lab photo picnic

Principal Investigator

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Nathan Clark, Ph.D.

Principal Investigator

nclark@utah.edu

Nathan is an Associate Professor in the Department of Human Genetics at the University of Utah. He received his PhD in Genome Sciences under the mentorship of Willie Swanson at the University of Washington. His NRSA-funded postdoctoral studies took place at Cornell under the guidance of Chip Aquadro. He began as an Assistant Professor in 2012 in the Department of Computational and Systems Biology at the University of Pittsburgh. There he received tenure and promotion to Associate Professor and remains a proud Adjunct member of that department. In 2019, the Clark lab moved to the University of Utah as part of an Evolutionary Genetics and Genomics hiring initiative. The Clark lab conducts evolutionary research at the interface of computational and experimental biology mostly within the themes of adaptive and convergent evolution. Major projects in the lab focus on the regressive evolution of eyesight in subterranean mammals, evolutionary adaptation to hypoxia and oxidative stress as encountered during diving and at high altitude, the evolution of long lifespan, and the creation of novel phylogenetic and comparative genomics methods to infer function from evolutionary patterns.

Lab

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Allie Graham

Post-doctoral Fellow

Allie received her PhD in 2017 from the University of Miami studying the genomic underpinnings of high-altitude adaptation in Andean ducks; from 2017 – 2020, she was an NSF Postdoctoral Research Fellow (PRFB) at Oregon State University, where she investigated the molecular mechanisms associated with hypoxia response in an intertidal copepod species. Her general interests lie in questions related to the genomic consequences of adaptations to “extreme” environmental cues​, and the roles of regulatory elements in facilitating adaptation and population divergence. She is also passionate about scientific outreach and broadening participation! Outside of science, she loves bird-watching, playing RPGs (D&D), video/board games, and reading science fiction.

Website: www.alliemgraham.weebly.com

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Amanda Kowalczyk

Ph.D. Student

Amanda uses evolution-based analyses to learn more about traits relevant to human health, such as longevity and vision. She is an active member of the RERconverge development team alongside her own research projects, which include RERconverge implementations, refining statistical methods, and incorporating data from numerous sources to complement computational analyses. Outside of her research endeavors, she has a strong interest in teaching, scientific outreach, and science writing.

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Elysia Saputra

Ph.D. Student

Elysia is a second-year PhD student in the CMU-Pitt Computational Biology program. Her current research focuses on finding regulatory elements that are correlated with the convergent evolution of the subterranean phenotype, using statistical and deep learning methods.

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Sarah Lucas

Ph.D. Student

Sarah is a 2nd year PhD student at the University of Utah. She looks forward to learning more about comparative genomics and the techniques needed to study them. Outside of lab, she enjoys playing board games and rock climbing, among other things.

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Jason Presnell

Senior Lab Specialist

Jason received his PhD from the University of Miami in 2017 working in the Browne lab where he studied KLF/SP gene family evolution and the roles of this gene family during development in the ctenophore Mnemiopsis leidyi. He worked on establishing protocols for performing gene knockdown via CRISPR/Cas9 in M. leidyi and for closing the life cycle of lab-cultured M. leidyi. He also published a re-examination of the presence of a through-gut in ctenophores. Jason then moved to the Weis lab at Oregon State University where he mostly worked on developing molecular genetic tools to investigate cnidarian-algal symbiosis in the model sea anemone Aiptasia. Additionally, he characterized tentacle patterning and the role of symbiosis during asexual reproduction in Aiptasia, a process known as pedal laceration. Broadly, his research interests are focused on evolutionary developmental biology, especially with regard to non-bilaterians and early metazoan trait evolution, and the role of gene regulation (non-coding regions, transcription factors) during development.

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Jaret Lieberth

Lab Technician

Jaret is a graduate of the University of Mississippi and is originally from Cleveland, Ohio. Currently, he is working as a research technician in the Clark lab. His project involves creating genetic constructs and using zebrafish to characterize regulatory elements presumed to play roles in the development and function of the eye. Eventually, he would like to gain acceptance to an NSF-funded MD/Ph.D. program.

Former Lab Members

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Raghav Partha

Ph.D. Student
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Wynn Meyer

Post-doctoral Associate
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Melissa Plakke

Ph.D. Student
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Camille Meslin

Post-doctoral Associate
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Zelia Ferreira

Post-doctoral Associate
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Jennifer Walker

Lab Manager
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Jerrica Jamison

Undergraduate
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Brandon Small

Undergraduate
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Jianxuan Yang

Visiting Scholar
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Luisa Cusick

Undergraduate