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Vcfanno: fast, flexible annotation of genetic variants.

Pedersen BS, Layer RM, Quinlan AR.

Genome Biol. 2016 Jun 1;17(1):118. doi: 10.1186/s13059-016-0973-5.


Targeted Deep Sequencing in Multiple-Affected Sibships of European Ancestry Identifies Rare Deleterious Variants in PTPN22 That Confer Risk for Type 1 Diabetes.

Ge Y, Onengut-Gumuscu S, Quinlan AR, Mackey AJ, Wright JA, Buckner JH, Habib T, Rich SS, Concannon P.

Diabetes. 2016 Mar;65(3):794-802. doi: 10.2337/db15-0322.


Efficient genotype compression and analysis of large genetic-variation data sets.

Layer RM, Kindlon N, Karczewski KJ; Exome Aggregation Consortium., Quinlan AR.

Nat Methods. 2016 Jan;13(1):63-5. doi: 10.1038/nmeth.3654.


SpeedSeq: ultra-fast personal genome analysis and interpretation.

Chiang C, Layer RM, Faust GG, Lindberg MR, Rose DB, Garrison EP, Marth GT, Quinlan AR, Hall IM.

Nat Methods. 2015 Oct;12(10):966-8. doi: 10.1038/nmeth.3505.


Rare and Coding Region Genetic Variants Associated With Risk of Ischemic Stroke: The NHLBI Exome Sequence Project.

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..

JAMA Neurol. 2015 Jul;72(7):781-8. doi: 10.1001/jamaneurol.2015.0582.


Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers.

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.

Nat Genet. 2015 Apr;47(4):381-6. doi: 10.1038/ng.3245.


Erratum: A reference bacterial genome dataset generated on the MinION(TM) portable single-molecule nanopore sequencer.

Quick J, Quinlan AR, Loman NJ.

Gigascience. 2015 Feb 13;4:6. doi: 10.1186/s13742-015-0043-z.


Extending reference assembly models.

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.

Genome Biol. 2015 Jan 24;16:13. doi: 10.1186/s13059-015-0587-3.


Population-based structural variation discovery with Hydra-Multi.

Lindberg MR, Hall IM, Quinlan AR.

Bioinformatics. 2015 Apr 15;31(8):1286-9. doi: 10.1093/bioinformatics/btu771.


A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer.

Quick J, Quinlan AR, Loman NJ.

Gigascience. 2014 Oct 20;3:22. doi: 10.1186/2047-217X-3-22. Erratum in: Gigascience. 2015;4:6.


BEDTools: The Swiss-Army Tool for Genome Feature Analysis.

Quinlan AR.

Curr Protoc Bioinformatics. 2014 Sep 8;47:11.12.1-34. doi: 10.1002/0471250953.bi1112s47.


SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization.

Qiao Y, Quinlan AR, Jazaeri AA, Verhaak RG, Wheeler DA, Marth GT.

Genome Biol. 2014 Aug 26;15(8):443. doi: 10.1186/s13059-014-0443-x.


Poretools: a toolkit for analyzing nanopore sequence data.

Loman NJ, Quinlan AR.

Bioinformatics. 2014 Dec 1;30(23):3399-401. doi: 10.1093/bioinformatics/btu555.


LUMPY: a probabilistic framework for structural variant discovery.

Layer RM, Chiang C, Quinlan AR, Hall IM.

Genome Biol. 2014 Jun 26;15(6):R84. doi: 10.1186/gb-2014-15-6-r84.


GEMINI: integrative exploration of genetic variation and genome annotations.

Paila U, Chapman BA, Kirchner R, Quinlan AR.

PLoS Comput Biol. 2013;9(7):e1003153. doi: 10.1371/journal.pcbi.1003153.


Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms.

Malhotra A, Lindberg M, Faust GG, Leibowitz ML, Clark RA, Layer RM, Quinlan AR, Hall IM.

Genome Res. 2013 May;23(5):762-76. doi: 10.1101/gr.143677.112.


Binary Interval Search: a scalable algorithm for counting interval intersections.

Layer RM, Skadron K, Robins G, Hall IM, Quinlan AR.

Bioinformatics. 2013 Jan 1;29(1):1-7. doi: 10.1093/bioinformatics/bts652.


Copy number variation detection and genotyping from exome sequence data.

Krumm N, Sudmant PH, Ko A, O'Roak BJ, Malig M, Coe BP; NHLBI Exome Sequencing Project., Quinlan AR, Nickerson DA, Eichler EE.

Genome Res. 2012 Aug;22(8):1525-32. doi: 10.1101/gr.138115.112.


Detection and interpretation of genomic structural variation in mammals.

Hall IM, Quinlan AR.

Methods Mol Biol. 2012;838:225-48. doi: 10.1007/978-1-61779-507-7_11. Review.


Characterizing complex structural variation in germline and somatic genomes.

Quinlan AR, Hall IM.

Trends Genet. 2012 Jan;28(1):43-53. doi: 10.1016/j.tig.2011.10.002. Review.

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