Publications by authors named "Aaron R Quinlan"

56Publications

Regulatory sharing between estrogen receptor α bound enhancers.

Nucleic Acids Res 2020 07;48(12):6597-6610

Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.

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http://dx.doi.org/10.1093/nar/gkaa454DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7337896PMC
July 2020

XPRESSyourself: Enhancing, standardizing, and automating ribosome profiling computational analyses yields improved insight into data.

PLoS Comput Biol 2020 01 31;16(1):e1007625. Epub 2020 Jan 31.

Department of Biochemistry, University of Utah, Salt Lake City, Utah, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1007625DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7015430PMC
January 2020

Duphold: scalable, depth-based annotation and curation of high-confidence structural variant calls.

Gigascience 2019 04;8(4)

Department of Human Genetics, University of Utah, Salt Lake City, UT, 84112.

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http://dx.doi.org/10.1093/gigascience/giz040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6479422PMC
April 2019

Overlooked roles of DNA damage and maternal age in generating human germline mutations.

Proc Natl Acad Sci U S A 2019 05 24;116(19):9491-9500. Epub 2019 Apr 24.

Department of Biological Sciences, Columbia University, New York, NY 10027;

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http://dx.doi.org/10.1073/pnas.1901259116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6511033PMC
May 2019

Coexpression patterns define epigenetic regulators associated with neurological dysfunction.

Genome Res 2019 04 11;29(4):532-542. Epub 2019 Mar 11.

McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.

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http://genome.cshlp.org/lookup/doi/10.1101/gr.239442.118
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http://dx.doi.org/10.1101/gr.239442.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6442390PMC
April 2019

A map of constrained coding regions in the human genome.

Nat Genet 2019 01 10;51(1):88-95. Epub 2018 Dec 10.

Department of Human Genetics, University of Utah, Salt Lake City, UT, USA.

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http://dx.doi.org/10.1038/s41588-018-0294-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6589356PMC
January 2019

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

Elife 2018 08 29;7. Epub 2018 Aug 29.

Department of Human Genetics, University of Utah, Salt Lake, United States.

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https://elifesciences.org/articles/35453
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http://dx.doi.org/10.7554/eLife.35453DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6115191PMC
August 2018

hts-nim: scripting high-performance genomic analyses.

Bioinformatics 2018 10;34(19):3387-3389

Department of Human Genetics, Department of Biomedical Informatics, and USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty358DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7190653PMC
October 2018

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

Nat Methods 2018 02 8;15(2):123-126. Epub 2018 Jan 8.

Department of Human Genetics, University of Utah, Salt Lake City, Utah, USA.

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http://dx.doi.org/10.1038/nmeth.4556DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5872823PMC
February 2018

Mosdepth: quick coverage calculation for genomes and exomes.

Bioinformatics 2018 03;34(5):867-868

Department of Human Genetics.

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http://dx.doi.org/10.1093/bioinformatics/btx699DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030888PMC
March 2018

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

Gigascience 2017 11;6(11):1-6

Department of Human Genetics, University of Utah, 15 S 2030 E, Salt Lake City, UT 84112, USA.

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http://dx.doi.org/10.1093/gigascience/gix090DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737511PMC
November 2017

Identification of ATIC as a Novel Target for Chemoradiosensitization.

Int J Radiat Oncol Biol Phys 2018 01 21;100(1):162-173. Epub 2017 Sep 21.

Genetics Institute and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida. Electronic address:

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http://dx.doi.org/10.1016/j.ijrobp.2017.08.033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5736427PMC
January 2018

A parallel algorithm for -way interval set intersection.

Proc IEEE Inst Electr Electron Eng 2017 Mar;105(3):542-551

Department of Human Genetics, University of Utah, Salt Lake City, UT, 84112. Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, 84112.

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http://ieeexplore.ieee.org/document/7289350/
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http://dx.doi.org/10.1109/JPROC.2015.2461494DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6188649PMC
March 2017

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

Am J Hum Genet 2017 Mar 9;100(3):406-413. Epub 2017 Feb 9.

Department of Human Genetics, University of Utah, Salt Lake City, UT 84105, USA; Department of Biomedical Informatics, University of Utah, Salt Lake City, UT 84105, USA; USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84105, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2017.01.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5339084PMC
March 2017

cyvcf2: fast, flexible variant analysis with Python.

Bioinformatics 2017 Jun;33(12):1867-1869

Department of Human Genetics, Department of Biomedical Informatics, and USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA.

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https://academic.oup.com/bioinformatics/article/33/12/1867/2
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http://dx.doi.org/10.1093/bioinformatics/btx057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870853PMC
June 2017

Vcfanno: fast, flexible annotation of genetic variants.

Genome Biol 2016 06 1;17(1):118. Epub 2016 Jun 1.

Department of Human Genetics, University of Utah, Salt Lake City, UT, 84105, USA.

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http://dx.doi.org/10.1186/s13059-016-0973-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4888505PMC
June 2016

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

Diabetes 2016 Mar 2;65(3):794-802. Epub 2015 Dec 2.

Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL Genetics Institute, University of Florida, Gainesville, FL

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http://dx.doi.org/10.2337/db15-0322DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4764149PMC
March 2016

SpeedSeq: ultra-fast personal genome analysis and interpretation.

Nat Methods 2015 Oct 10;12(10):966-8. Epub 2015 Aug 10.

McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA.

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http://dx.doi.org/10.1038/nmeth.3505DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4589466PMC
October 2015

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

Gigascience 2015 13;4. Epub 2015 Feb 13.

Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT UK.

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http://dx.doi.org/10.1186/s13742-015-0043-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4332450PMC
September 2016

Population-based structural variation discovery with Hydra-Multi.

Bioinformatics 2015 Apr 2;31(8):1286-9. Epub 2014 Dec 2.

Department of Biochemistry and Molecular Genetics, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA, Department of Medicine, The Genome Institute, Washington University School of Medicine, St. Louis MO, USA and Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA Department of Biochemistry and Molecular Genetics, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA, Department of Medicine, The Genome Institute, Washington University School of Medicine, St. Louis MO, USA and Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA Department of Biochemistry and Molecular Genetics, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA, Department of Medicine, The Genome Institute, Washington University School of Medicine, St. Louis MO, USA and Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu771DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393510PMC
April 2015

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

Gigascience 2014 20;3:22. Epub 2014 Oct 20.

Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK.

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http://dx.doi.org/10.1186/2047-217X-3-22DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4226419PMC
November 2014

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

Authors:
Aaron R Quinlan

Curr Protoc Bioinformatics 2014 Sep 8;47:11.12.1-34. Epub 2014 Sep 8.

Department of Public Health Sciences, Center for Public Health Genomics, Department of Biochemistry and Molecular Genetics, and Department of Computer Science. University of Virginia, Charlottesville, Virginia.

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http://dx.doi.org/10.1002/0471250953.bi1112s47DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4213956PMC
September 2014

Poretools: a toolkit for analyzing nanopore sequence data.

Bioinformatics 2014 Dec 20;30(23):3399-401. Epub 2014 Aug 20.

Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK and Department of Public Health Sciences, University of Virginia, Charlottesville 22932, VA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu555DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4296151PMC
December 2014

GEMINI: integrative exploration of genetic variation and genome annotations.

PLoS Comput Biol 2013 18;9(7):e1003153. Epub 2013 Jul 18.

Department of Public Health Sciences and Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA.

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http://dx.doi.org/10.1371/journal.pcbi.1003153DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715403PMC
February 2014

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

Genome Res 2013 May 14;23(5):762-76. Epub 2013 Feb 14.

Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22903, USA.

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http://dx.doi.org/10.1101/gr.143677.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3638133PMC
May 2013

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

Bioinformatics 2013 Jan 4;29(1):1-7. Epub 2012 Nov 4.

Department of Computer Science, University of Virginia, Charlottesville, VA 22904, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts652DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530906PMC
January 2013

Copy number variation detection and genotyping from exome sequence data.

Genome Res 2012 Aug 14;22(8):1525-32. Epub 2012 May 14.

Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA.

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http://dx.doi.org/10.1101/gr.138115.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3409265PMC
August 2012

Detection and interpretation of genomic structural variation in mammals.

Methods Mol Biol 2012 ;838:225-48

Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA.

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http://dx.doi.org/10.1007/978-1-61779-507-7_11DOI Listing
April 2012

Characterizing complex structural variation in germline and somatic genomes.

Trends Genet 2012 Jan 15;28(1):43-53. Epub 2011 Nov 15.

Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.

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http://dx.doi.org/10.1016/j.tig.2011.10.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3249479PMC
January 2012

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

Bioinformatics 2011 Dec 23;27(24):3423-4. Epub 2011 Sep 23.

Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr539DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232365PMC
December 2011

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

Bioinformatics 2011 Jun 14;27(12):1691-2. Epub 2011 Apr 14.

Department of Biology, Boston College, Chestnut Hill, MA 02467, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr174DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3106182PMC
June 2011

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

Genome Res 2010 May 22;20(5):623-35. Epub 2010 Mar 22.

Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA.

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http://dx.doi.org/10.1101/gr.102970.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2860164PMC
May 2010

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

Bioinformatics 2010 Mar 28;26(6):841-2. Epub 2010 Jan 28.

Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.

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http://dx.doi.org/10.1093/bioinformatics/btq033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832824PMC
March 2010

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

Nat Methods 2008 Feb 20;5(2):183-8. Epub 2008 Jan 20.

Washington University School of Medicine, Department of Genetics and Genome Sequencing Center, 4444 Forest Park Blvd., St. Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nmeth.1179DOI Listing
February 2008

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

Nat Methods 2008 Feb 13;5(2):179-81. Epub 2008 Jan 13.

Department of Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, Massachusetts 02467, USA.

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http://lysine.umiacs.umd.edu/files/teaching/quinlan_et_al_su
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http://www.nature.com/doifinder/10.1038/nmeth.1172
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http://dx.doi.org/10.1038/nmeth.1172DOI Listing
February 2008

Primer-site SNPs mask mutations.

Nat Methods 2007 Mar;4(3):192

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http://dx.doi.org/10.1038/nmeth0307-192DOI Listing
March 2007