Publications and posts from Petar Pajic, NSF Postdoctoral Fellow at Yale University.https://petarpajic.com/https://petarpajic.com/posts/new-paper-vntr-balancing/https://petarpajic.com/posts/new-paper-vntr-balancing/Petar Pajic, currently an NSF Postdoctoral Fellow at Yale University, has published a new review article in Genome Biology and Evolution exploring how VNTRs drive evolutionary innovation in mammals while carrying functional risk.Tue, 20 Jan 2026 00:00:00 GMThttps://doi.org/10.1093/gbe/evaf250https://doi.org/10.1093/gbe/evaf250Understanding genomic function has historically relied on sequence conservation across evolutionary time. However, functional innovations often arise from rapidly evolving, nonconserved elements. Variable number tandem repeats (VNTRs) act as engines of both functional innovation and phenotypic consequence, influencing gene regulation, protein structure, and phenotypic diversity. This review synthesizes emerging insights into the functional and evolutionary impact of VNTRs in mammals, outlining the mutational mechanisms driving their evolution, the selective forces maintaining structural heterogeneity, and a theoretical framework for their persistence through evolutionary tradeoffs.Thu, 01 Jan 2026 00:00:00 GMThttps://doi.org/10.1093/gbe/evaf165https://doi.org/10.1093/gbe/evaf165The secretory calcium-binding phosphoprotein (SCPP) gene family, which includes genes expressed abundantly in human saliva, evolved alongside major evolutionary milestones in vertebrates. We explored the evolution of saliva-related SCPP genes using genomic and transcriptomic resources, finding previously undocumented convergent gene duplications in primate genomes. These saliva-related genes show signatures of positive selection while neighboring genes remain conserved, suggesting dietary and pathogenic pressures drove adaptive diversification of saliva composition in primates, including humans.Fri, 22 Aug 2025 00:00:00 GMThttps://petarpajic.com/posts/nsf-fellowship-mucus-pregnancy/https://petarpajic.com/posts/nsf-fellowship-mucus-pregnancy/I've been awarded a prestigious Postdoctoral Research Fellowship in Biology (PRFB) from the National Science Foundation, joining Dr. Stacy Malaker's lab at Yale University to study glycoproteomics and the evolutionary genetics of mucins.Wed, 20 Aug 2025 00:00:00 GMThttps://doi.org/10.1093/nar/gkaf133https://doi.org/10.1093/nar/gkaf133SARS-CoV-2 virus-like particles (VLPs) are ~100-nm bioinspired mimetics of the authentic virus, engineered here as a platform for mRNA delivery. A three-plasmid VLP system displayed ~7-fold higher viral entry efficiency than four-plasmid co-transfection, transducing over 90% of human ACE2-expressing cells. Viral tropism could be reprogrammed by swapping glycoproteins from other viral strains, and VLPs carried up to four transgenes, including functional Cas9 mRNA for genome editing, with successful delivery to mouse lungs.Mon, 24 Mar 2025 00:00:00 GMThttps://petarpajic.com/posts/amylase-paper-press/https://petarpajic.com/posts/amylase-paper-press/My latest paper on the evolutionary history of the AMY1 gene has garnered significant attention from CNN, The New York Times, and scientists in the field, shedding light on how our ancestors adapted to carbohydrate-rich diets long before the advent of agriculture.Sun, 02 Feb 2025 00:00:00 GMThttps://doi.org/10.1126/science.adn0609https://doi.org/10.1126/science.adn0609Human adaptation to a wide range of diets is a hallmark of our species, sometimes even reflected in our genomic diversity. The amylase gene encodes an enzyme that digests starch, a complex carbohydrate found in many modern human diets. Genomic studies have found substantial variation in the number of amylase gene copies, believed to be an adaptive response to dietary changes among human populations after the advent of agriculture. We reconstruct the locus's evolutionary history, tracing duplications that predate agriculture and seeded modern structural variation.Thu, 24 Oct 2024 00:00:00 GMThttps://petarpajic.com/publications/ancient-amy1-duplications/https://petarpajic.com/publications/ancient-amy1-duplications/Starch digestion is a cornerstone of human nutrition, and the amylase enzyme plays a key role in starch metabolism. The copy number of the human amylase gene (AMY1) has been associated with metabolic diseases and adaptation to agricultural diets. We show that amylase gene duplications originated over 700,000 years ago, predating the human-Neanderthal divergence, and likely primed the locus for rapid dietary adaptation during the agricultural transition through nonallelic homologous recombination.Tue, 28 Nov 2023 00:00:00 GMThttps://petarpajic.com/posts/contributing-one-puzzle-piece/https://petarpajic.com/posts/contributing-one-puzzle-piece/When I first entered Dr. Gokcumen's lab, I carried with me a heavy bag of naivety about the value of basic science. One story about the Manhattan Project reshaped my perspective on applied versus basic research entirely.Mon, 21 Aug 2023 00:00:00 GMThttps://doi.org/10.1038/s42003-023-05047-yhttps://doi.org/10.1038/s42003-023-05047-yChemosensation (olfaction, taste) is essential for detecting and assessing foods, such that dietary shifts elicit evolutionary changes in vertebrate chemosensory genes. We explore the effects of subsistence behaviors on olfactory and taste receptor genes among rainforest foragers and neighboring agriculturalists in Africa and Southeast Asia, analyzing 378 functional OR and 26 functional TASR genes across 133 individuals. We find no evidence of relaxed selection in agricultural populations but identify subsistence-related signatures of local adaptation within each geographic region.Mon, 03 Jul 2023 00:00:00 GMThttps://petarpajic.com/publications/mucin-function-gene-evolution/https://petarpajic.com/publications/mucin-function-gene-evolution/How novel gene functions evolve is a fundamental question in biology. Mucin proteins, a functionally but not evolutionarily defined group of proteins, allow the study of convergent evolution of gene function. By analyzing the genomic variation of mucins across a wide range of mammalian genomes, we propose that exonic repeats and their copy number variation contribute substantially to the de novo evolution of new gene functions, identifying 15 undescribed instances of evolutionary convergence in mucin origin.Fri, 26 Aug 2022 00:00:00 GMThttps://petarpajic.com/posts/mucus-slime-new-way-to-evolve/https://petarpajic.com/posts/mucus-slime-new-way-to-evolve/I led this project with the Stefan Ruhl Laboratory on how mucin proteins have evolved. Our work shows that the gain of exonic repeats on existing precursor genes led to the de novo evolution of mucin function in multiple mammalian lineages.Fri, 19 Aug 2022 00:00:00 GMThttps://petarpajic.com/publications/modified-sialic-acids-influenza/https://petarpajic.com/publications/modified-sialic-acids-influenza/Sialic acids (Sia) are the primary receptors for influenza viruses and are widely displayed on cell surfaces and in secreted mucus. Modifications of Sia in mucus may have potent effects on the functions of influenza A virus (IAV) hemagglutinin and neuraminidase, affecting both pathogens and the normal flora of different mucosal sites.Thu, 16 Apr 2020 00:00:00 GMThttps://petarpajic.com/publications/independent-amylase-bursts/https://petarpajic.com/publications/independent-amylase-bursts/The amylase gene (AMY), which codes for a starch-digesting enzyme, underwent several gene copy number gains in humans, dogs, and mice, possibly along with increased starch consumption during the evolution of these species. We present comprehensive evidence for AMY copy number expansions that independently occurred in several mammalian species which consume starch-rich diets, and provide correlative evidence that AMY duplications may be an essential first step for amylase to gain expression in saliva.Tue, 14 May 2019 00:00:00 GMThttps://petarpajic.com/publications/lce3b-lce3c-balancing-selection/https://petarpajic.com/publications/lce3b-lce3c-balancing-selection/A common, 32kb deletion of LCE3B and LCE3C genes is strongly associated with psoriasis and is ancient, predating Human-Denisovan divergence. We show that the haplotype harboring the deletion retains high allele frequency among extant and ancient human populations, harbors unusually high nucleotide variation, and has an unusually long coalescence time, consistent with the LCE3BC deletion having evolved under balancing selection — possibly a tradeoff between autoimmunity and pathogen exposure.Mon, 05 Dec 2016 00:00:00 GMT