., Romano R-A., Garneau, D., Globig, A., Ruhl, S., Gokcumen, O. (2019). Independent amylase gene copy number bursts correlate with dietary preferences in mammals. eLife. 8:e44628 [Corresponding Author].
- Chow J, Starr I*, Jamalzadeh S, Muniz O, Kumar A, Gokcumen, O.*, Ferkey DM, Cullen PJ. 2019. Filamentation Regulatory Pathways Control Adhesion-Dependent Surface Responses in Yeast. Genetics [Internet]:genetics.302004.2019. Available from: http://dx.doi.org/10.1534/genetics.119.302004
- Lin, Y.-L.*, & Gokcumen, O.* (2019). Fine-Scale Characterization of Genomic Structural Variation in the Human Genome Reveals Adaptive and Biomedically Relevant Hotspots. Genome Biology and Evolution, 11(4), 1136–1151. [Corresponding Author].Lin, Y-L., Gokcumen, O. (2018). Fine-scale characterization of genomic structural variation in the human genome reveals adaptive and biomedically relevant hotspots. BioRxiv [preprint]. April 4, 2018. Available here.
- Pajic, P., Pavlidis, P., Dean, K., Neznanova, L., Daugherity, E., Romano R-A., Garneau, D., Globig, A., Ruhl, S., Gokcumen, O. (2018). Amylase copy number analysis in several mammalian lineages reveals convergent adaptive bursts shaped by diet. BioRxiv [preprint]. June 5, 2018. Available here.
- Saito, M.*, Satta, Y., Gokcumen, O.* (2018). Complex haplotypes of GSTM1 gene deletions harbor signatures of a selective sweep in East Asian populations. G3. 8:2953.
- Saito, M*. Lizardo, D., Taskent, R. O.*, Millner, A., Gokcumen, O., Atilla-Gokcumen, G. (2018). An evolutionary transcriptomics approach links CD36 to membrane remodeling in replicative senescence. Mol Omics 14, 237 (a journal of Royal Society of Chemistry). [Cover article, co-Corresponding Author].
- Saito, M.*, Satta, Y., Gokcumen, O.*, Ishida, T. (2018). Complex evolution of the GSTM gene family involves sharing of GSTM1 deletion polymorphism in humans and chimpanzees. BMC Genomics. 19:293. [co-Corresponding Author, IF:4.3].
- Quillen, E., Norton, H., Parra, E., Lona-Durazo, F., Ang, K., I, Florin M., Pearson, L., Shriver, M., Lasisi, T., Gokcumen, O., Starr, I*., Lin, YL*., Martin, A., Jablonski, N. (2018). Shades of complexity: New perspectives on the evolution and genetic architecture of human skin. Yearbook of Physical Anthropology. (Early View).
- Gokcumen, O. (2018). The Year in Genetics Anthropology: New Lands, New Technologies, New Questions. American Anthropologist. 120:266. [Also highlighted in the special virtual issue: “Genetics, Biology, and Race: Understanding Human Difference”].
- Resendez, S.D.*, Bradley, J.*, Xu, D.*, Gokcumen, O.* (2018). Structural variants in ancient genomes. In: Rajora and Lindqvist, eds. Paleogenomics. Springer Population Genomics Series.
- Schmidt, C. and Gokcumen, O.* Primate Genomics and Phylogenetics. In: O’Rourke, eds. A Companion to Anthropological Genetics. Wiley Press
- Taskent et al. (2017). Variation and functional impact of Neanderthal ancestry in Western Asia. Genome Biology and Evolution. evx216. For press release.
- Xu et al. (2017). VCFtoTree: a user-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences. BMC Bioinformatics. 18:426.
- Xu et al. (2017). Archaic hominin introgression in Africa contributes to functional salivary MUC7 genetic variation. Mol Biol Evol. Press release from UB Press Office. A write-up in the Guardian is here. For further media coverage, please see its Altmetric page.
- Taskent and Gokcumen (2017). The multiple histories of Western Asia: Perspectives from ancient, and modern genomes. PrePrint (before proofs). Hum. Bio.
- Lizardo et al. (2017). Regulation of lipids is central to replicative senescence. Molecular BioSystems. 13, 498-509 – This study was also recognized by the Royal Society of Chemistry as an article of particular interest.
- Pajic et al. (2016). The psoriasis-associated deletion of late cornified envelope genes LCE3B and LCE3C has been maintained under balancing selection since Human Denisovan divergence. BMC Evolutionary Biology. 16,265.
- Muthukrishnan et al. (2016). Atopic Dermatitis Susceptibility Variants In Filaggrin Hitchhike Hornerin Selective Sweep. Genome Biology and Evolution. 8, 3240 – For media coverage, please see its Altmetric page.
- Xu et al. Recent Evolution of the salivary mucin MUC7. (2016). Scientific Reports. 6, 31791. Press release from UB Press Office. For further media coverage, please see its Altmetric page.
- Lin et al. (2015). The evolution and functional impact of human deletion variants shared with archaic hominin genomes. Mol Biol Evol. Early Access. [Corresponding Author]. – Press release from UB Press Office. For further media coverage, please see its Altmetric page. Here is also Omer’s Talk on this paper at EMPH @Tempe 2015.
- Muthukrishan et al. (2014). Geographic Distribution And Adaptive Significance Of Genomic Structural Variants: An Anthropological Genetics Perspective. Hum Bio. 86(4):260-275. 2014. [Cover Article].
- Pradhani et al. (2021). Protein acylation by saturated very long chain fatty acids and endocytosis are involved in necroptosis. Cell Chemical Biology. (In Press)
- Xu, D., Gokcumen, O*., Khurana, E. (2020). Loss-of-function tolerance of enhancers in the human genome. PLoS Genetics. 6:e1008663.
- Eaaswarkhanth, E., dos Santos, A.L.*, Gokcumen, O.*, Al-Mulla, F., Thanaraj, T.A. (2020). Genome-Wide Selection Scan in an Arabian Peninsula Population Identifies a TNKS Haplotype Linked to Metabolic Traits and Hypertension. Genome Biology and Evolution, 12: 77–87 [Highlighted in Human Genetics].
- Gokcumen, O. (2020) Archaic hominin introgression into modern human genomes. Yearbook of Physical Anthropology. 171: 60.
- Saitou, M.* & Gokcumen, O. (2020). An Evolutionary Perspective on the Impact of Genomic Copy Number Variation on Human Health. Journal of Molecular Evolution. 88: 104.
- Thamadilok, S., Choi, K.-S., Ruhl, L., Schulte, F., Kazim, A. L., Hardt, M., Gokcumen, O*., Ruhl, S. (2020).Human and Non-Human Primate Lineage-Specific Footprints in the Salivary Proteome. Molecular Biology and Evolution. 37:39-405.
- O Gokcumen, M Frachetti. The Impact of Ancient Genome Studies in Archaeology. Annual Review of Anthropology. (2020) 49:277–98
- Saitou, M*., Gaylord, E., Xu, D.,Neznanova, L., Nathan, S., Grawe, A., Chang, J., Ryan, William., Ruhl, S., Knox, S.M., and Gokcumen, O*. (2020). Functional Specialization of Human Salivary Glands and Origins of Proteins Intrinsic to Human Saliva. Cell Reports. 33, 108402. [Corresponding Author].
- Ozgur Taskent, Yen Lung Lin, Ioannis Patramanis, Pavlos Pavlidis and Omer Gokcumen, 2020. Analysis of Haplotypic Variation and Deletion Polymorphisms Point to Multiple Archaic Introgression Events, Including from Altai Neanderthal Lineage. https://doi.org/10.1534/genetics.120.303167
- Saito, M., Gokcumen, O. (2019). Resolving the insertion sites of polymorphic duplications reveals a HERC2 haplotype under selection. Genome Biology and Evolution. evz107 [Corresponding Author].
- Pajic, P., Pavlidis, P., Dean, K., Neznanova, L., Daugherity, E., Romano R-A., Garneau, D., Globig, A., Ruhl, S., Gokcumen, O. (2019). Independent amylase gene copy number bursts correlate with dietary preferences in mammals. eLife. 8:e44628 [Corresponding Author].
- Chow J, Starr I*, Jamalzadeh S, Muniz O, Kumar A, Gokcumen, O.*, Ferkey DM, Cullen PJ. 2019. Filamentation Regulatory Pathways Control Adhesion-Dependent Surface Responses in Yeast. Genetics [Internet]:genetics.302004.2019. Available from: http://dx.doi.org/10.1534/genetics.119.302004
- Lin, Y.-L.*, & Gokcumen, O.* (2019). Fine-Scale Characterization of Genomic Structural Variation in the Human Genome Reveals Adaptive and Biomedically Relevant Hotspots. Genome Biology and Evolution, 11(4), 1136–1151. [Corresponding Author].Lin, Y-L., Gokcumen, O. (2018). Fine-scale characterization of genomic structural variation in the human genome reveals adaptive and biomedically relevant hotspots. BioRxiv [preprint]. April 4, 2018. Available here.
- Pajic, P., Pavlidis, P., Dean, K., Neznanova, L., Daugherity, E., Romano R-A., Garneau, D., Globig, A., Ruhl, S., Gokcumen, O. (2018). Amylase copy number analysis in several mammalian lineages reveals convergent adaptive bursts shaped by diet. BioRxiv [preprint]. June 5, 2018. Available here.
- Saito, M.*, Satta, Y., Gokcumen, O.* (2018). Complex haplotypes of GSTM1 gene deletions harbor signatures of a selective sweep in East Asian populations. G3. 8:2953.
- Saito, M*. Lizardo, D., Taskent, R. O.*, Millner, A., Gokcumen, O., Atilla-Gokcumen, G. (2018). An evolutionary transcriptomics approach links CD36 to membrane remodeling in replicative senescence. Mol Omics 14, 237 (a journal of Royal Society of Chemistry). [Cover article, co-Corresponding Author].
- Saito, M.*, Satta, Y., Gokcumen, O.*, Ishida, T. (2018). Complex evolution of the GSTM gene family involves sharing of GSTM1 deletion polymorphism in humans and chimpanzees. BMC Genomics. 19:293. [co-Corresponding Author, IF:4.3].
- Quillen, E., Norton, H., Parra, E., Lona-Durazo, F., Ang, K., I, Florin M., Pearson, L., Shriver, M., Lasisi, T., Gokcumen, O., Starr, I*., Lin, YL*., Martin, A., Jablonski, N. (2018). Shades of complexity: New perspectives on the evolution and genetic architecture of human skin. Yearbook of Physical Anthropology. (Early View).
- Gokcumen, O. (2018). The Year in Genetics Anthropology: New Lands, New Technologies, New Questions. American Anthropologist. 120:266. [Also highlighted in the special virtual issue: “Genetics, Biology, and Race: Understanding Human Difference”].
- Resendez, S.D.*, Bradley, J.*, Xu, D.*, Gokcumen, O.* (2018). Structural variants in ancient genomes. In: Rajora and Lindqvist, eds. Paleogenomics. Springer Population Genomics Series.
- Schmidt, C. and Gokcumen, O.* (In press). Primate Genomics and Phylogenetics. In: O’Rourke, eds. A Companion to Anthropological Genetics. Wiley Press
- Taskent et al. (2017). Variation and functional impact of Neanderthal ancestry in Western Asia. Genome Biology and Evolution. evx216. For press release.
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