Rick McLaughlin, Ph.D. (he/him/his)

Assistant Professor

Affiliate Assistant Professor, UW Genome Sciences

Rick McLaughlin, Ph.D. (he/him/his)

Assistant Professor

Affiliate Assistant Professor, UW Genome Sciences

Dr. Rick McLaughlin studies genome evolution and the interactions between mobile genetic elements and the immune system. His research focuses on transposable elements (DNA sequences that copy themselves within genomes) and the evolutionary conflicts that have shaped them and our cellular defenses. He previously led a research group at the Pacific Northwest Research Institute, trained as a postdoctoral fellow at Fred Hutchinson Cancer Center and received his doctorate from UT Southwestern Medical Center. McLaughlin works to create opportunities for undergraduates to participate directly in scientific discovery. His teaching emphasizes active learning, scientific communication and helping students develop the confidence and skills to think and work as scientists, regardless of their prior experience.

Education

  • Fred Hutch Cancer Center – Seattle, WA
    • Postdoctoral Fellow – Genome Evolution
  • University of Texas Southwestern Medical Center, Dallas, TX
    • Ph.D. – Biophysics, Cell Regulation
  • Trinity University, San Antonio, TX
    • B.S. – Biology, Business

Courses

  • BST 301 Scientific Writing
  • BIO 495 Investigative Biology

Teaching Interests

Dr. McLaughlin’s goal as an educator is to help students move beyond memorizing biological terms and pathways to thinking mechanistically and creatively about how living systems work. He wants students to understand how molecules, cells, genomes, and ecosystems give rise to the diversity of biological phenomena and to develop the skills to question, reason and communicate like scientists. He is excited to create classrooms and research environments that empower students to develop scientific identity and confidence, no matter where they begin or where they ultimately find professional fulfillment.

Research and Scholarship Interests

Our research program investigates how genomes function in the presence of vast amounts of repetitive DNA, particularly transposable elements (TEs) and retrocopy-derived genes, and how these elements influence cellular processes, immune signaling, and evolutionary change. Although originally dismissed as “junk,” repetitive sequences shape genome structure, gene regulation, mutation rates, and host–pathogen interactions. They also provide accessible avenues for undergraduate research: the questions are compelling (sometimes bordering on sci-fi), datasets are abundant and public, and analyses can range from conceptual reasoning to fully computational workflows or low-cost wet-lab experiments.

My goal is to build a research program that is simultaneously rigorous, creative, and highly participatory. I envision a lab where undergraduates are the primary drivers of discovery: an environment where students gain experience in the innate immune system, host-pathogen interactions, modern genomics, computational biology, molecular evolution, and hands-on experimental design while contributing to publishable research.

Creative Interests

Nature, mushroom foraging, bicycles, board games, parenting

Publications

  • Gustafson JA, Gibson SB, Damaraju N, Zalusky MPG, Hoekzema K, Twesigomwe D, Yang L, Snead AA, Richmond PA, De Coster W, Olson ND, Guarracino A, Li Q, Miller AL, Goffena J, Anderson ZB, Storz SHR, Ward SA, Sinha M, Gonzaga-Jauregui C, Clarke WE, Basile AO, Corvelo A, Reeves C, Helland A, Musunuri RL, Revsine M, Patterson KE, Paschal CR, Zakarian C, Goodwin S, Jensen TD, Robb E; 1000 Genomes ONT Sequencing Consortium; University of Washington Center for Rare Disease Research (UW-CRDR); Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium; McCombie WR, Sedlazeck FJ, Zook JM, Montgomery SB, Garrison E, Kolmogorov M, Schatz MC, McLaughlin RN, Dashnow H, Zody MC, Loose M, Jain M, Eichler EE, Miller DE. High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation. Genome Research (2024) PMID: 39358015.
  • Yang L, Metzger GA, Padilla Del Valle R, Delgadillo Rubalcaba D, McLaughlin RN. Evolutionary insights from profiling LINE-1 activity at allelic resolution in a single human genome. The EMBO Journal. (2024) PMID: 38177314
  • Xie MJ, Cromie GA, Owens K, Timour MS, Tang M, Kutz JN, El-Hattab AW, McLaughlin RN, Dudley AM. Constructing and interpreting a large-scale variant effect map for an ultrarare disease gene: Comprehensive prediction of the functional impact of PSAT1 genotypes. PLoS Genetics. (2023) PMID: 37812589.
  • Zhang L, Wang Y, Dong Y, Pant A, Liu Y, Masserman L, Xu Y, McLaughlin RN, Bai J. The endophilin curvature-sensitive motif requires electrostatic guidance to recycle synaptic vesicles in vivo. Developmental Cell. (2022) PMID: 35303431.
  • Yang L, Emerman M, Malik H, McLaughlin RN. Retrocopying expands the functional repertoire of APOBEC3 antiviral proteins in primates. eLife. (2020) PMID: 32479260.
  • Sharma A, McLaughlin RN, Basom RS, Kikawa C, OhAinle M, Yount JS, Emerman M, Overbaugh J. Macaque interferon-induced transmembrane proteins limit replication of SHIV strains in an Envelope-dependent manner. PLoS Pathogens. (2020) PMID: 31260493.
  • Colón-Thillet R, Hsieh E, Graf L, McLaughlin RN, Young JM, Kochs G, Emerman M, Malik HS. Combinatorial mutagenesis of rapidly evolving residues yields super-restrictor antiviral proteins. PLoS biology. (2019) PMID: 31574080.
  • McLaughlin RN, Gable JT, Wittkopp CJ, Emerman M, Malik HS. Conservation and innovation of APOBEC3A restriction functions during primate evolution. Molecular Biology and Evolution (2016) PMID: 27189538.
  • McLaughlin RN, Young JM, Yang L, Neme R, Wichman HA, Malik HS. Positive selection and multiple losses of the LINE-1-derived L1TD1 gene in mammals suggest a dual role in genome defense and pluripotency. PLoS Genetics. (2014) PMID: 25211013.
  • McLaughlin RN, Poelwijk FJ, Gosal WS, Ranganathan R. The spatial architecture of protein robustness and adaptation. Nature. (2012) PMID: 23041932.
  • Reynolds K, McLaughlin RN, Ranganathan R. Hotspots for allosteric regulation of a protein surface. Cell. (2011) PMID: 22196731.

Reviews, perspectives, primers

  • Padilla Del Valle R and McLaughlin RN. Stealing genes and facing consequences. Science. (2022) PMID: 36302006. (Perspective)
  • McLaughlin RN. Reading the tea leaves: dead transposon copies reveal novel host and transposon biology. PLOS Biology (2018) PMID: 29505560. (Primer)
  • McLaughlin RN and Malik HS. Genetic conflicts: the usual suspects and beyond. Journal of Experimental Biology (2017) PMID: 28057823. (Review)
  • McLaughlin RN and Malik HS. LINE-1 retroelements get ZAPped! PLoS Genetics. (2015) PMID: 26182081. (Perspective)

Preprints

  • Yang L, Nematbakhsh S, Norsemen A, McLaughlin RN Jr. Pangenome reference assemblies reveal the variation and recent activity of human LINE-1 retrotransposons. bioRxiv. 2026 May 16;. doi: 10.64898/2026.05.14.725010.
  • Lo RS, Cromie GA, Tang M, Teng K, Owens K, Sirr A, Kutz JN, McLaughlin RN, Morizono H, Caldovic L, Dudley A. The functional impact of 1,570 SNP-accessible missense variants in human OTC. bioRxiv (2022) doi: 10.1101/2022.10.26.513893.
  • Yang L, Metzger GA, and McLaughlin RN. Characterization of LINE-1 transposons in a human genome at allelic resolution. bioRxiv (2019) doi: 10.1101/594200.
  • 2023-2025, NIH R35 Maximizing Investigators’ Research Award Administrative Supplement Leveraging natural and directed evolution to dissect the functional consequences of sequence variation in human L1 retrotransposons. NIGMS 3R35GM142773-03S1.
  • 2022-2024, NIH R21 Exploratory/Developmental Research Grant Award Reverse transcriptase-mediated expansion of the host innate immune system. NIAID 1R21AI174130.
  • 2021-2026, NIH R35 Maximizing Investigators’ Research Award Leveraging natural and directed evolution to dissect the functional consequences of sequence variation in human L1 retrotransposons. NIGMS 1R35GM142773.
  • 2015-2021, NIH K99/R00 Pathway to Independence Award Causes and human health consequences of the evolution of retroelements and host restriction factors. NIGMS 1K99GM112941.
  • 2014, Fred Hutchinson Pilot and Feasibility Grant for CRISPR/Cas Technologies
    Investigating the essentiality of retrotransposon silencing in pluripotency induction and maintenance. NIDDK 5P30DK056465. R. McLaughlin and A. Molaro.
  • 2012-2014, Lupus Research Institute Novel Research Grant Genetic conflicts between TREX1 and endogenous retroelements. H. Malik (PI), Conceived and written with H. Malik.
  • 2012-2016, Helen Hay Whitney Foundation Postdoctoral Fellowship Sponsored by the Howard Hughes Medical Institute.
  • 2006-2008, Department of Pharmacology NIH Predoctoral Training Grant, UT Southwestern Medical Center. NIGMS 5T32GM007062.