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Items: 1 to 50 of 108

1.

Fine-mapping and functional studies highlight potential causal variants for rheumatoid arthritis and type 1 diabetes.

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.

Nat Genet. 2018 Oct;50(10):1366-1374. doi: 10.1038/s41588-018-0216-7. Epub 2018 Sep 17.

PMID:
30224649
2.

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.

3.

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.

4.

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.

5.

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.

6.

Quantifying patient preferences for symptomatic breast clinic referral: a decision analysis study.

Quinlan A, O'Brien KK, Galvin R, Hardy C, McDonnell R, Joyce D, McDowell RD, Aherne E, Keogh C, O'Sullivan K, Fahey T.

BMJ Open. 2018 May 31;8(5):e017286. doi: 10.1136/bmjopen-2017-017286.

7.

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
8.

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.

9.

Family Exergaming: Correlates and Preferences.

Rhodes RE, Nwachukwu N, Quinlan A.

Games Health J. 2018 Jun;7(3):188-196. doi: 10.1089/g4h.2017.0177. Epub 2018 Apr 24.

PMID:
29688819
10.

Prevalence of chronic kidney disease among patients undergoing transradial percutaneous coronary interventions.

Hossain MA, Quinlan A, Heck-Kanellidis J, Calderon D, Patel T, Gandhi B, Patel S, Hetavi M, Costanzo EJ, Cosentino J, Patel C, Dewan A, Kuo YH, Salman L, Vachharajani TJ.

J Vasc Access. 2018 Jul;19(4):346-349. doi: 10.1177/1129729817752874. Epub 2018 Mar 12.

PMID:
29529964
11.

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.

12.

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.

13.

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.

14.

Evaluation of a physical activity intervention for new parents: protocol paper for a randomized trial.

Quinlan A, Rhodes RE, Beauchamp MR, Symons Downs D, Warburton DER, Blanchard CM.

BMC Public Health. 2017 Nov 9;17(1):875. doi: 10.1186/s12889-017-4874-7.

15.

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.

16.

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.

17.

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.

18.

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
19.

Understanding medulloblastoma.

Quinlan A, Rizzolo D.

JAAPA. 2017 Oct;30(10):30-36. doi: 10.1097/01.JAA.0000524717.71084.50. Review.

PMID:
28953021
20.

Settling the score: variant prioritization and Mendelian disease.

Eilbeck K, Quinlan A, Yandell M.

Nat Rev Genet. 2017 Oct;18(10):599-612. doi: 10.1038/nrg.2017.52. Epub 2017 Aug 14. Review.

21.

The ABCs of finding a good antibody: How to find a good antibody, validate it, and publish meaningful data.

Acharya P, Quinlan A, Neumeister V.

F1000Res. 2017 Jun 8;6:851. doi: 10.12688/f1000research.11774.1. eCollection 2017.

22.

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.

23.

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.

24.

cyvcf2: fast, flexible variant analysis with Python.

Pedersen BS, Quinlan AR.

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

25.

Do other goals influence physical activity? A systematic review examining the relationship between other goals and physical activity behavior.

Rhodes RE, Quinlan A, Mistry CD.

Prev Med. 2016 Oct;91:306-317. doi: 10.1016/j.ypmed.2016.08.033. Epub 2016 Aug 25. Review.

PMID:
27568235
26.

Interventions to Address Potentially Inappropriate Prescribing in Community-Dwelling Older Adults: A Systematic Review of Randomized Controlled Trials.

Clyne B, Fitzgerald C, Quinlan A, Hardy C, Galvin R, Fahey T, Smith SM.

J Am Geriatr Soc. 2016 Jun;64(6):1210-22. doi: 10.1111/jgs.14133. Review.

PMID:
27321600
27.

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.

28.

Is physical activity a part of who I am? A review and meta-analysis of identity, schema and physical activity.

Rhodes RE, Kaushal N, Quinlan A.

Health Psychol Rev. 2016 Jun;10(2):204-25. doi: 10.1080/17437199.2016.1143334. Epub 2016 Mar 2.

PMID:
26805431
29.

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.

30.

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.

31.

Family planning to promote physical activity: a randomized controlled trial protocol.

Quinlan A, Rhodes RE, Blanchard CM, Naylor PJ, Warburton DE.

BMC Public Health. 2015 Oct 5;15:1011. doi: 10.1186/s12889-015-2309-x.

32.

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.

33.

Cas9-chromatin binding information enables more accurate CRISPR off-target prediction.

Singh R, Kuscu C, Quinlan A, Qi Y, Adli M.

Nucleic Acids Res. 2015 Oct 15;43(18):e118. doi: 10.1093/nar/gkv575. Epub 2015 Jun 1.

34.

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.

35.

Response to "a comparison of paper documentation to electronic documentation for trauma resuscitations at a level I pediatric trauma center".

Quinlan A.

J Emerg Nurs. 2015 May;41(3):181-2. doi: 10.1016/j.jen.2015.02.010. Epub 2015 Mar 23. No abstract available.

PMID:
25814097
36.

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.

37.

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.

38.

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.

39.

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.

40.

Genetics of systemic lupus erythematosus: immune responses and end organ resistance to damage.

Dai C, Deng Y, Quinlan A, Gaskin F, Tsao BP, Fu SM.

Curr Opin Immunol. 2014 Dec;31:87-96. doi: 10.1016/j.coi.2014.10.004. Epub 2014 Oct 25. Review.

41.

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.

42.

Predictors of physical activity change among adults using observational designs.

Rhodes RE, Quinlan A.

Sports Med. 2015 Mar;45(3):423-41. doi: 10.1007/s40279-014-0275-6. Review.

PMID:
25312706
43.

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.

44.

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.

45.

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.

46.

PEGylated cyclodextrins as novel siRNA nanosystems: correlations between polyethylene glycol length and nanoparticle stability.

Godinho BM, Ogier JR, Quinlan A, Darcy R, Griffin BT, Cryan JF, O'Driscoll CM.

Int J Pharm. 2014 Oct 1;473(1-2):105-12. doi: 10.1016/j.ijpharm.2014.06.054. Epub 2014 Jun 30.

PMID:
24992319
47.

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.

48.

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.

49.

A novel IFITM5 mutation in severe atypical osteogenesis imperfecta type VI impairs osteoblast production of pigment epithelium-derived factor.

Farber CR, Reich A, Barnes AM, Becerra P, Rauch F, Cabral WA, Bae A, Quinlan A, Glorieux FH, Clemens TL, Marini JC.

J Bone Miner Res. 2014 Jun;29(6):1402-11.

50.

Differential nanotoxicological and neuroinflammatory liabilities of non-viral vectors for RNA interference in the central nervous system.

Godinho BM, McCarthy DJ, Torres-Fuentes C, Beltrán CJ, McCarthy J, Quinlan A, Ogier JR, Darcy R, O'Driscoll CM, Cryan JF.

Biomaterials. 2014 Jan;35(1):489-99. doi: 10.1016/j.biomaterials.2013.09.068. Epub 2013 Oct 16.

PMID:
24138827

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