Aaron R Quinlan

Summary

Publications

  1. pmc BEDTools: a flexible suite of utilities for comparing genomic features
    Aaron R Quinlan
    Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
    Bioinformatics 26:841-2. 2010
  2. pmc Binary Interval Search: a scalable algorithm for counting interval intersections
    Ryan M Layer
    Department of Computer Science, University of Virginia, Charlottesville, VA 22904, USA
    Bioinformatics 29:1-7. 2013
  3. pmc Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms
    Ankit Malhotra
    Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22903, USA
    Genome Res 23:762-76. 2013
  4. doi request reprint Detection and interpretation of genomic structural variation in mammals
    Ira M Hall
    Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
    Methods Mol Biol 838:225-48. 2012
  5. pmc Pybedtools: a flexible Python library for manipulating genomic datasets and annotations
    Ryan K Dale
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Bioinformatics 27:3423-4. 2011
  6. doi request reprint Genome sequencing of mouse induced pluripotent stem cells reveals retroelement stability and infrequent DNA rearrangement during reprogramming
    Aaron R Quinlan
    Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, USA
    Cell Stem Cell 9:366-73. 2011
  7. pmc Characterizing complex structural variation in germline and somatic genomes
    Aaron R Quinlan
    Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
    Trends Genet 28:43-53. 2012
  8. pmc Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome
    Aaron R Quinlan
    Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
    Genome Res 20:623-35. 2010

Collaborators

  • Ira M Hall
  • Brent S Pedersen
  • Ryan M Layer
  • Ankit Malhotra
  • Ryan K Dale
  • Michael Lindberg
  • Mitchell L Leibowitz
  • Gabriel Robins
  • Kevin Skadron
  • Gregory G Faust
  • Royden A Clark

Detail Information

Publications8

  1. pmc BEDTools: a flexible suite of utilities for comparing genomic features
    Aaron R Quinlan
    Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
    Bioinformatics 26:841-2. 2010
    ..Fast and flexible tools are therefore required to ask complex questions of these data in an efficient manner...
  2. pmc Binary Interval Search: a scalable algorithm for counting interval intersections
    Ryan M Layer
    Department of Computer Science, University of Virginia, Charlottesville, VA 22904, USA
    Bioinformatics 29:1-7. 2013
    ..Given the continued advances in DNA sequencing technologies, efficient methods for measuring statistically significant relationships between many sets of genomic features are crucial for future discovery...
  3. pmc Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms
    Ankit Malhotra
    Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22903, USA
    Genome Res 23:762-76. 2013
    ....
  4. doi request reprint Detection and interpretation of genomic structural variation in mammals
    Ira M Hall
    Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
    Methods Mol Biol 838:225-48. 2012
    ..Finally, we explore a few of the key biological insights that can be gained by applying NGS methods to model organisms...
  5. pmc Pybedtools: a flexible Python library for manipulating genomic datasets and annotations
    Ryan K Dale
    Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Bioinformatics 27:3423-4. 2011
    ..The library is well documented and efficient, and allows researchers to quickly develop simple, yet powerful scripts that enable complex genomic analyses...
  6. doi request reprint Genome sequencing of mouse induced pluripotent stem cells reveals retroelement stability and infrequent DNA rearrangement during reprogramming
    Aaron R Quinlan
    Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, USA
    Cell Stem Cell 9:366-73. 2011
    ..These results show that genome stability can persist throughout reprogramming, and argue that it is possible to generate iPSCs lacking gene-disrupting mutations using current reprogramming methods...
  7. pmc Characterizing complex structural variation in germline and somatic genomes
    Aaron R Quinlan
    Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
    Trends Genet 28:43-53. 2012
    ..Here, we review current knowledge of complex SV in mammals, and outline techniques for identifying and characterizing complex variants using next-generation DNA sequencing...
  8. pmc Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome
    Aaron R Quinlan
    Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
    Genome Res 20:623-35. 2010
    ..This result suggests that the genetic instability of such regions is often the cause rather than the consequence of duplicated genomic architecture...