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Aaron Quinlan, PhD - Publications

Affiliations: 
1997 College of William and Mary, Williamsburg, VA 
 2008 Boston College, Newton, MA, United States 
 2008-2015 University of Virginia, Charlottesville, VA 
 2015- Human Genetics University of Utah, Salt Lake City, UT 
Website:
http://quinlanlab.org/
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66 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Chamberlin JT, Gillen AE, Quinlan AR. Improved characterization of 3' single-cell RNA-seq libraries with paired-end avidity sequencing. Nar Genomics and Bioinformatics. 6: lqae175. PMID 39703419 DOI: 10.1093/nargab/lqae175  0.308
2024 Thorpe HJ, Pedersen BS, Dietze M, Link N, Quinlan AR, Bonkowsky JL, Thomas A, Chow CY. Identification of as a genetic modifier of PIGA-CDG through pedigree analysis of a family with incomplete penetrance and functional testing in . Biorxiv : the Preprint Server For Biology. PMID 39211166 DOI: 10.1101/2024.08.12.607501  0.302
2024 Porubsky D, Dashnow H, Sasani TA, Logsdon GA, Hallast P, Noyes MD, Kronenberg ZN, Mokveld T, Koundinya N, Nolan C, Steely CJ, Guarracino A, Dolzhenko E, Harvey WT, Rowell WJ, ... ... Quinlan AR, et al. A familial, telomere-to-telomere reference for human mutation and recombination from a four-generation pedigree. Biorxiv : the Preprint Server For Biology. PMID 39149261 DOI: 10.1101/2024.08.05.606142  0.38
2024 Chamberlin JT, Gillen AE, Quinlan AR. Improved characterization of single-cell RNA-seq libraries with paired-end avidity sequencing. Biorxiv : the Preprint Server For Biology. PMID 39026715 DOI: 10.1101/2024.07.10.602909  0.334
2024 Chamberlin JT, Lee Y, Marth G, Quinlan AR. Differences in molecular sampling and data processing explain variation among single-cell and single-nucleus RNA-seq experiments. Genome Research. PMID 38355308 DOI: 10.1101/gr.278253.123  0.551
2024 Hou H, Pedersen B, Quinlan A. Author Correction: Balancing efficient analysis and storage of quantitative genomics data with the D4 format and d4tools. Nature Computational Science. 2: 132. PMID 38177525 DOI: 10.1038/s43588-022-00211-6  0.3
2024 Dolzhenko E, English A, Dashnow H, De Sena Brandine G, Mokveld T, Rowell WJ, Karniski C, Kronenberg Z, Danzi MC, Cheung WA, Bi C, Farrow E, Wenger A, Chua KP, Martínez-Cerdeño V, ... ... Quinlan AR, et al. Characterization and visualization of tandem repeats at genome scale. Nature Biotechnology. PMID 38168995 DOI: 10.1038/s41587-023-02057-3  0.398
2023 Khan MR, Akbari A, Nicholas TJ, Castillo-Madeen H, Ajmal M, Haq TU, Laan M, Quinlan AR, Ahuja JS, Shah AA, Conrad DF. Genome sequencing of Pakistani families with male infertility identifies deleterious genotypes in SPAG6, CCDC9, TKTL1, TUBA3C, and M1AP. Andrology. PMID 38073178 DOI: 10.1111/andr.13570  0.363
2022 Dashnow H, Pedersen BS, Hiatt L, Brown J, Beecroft SJ, Ravenscroft G, LaCroix AJ, Lamont P, Roxburgh RH, Rodrigues MJ, Davis M, Mefford HC, Laing NG, Quinlan AR. STRling: a k-mer counting approach that detects short tandem repeat expansions at known and novel loci. Genome Biology. 23: 257. PMID 36517892 DOI: 10.1186/s13059-022-02826-4  0.315
2022 Goldstein SA, Brown J, Pedersen BS, Quinlan AR, Elde NC. Extensive Recombination-driven Coronavirus Diversification Expands the Pool of Potential Pandemic Pathogens. Genome Biology and Evolution. 14. PMID 36477201 DOI: 10.1093/gbe/evac161  0.329
2022 Cormier MJ, Pedersen BS, Bayrak-Toydemir P, Quinlan AR. Combining genetic constraint with predictions of alternative splicing to prioritize deleterious splicing in rare disease studies. Bmc Bioinformatics. 23: 482. PMID 36376793 DOI: 10.1186/s12859-022-05041-x  0.354
2022 Chowdhury M, Pedersen BS, Sedlazeck FJ, Quinlan AR, Layer RM. Author Correction: Searching thousands of genomes to classify somatic and novel structural variants using STIX. Nature Methods. 19: 770. PMID 35618956 DOI: 10.1038/s41592-022-01538-8  0.424
2022 Chowdhury M, Pedersen BS, Sedlazeck FJ, Quinlan AR, Layer RM. Searching thousands of genomes to classify somatic and novel structural variants using STIX. Nature Methods. 19: 445-448. PMID 35396485 DOI: 10.1038/s41592-022-01423-4  0.34
2022 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, ... ... Quinlan AR, et al. Comprehensive variant calling from whole-genome sequencing identifies a complex inversion that disrupts ZFPM2 in familial congenital diaphragmatic hernia. Molecular Genetics & Genomic Medicine. e1888. PMID 35119225 DOI: 10.1002/mgg3.1888  0.713
2021 Hou H, Pedersen B, Quinlan A. Balancing efficient analysis and storage of quantitative genomics data with the D4 format and d4tools. Nature Computational Science. 1: 441-447. PMID 35936573 DOI: 10.1038/s43588-021-00085-0  0.333
2021 McHale P, Quinlan AR. trfermikit: a tool to discover VNTR-associated deletions. Bioinformatics (Oxford, England). PMID 34864893 DOI: 10.1093/bioinformatics/btab805  0.395
2021 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. Effective variant filtering and expected candidate variant yield in studies of rare human disease. Npj Genomic Medicine. 6: 60. PMID 34267211 DOI: 10.1038/s41525-021-00227-3  0.351
2021 Cormier MJ, Belyeu JR, Pedersen BS, Brown J, Köster J, Quinlan AR. Go Get Data (GGD) is a framework that facilitates reproducible access to genomic data. Nature Communications. 12: 2151. PMID 33846313 DOI: 10.1038/s41467-021-22381-z  0.362
2021 Wallace AD, Sasani TA, Swanier J, Gates BL, Greenland J, Pedersen BS, Varley KE, Quinlan AR. CaBagE: A Cas9-based Background Elimination strategy for targeted, long-read DNA sequencing. Plos One. 16: e0241253. PMID 33830997 DOI: 10.1371/journal.pone.0241253  0.371
2021 Nicholas TJ, Cormier MJ, Huang X, Qiao Y, Marth GT, Quinlan AR. OncoGEMINI: software for investigating tumor variants from multiple biopsies with integrated cancer annotations. Genome Medicine. 13: 46. PMID 33771218 DOI: 10.1186/s13073-021-00854-6  0.609
2021 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. De novo structural mutation rates and gamete-of-origin biases revealed through genome sequencing of 2,396 families. American Journal of Human Genetics. PMID 33675682 DOI: 10.1016/j.ajhg.2021.02.012  0.341
2020 Pedersen BS, Bhetariya PJ, Brown J, Kravitz SN, Marth G, Jensen RL, Bronner MP, Underhill HR, Quinlan AR. Somalier: rapid relatedness estimation for cancer and germline studies using efficient genome sketches. Genome Medicine. 12: 62. PMID 32664994 DOI: 10.1186/S13073-020-00761-2  0.656
2020 Layer RM, Quinlan AR. A parallel algorithm for -way interval set intersection. Proceedings of the Ieee. Institute of Electrical and Electronics Engineers. 105: 542-551. PMID 30333632 DOI: 10.1109/JPROC.2015.2461494  0.375
2019 Pedersen BS, Quinlan AR. Duphold: scalable, depth-based annotation and curation of high-confidence structural variant calls. Gigascience. 8. PMID 31222198 DOI: 10.1093/Gigascience/Giz040  0.361
2019 Havrilla JM, Pedersen BS, Layer RM, Quinlan AR. A map of constrained coding regions in the human genome. Nature Genetics. 51: 88-95. PMID 30531870 DOI: 10.1038/S41588-018-0294-6  0.324
2018 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, ... ... Quinlan AR, et al. Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder. Science (New York, N.Y.). 362. PMID 30545852 DOI: 10.1126/Science.Aat6576  0.667
2018 Sasani TA, Cone KR, Quinlan AR, Elde NC. Long read sequencing reveals poxvirus evolution through rapid homogenization of gene arrays. Elife. 7. PMID 30156554 DOI: 10.7554/Elife.35453  0.351
2018 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. Whole-genome analysis for effective clinical diagnosis and gene discovery in early infantile epileptic encephalopathy. Npj Genomic Medicine. 3: 22. PMID 30109124 DOI: 10.1038/S41525-018-0061-8  0.693
2018 Pedersen BS, Quinlan AR. hts-nim: scripting high-performance genomic analyses. Bioinformatics (Oxford, England). PMID 29718142 DOI: 10.1093/Bioinformatics/Bty358  0.33
2018 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, ... ... Quinlan AR, et al. An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder. Nature Genetics. PMID 29700473 DOI: 10.1038/S41588-018-0107-Y  0.705
2018 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, ... ... Quinlan AR, et al. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nature Biotechnology. PMID 29431738 DOI: 10.1038/Nbt.4060  0.411
2018 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, ... ... Quinlan AR, et al. Publisher Correction: Combating subclonal evolution of resistant cancer phenotypes. Nature Communications. 9: 572. PMID 29402882 DOI: 10.1038/S41467-017-02383-6  0.549
2018 Layer RM, Pedersen BS, DiSera T, Marth GT, Gertz J, Quinlan AR. GIGGLE: a search engine for large-scale integrated genome analysis. Nature Methods. PMID 29309061 DOI: 10.1038/Nmeth.4556  0.686
2017 Pedersen BS, Quinlan AR. mosdepth: quick coverage calculation for genomes and exomes. Bioinformatics (Oxford, England). PMID 29096012 DOI: 10.1093/Bioinformatics/Btx699  0.394
2017 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, ... ... Quinlan AR, et al. Combating subclonal evolution of resistant cancer phenotypes. Nature Communications. 8: 1231. PMID 29093439 DOI: 10.1038/S41467-017-01174-3  0.566
2017 Pedersen BS, Collins RL, Talkowski ME, Quinlan AR. Indexcov: fast coverage quality control for whole-genome sequencing. Gigascience. PMID 29048539 DOI: 10.1093/Gigascience/Gix090  0.46
2017 Eilbeck K, Quinlan A, Yandell M. Settling the score: variant prioritization and Mendelian disease. Nature Reviews. Genetics. PMID 28804138 DOI: 10.1038/Nrg.2017.52  0.401
2017 Pedersen BS, Quinlan AR. Who's Who? Detecting and Resolving Sample Anomalies in Human DNA Sequencing Studies with Peddy. American Journal of Human Genetics. PMID 28190455 DOI: 10.1016/J.Ajhg.2017.01.017  0.335
2017 Pedersen BS, Quinlan AR. cyvcf2: fast, flexible variant analysis with Python. Bioinformatics (Oxford, England). PMID 28165109 DOI: 10.1093/Bioinformatics/Btx057  0.348
2016 Pedersen BS, Layer RM, Quinlan AR. Vcfanno: fast, flexible annotation of genetic variants. Genome Biology. 17: 118. PMID 27250555 DOI: 10.1186/S13059-016-0973-5  0.438
2015 Layer RM, Kindlon N, Karczewski KJ, Quinlan AR. Efficient genotype compression and analysis of large genetic-variation data sets. Nature Methods. 13: 63-5. PMID 26550772 DOI: 10.1038/nmeth.3654  0.338
2015 Chiang C, Layer RM, Faust GG, Lindberg MR, Rose DB, Garrison EP, Marth GT, Quinlan AR, Hall IM. SpeedSeq: ultra-fast personal genome analysis and interpretation. Nature Methods. 12: 966-8. PMID 26258291 DOI: 10.1038/nmeth.3505  0.776
2015 Quick J, Quinlan AR, Loman NJ. Erratum: A reference bacterial genome dataset generated on the MinION(TM) portable single-molecule nanopore sequencer. Gigascience. 4: 6. PMID 25695306 DOI: 10.1186/s13742-015-0043-z  0.366
2015 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. Extending reference assembly models. Genome Biology. 16: 13. PMID 25651527 DOI: 10.1186/S13059-015-0587-3  0.693
2015 Lindberg MR, Hall IM, Quinlan AR. Population-based structural variation discovery with Hydra-Multi. Bioinformatics (Oxford, England). 31: 1286-9. PMID 25527832 DOI: 10.1093/bioinformatics/btu771  0.752
2014 Quick J, Quinlan AR, Loman NJ. A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer. Gigascience. 3: 22. PMID 25386338 DOI: 10.1186/2047-217X-3-22  0.324
2014 Quinlan AR. BEDTools: The Swiss-Army Tool for Genome Feature Analysis. Current Protocols in Bioinformatics. 47: 11.12.1-34. PMID 25199790 DOI: 10.1002/0471250953.bi1112s47  0.437
2014 Qiao Y, Quinlan AR, Jazaeri AA, Verhaak RG, Wheeler DA, Marth GT. SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization. Genome Biology. 15: 443. PMID 25160522 DOI: 10.1186/s13059-014-0443-x  0.619
2014 Loman NJ, Quinlan AR. Poretools: a toolkit for analyzing nanopore sequence data. Bioinformatics (Oxford, England). 30: 3399-401. PMID 25143291 DOI: 10.1093/bioinformatics/btu555  0.357
2014 Layer RM, Chiang C, Quinlan AR, Hall IM. LUMPY: a probabilistic framework for structural variant discovery. Genome Biology. 15: R84. PMID 24970577 DOI: 10.1186/gb-2014-15-6-r84  0.632
2013 Paila U, Chapman BA, Kirchner R, Quinlan AR. GEMINI: integrative exploration of genetic variation and genome annotations. Plos Computational Biology. 9: e1003153. PMID 23874191 DOI: 10.1371/journal.pcbi.1003153  0.397
2013 Malhotra A, Lindberg M, Faust GG, Leibowitz ML, Clark RA, Layer RM, Quinlan AR, Hall IM. Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms. Genome Research. 23: 762-76. PMID 23410887 DOI: 10.1101/Gr.143677.112  0.649
2013 Layer RM, Skadron K, Robins G, Hall IM, Quinlan AR. Binary Interval Search: a scalable algorithm for counting interval intersections. Bioinformatics (Oxford, England). 29: 1-7. PMID 23129298 DOI: 10.1093/Bioinformatics/Bts652  0.743
2012 Krumm N, Sudmant PH, Ko A, O'Roak BJ, Malig M, Coe BP, Quinlan AR, Nickerson DA, Eichler EE. Copy number variation detection and genotyping from exome sequence data. Genome Research. 22: 1525-32. PMID 22585873 DOI: 10.1101/Gr.138115.112  0.411
2012 Hall IM, Quinlan AR. Detection and interpretation of genomic structural variation in mammals. Methods in Molecular Biology (Clifton, N.J.). 838: 225-48. PMID 22228015 DOI: 10.1007/978-1-61779-507-7_11  0.728
2011 Quinlan AR, Hall IM. Characterizing complex structural variation in germline and somatic genomes. Trends in Genetics : Tig. 28: 43-53. PMID 22094265 DOI: 10.1016/j.tig.2011.10.002  0.713
2011 Quinlan AR, Boland MJ, Leibowitz ML, Shumilina S, Pehrson SM, Baldwin KK, Hall IM. Genome sequencing of mouse induced pluripotent stem cells reveals retroelement stability and infrequent DNA rearrangement during reprogramming. Cell Stem Cell. 9: 366-73. PMID 21982236 DOI: 10.1016/J.Stem.2011.07.018  0.715
2011 Dale RK, Pedersen BS, Quinlan AR. Pybedtools: a flexible Python library for manipulating genomic datasets and annotations. Bioinformatics (Oxford, England). 27: 3423-4. PMID 21949271 DOI: 10.1093/Bioinformatics/Btr539  0.439
2011 Barnett DW, Garrison EK, Quinlan AR, Strömberg MP, Marth GT. BamTools: a C++ API and toolkit for analyzing and managing BAM files. Bioinformatics (Oxford, England). 27: 1691-2. PMID 21493652 DOI: 10.1093/bioinformatics/btr174  0.645
2010 Quinlan AR, Clark RA, Sokolova S, Leibowitz ML, Zhang Y, Hurles ME, Mell JC, Hall IM. Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome. Genome Research. 20: 623-35. PMID 20308636 DOI: 10.1101/gr.102970.109  0.743
2010 Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics (Oxford, England). 26: 841-2. PMID 20110278 DOI: 10.1093/bioinformatics/btq033  0.722
2009 Sackton TB, Kulathinal RJ, Bergman CM, Quinlan AR, Dopman EB, Carneiro M, Marth GT, Hartl DL, Clark AG. Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster. Genome Biology and Evolution. 1: 449-65. PMID 20333214 DOI: 10.1093/Gbe/Evp048  0.723
2008 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, et al. Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Research. 18: 1638-42. PMID 18775913 DOI: 10.1101/Gr.077776.108  0.676
2008 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, et al. Whole-genome sequencing and variant discovery in C. elegans. Nature Methods. 5: 183-8. PMID 18204455 DOI: 10.1038/Nmeth.1179  0.718
2008 Quinlan AR, Stewart DA, Strömberg MP, Marth GT. Pyrobayes: An improved base caller for SNP discovery in pyrosequences Nature Methods. 5: 179-181. PMID 18193056 DOI: 10.1038/nmeth.1172  0.612
2007 Quinlan AR, Marth GT. Primer-site SNPs mask mutations. Nature Methods. 4: 192. PMID 17327845 DOI: 10.1038/nmeth0307-192  0.576
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