Skip to content

Aaron Quinlan

Professor of Human Genetics and
of Biomedical Informatics

Quinlan Photo

B.S. College of William and Mary

Ph.D. Boston College



Aaron Quinlan's Lab Page

Aaron Quinlan USTAR Center

Aaron Quinlan's PubMed Literature Search


Molecular Biology Program

Genomics, Computational Biology, Bioinformatics, Human Genetics, Cancer Genomics, Rare disease genetics, Ovarian Cancer


Broadly speaking, my group’s research marries genetics and genomics techniques with computer science, machine learning, and engineering to develop new ways of gaining insight into genome biology and the genetic basis of traits. We try to tackle problems with practical importance to understanding genome variation, chromosome evolution and mining genetic variation for improved understanding of human disease. For more details about our research, the laboratory, and living in Utah, please visit


  1. James M. Havrilla, Brent S. Pedersen, Ryan M. Layer, Aaron R. Quinlan. (2018) A map of constrained coding regions in the human genome.doi: 
  2. Simovski B, Kanduri C, Gundersen S, Titov D, Domanska D, Bock C, Bossini-Castillo L, Chikina M, Favorov A, Layer RM, Mironov AA, Quinlan AR, Sheffield NC, Trynka G, Sandve GK. Coloc-stats: a unified web interface to perform colocalization analysis of genomic features. (2018) Nucleic Acids Research, doi: 10.1093/nar/gky474.
  3. Belyeu JR, Nicholas TJ, Pedersen BS, Sasani TA, Havrilla JM, Kravitz SN, Conway ME, Lohman BK, Quinlan AR, Layer RM. SV-plaudit: A cloud-based framework for manually curating thousands of structural variants. (2018) Gigascience, doi: 10.1093/gigascience/giy064. 
  4. Pedersen BS, Quinlan AR. hts-nim: scripting high-performance genomic analyses.(2018) Bioinformatics, doi: 10.1093/bioinformatics/bty358.
  5. Donna M Werling, Harrison Brand, Joon-Yong An, Matthew R Stone, Joseph T Glessner, Lingxue Zhu, Ryan L Collins, Shan Dong, Ryan M Layer, Eiriene-Chloe Markenscoff-Papadimitriou, Andrew Farrell, Grace B Schwartz, Benjamin B Currall, Jeanselle Dea, Clif Duhn, Carolyn Erdman, Michael Gilson, Robert E Handsaker, Seva Kashin, Lambertus Klei, Jeffrey D Mandell, Tomasz J Nowakowski, Yuwen Liu, Sirisha Pochareddy, Louw Smith, Michael F Walker, Harold Z Wang, Mathew J Waterman, Xin He, Arnold R Kriegstein, John L Rubenstein, Nenad Sestan, Steven A McCarroll, Ben M Neale, Hilary Coon, A. Jeremy Willsey, Joseph D Buxbaum, Mark J Daly, Matthew W State, Aaron Quinlan, Gabor T Marth, Kathryn Roeder, Bernie Devlin, Michael E Talkowski, Stephan J Sanders.  An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder. (2018) Nature Genetics, DOI: 10.1038/s41588-018-0107-y. 
  6. Miten Jain, Sergey Koren, Josh Quick, Arthur C Rand, Thomas A Sasani, John R Tyson, Andrew D Beggs, Alexander T Dilthey, Ian T Fiddes, Sunir Malla, Hannah Marriott, Karen H Miga, Tom Nieto, Justin O'Grady, Hugh E Olsen, Brent S Pedersen, Arang Rhie, Hollian Richardson, Aaron Quinlan, Terrance P Snutch, Louise Tee, Benedict Paten, Adam M. Phillippy, Jared T Simpson, Nicholas James Loman, View ORCID ProfileMatthew Loose. Nanopore sequencing and assembly of a human genome with ultra-long reads. (2018) Nature Biotechnology, DOI: 10.1038/nbt.4060. 
  7. Ryan M. Layer, Brent S. Pedersen, Tonya DiSera, Gabor T. Marth, Jason Gertz, Aaron R. Quinlan.  GIGGLE: a search engine for large-scale integrated genome analysis. (2018) Nature Methods, doi: 10.1038/nmeth.4556. 
  8. Brent S. Pedersen and Aaron Quinlan. mosdepth: quick coverage calculation for genomes and exomes. (2018) Bioinformatics 
  9. Brent S. Pedersen, Ryan L Collins, Michael E Talkowski, Aaron Quinlan.  Indexcov: fast coverage quality control for whole-genome sequencing. (2017). GigaScience 
  10. Karen Eilbeck*, Aaron Quinlan*, Mark Yandell. Settling the score: variant prioritization and Mendelian disease. (2017) Nature Reviews Genetics doi:10.1038/nrg.2017.52. 
  11. Andrea Bild, Samuel Brady, Jasmine McQuerry, Yi Qiao, Stephen Piccolo, Gajendra Shrestha, Ryan Layer, Brent Pedersen, David Jenkins, Ryan Miller, Amanda Esch, Sara Selitsky, Joel Parker, Layla Anderson, Chakravarthy Reddy, Jonathan Boltax, Dean Li, Philip Moos, Joe Gray, Laura Heiser, W. Evan Johnson, Saundra Buys, Adam Cohen, Quinlan AR, Gabor Marth, Theresa Werner, Brian Dalley, and Rachel Factor.  Combating subclonal evolution of resistant cancer phenotypes. (2017)Nature Communications, doi:10.1038/s41467-017-01174-3. 
  12. Xiangfei Liu, Uma Devi Paila, Sharon N. Teraoka, Jocyndra A. Wright, Xin Huang, Quinlan AR, Richard A. Gatti and Patrick Concannon. Identification of ATIC as a novel target for chemoradiosensitization. (2017) International Journal of Radiation Oncology, doi:10.1016/j.ijrobp.2017.08.033.
  13. Pedersen BS, Quinlan AR†.  Who’s Who? Detecting and Resolving Sample Anomalies in Human DNA Sequencing Studies with Peddy. (2017) AJHG doi: 10.1016/j.ajhg.2017.01.017.
  14. Pedersen BS, Quinlan AR†. cyvcf2: fast, flexible variant analysis with Python. (2017) Bioinformatics doi: 10.1093/bioinformatics/btx057
  15. Pedersen BS, Layer RM, Quinlan AR†. Vcfanno: fast, flexible annotation of genetic variants. (2016) Genome Biol. doi: 10.1186/s13059-016-0973-5.
  16. Ge Y, Onengut-Gumuscu S, Quinlan AR, Mackey AJ, Wright JA, Buckner JH, Habib T, Rich SS, Concannon P.  Targeted Deep Sequencing in Multiple-Affected Sibships of European Ancestry Identifies Rare Deleterious Variants in PTPN22 that Confer Risk for Type 1 Diabetes. (2016) Diabetes. pii: db150322.
  17. Layer RM, Kindlon N, Karczewski K, Exome Aggregation Consortium, Quinlan AR.  Efficient genotype compression and analysis of large genetic-variation data sets. (2015) Nature Methods. doi:10.1038/nmeth.3654
  18. Layer RM, Quinlan AR. A parallel algorithm for N-way interval set intersection. (2015) IEEE Proceedings.
  19. Chiang C, Layer RM, Faust GG, Lindberg MR, Rose DB, Garrison EP, Marth GT, Quinlan AR, Hall IM. Speedseq: Ultra-fast personal genome analysis and interpretation. (2015). Nature Methods. doi:10.1038/nmeth.3505
  20. Paul L. Auer, PhD; Mike Nalls, PhD; James F. Meschia, MD; Bradford B. Worrall, MD; W. T. Longstreth Jr, MD; Sudha Seshadri, MD; Charles Kooperberg, PhD; Kathleen M. Burger, DO; Christopher S. Carlson, PhD; Cara L. Carty, PhD; Wei-Min Chen, PhD; L. Adrienne Cupples, PhD; Anita L. DeStefano, PhD; Myriam Fornage, PhD; John Hardy, PhD; Li Hsu, PhD; Rebecca D. Jackson, MD; Gail P. Jarvik, MD, PhD; Daniel S. Kim, BS; Kamakshi Lakshminarayan, MD; Leslie A. Lange, PhD; Ani Manichaikul, PhD; Aaron R. Quinlan, PhD; Andrew B. Singleton, PhD; Timothy A. Thornton, PhD; Deborah A. Nickerson, PhD;Ulrike Peters, PhD; Stephen S. Rich, PhD;
    Rare and Coding Region Genetic Variants Associated With Risk of Ischemic Stroke. (2015) JAMA Neurol. 2015;72(7):781-788. doi:10.1001/jamaneurol.2015.0582
  21. Suna Onengut-Gumuscu,Wei-Min Chen, Oliver Burren, Nick J. Cooper, Aaron R. Quinlan, et. al. Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers. Nature Genetics, (2015), 47(4): 381-6. doi: 10.1038/ng.3245
  22. Nicholas Loman and Aaron R. Quinlan. PORETOOLS: a toolkit for working with nanopore sequencing data from Oxford Nanopore. Bioinformatics, (2014), 30(23): 3399-401. doi:10.1093/bioinformatics/btu555
  23. Ryan M Layer, Colby Chiang, Aaron R Quinlan, and Ira M Hall. LUMPY: a probabilistic framework for structural variant discovery. Genome Biology, (2014), 15(6): R84. doi:10.1186/gb-2014-15-6-r84
  24. Yi Qiao, Aaron R Quinlan, Amir A Jazaeri, Roeland GW Verhaak, David A Wheeler, and Gabor T Marth. SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization. Genome Biology, (2014),15(8): 443. doi: 10.1186/s13059-014-0443-x
  25. Umadevi Paila, Brad A. Chapman, Rory Kirchner, and Aaron R. Quinlan. GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations. PLoS Computational Biology, (2013), 9(7): e1003153. doi:10.1371/journal.pcbi.1003153
  26. Ankit Malhotra, Michael Lindberg, Gregory G. Faust, Mitchell L. Leibowitz, Royden A. Clark, Ryan M. Layer, Aaron R. Quinlan, and Ira M. Hall. Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms Genome Research, (2013), 23(5): 762-76. doi: 10.1101/gr.143677.112
  27. The 1000 Genomes Project Consortium. A map of human genome variation from population scale sequencing. Nature, (2011), 467(7319): 1061–1073. doi: 10.1038/nature09534

to page top

Last Updated: 5/5/21