Aaron Quinlan portrait
  • Professor, Biomedical Informatics Resrch
  • Associate Professor, Human Genetics
  • Professor, Human Genetics
801-585-0406

Research Keywords

  • 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

Presentations

  • Quinlan AR. Patterns and consequences of mutation in the human germline; Medical University of South Carolina; (via Webex). , , 2021.
  • Quinlan AR. We are all mutants: patterns of mutation in the human genome revealed by DNA sequencing of large, multigenerational families; Western Colorado University; Gunnison, CO. , , 2019.
  • Quinlan AR. Constrained coding regions and implications for somatic genome evolution; Huntsman Cancer Institute; Salt Lake City, UT. , , 2019.
  • Quinlan AR. Large, three-generation CEPH families reveal post-zygotic mosaicism and variability in germline mutation accumulation; University of Michigan; Ann Arbor, MI. , , 2019.
  • Quinlan AR. Tools for undiagnosed disease research; NIH; Bethesda, MD. , , 2019.
  • Quinlan AR. Constrained coding regions and patterns of mutation in the human genome; Penn State University; State College, PA. , , 2018.
  • Quinlan AR. A map of constrained coding regions in the human genome; 23AndMe; Mountain View, CA. , , 2018.
  • Quinlan AR. Computing the human genome; Goldman Sachs; Salt Lake City, UT. , , 2018.
  • Quinlan AR. Computing the genome; Chan Zuckerberg Initiative; Palo Alto, CA;. , , 2018.
  • Quinlan AR. Inferring function from highly constrained coding regions; UW Center for Mendelian Genomics; Seattle, WA;. , , 2017.
  • Quinlan AR. Variation deserts and recombination jungles; UCSD (Yeo Lab); San Diego, CA. , , 2016.
  • Quinlan AR. Querying the Genome. Invited lecture at Sanger Institute, Sanger Institute, Hinxton, UK. , , 2015.
  • Quinlan AR. Challenges and (some) solutions for scanning the genome in studies of human disease, Human Genetics Interest Group, University of Utah, Salt Lake City, UT. , , 2015.
  • Quinlan AR. Variant Calling while Accounting for Alternate Haplotypes. Presented at Genome Reference Consortium Workshop 2014, Cambridge, UK. , , 2014.
  • Quinlan AR. Prioritizing germline and somatic variation in studies of human disease. Johns Hopkins School of Medicine, Baltimore, MD. , , 2014.
  • Quinlan AR. Comprehensive discovery and prioritization of genetic variationin studies of human disease. Biomedical Engineering Seminar Series, University of Virginia, Charlottesville, VA. , , 2014.
  • Quinlan AR. Algorithms for chromosomal rearrangement detection and DNA classification. Quantitative Biology Seminar Series, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. , , 2014.
  • Quinlan AR. Comprehensive discovery and prioritization of genetic variation in studies of human disease. University of Florida Genetics Institute, Gainesville, FL. , , 2014.
  • Quinlan AR. Comprehensive discovery and prioritization of genetic variation in studies of human disease. Department of Human Genetics, University of Utah, Salt Lake City, UT. , , 2014.
  • Quinlan AR. Detection and characterization of complex rearrangements in tumor genomes. BioConductor 2013, Seattle, WA. , , 2013.
  • Quinlan AR. Mining the structure and function of the genome. Host: Anton Nekreutenko, Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, State College, PA. , , 2012.
  • Quinlan AR. Exploring the origin and extent of structural variation in human genomes. Deans New Faculty Seminar Series, University of Virginia School of Medicine, Charlottesville, VA. , , 2012.
  • Quinlan AR. Patterns and consequences of mutation in the human germline; UCONN Health; (via Webex). , , 2020.
  • Quinlan AR. Strateges for diagnosing rare disease; 2nd year medical students at UU; (via Webex). , , 2020.
  • Quinlan AR. Germline mutation rates in young adults predict longevity; EMGS 2020; (via Webex). , , 2020.
  • Quinlan AR. Annotation and curation of high-confidence structural variation; ESHG 2020; (via Webex). , , 2020.
  • Quinlan AR. Mutation in the human genome; University of Utah, Dept. of Human Genetics; Salt Lake City, UT. , , 2018.
  • Quinlan AR. A map of constrained coding regions in the human genome; UCLA; Los Angeles, CA;. , , 2018.
  • Quinlan AR. Inferring function from highly constrained coding regions; BIRS Conference; Banff, Alberta;. , , 2017.
  • Quinlan AR. Variation deserts and recombination jungles; BYU; Provo, UT. , , 2017.
  • Quinlan AR. Direct measurement of the mutagenic impact of recombination through deep genome sequencing of 519 families; ASHG 2016; Vancouver, BC. , , 2016.
  • Quinlan AR. Genetic analysis software for any species; PAG 2016; San Diego, CA. , , 2016.
  • Quinlan AR. Making queries of the genome less difficult. Abstract presented at BIOT 2015, BYU, Cold Provo, UT. , , 2015.
  • Quinlan AR. Making queries of the genome less difficult. Abstract presented at Genome Informatics 2015, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. , , 2015.
  • Quinlan AR. How does ovarian cancer become resistant to chemotherapy? Abstract presented at The Biology of Genomes, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. , , 2014.
  • Quinlan AR. Disease variant interpretation and prioritization with GEMINI. Abstract presented at Genome Informatics 2013, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. , , 2013.
  • Quinlan AR. Mining genomic feature sets and identifying significant biological relationships with BedTools2. Abstract presented at the American Society of Human Genetics Meeting, Boston, MA. , , 2013.
  • Quinlan AR. Disease variant interpretation and prioritization with GEMINI. Abstract presented at Beyond the Genome 2013, San Francisco, CA. , , 2013.
  • Quinlan AR. Exploring disease genetics among thousands of human genomes with GEMINI. Abstract presented at SciPy 2013, Austin, TX. , , 2013.
  • Quinlan AR. Computational Genomics. Big Data Summit 2, University of Virginia, Charlottesville, VA. , , 2013.
  • Quinlan AR. Exploring genetic variation with a tour guide. International Stroke Genetics Consortium Meeting, Charlottesville, VA. , , 2013.
  • Quinlan AR. LUMPY: A probabilistic framework for SV discovery. Abstract presented at the Advances in Genome Biology and Technology (AGBT) Meeting, Marco Island, FL. , , 2013.
  • Quinlan AR. Mining the genome. Center for Public Health Genomics Genome Sciences Seminar Series, University of Virginia, Charlottesville, VA. , , 2012.
  • Quinlan AR. Exploring high-dimension genomic data. Advanced Sequencing Technologies Course, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. , , 2012.
  • Quinlan AR. Towards a map of structural variation in the Exome Sequencing Project. NHLBI Exome Sequencing Project In-Person Meeting, National Heart, Lung, and Blood Institute, Bethesda, MD. , , 2012.
  • Quinlan AR. ESP Structural Variation Project Group: goals, initial results, and future work. NHLBI Exome Sequencing Project In-Person Meeting, National Heart, Lung, and Blood Institute, Bethesda, MD. , , 2011.
  • Quinlan AR. Large-Scale Characterization of SV Breakpoints in Cancer. Abstract presented at the Keystone Symposium on The Functional Impact of Structural Variation, Steamboat Springs, CO. , , 2011.
  • Quinlan AR. Efficient discovery of structural instability in repetitive regions of mammalian genomes. Abstract presented at the Advances in Genome Biology and Technology (AGBT) Meeting, Marco Island, FL. , , 2009.
  • Quinlan AR. Approaches to rare allele discovery: More samples or more depth per sample? 1000 Genomes Analysis Meeting, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. , , 2008.

Grants, Contracts & Research Gifts

  • New algorithms and tools for large-scale genomic analyses. PI: - 2027. Total project budget to date:
  • Improving the analytical flexibility of bedtools (EOSS4). PI: - 2023. Total project budget to date:
  • GEMS: Genomic approach to connecting Elevated germline Mutation rates with male infertility and Somatic health. PI: - 2026. Total project budget to date:
  • Scalable detection and interpretation of structural variation in human genomes. PI: - 2024. Total project budget to date:

Languages

  • English, Fluent.

Publications

  • Hall IM, Quinlan AR (date unknown). Detection and interpretation of genomic structural variation in mammals.. (pp. 225-48). Vol. 838. Accepted, .
  • Kunisaki J, Quinlan A, Aston KI, Hotaling J (date unknown). Integrating Precision Medicine into the Standard of Care for Male Infertility: What Will it Take?. Accepted, .
  • Dale RK, Pedersen BS, Quinlan AR (date unknown). Pybedtools: a flexible Python library for manipulating genomic datasets and annotations. Vol. 27, 3423-4. Accepted, .
  • 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 (date unknown). Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder. Vol. 362. Accepted, .
  • Rosenthal EA, Ranchalis J, Crosslin DR, Burt A, Brunzell JD, Motulsky AG, NickersonDA, NHLBI GO Exome Sequencing Project, Wijsman EM, Jarvik GP. (date unknown). Joint linkage and association analysis with exome sequence data implicates SLC25A40 in hypertriglyceridemia. Vol. 93, 1035-45. Accepted, .
  • McHale P, Quinlan AR (date unknown). trfermikit: a tool to discover VNTR-associated deletions. Accepted, .
  • Loman NJ, Quinlan AR (date unknown). Poretools: a toolkit for analyzing nanopore sequence data. Vol. 30, 3399-401. Accepted, .
  • Sackton TB, Kulathinal RJ, Bergman CM, Quinlan AR, Dopman EB, Carneiro M, Marth GT, Hartl DL, Clark AG (date unknown). Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster. Vol. 1, 449-65. Accepted, .
  • Pedersen BS, Collins RL, Talkowski ME, Quinlan AR (date unknown). Indexcov: fast coverage quality control for whole-genome sequencing. Vol. 6, 1-6. Accepted, .
  • 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 (date unknown). Combating subclonal evolution of resistant cancer phenotypes. Vol. 8, 1231. Accepted, .
  • Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA (date unknown). A map of human genome variation from population-scale sequencing. Vol. 467, 1061-73. Accepted, .
  • Quick J, Quinlan AR, Loman NJ (date unknown). A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer. Vol. 3, 22. Accepted, .
  • Singh R, Kuscu C, Quinlan A, Qi Y, Adli M (date unknown). Cas9-chromatin binding information enables more accurate CRISPR off-target prediction. Vol. 43, e118. Accepted, .
  • Quinlan AR, Boland MJ, Leibowitz ML, Shumilina S, Pehrson SM, Baldwin KK, Hall IM (date unknown). Genome sequencing of mouse induced pluripotent stem cells reveals retroelement stability and infrequent DNA rearrangement during reprogramming. Vol. 9, 366-73. Accepted, .
  • Pedersen BS, Quinlan AR (date unknown). hts-nim: scripting high-performance genomic analyses. Vol. 34, 3387-3389. Accepted, .
  • Eilbeck K, Quinlan A, Yandell M (date unknown). Settling the score: variant prioritization and Mendelian disease. Vol. 18, 599-612. Accepted, .
  • Chiang C, Layer RM, Faust GG, Lindberg MR, Rose DB, Garrison EP, Marth GT, Quinlan AR, Hall IM (date unknown). SpeedSeq: ultra-fast personal genome analysis and interpretation. Vol. 12, 966-8. Accepted, .
  • 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 (date unknown). Rapid whole-genome mutational profiling using next-generation sequencing technologies. Vol. 18, 1638-42. Accepted, .
  • Sasani TA, Pedersen BS, Gao Z, Baird L, Przeworski M, Jorde LB, Quinlan AR (date unknown). Large, three-generation human families reveal post-zygotic mosaicism and variability in germline mutation accumulation. Vol. 8. Accepted, .
  • Quinlan AR (date unknown). BEDTools: The Swiss-Army Tool for Genome Feature Analysis. Vol. 47, 11.12.1-34. Accepted, .
  • Gupta M, Liu X, Teraoka SN, Wright JA, Gatti RA, Quinlan A, Concannon P (date unknown). Genes affecting ionizing radiation survival identified through combined exome sequencing and functional screening. Vol. 42, 1124-1138. Accepted, .
  • Sasani TA, Cone KR, Quinlan AR, Elde NC (date unknown). Long read sequencing reveals poxvirus evolution through rapid homogenization of gene arrays. Vol. 7. Accepted, .
  • Qiao Y, Quinlan AR, Jazaeri AA, Verhaak RG, Wheeler DA, Marth GT (date unknown). SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization. Vol. 15, 443. Accepted, .
  • 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 (date unknown). Whole-genome analysis for effective clinical diagnosis and gene discovery in early infantile epileptic encephalopathy. Vol. 3, 22. Accepted, .
  • 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. (date unknown). Recurrent gain-of-function mutation in PRKG1 causes thoracic aortic aneurysms and acute aortic dissections. Vol. 93, 398-404. Accepted, .
  • Krumm N, Sudmant PH, Ko A, O'Roak BJ, Malig M, Coe BP, NHLBI Exome Sequencing Project., Quinlan AR, Nickerson DA, Eichler EE (date unknown). Copy number variation detection and genotyping from exome sequence data. Vol. 22, 1525-32. Accepted, .
  • Tabor HK, Auer PL, Jamal SM, Chong JX, Yu JH, Gordon AS, Graubert TA, O’Donnell CJ, Rich SS, Nickerson DA (date unknown). Pathogenic variants for Mendelian and complex traits in exomes of 6,517 European and African Americans: implications for the return of incidental results. Vol. 95, 183–193. Accepted, .
  • 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 (date unknown). Common and rare von Willebrand factor (VWF) coding variants, VWF levels, and factor VIII levels in African Americans: the NHLBI Exome Sequencing Project. Vol. 122, 590-7. Accepted, .
  • 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 (date unknown). Effective variant filtering and expected candidate variant yield in studies of rare human disease. Vol. 6, 60. Accepted, .
  • Pedersen BS, Bhetariya PJ, Brown J, Kravitz SN, Marth G, Jensen RL, Bronner MP, Underhill HR, Quinlan AR (date unknown). Somalier: rapid relatedness estimation for cancer and germline studies using efficient genome sketches. Vol. 12, 62. Accepted, .
  • Carleton JB, Ginley-Hidinger M, Berrett KC, Layer RM, Quinlan AR, Gertz J (date unknown). Regulatory sharing between estrogen receptor α bound enhancers. Vol. 48, 6597-6610. Accepted, .
  • 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 (date unknown). Exome sequencing of extreme phenotypes identifies DCTN4 as a modifier of chronic Pseudomonas aeruginosa infection in cystic fibrosis. Vol. 44, 886-9. Accepted, .
  • 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 (date unknown). TGFB2 mutations cause familial thoracic aortic aneurysms and dissections associated with mild systemic features of Marfan syndrome. Vol. 44, 916-21. Accepted, .
  • 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 (date unknown). Coloc-stats: a unified web interface to perform colocalization analysis of genomic features. Vol. 46, W186-W193. Accepted, .
  • Belyeu JR, Nicholas TJ, Pedersen BS, Sasani TA, Havrilla JM, Kravitz SN, Conway ME, Lohman BK, Quinlan AR, Layer RM (date unknown). SV-plaudit: A cloud-based framework for manually curating thousands of structural variants. Vol. 7. Accepted, .
  • 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. (date unknown). Rare and Coding Region Genetic Variants Associated With Risk of Ischemic Stroke: The NHLBI Exome Sequence Project. Vol. 72, 781-8. Accepted, .
  • Layer RM, Chiang C, Quinlan AR, Hall IM (date unknown). LUMPY: a probabilistic framework for structural variant discovery. Vol. 15, R84. Accepted, .
  • Hou H, Pedersen BS Quinlan AR (date unknown). Efficient storage and analysis of quantitative genomics data with the Dense Depth Data Dump (D4) format and d4tools. Accepted, .
  • Belyeu JR, Sasani TA, Pedersen BS, Quinlan AR (date unknown). Unfazed: parent-of-origin detection for large and small de novo variants. Accepted, .
  • Cawthon RM, Meeks HD, Sasani TA, Smith KR, Kerber RA, O'Brien E, Baird L, Dixon MM, Peiffer AP, Leppert MF, Quinlan AR, Jorde LB (date unknown). Germline mutation rates in young adults predict longevity and reproductive lifespan. Vol. 10, 10001. Accepted, .
  • Pedersen BS, Quinlan AR (date unknown). cyvcf2: fast, flexible variant analysis with Python. Vol. 33, 1867-1869. Accepted, .
  • Barnett DW, Garrison EK, Quinlan AR, Strömberg MP, Marth GT (date unknown). BamTools: a C++ API and toolkit for analyzing and managing BAM files. Vol. 27, 1691-2. Accepted, .
  • Pedersen BS, Layer RM, Quinlan AR (date unknown). Vcfanno: fast, flexible annotation of genetic variants. Vol. 17, 118. Accepted, .
  • Layer R, Quinlan AR (date unknown). A parallel algorithm for N-way interval set intersection. Accepted, .
  • Farber CR, Reich A, Barnes AM, Becerra P, Rauch F, Cabral WA, Bae A, Quinlan A, Glorieux FH, Clemens TL, Marini JC (date unknown). A novel IFITM5 mutation in severe atypical osteogenesis imperfecta type VI impairs osteoblast production of pigment epithelium-derived factor. Vol. 29, 1402-11. Accepted, .
  • Belyeu JR, Chowdhury M, Brown J, Pedersen BS, Cormier MJ, Quinlan AR, Layer RM (date unknown). Samplot: a platform for structural variant visual validation and automated filtering. Vol. 22, 161. Accepted, .
  • Gao Z, Moorjani P, Sasani TA, Pedersen BS, Quinlan AR, Jorde LB, Amster G, Przeworski M (date unknown). Overlooked roles of DNA damage and maternal age in generating human germline mutations. Vol. 116, 9491-9500. Accepted, .
  • Malhotra A, Lindberg M, Faust GG, Leibowitz ML, Clark RA, Layer RM, Quinlan AR, Hall IM (date unknown). Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms. Vol. 23, 762-76. Accepted, .
  • Quinlan AR, Clark RA, Sokolova S, Leibowitz ML, Zhang Y, Hurles ME, Mell JC, Hall IM (date unknown). Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome. Vol. 20, 623-35. Accepted, .
  • 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 (date unknown). An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder. Vol. 50, 727-736. Accepted, .
  • Lindberg MR, Hall IM, Quinlan AR (date unknown). Population-based structural variation discovery with Hydra-Multi. Vol. 31, 1286-9. Accepted, .
  • 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. (date unknown). Quantifying rare, deleterious variation in 12 human cytochrome P450 drug-metabolism genes in a large-scale exome dataset. Vol. 23, 1957–1963. Accepted, .
  • Cormier MJ, Belyeu JR, Pedersen BS, Brown J, Köster J, Quinlan AR (date unknown). Go Get Data (GGD) is a framework that facilitates reproducible access to genomic data. Vol. 12, 2151. Accepted, .
  • Wallace AD, Sasani TA, Swanier J, Gates BL, Greenland J, Pedersen BS, Varley KE, Quinlan AR (date unknown). CaBagE: A Cas9-based Background Elimination strategy for targeted, long-read DNA sequencing. Vol. 16, e0241253. Accepted, .
  • Chowdhury M, Pedersen BS, Sedlazeck FJ, Quinlan AR, Layer RM (date unknown). Searching thousands of genomes to classify somatic and novel structural variants using STIX. Vol. 19, 445-448. Accepted, .
  • 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 (date unknown). De novo structural mutation rates and gamete-of-origin biases revealed through genome sequencing of 2,396 families. Vol. 108, 597-607. Accepted, .
  • Boukas L, Havrilla JM, Hickey PF, Quinlan AR, Bjornsson HT, Hansen KD (date unknown). Coexpression patterns define epigenetic regulators associated with neurological dysfunction. Vol. 29, 532-542. Accepted, .
  • Pedersen BS, Quinlan AR (date unknown). Duphold: scalable, depth-based annotation and curation of high-confidence structural variant calls. Vol. 8. Accepted, .
  • 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 M (date unknown). Nanopore sequencing and assembly of a human genome with ultra-long reads. Vol. 36, 338-345. Accepted, .
  • 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 (date unknown). Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers. Vol. 47, 381-6. Accepted, .
  • 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 (date unknown). Exome sequencing and genome-wide linkage analysis in 17 families illustrate the complex contribution of TTN truncating variants to dilated cardiomyopathy. Vol. 6, 144-53. Accepted, .
  • Nicholas TJ, Cormier MJ, Huang X, Qiao Y, Marth GT, Quinlan AR (date unknown). OncoGEMINI: software for investigating tumor variants from multiple biopsies with integrated cancer annotations. Vol. 13, 46. Accepted, .
  • 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 (date unknown). Homozygous mutation of MTPAP causes cellular radiosensitivity and persistent DNA double-strand breaks. Vol. 5, e1130. Accepted, .
  • Quinlan AR, Hall IM (date unknown). BEDTools: a flexible suite of utilities for comparing genomic features. Vol. 26, 841-2. Accepted, .
  • Pedersen BS, Quinlan AR (date unknown). Who's Who? Detecting and Resolving Sample Anomalies in Human DNA Sequencing Studies with Peddy. Vol. 100, 406-413. Accepted, .
  • Pedersen BS, Quinlan AR (date unknown). Mosdepth: quick coverage calculation for genomes and exomes. Vol. 34, 867-868. Accepted, .
  • Layer RM, Quinlan AR (date unknown). A parallel algorithm for N-way interval set intersection. Vol. 105, 542-551. Accepted, .
  • Ge Y, Onengut-Gumuscu S, Quinlan AR, Mackey AJ, Wright JA, Buckner JH, Habib T, Rich SS, Concannon P (date unknown). Targeted Deep Sequencing in Multiple-Affected Sibships of European Ancestry Identifies Rare Deleterious Variants in PTPN22 That Confer Risk for Type 1 Diabetes. Vol. 65, 794-802. Accepted, .
  • Quinlan AR, Marth GT (date unknown). Primer-site SNPs mask mutations. (pp. 192). Vol. 4. Accepted, .
  • 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. (date unknown). Whole-exome sequencing identifies rare and low-frequency coding variants associated with LDL cholesterol. Vol. 94, 233–245. Accepted, .
  • 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. (date unknown). Exome sequencing identifies rare LDLR and APOA5 alleles conferring risk for myocardial infarction. Vol. 518, 102–106. Accepted, .
  • 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 (date unknown). Comprehensive variant calling from whole-genome sequencing identifies a complex inversion that disrupts ZFPM2 in familial congenital diaphragmatic hernia. e1888. Accepted, .
  • Layer RM, Pedersen BS, DiSera T, Marth GT, Gertz J, Quinlan AR (date unknown). GIGGLE: a search engine for large-scale integrated genome analysis. Vol. 15, 123-126. Accepted, .
  • Quinlan AR, Stewart DA, Stromberg MP, Marth GT (date unknown). Pyrobayes: an improved base caller for SNP discovery in pyrosequences. Vol. 5, 179-81. Accepted, .
  • 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 (date unknown). Whole-genome sequencing and variant discovery in C. elegans. Vol. 5, 183-8. Accepted, .
  • Berg JA, Belyeu JR, Morgan JT, Ouyang Y, Bott AJ, Quinlan AR, Gertz J, Rutter J (date unknown). XPRESSyourself: Enhancing, standardizing, and automating ribosome profiling computational analyses yields improved insight into data. Vol. 16, e1007625. Accepted, .
  • 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 (date unknown). Extending reference assembly models. Vol. 16, 13. Accepted, .
  • 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 JM (date unknown). Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants. Vol. 493, 216-20. Accepted, .
  • Carey AZ, Blue NR, Varner MW, Page JM, Chaiyakunapruk N, Quinlan AR, Branch DW, Silver RM, Workalemahu T (date unknown). A systematic review to guide future efforts in the determination of genetic causes of pregnancy loss. Vol. 3. Accepted, .
  • Havrilla JM, Pedersen BS, Layer RM, Quinlan AR (date unknown). A map of constrained coding regions in the human genome. Vol. 51, 88-95. Accepted, .
  • Liu X, Paila UD, Teraoka SN, Wright JA, Huang X, Quinlan AR, Gatti RA, Concannon P (date unknown). Identification of ATIC as a Novel Target for Chemoradiosensitization. Vol. 100, 162-173. Accepted, .
  • Layer RM, Kindlon N, Karczewski KJ, Exome Aggregation Consortium., Quinlan AR (date unknown). Efficient genotype compression and analysis of large genetic-variation data sets. Vol. 13, 63-5. Accepted, .
  • Layer RM, Skadron K, Robins G, Hall IM, Quinlan AR (date unknown). Binary Interval Search: a scalable algorithm for counting interval intersections. Vol. 29, 1-7. Accepted, .
  • Paila U, Chapman BA, Kirchner R, Quinlan AR (date unknown). GEMINI: integrative exploration of genetic variation and genome annotations. Vol. 9, e1003153. Accepted, .
  • O'Connor TD, Kiezun A, Bamshad M, Rich SS, Smith JD, Turner E, Leal SM, Akey JM (date unknown). Fine-scale patterns of population stratification confound rare variant association tests. Vol. 8, e65834. Accepted, .
  • Quinlan AR, Hall IM (date unknown). Characterizing complex structural variation in germline and somatic genomes. Vol. 28, 43-53. Accepted, .
  • Keene KL, Quinlan AR, Hou X, Hall IM, Mychaleckyj JC, Onengut-Gumuscu S, Concannon P (date unknown). Evidence for two independent associations with type 1 diabetes at the 12q13 locus. Vol. 13, 66-70. Accepted, .
  • Westra HJ, Martínez-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 (date unknown). Fine-mapping and functional studies highlight potential causal variants for rheumatoid arthritis and type 1 diabetes. (pp. 1366-1374). Vol. 50. Accepted, .
  • Goldstein SA, Brown J, Pedersen BS, Quinlan AR, Elde NC (date unknown). Extensive recombination-driven coronavirus diversification expands the pool of potential pandemic pathogens. Accepted, .
  • Dai C, Deng Y, Quinlan A, Gaskin F, Tsao BP, Fu SM (date unknown). Genetics of systemic lupus erythematosus: immune responses and end organ resistance to damage. Vol. 31, 87-96. Accepted, .