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Items: 48

1.

Long read sequencing reveals poxvirus evolution through rapid homogenization of gene arrays.

Sasani TA, Cone KR, Quinlan AR, Elde NC.

Elife. 2018 Aug 29;7. pii: e35453. doi: 10.7554/eLife.35453.

2.

Whole-genome analysis for effective clinical diagnosis and gene discovery in early infantile epileptic encephalopathy.

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.

NPJ Genom Med. 2018 Aug 13;3:22. doi: 10.1038/s41525-018-0061-8. eCollection 2018.

3.

Coloc-stats: a unified web interface to perform colocalization analysis of genomic features.

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.

Nucleic Acids Res. 2018 Jul 2;46(W1):W186-W193. doi: 10.1093/nar/gky474.

4.

SV-plaudit: A cloud-based framework for manually curating thousands of structural variants.

Belyeu JR, Nicholas TJ, Pedersen BS, Sasani TA, Havrilla JM, Kravitz SN, Conway ME, Lohman BK, Quinlan AR, Layer RM.

Gigascience. 2018 Jul 1;7(7). doi: 10.1093/gigascience/giy064.

5.

hts-nim: scripting high-performance genomic analyses.

Pedersen BS, Quinlan AR.

Bioinformatics. 2018 Oct 1;34(19):3387-3389. doi: 10.1093/bioinformatics/bty358.

PMID:
29718142
6.

An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder.

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.

Nat Genet. 2018 May;50(5):727-736. doi: 10.1038/s41588-018-0107-y. Epub 2018 Apr 26.

7.

Nanopore sequencing and assembly of a human genome with ultra-long reads.

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.

Nat Biotechnol. 2018 Apr;36(4):338-345. doi: 10.1038/nbt.4060. Epub 2018 Jan 29.

8.

Publisher Correction: Combating subclonal evolution of resistant cancer phenotypes.

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.

Nat Commun. 2018 Feb 5;9(1):572. doi: 10.1038/s41467-017-02383-6.

9.

GIGGLE: a search engine for large-scale integrated genome analysis.

Layer RM, Pedersen BS, DiSera T, Marth GT, Gertz J, Quinlan AR.

Nat Methods. 2018 Feb;15(2):123-126. doi: 10.1038/nmeth.4556. Epub 2018 Jan 8.

10.

Mosdepth: quick coverage calculation for genomes and exomes.

Pedersen BS, Quinlan AR.

Bioinformatics. 2018 Mar 1;34(5):867-868. doi: 10.1093/bioinformatics/btx699.

11.

Combating subclonal evolution of resistant cancer phenotypes.

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.

Nat Commun. 2017 Nov 1;8(1):1231. doi: 10.1038/s41467-017-01174-3. Erratum in: Nat Commun. 2018 Feb 5;9(1):572.

12.

Indexcov: fast coverage quality control for whole-genome sequencing.

Pedersen BS, Collins RL, Talkowski ME, Quinlan AR.

Gigascience. 2017 Nov 1;6(11):1-6. doi: 10.1093/gigascience/gix090.

13.

Identification of ATIC as a Novel Target for Chemoradiosensitization.

Liu X, Paila UD, Teraoka SN, Wright JA, Huang X, Quinlan AR, Gatti RA, Concannon P.

Int J Radiat Oncol Biol Phys. 2018 Jan 1;100(1):162-173. doi: 10.1016/j.ijrobp.2017.08.033. Epub 2017 Sep 21.

PMID:
29029884
14.

A parallel algorithm for N-way interval set intersection.

Layer RM, Quinlan AR.

Proc IEEE Inst Electr Electron Eng. 2017 Mar;105(3):542-551. doi: 10.1109/JPROC.2015.2461494.

15.

Who's Who? Detecting and Resolving Sample Anomalies in Human DNA Sequencing Studies with Peddy.

Pedersen BS, Quinlan AR.

Am J Hum Genet. 2017 Mar 2;100(3):406-413. doi: 10.1016/j.ajhg.2017.01.017. Epub 2017 Feb 9.

16.

cyvcf2: fast, flexible variant analysis with Python.

Pedersen BS, Quinlan AR.

Bioinformatics. 2017 Jun 15;33(12):1867-1869. doi: 10.1093/bioinformatics/btx057.

17.

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.

18.

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. Epub 2015 Dec 2.

19.

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. Epub 2015 Nov 9.

20.

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. Epub 2015 Aug 10.

21.

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.

22.

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. Epub 2015 Mar 9.

23.

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. eCollection 2015.

24.

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.

25.

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. Epub 2014 Dec 2.

26.

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. eCollection 2014. Erratum in: Gigascience. 2015;4:6.

27.

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.

28.

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.

29.

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. Epub 2014 Aug 20.

30.

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.

31.

Homozygous mutation of MTPAP causes cellular radiosensitivity and persistent DNA double-strand breaks.

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.

Cell Death Dis. 2014 Mar 20;5:e1130. doi: 10.1038/cddis.2014.99.

32.

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. Epub 2013 Jul 18.

33.

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. Epub 2013 Feb 14.

34.

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. Epub 2012 Nov 4.

35.

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. Epub 2012 May 14.

36.

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.

PMID:
22228015
37.

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. Epub 2011 Nov 15. Review.

38.

Genome sequencing of mouse induced pluripotent stem cells reveals retroelement stability and infrequent DNA rearrangement during reprogramming.

Quinlan AR, Boland MJ, Leibowitz ML, Shumilina S, Pehrson SM, Baldwin KK, Hall IM.

Cell Stem Cell. 2011 Oct 4;9(4):366-73. doi: 10.1016/j.stem.2011.07.018.

39.

Pybedtools: a flexible Python library for manipulating genomic datasets and annotations.

Dale RK, Pedersen BS, Quinlan AR.

Bioinformatics. 2011 Dec 15;27(24):3423-4. doi: 10.1093/bioinformatics/btr539. Epub 2011 Sep 23.

40.

Evidence for two independent associations with type 1 diabetes at the 12q13 locus.

Keene KL, Quinlan AR, Hou X, Hall IM, Mychaleckyj JC, Onengut-Gumuscu S, Concannon P.

Genes Immun. 2012 Jan;13(1):66-70. doi: 10.1038/gene.2011.56. Epub 2011 Aug 18.

41.

BamTools: a C++ API and toolkit for analyzing and managing BAM files.

Barnett DW, Garrison EK, Quinlan AR, Strömberg MP, Marth GT.

Bioinformatics. 2011 Jun 15;27(12):1691-2. doi: 10.1093/bioinformatics/btr174. Epub 2011 Apr 14.

42.

Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome.

Quinlan AR, Clark RA, Sokolova S, Leibowitz ML, Zhang Y, Hurles ME, Mell JC, Hall IM.

Genome Res. 2010 May;20(5):623-35. doi: 10.1101/gr.102970.109. Epub 2010 Mar 22.

43.

BEDTools: a flexible suite of utilities for comparing genomic features.

Quinlan AR, Hall IM.

Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28.

44.

Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster.

Sackton TB, Kulathinal RJ, Bergman CM, Quinlan AR, Dopman EB, Carneiro M, Marth GT, Hartl DL, Clark AG.

Genome Biol Evol. 2009 Nov 18;1:449-65. doi: 10.1093/gbe/evp048.

45.

Rapid whole-genome mutational profiling using next-generation sequencing technologies.

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.

Genome Res. 2008 Oct;18(10):1638-42. doi: 10.1101/gr.077776.108. Epub 2008 Sep 4.

46.

Whole-genome sequencing and variant discovery in C. elegans.

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.

Nat Methods. 2008 Feb;5(2):183-8. doi: 10.1038/nmeth.1179. Epub 2008 Jan 20.

PMID:
18204455
47.

Pyrobayes: an improved base caller for SNP discovery in pyrosequences.

Quinlan AR, Stewart DA, Strömberg MP, Marth GT.

Nat Methods. 2008 Feb;5(2):179-81. doi: 10.1038/nmeth.1172. Epub 2008 Jan 13.

PMID:
18193056
48.

Primer-site SNPs mask mutations.

Quinlan AR, Marth GT.

Nat Methods. 2007 Mar;4(3):192. No abstract available.

PMID:
17327845

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