Aaron Quinlan

Aaron Quinlan, PhD

Languages spoken: English

Academic Information

Departments Adjunct - Biomedical Informatics , Primary - Human Genetics

Academic Office Information

aaron.quinlan@utah.edu

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

Undergraduate College of William and Mary
 BS
Doctoral Training Boston College
 PhD
Postdoctoral Fellowship University of Virginia
 Postdoctoral Fellow

Selected Publications

Journal Article

  1. 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 (2022). Comprehensive variant calling from whole-genome sequencing identifies a complex inversion that disrupts ZFPM2 in familial congenital diaphragmatic hernia. Molecular genetics & genomic medicine, 10(4), e1888.
  2. Chowdhury M, Pedersen BS, Sedlazeck FJ, Quinlan AR, Layer R (2022). Searching thousands of genomes to classify somatic and novel structural variants using STIX. Nature methods, 19(4), 445-448.
  3. 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.
  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. Belyeu JR, Sasani TA, Pedersen BS, Quinlan A (2021). Unfazed: parent-of-origin detection for large and small de novo variants. Bioinformatics (Oxford, England),
  6. McHale P, Quinlan A (2021). trfermikit: a tool to discover VNTR-associated deletions. Bioinformatics (Oxford, England),
  7. Belyeu JR, Chowdhury M, Brown J, Pedersen BS, Cormier MJ, Quinlan AR, Layer R (2021). Samplot: a platform for structural variant visual validation and automated filtering. Genome biology, 22(1), 161.
  8. Wallace AD, Sasani TA, Swanier J, Gates BL, Greenland J, Pedersen BS, Varley KE, Quinlan A (2021). CaBagE: A Cas9-based Background Elimination strategy for targeted, long-read DNA sequencing. PloS one, 16(4), e0241253.
  9. Nicholas TJ, Cormier MJ, Huang X, Qiao Y, Marth GT, Quinlan A (2021). OncoGEMINI: software for investigating tumor variants from multiple biopsies with integrated cancer annotations. Genome medicine, 13(1), 46.
  10. Cormier MJ, Belyeu JR, Pedersen BS, Brown J, Köster J, Quinlan A (2021). Go Get Data (GGD) is a framework that facilitates reproducible access to genomic data. Nature communications, 12(1), 2151.
  11. 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 A (2021). Effective variant filtering and expected candidate variant yield in studies of rare human disease. NPJ genomic medicine, 6(1), 60.
  12. Carey AZ, Blue NR, Varner MW, Page JM, Chaiyakunapruk N, Quinlan AR, Branch DW, Silver RM, Workalemahu (2021). A systematic review to guide future efforts in the determination of genetic causes of pregnancy loss. Frontiers in reproductive health, 3,
  13. Hou H, Pedersen BS Quinlan A (2021). Efficient storage and analysis of quantitative genomics data with the Dense Depth Data Dump (D4) format and d4tools. Nature computational science,
  14. Hou H, Pedersen B, Quinlan (2021). Balancing efficient analysis and storage of quantitative genomics data with the D4 format and d4tools. Nature computational science, 1(6), 441-447.
  15. Carleton JB, Ginley-Hidinger M, Berrett KC, Layer RM, Quinlan AR, Gertz (2020). Regulatory sharing between estrogen receptor ¿ bound enhancers. Nucleic acids research, 48(12), 6597-6610.
  16. Berg JA, Belyeu JR, Morgan JT, Ouyang Y, Bott AJ, Quinlan AR, Gertz J, Rutter (2020). XPRESSyourself: Enhancing, standardizing, and automating ribosome profiling computational analyses yields improved insight into data. PLoS computational biology, 16(1), e1007625.
  17. Pedersen BS, Bhetariya PJ, Brown J, Kravitz SN, Marth G, Jensen RL, Bronner MP, Underhill HR, Quinlan A (2020). Somalier: rapid relatedness estimation for cancer and germline studies using efficient genome sketches. Genome medicine, 12(1), 62.
  18. Cawthon RM, Meeks HD, Sasani TA, Smith KR, Kerber RA, O'Brien E, Baird L, Dixon MM, Peiffer AP, Leppert MF, Quinlan AR, Jorde L (2020). Germline mutation rates in young adults predict longevity and reproductive lifespan. Scientific reports, 10(1), 10001.
  19. 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.
  20. Gao Z, Moorjani P, Sasani TA, Pedersen BS, Quinlan AR, Jorde LB, Amster G, Przeworski (2019). Overlooked roles of DNA damage and maternal age in generating human germline mutations. Proceedings of the National Academy of Sciences of the United States of America, 116(19), 9491-9500.
  21. Boukas L, Havrilla JM, Hickey PF, Quinlan AR, Bjornsson HT, Hansen K (2019). Coexpression patterns define epigenetic regulators associated with neurological dysfunction. Genome research, 29(4), 532-542.
  22. Sasani TA, Pedersen BS, Gao Z, Baird L, Przeworski M, Jorde LB, Quinlan A (2019). Large, three-generation human families reveal post-zygotic mosaicism and variability in germline mutation accumulation. eLife, 8,
  23. Pedersen BS, Quinlan A (2019). Duphold: scalable, depth-based annotation and curation of high-confidence structural variant calls. GigaScience, 8(4),
  24. 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.
  25. Liu X, Paila UD, Teraoka SN, Wright JA, Huang X, Quinlan AR, Gatti RA, Concannon (2018). Identification of ATIC as a Novel Target for Chemoradiosensitization. International journal of radiation oncology, biology, physics, 100(1), 162-173.
  26. 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 G (2018). Coloc-stats: a unified web interface to perform colocalization analysis of genomic features. Nucleic acids research, 46(W1), W186-W193.
  27. 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 S (2018). Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder. Science (New York, N.Y.), 362(6420),
  28. 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, O'Grady J, Olsen HE, Pedersen BS, Rhie A, Richardson H, Quinlan AR, Snutch TP, Tee L, Paten B, Phillippy AM, Simpson JT, Loman NJ, Loose (2018). Nanopore sequencing and assembly of a human genome with ultra-long reads. Nature biotechnology, 36(4), 338-345.
  29. Pedersen BS, Quinlan A (2018). Mosdepth: quick coverage calculation for genomes and exomes. Bioinformatics (Oxford, England), 34(5), 867-868.
  30. Pedersen BS, Quinlan A (2018). hts-nim: scripting high-performance genomic analyses. Bioinformatics (Oxford, England), 34(19), 3387-3389.
  31. Layer RM, Pedersen BS, DiSera T, Marth GT, Gertz J, Quinlan A (2018). GIGGLE: a search engine for large-scale integrated genome analysis. Nature methods, 15(2), 123-126.
  32. Sasani TA, Cone KR, Quinlan AR, Elde N (2018). Long read sequencing reveals poxvirus evolution through rapid homogenization of gene arrays. eLife, 7,
  33. Belyeu JR, Nicholas TJ, Pedersen BS, Sasani TA, Havrilla JM, Kravitz SN, Conway ME, Lohman BK, Quinlan AR, Layer R (2018). SV-plaudit: A cloud-based framework for manually curating thousands of structural variants. GigaScience, 7(7),
  34. 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 A (2018). Whole-genome analysis for effective clinical diagnosis and gene discovery in early infantile epileptic encephalopathy. NPJ genomic medicine, 3, 22.
  35. 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.
  36. Pedersen BS, Quinlan A (2017). cyvcf2: fast, flexible variant analysis with Python. Bioinformatics (Oxford, England), 33(12), 1867-1869.
  37. Eilbeck K, Quinlan A, Yandell (2017). Settling the score: variant prioritization and Mendelian disease. Nature reviews. Genetics, 18(10), 599-612.
  38. Layer RM, Quinlan A (2017). A parallel algorithm for N-way interval set intersection. Proceedings of the IEEE. Institute of Electrical and Electronics Engineers, 105(3), 542-551.
  39. 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 A (2017). Combating subclonal evolution of resistant cancer phenotypes. Nature communications, 8(1), 1231.
  40. Pedersen BS, Collins RL, Talkowski ME, Quinlan A (2017). Indexcov: fast coverage quality control for whole-genome sequencing. GigaScience, 6(11), 1-6.
  41. Ge Y, Onengut-Gumuscu S, Quinlan AR, Mackey AJ, Wright JA, Buckner JH, Habib T, Rich SS, Concannon (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.
  42. Pedersen BS, Layer RM, Quinlan A (2016). Vcfanno: fast, flexible annotation of genetic variants. Genome biology, 17(1), 118.
  43. Layer RM, Kindlon N, Karczewski KJ, Exome Aggregation Consortium., Quinlan A (2016). Efficient genotype compression and analysis of large genetic-variation data sets. Nature methods, 13(1), 63-5.
  44. 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.
  45. 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, O'Donnell 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.
  46. Singh R, Kuscu C, Quinlan A, Qi Y, Adli (2015). Cas9-chromatin binding information enables more accurate CRISPR off-target prediction. Nucleic acids research, 43(18), e118.
  47. Lindberg MR, Hall IM, Quinlan A (2015). Population-based structural variation discovery with Hydra-Multi. Bioinformatics (Oxford, England), 31(8), 1286-9.
  48. 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 (2015). Extending reference assembly models. Genome biology, 16, 13.
  49. Layer R, Quinlan A (2015). A parallel algorithm for N-way interval set intersection. Proceedings of the IEEE. Institute of Electrical and Electronics Engineers,
  50. Chiang C, Layer RM, Faust GG, Lindberg MR, Rose DB, Garrison EP, Marth GT, Quinlan AR, Hall I (2015). SpeedSeq: ultra-fast personal genome analysis and interpretation. Nature methods, 12(10), 966-8.
  51. 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 neurology, 72(7), 781-8.
  52. 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.
  53. Tabor HK, Auer PL, Jamal SM, Chong JX, Yu JH, Gordon AS, Graubert TA, O�Donnell 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.
  54. 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, O�Donnell 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.
  55. 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.
  56. 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, O�Donnell 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.
  57. Loman NJ, Quinlan A (2014). Poretools: a toolkit for analyzing nanopore sequence data. Bioinformatics (Oxford, England), 30(23), 3399-401.
  58. Layer RM, Chiang C, Quinlan AR, Hall I (2014). LUMPY: a probabilistic framework for structural variant discovery. Genome biology, 15(6), R84.
  59. Qiao Y, Quinlan AR, Jazaeri AA, Verhaak RG, Wheeler DA, Marth G (2014). SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization. Genome biology, 15(8), 443.
  60. Quinlan A (2014). BEDTools: The Swiss-Army Tool for Genome Feature Analysis. Current protocols in bioinformatics, 47, 11.12.1-34.
  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 (2014). Homozygous mutation of MTPAP causes cellular radiosensitivity and persistent DNA double-strand breaks. Cell death & disease, 5, e1130.
  62. Quick J, Quinlan AR, Loman N (2014). A reference bacterial genome dataset generated on the MinION¿ portable single-molecule nanopore sequencer. GigaScience, 3, 22.
  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. Fu W, O'Connor TD, Jun G, Kang HM, Abecasis G, Leal SM, Gabriel S, Rieder MJ, Altshuler D, Shendure J, Nickerson DA, Bamshad MJ, Akey J (2013). Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants. Nature, 493(7431), 216-20.
  67. Malhotra A, Lindberg M, Faust GG, Leibowitz ML, Clark RA, Layer RM, Quinlan AR, Hall I (2013). Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms. Genome research, 23(5), 762-76.
  68. Layer RM, Skadron K, Robins G, Hall IM, Quinlan A (2013). Binary Interval Search: a scalable algorithm for counting interval intersections. Bioinformatics (Oxford, England), 29(1), 1-7.
  69. Paila U, Chapman BA, Kirchner R, Quinlan A (2013). GEMINI: integrative exploration of genetic variation and genome annotations. PLoS computational biology, 9(7), e1003153.
  70. O'Connor TD, Kiezun A, Bamshad M, Rich SS, Smith JD, Turner E, Leal SM, Akey J (2013). Fine-scale patterns of population stratification confound rare variant association tests. PloS one, 8(7), e65834.
  71. 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 R (2013). Exome sequencing and genome-wide linkage analysis in 17 families illustrate the complex contribution of TTN truncating variants to dilated cardiomyopathy. Circulation. Cardiovascular genetics, 6(2), 144-53.
  72. 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.
  73. Boileau C, Guo DC, Hanna N, Regalado ES, Detaint D, Gong L, Varret M, Prakash SK, Li AH, d'Indy 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. Quinlan AR, Hall I (2012). Characterizing complex structural variation in germline and somatic genomes. Trends in genetics, 28(1), 43-53.
  75. Krumm N, Sudmant PH, Ko A, O'Roak BJ, Malig M, Coe BP, NHLBI Exome Sequencing Project., Quinlan AR, Nickerson DA, Eichler E (2012). Copy number variation detection and genotyping from exome sequence data. Genome research, 22(8), 1525-32.
  76. Keene KL, Quinlan AR, Hou X, Hall IM, Mychaleckyj JC, Onengut-Gumuscu S, Concannon (2012). Evidence for two independent associations with type 1 diabetes at the 12q13 locus. Genes and immunity, 13(1), 66-70.
  77. Barnett DW, Garrison EK, Quinlan AR, Strömberg MP, Marth G (2011). BamTools: a C++ API and toolkit for analyzing and managing BAM files. Bioinformatics (Oxford, England), 27(12), 1691-2.
  78. Dale RK, Pedersen BS, Quinlan A (2011). Pybedtools: a flexible Python library for manipulating genomic datasets and annotations. Bioinformatics (Oxford, England), 27(24), 3423-4.
  79. Quinlan AR, Boland MJ, Leibowitz ML, Shumilina S, Pehrson SM, Baldwin KK, Hall I (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.
  80. Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean G (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 I (2010). Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome. Genome research, 20(5), 623-35.
  82. Quinlan AR, Hall I (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics (Oxford, England), 26(6), 841-2.
  83. Sackton TB, Kulathinal RJ, Bergman CM, Quinlan AR, Dopman EB, Carneiro M, Marth GT, Hartl DL, Clark A (2009). Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster. Genome biology and evolution, 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 P (2008). Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome research, 18(10), 1638-42.
  85. Quinlan AR, Stewart DA, Stromberg MP, Marth G (2008). Pyrobayes: an improved base caller for SNP discovery in pyrosequences. Nature methods, 5(2), 179-81.
  86. 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 E (2008). Whole-genome sequencing and variant discovery in C. elegans. Nature methods, 5(2), 183-8.

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.

Editorial

  1. Kunisaki J, Quinlan A, Aston KI, Hotaling (2022). Integrating Precision Medicine into the Standard of Care for Male Infertility: What Will it Take?. European urology, 82(4), 339-340.

Letter

  1. Westra HJ, Mart�nez-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 G (2007). Primer-site SNPs mask mutations. Nature methods, 4(3), 192.

Other

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