Skip to main content
Aaron Quinlan

Aaron Quinlan, PhD

Languages spoken: English

Academic Information

Departments Primary - Human Genetics , Primary - Biomedical Informatics

Academic Office Information

Research Interests

  • Human Genome Interpretation
  • Application of Genomics to Clinical Care
  • Chromosome Stability and Somatic Genome Evolution
  • Algorithm and Genomics Software Development
  • Cancer Genetics
  • Nucleotide Repeat Disorders
  • Population Genomics
  • Genetics of Complex Disease

Aaron Quinlan, Ph.D., is a Professor in the Departments of Human Genetics and Biomedical Informatics at the University of Utah. He received his bachelor’s degree in Computer Science from the College of William and Mary and his Ph.D. from Boston College where he focused on population genetics, new methods for emerging DNA sequencing technologies, and the discovery and characterization of genetic variation. During his NRSA postdoctoral fellowship at the University of Virginia he developed expertise in structural variation of mammalian genomes and somatic genome mutation. He started his laboratory at the University of Virginia in 2011. He was recruited to the University of Utah in early 2015 to become the Associate Director of the Utah Center for Genetic Discovery. Broadly speaking, the Quinlan laboratory is interested in the development and application of new computational and statistical techniques for understanding the biology of genomes. His team tackles problems with practical importance to identifying genome variation, understanding genome evolution, and mining genetic variation underlying rare genetic disease. The Quinlan laboratory’s ultimate goal is to develop and apply computational technologies that improve our understanding of human disease.

Education History

Postdoctoral Fellowship University of Virginia
Postdoctoral Fellow
Boston College
Undergraduate College of William and Mary

Selected Publications

Journal Article

  1. Chowdhury M, Pedersen BS, Sedlazeck FJ, Quinlan AR, Layer RM (2022). Searching thousands of genomes to classify somatic and novel structural variants using STIX. Nat Methods, 19(4), 445-448.
  2. Nicholas TJ, Al-Sweel N, Farrell A, Mao R, Bayrak-Toydemir P, Miller CE, Bentley D, Palmquist R, Moore B, Hernandez EJ, Cormier MJ, Fredrickson E, Noble K, Rynearson S, Holt C, Karren MA, Bonkowsky JL, Tristani-Firouzi M, Yandell M, Marth G, Quinlan AR, Brunelli L, Toydemir RM, Shayota BJ, Carey JC, Boyden SE, Malone Jenkins S (2022). Comprehensive variant calling from whole-genome sequencing identifies a complex inversion that disrupts ZFPM2 in familial congenital diaphragmatic hernia. Mol Genet Genomic Med, 10, e1888.
  3. McHale P, Quinlan AR (2021). trfermikit: a tool to discover VNTR-associated deletions. Bioinformatics.
  4. Gupta M, Liu X, Teraoka SN, Wright JA, Gatti RA, Quinlan A, Concannon P (2021). Genes affecting ionizing radiation survival identified through combined exome sequencing and functional screening. Hum Mutat, 42(9), 1124-1138.
  5. Pedersen BS, Brown JM, Dashnow H, Wallace AD, Velinder M, Tristani-Firouzi M, Schiffman JD, Tvrdik T, Mao R, Best DH, Bayrak-Toydemir P, Quinlan AR (2021). Effective variant filtering and expected candidate variant yield in studies of rare human disease. NPJ Genom Med, 6(1), 60.
  6. Hou H, Pedersen BS Quinlan AR (2021). Efficient storage and analysis of quantitative genomics data with the Dense Depth Data Dump (D4) format and d4tools. Nat Comput Sci.
  7. Belyeu JR, Sasani TA, Pedersen BS, Quinlan AR (2021). Unfazed: parent-of-origin detection for large and small de novo variants. Bioinformatics.
  8. Hou H, Pedersen B, Quinlan A (2021). Balancing efficient analysis and storage of quantitative genomics data with the D4 format and d4tools. Nat Comput Sci, 1(6), 441-447.
  9. Belyeu JR, Chowdhury M, Brown J, Pedersen BS, Cormier MJ, Quinlan AR, Layer RM (2021). Samplot: a platform for structural variant visual validation and automated filtering. Genome Biol, 22(1), 161.
  10. Cormier MJ, Belyeu JR, Pedersen BS, Brown J, Kster J, Quinlan AR (2021). Go Get Data (GGD) is a framework that facilitates reproducible access to genomic data. Nat Commun, 12(1), 2151.
  11. Wallace AD, Sasani TA, Swanier J, Gates BL, Greenland J, Pedersen BS, Varley KE, Quinlan AR (2021). CaBagE: A Cas9-based Background Elimination strategy for targeted, long-read DNA sequencing. PLoS One, 16(4), e0241253.
  12. Belyeu JR, Brand H, Wang H, Zhao X, Pedersen BS, Feusier J, Gupta M, Nicholas TJ, Brown J, Baird L, Devlin B, Sanders SJ, Jorde LB, Talkowski ME, Quinlan AR (2021). De novo structural mutation rates and gamete-of-origin biases revealed through genome sequencing of 2,396 families. Am J Hum Genet, 108(4), 597-607.
  13. Nicholas TJ, Cormier MJ, Huang X, Qiao Y, Marth GT, Quinlan AR (2021). OncoGEMINI: software for investigating tumor variants from multiple biopsies with integrated cancer annotations. Genome Med, 13(1), 46.
  14. Carey AZ, Blue NR, Varner MW, Page JM, Chaiyakunapruk N, Quinlan AR, Branch DW, Silver RM, Workalemahu T (2021). A systematic review to guide future efforts in the determination of genetic causes of pregnancy loss. Front Reprod Health, 3.
  15. Pedersen BS, Bhetariya PJ, Brown J, Kravitz SN, Marth G, Jensen RL, Bronner MP, Underhill HR, Quinlan AR (2020). Somalier: rapid relatedness estimation for cancer and germline studies using efficient genome sketches. Genome Med, 12(1), 62.
  16. Carleton JB, Ginley-Hidinger M, Berrett KC, Layer RM, Quinlan AR, Gertz J (2020). Regulatory sharing between estrogen receptor α bound enhancers. Nucleic Acids Res, 48(12), 6597-6610.
  17. Cawthon RM, Meeks HD, Sasani TA, Smith KR, Kerber RA, OBrien E, Baird L, Dixon MM, Peiffer AP, Leppert MF, Quinlan AR, Jorde LB (2020). Germline mutation rates in young adults predict longevity and reproductive lifespan. Sci Rep, 10(1), 10001.
  18. Berg JA, Belyeu JR, Morgan JT, Ouyang Y, Bott AJ, Quinlan AR, Gertz J, Rutter J (2020). XPRESSyourself: Enhancing, standardizing, and automating ribosome profiling computational analyses yields improved insight into data. PLoS Comput Biol, 16(1), e1007625.
  19. Sasani TA, Pedersen BS, Gao Z, Baird L, Przeworski M, Jorde LB, Quinlan AR (2019). Large, three-generation human families reveal post-zygotic mosaicism and variability in germline mutation accumulation. Elife, 8.
  20. Gao Z, Moorjani P, Sasani TA, Pedersen BS, Quinlan AR, Jorde LB, Amster G, Przeworski M (2019). Overlooked roles of DNA damage and maternal age in generating human germline mutations. Proc Natl Acad Sci U S A, 116(19), 9491-9500.
  21. Pedersen BS, Quinlan AR (2018). Duphold: scalable, depth-based annotation and curation of high-confidence structural variant calls. Gigascience, 8(4).
  22. Boukas L, Havrilla JM, Hickey PF, Quinlan AR, Bjornsson HT, Hansen KD (2019). Coexpression patterns define epigenetic regulators associated with neurological dysfunction. Genome Res, 29(4), 532-542.
  23. Havrilla JM, Pedersen BS, Layer RM, Quinlan AR (2018). A map of constrained coding regions in the human genome. Nat Genet, 51(1), 88-95.
  24. An JY, Lin K, Zhu L, Werling DM, Dong S, Brand H, Wang HZ, Zhao X, Schwartz GB, Collins RL, Currall BB, Dastmalchi C, Dea J, Duhn C, Gilson MC, Klei L, Liang L, Markenscoff-Papadimitriou E, Pochareddy S, Ahituv N, Buxbaum JD, Coon H, Daly MJ, Kim YS, Marth GT, Neale BM, Quinlan AR, Rubenstein JL, Sestan N, State MW, Willsey AJ, Talkowski ME, Devlin B, Roeder K, Sanders SJ (2018). Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder. Science, 362(6420).
  25. Pedersen BS, Quinlan AR (2018). hts-nim: scripting high-performance genomic analyses. Bioinformatics, 34(19), 3387-3389.
  26. Sasani TA, Cone KR, Quinlan AR, Elde NC (2018). Long read sequencing reveals poxvirus evolution through rapid homogenization of gene arrays. Elife, 7.
  27. Ostrander BEP, Butterfield RJ, Pedersen BS, Farrell AJ, Layer RM, Ward A, Miller C, DiSera T, Filloux FM, Candee MS, Newcomb T, Bonkowsky JL, Marth GT, Quinlan AR (2018). Whole-genome analysis for effective clinical diagnosis and gene discovery in early infantile epileptic encephalopathy. NPJ Genom Med, 3, 22.
  28. 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 (2018). Coloc-stats: a unified web interface to perform colocalization analysis of genomic features. Nucleic Acids Res, 46(W1), W186-W193.
  29. Belyeu JR, Nicholas TJ, Pedersen BS, Sasani TA, Havrilla JM, Kravitz SN, Conway ME, Lohman BK, Quinlan AR, Layer RM (2018). SV-plaudit: A cloud-based framework for manually curating thousands of structural variants. Gigascience, 7(7).
  30. Werling DM, Brand H, An JY, Stone MR, Zhu L, Glessner JT, Collins RL, Dong S, Layer RM, Markenscoff-Papadimitriou E, Farrell A, Schwartz GB, Wang HZ, Currall BB, Zhao X, Dea J, Duhn C, Erdman CA, Gilson MC, Yadav R, Handsaker RE, Kashin S, Klei L, Mandell JD, Nowakowski TJ, Liu Y, Pochareddy S, Smith L, Walker MF, Waterman MJ, He X, Kriegstein AR, Rubenstein JL, Sestan N, McCarroll SA, Neale BM, Coon H, Willsey AJ, Buxbaum JD, Daly MJ, State MW, Quinlan AR, Marth GT, Roeder K, Devlin B, Talkowski ME, Sanders SJ (2018). An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder. Nat Genet, 50(5), 727-736.
  31. Jain M, Koren S, Miga KH, Quick J, Rand AC, Sasani TA, Tyson JR, Beggs AD, Dilthey AT, Fiddes IT, Malla S, Marriott H, Nieto T, OGrady J, Olsen HE, Pedersen BS, Rhie A, Richardson H, Quinlan AR, Snutch TP, Tee L, Paten B, Phillippy AM, Simpson JT, Loman NJ, Loose M (2018). Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat Biotechnol, 36(4), 338-345.
  32. Pedersen BS, Quinlan AR (2018). Mosdepth: quick coverage calculation for genomes and exomes. Bioinformatics, 34(5), 867-868.
  33. Layer RM, Pedersen BS, DiSera T, Marth GT, Gertz J, Quinlan AR (2018). GIGGLE: a search engine for large-scale integrated genome analysis. Nat Methods, 15(2), 123-126.
  34. Liu X, Paila UD, Teraoka SN, Wright JA, Huang X, Quinlan AR, Gatti RA, Concannon P (2018). Identification of ATIC as a Novel Target for Chemoradiosensitization. Int J Radiat Oncol Biol Phys, 100(1), 162-173.
  35. Brady SW, McQuerry JA, Qiao Y, Piccolo SR, Shrestha G, Jenkins DF, Layer RM, Pedersen BS, Miller RH, Esch A, Selitsky SR, Parker JS, Anderson LA, Dalley BK, Factor RE, Reddy CB, Boltax JP, Li DY, Moos PJ, Gray JW, Heiser LM, Buys SS, Cohen AL, Johnson WE, Quinlan AR, Marth G, Werner TL, Bild AH (2017). Combating subclonal evolution of resistant cancer phenotypes. Nat Commun, 8(1), 1231.
  36. Pedersen BS, Collins RL, Talkowski ME, Quinlan AR (2017). Indexcov: fast coverage quality control for whole-genome sequencing. Gigascience, 6(11), 1-6.
  37. Eilbeck K, Quinlan A, Yandell M (2017). Settling the score: variant prioritization and Mendelian disease. Nat Rev Genet, 18(10), 599-612.
  38. Pedersen BS, Quinlan AR (2017). cyvcf2: fast, flexible variant analysis with Python. Bioinformatics, 33(12), 1867-1869.
  39. Pedersen BS, Quinlan AR (2017). Who's Who? Detecting and Resolving Sample Anomalies in Human DNA Sequencing Studies with Peddy. Am J Hum Genet, 100(3), 406-413.
  40. Layer RM, Quinlan AR (2017). A parallel algorithm for N-way interval set intersection. Proc IEEE Inst Electr Electron Eng, 105(3), 542-551.
  41. Pedersen BS, Layer RM, Quinlan AR (2016). Vcfanno: fast, flexible annotation of genetic variants. Genome Biol, 17(1), 118.
  42. Ge Y, Onengut-Gumuscu S, Quinlan AR, Mackey AJ, Wright JA, Buckner JH, Habib T, Rich SS, Concannon P (2016). Targeted Deep Sequencing in Multiple-Affected Sibships of European Ancestry Identifies Rare Deleterious Variants in PTPN22 That Confer Risk for Type 1 Diabetes. Diabetes, 65(3), 794-802.
  43. Layer RM, Kindlon N, Karczewski KJ, Exome Aggregation Consortium, Quinlan AR (2016). Efficient genotype compression and analysis of large genetic-variation data sets. Nat Methods, 13(1), 63-5.
  44. Singh R, Kuscu C, Quinlan A, Qi Y, Adli M (2015). Cas9-chromatin binding information enables more accurate CRISPR off-target prediction. Nucleic Acids Res, 43(18), e118.
  45. Chiang C, Layer RM, Faust GG, Lindberg MR, Rose DB, Garrison EP, Marth GT, Quinlan AR, Hall IM (2015). SpeedSeq: ultra-fast personal genome analysis and interpretation. Nat Methods, 12(10), 966-8.
  46. Auer PL, Nalls M, Meschia JF, Worrall BB, Longstreth WT Jr, Seshadri S, Kooperberg C, Burger KM, Carlson CS, Carty CL, Chen WM, Cupples LA, DeStefano AL, Fornage M, Hardy J, Hsu L, Jackson RD, Jarvik GP, Kim DS, Lakshminarayan K, Lange LA, Manichaikul A, Quinlan AR, Singleton AB, Thornton TA, Nickerson DA, Peters U, Rich SS, National Heart Lung and Blood Institute Exome Sequencing Project (2015). Rare and Coding Region Genetic Variants Associated With Risk of Ischemic Stroke: The NHLBI Exome Sequence Project. JAMA Neurol, 72(7), 781-8.
  47. Layer R, Quinlan AR (2015). A parallel algorithm for N-way interval set intersection. Proc IEEE Inst Electr Electron Eng.
  48. Lindberg MR, Hall IM, Quinlan AR (2015). Population-based structural variation discovery with Hydra-Multi. Bioinformatics, 31(8), 1286-9.
  49. Onengut-Gumuscu S, Chen WM, Burren O, Cooper NJ, Quinlan AR, Mychaleckyj JC, Farber E, Bonnie JK, Szpak M, Schofield E, Achuthan P, Guo H, Fortune MD, Stevens H, Walker NM, Ward LD, Kundaje A, Kellis M, Daly MJ, Barrett JC, Cooper JD, Deloukas P, Type 1 Diabetes Genetics Consortium, Todd JA, Wallace C, Concannon P, Rich SS (2015). Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers. Nat Genet, 47(4), 381-6.
  50. Do R, Stitziel NO, Won HH, Jrgensen AB, Duga S, Angelica Merlini P, Kiezun A, FarrallM, Goel A, Zuk O, Guella I, Asselta R, Lange LA, Peloso GM, Auer PL, NHLBI ExomeSequencing Project, Girelli D, Martinelli N, Farlow DN, DePristo MA, Roberts R, StewartAF, Saleheen D, Danesh J, Epstein SE, Sivapalaratnam S, Hovingh GK, Kastelein JJ, SamaniNJ, Schunkert H, Erdmann J, Shah SH, Kraus WE, Davies R, Nikpay M, Johansen CT, Wang J, Hegele RA, Hechter E, Marz W, Kleber ME, Huang J, Johnson AD, Li M, BurkeGL, Gross M, Liu Y, Assimes TL, Heiss G, Lange EM, Folsom AR, Taylor HA, OlivieriO, Hamsten A, Clarke R, Reilly DF, Yin W, Rivas MA, Donnelly P, Rossouw JE, PsatyBM, Herrington DM, Wilson JG, Rich SS, Bamshad MJ, Tracy RP, Cupples LA, Rader DJ, Reilly MP, Spertus JA, Cresci S, Hartiala J, Tang WH, Hazen SL, Allayee H, Reiner AP, Carlson CS, Kooperberg C, Jackson RD, Boerwinkle E, Lander ES, Schwartz SM, SiscovickDS, McPherson R, Tybjaerg-Hansen A, Abecasis GR, Watkins H, Nickerson DA, ArdissinoD, Sunyaev SR, ODonnell CJ, Altshuler D, Gabriel S, Kathiresan S (2015). Exome sequencing identifies rare LDLR and APOA5 alleles conferring risk for myocardial infarction. Nature, 518(7537), 102–106.
  51. Church DM, Schneider VA, Steinberg KM, Schatz MC, Quinlan AR, Chin CS, Kitts PA, Aken B, Marth GT, Hoffman MM, Herrero J, Mendoza ML, Durbin R, Flicek P (2015). Extending reference assembly models. Genome Biol, 16, 13.
  52. Loman NJ, Quinlan AR (2014). Poretools: a toolkit for analyzing nanopore sequence data. Bioinformatics, 30(23), 3399-401.
  53. Dai C, Deng Y, Quinlan A, Gaskin F, Tsao BP, Fu SM (2014). Genetics of systemic lupus erythematosus: immune responses and end organ resistance to damage. Curr Opin Immunol, 31, 87-96.
  54. Quick J, Quinlan AR, Loman NJ (2014). A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer. Gigascience, 3, 22.
  55. Quinlan AR (2014). BEDTools: The Swiss-Army Tool for Genome Feature Analysis. Curr Protoc Bioinformatics, 47, 11.12.1-34.
  56. Qiao Y, Quinlan AR, Jazaeri AA, Verhaak RG, Wheeler DA, Marth GT (2014). SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization. Genome Biol, 15(8), 443.
  57. Tabor HK, Auer PL, Jamal SM, Chong JX, Yu JH, Gordon AS, Graubert TA, ODonnell CJ, Rich SS, Nickerson DA (2014). Pathogenic variants for Mendelian and complex traits in exomes of 6,517 European and African Americans: implications for the return of incidental results. Am J Hum Genet, 95(2), 183–193.
  58. Layer RM, Chiang C, Quinlan AR, Hall IM (2014). LUMPY: a probabilistic framework for structural variant discovery. Genome Biol, 15(6), R84.
  59. Farber CR, Reich A, Barnes AM, Becerra P, Rauch F, Cabral WA, Bae A, Quinlan A, Glorieux FH, Clemens TL, Marini JC (2014). A novel IFITM5 mutation in severe atypical osteogenesis imperfecta type VI impairs osteoblast production of pigment epithelium-derived factor. J Bone Miner Res, 29(6), 1402-11.
  60. Gordon AS, Tabor HK, Johnson AD, Snively BM, Assimes TL, Auer PL, Ioannidis JP, PetersU, Robinson JG, Sucheston LE, Wang D, Sotoodehnia N, Rotter JI, Psaty BM, Jackson RD, Herrington DM, ODonnell CJ, Reiner AP, Rich SS, Rieder MJ, Bamshad MJ, NickersonDA, NHLBI GO Exome Sequencing Project (2014). Quantifying rare, deleterious variation in 12 human cytochrome P450 drug-metabolism genes in a large-scale exome dataset. Hum Mol Genet, 23(8), 1957–1963.
  61. Martin NT, Nakamura K, Paila U, Woo J, Brown C, Wright JA, Teraoka SN, Haghayegh S, McCurdy D, Schneider M, Hu H, Quinlan AR, Gatti RA, Concannon P (2014). Homozygous mutation of MTPAP causes cellular radiosensitivity and persistent DNA double-strand breaks. Cell Death Dis, 5, e1130.
  62. Lange LA, Hu Y, Zhang H, Xue C, Schmidt EM, Tang ZZ, Bizon C, Lange EM, Smith JD, Turner EH, Jun G, Kang HM, Peloso G, Auer P, Li KP, Flannick J, Zhang J, FuchsbergerC, Gaulton K, Lindgren C, Locke A, Manning A, Sim X, Rivas MA, Holmen OL, GottesmanO, Lu Y, Ruderfer D, Stahl EA, Duan Q, Li Y, Durda P, Jiao S, Isaacs A, Hofman A, BisJC, Correa A, Griswold ME, Jakobsdottir J, Smith AV, Schreiner PJ, Feitosa MF, Zhang Q, Huffman JE, Crosby J, Wassel CL, Do R, Franceschini N, Martin LW, Robinson JG, AssimesTL, Crosslin DR, Rosenthal EA, Tsai M, Rieder MJ, Farlow DN, Folsom AR, Lumley T, FoxER, Carlson CS, Peters U, Jackson RD, van Duijn CM, Uitterlinden AG, Levy D, RotterJI, Taylor HA, Gudnason V Jr, Siscovick DS, Fornage M, Borecki IB, Hayward C, RudanI, Chen YE, Bottinger EP, Loos RJ, Strom P, Hveem K, Boehnke M, Groop L, McCarthyM, Meitinger T, Ballantyne CM, Gabriel SB, ODonnell CJ, Post WS, North KE, ReinerAP, Boerwinkle E, Psaty BM, Altshuler D, Kathiresan S, Lin DY, Jarvik GP, Cupples LA, Kooperberg C, Wilson JG, Nickerson DA, Abecasis GR, Rich SS, Tracy RP, Willer CJ, NHLBI Grand Opportunity Exome Sequencing Project (2014). Whole-exome sequencing identifies rare and low-frequency coding variants associated with LDL cholesterol. Am J Hum Genet, 94(2), 233–245.
  63. Rosenthal EA, Ranchalis J, Crosslin DR, Burt A, Brunzell JD, Motulsky AG, NickersonDA, NHLBI GO Exome Sequencing Project, Wijsman EM, Jarvik GP (2013). Joint linkage and association analysis with exome sequence data implicates SLC25A40 in hypertriglyceridemia. Am J Hum Genet, 93(6), 1035-45.
  64. Guo DC, Regalado E, Casteel DE, Santos-Cortez RL, Gong L, Kim JJ, Dyack S, HorneSG, Chang G, Jondeau G, Boileau C, Coselli JS, Li Z, Leal SM, Shendure J, Rieder MJ, Bamshad MJ, Nickerson DA, GenTAC Registry Consortium, National Heart, Lung, Blood Institute Grand Opportunity Exome Sequencing Project, Kim C, Milewicz DM (2013). Recurrent gain-of-function mutation in PRKG1 causes thoracic aortic aneurysms and acute aortic dissections. Am J Hum Genet, 93(2), 398-404.
  65. Johnsen JM, Auer PL, Morrison AC, Jiao S, Wei P, Haessler J, Fox K, McGee SR, Smith JD, Carlson CS, Smith N, Boerwinkle E, Kooperberg C, Nickerson DA, Rich SS, Green D, Peters U, Cushman M, Reiner AP (2013). Common and rare von Willebrand factor (VWF) coding variants, VWF levels, and factor VIII levels in African Americans: the NHLBI Exome Sequencing Project. Blood, 122(4), 590-7.
  66. Malhotra A, Lindberg M, Faust GG, Leibowitz ML, Clark RA, Layer RM, Quinlan AR, Hall IM (2013). Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms. Genome Res, 23(5), 762-76.
  67. Norton N, Li D, Rampersaud E, Morales A, Martin ER, Zuchner S, Guo S, Gonzalez M, Hedges DJ, Robertson PD, Krumm N, Nickerson DA, Hershberger RE (2013). Exome sequencing and genome-wide linkage analysis in 17 families illustrate the complex contribution of TTN truncating variants to dilated cardiomyopathy. Circ Cardiovasc Genet, 6(2), 144-53.
  68. Fu W, OConnor TD, Jun G, Kang HM, Abecasis G, Leal SM, Gabriel S, Rieder MJ, Altshuler D, Shendure J, Nickerson DA, Bamshad MJ, Akey JM (2013). Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants. Nature, 493(7431), 216-20.
  69. Paila U, Chapman BA, Kirchner R, Quinlan AR (2013). GEMINI: integrative exploration of genetic variation and genome annotations. PLoS Comput Biol, 9(7), e1003153.
  70. Layer RM, Skadron K, Robins G, Hall IM, Quinlan AR (2013). Binary Interval Search: a scalable algorithm for counting interval intersections. Bioinformatics, 29(1), 1-7.
  71. OConnor TD, Kiezun A, Bamshad M, Rich SS, Smith JD, Turner E, Leal SM, Akey JM (2013). Fine-scale patterns of population stratification confound rare variant association tests. PLoS One, 8(7), e65834.
  72. Krumm N, Sudmant PH, Ko A, ORoak BJ, Malig M, Coe BP, NHLBI Exome Sequencing Project, Quinlan AR, Nickerson DA, Eichler EE (2012). Copy number variation detection and genotyping from exome sequence data. Genome Res, 22(8), 1525-32.
  73. Boileau C, Guo DC, Hanna N, Regalado ES, Detaint D, Gong L, Varret M, Prakash SK, Li AH, dIndy H, Braverman AC, Grandchamp B, Kwartler CS, Gouya L, Santos-Cortez RL, Abifadel M, Leal SM, Muti C, Shendure J, Gross MS, Rieder MJ, Vahanian A, Nickerson DA, Michel JB, Jondeau G, Milewicz DM (2012). TGFB2 mutations cause familial thoracic aortic aneurysms and dissections associated with mild systemic features of Marfan syndrome. Nat Genet, 44(8), 916-21.
  74. Emond MJ, Louie T, Emerson J, Zhao W, Mathias RA, Knowles MR, Wright FA, Rieder MJ, Tabor HK, Nickerson DA, Barnes KC, Gibson RL, Bamshad MJ (2012). Exome sequencing of extreme phenotypes identifies DCTN4 as a modifier of chronic Pseudomonas aeruginosa infection in cystic fibrosis. Nat Genet, 44(8), 886-9.
  75. Quinlan AR, Hall IM (2012). Characterizing complex structural variation in germline and somatic genomes. Trends Genet, 28(1), 43-53.
  76. Keene KL, Quinlan AR, Hou X, Hall IM, Mychaleckyj JC, Onengut-Gumuscu S, Concannon P (2012). Evidence for two independent associations with type 1 diabetes at the 12q13 locus. Genes Immun, 13(1), 66-70.
  77. Dale RK, Pedersen BS, Quinlan AR (2011). Pybedtools: a flexible Python library for manipulating genomic datasets and annotations. Bioinformatics, 27(24), 3423-4.
  78. Quinlan AR, Boland MJ, Leibowitz ML, Shumilina S, Pehrson SM, Baldwin KK, Hall IM (2011). Genome sequencing of mouse induced pluripotent stem cells reveals retroelement stability and infrequent DNA rearrangement during reprogramming. Cell Stem Cell, 9(4), 366-73.
  79. Barnett DW, Garrison EK, Quinlan AR, Strmberg MP, Marth GT (2011). BamTools: a C++ API and toolkit for analyzing and managing BAM files. Bioinformatics, 27(12), 1691-2.
  80. Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA (2010). A map of human genome variation from population-scale sequencing. Nature, 467(7319), 1061-73.
  81. Quinlan AR, Clark RA, Sokolova S, Leibowitz ML, Zhang Y, Hurles ME, Mell JC, Hall IM (2010). Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome. Genome Res, 20(5), 623-35.
  82. Quinlan AR, Hall IM (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26(6), 841-2.
  83. Sackton TB, Kulathinal RJ, Bergman CM, Quinlan AR, Dopman EB, Carneiro M, Marth GT, Hartl DL, Clark AG (2009). Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster. Genome Biol Evol, 1, 449-65.
  84. Smith DR, Quinlan AR, Peckham HE, Makowsky K, Tao W, Woolf B, Shen L, Donahue WF, Tusneem N, Stromberg MP, Stewart DA, Zhang L, Ranade SS, Warner JB, Lee CC, Coleman BE, Zhang Z, McLaughlin SF, Malek JA, Sorenson JM, Blanchard AP, Chapman J, Hillman D, Chen F, Rokhsar DS, McKernan KJ, Jeffries TW, Marth GT, Richardson PM (2008). Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Res, 18(10), 1638-42.
  85. Hillier LW, Marth GT, Quinlan AR, Dooling D, Fewell G, Barnett D, Fox P, Glasscock JI, Hickenbotham M, Huang W, Magrini VJ, Richt RJ, Sander SN, Stewart DA, Stromberg M, Tsung EF, Wylie T, Schedl T, Wilson RK, Mardis ER (2008). Whole-genome sequencing and variant discovery in C. elegans. Nat Methods, 5(2), 183-8.
  86. Quinlan AR, Stewart DA, Stromberg MP, Marth GT (2008). Pyrobayes: an improved base caller for SNP discovery in pyrosequences. Nat Methods, 5(2), 179-81.

Book Chapter

  1. Hall IM, Quinlan AR (2012). Detection and interpretation of genomic structural variation in mammals. In Methods Mol Biol (838, pp. 225-48). United States.


  1. Kunisaki J, Quinlan A, Aston KI, Hotaling J (2022). Integrating Precision Medicine into the Standard of Care for Male Infertility: What Will it Take? Eur Urol.


  1. Westra HJ, Martnez-Bonet M, Onengut-Gumuscu S, Lee A, Luo Y, Teslovich N, Worthington J, Martin J, Huizinga T, Klareskog L, Rantapaa-Dahlqvist S, Chen WM, Quinlan A, Todd JA, Eyre S, Nigrovic PA, Gregersen PK, Rich SS, Raychaudhuri S (2018). Fine-mapping and functional studies highlight potential causal variants for rheumatoid arthritis and type 1 diabetes. [Letter to the editor]. Nat Genet, 50(10), 1366-1374.
  2. Quinlan AR, Marth GT (2007). Primer-site SNPs mask mutations. [Letter to the editor]. Nat Methods, 4(3), 192.


  1. Goldstein SA, Brown J, Pedersen BS, Quinlan AR, Elde NC (2021). Extensive recombination-driven coronavirus diversification expands the pool of potential pandemic pathogens. bioRxiv. United States.