BEDTools: a flexible suite of utilities for comparing genomic features. - Aaron R. Quinlan; Ira M. Hall (Bioinform., 2010)

BamTools: a C++ API and toolkit for analyzing and managing BAM files. - Derek W. Barnett; Erik K. Garrison; Aaron R. Quinlan; Michael Strömberg; Gabor T. Marth (Bioinform., 2011)

Pybedtools: a flexible Python library for manipulating genomic datasets and annotations. - Ryan K. Dale; Brent S. Pedersen; Aaron R. Quinlan (Bioinform., 2011)

Binary Interval Search: a scalable algorithm for counting interval intersections. - Ryan M. Layer; Kevin Skadron; Gabriel Robins; Ira M. Hall; Aaron R. Quinlan (Bioinform., 2013)

GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations. - Umadevi Paila; Brad A. Chapman; Rory D. Kirchner; Aaron R. Quinlan (PLoS Comput. Biol., 2013)

Poretools: a toolkit for analyzing nanopore sequence data. - Nicholas J. Loman; Aaron R. Quinlan (Bioinform., 2014)

Population-based structural variation discovery with Hydra-Multi. - Michael R. Lindberg; Ira M. Hall; Aaron R. Quinlan (Bioinform., 2015)

cyvcf2: fast, flexible variant analysis with Python. - Brent S. Pedersen; Aaron R. Quinlan (Bioinform., 2017)

A Parallel Algorithm for $N$-Way Interval Set Intersection. - Ryan M. Layer; Aaron R. Quinlan (Proc. IEEE, 2017)

Mosdepth: quick coverage calculation for genomes and exomes. - Brent S. Pedersen; Aaron R. Quinlan (Bioinform., 2018)

hts-nim: scripting high-performance genomic analyses. - Brent S. Pedersen; Aaron R. Quinlan (Bioinform., 2018)

Coloc-stats: a unified web interface to perform colocalization analysis of genomic features. - Boris Simovski; Chakravarthi Kanduri; Sveinung Gundersen; Dmytro Titov; Diana Domanska; Christoph Bock; Lara Bossini-Castillo; Maria Chikina; Alexander V. Favorov; Ryan M. Layer; Andrey A. Mironov; Aaron R. Quinlan; et al. (Nucleic Acids Res., 2018)

XPRESSyourself: Enhancing, standardizing, and automating ribosome profiling computational analyses yields improved insight into data. - Jordan A. Berg; Jonathan R. Belyeu; Jeffrey T. Morgan; Yeyun Ouyang; Alex J. Bott; Aaron R. Quinlan; Jason Gertz; Jared Rutter (PLoS Comput. Biol., 2020)

Unfazed: parent-of-origin detection for large and small de novo variants. - Jonathan R. Belyeu; Thomas A. Sasani; Brent S. Pedersen; Aaron R. Quinlan (Bioinform., 2021)

Balancing efficient analysis and storage of quantitative genomics data with the D4 format and d4tools. - Hao Hou; Brent S. Pedersen; Aaron R. Quinlan (Nat. Comput. Sci., 2021)

trfermikit: a tool to discover VNTR-associated deletions. - Peter McHale; Aaron R. Quinlan (Bioinform., 2022)

Combining genetic constraint with predictions of alternative splicing to prioritize deleterious splicing in rare disease studies. - Michael J. Cormier; Brent S. Pedersen; Pinar Bayrak-Toydemir; Aaron R. Quinlan (BMC Bioinform., 2022)

Annotation of structural variants with reported allele frequencies and related metrics from multiple datasets using SVAFotate. - Thomas J. Nicholas; Michael J. Cormier; Aaron R. Quinlan (BMC Bioinform., 2022)

Author Correction: Balancing efficient analysis and storage of quantitative genomics data with the D4 format and d4tools. - Hao Hou; Brent S. Pedersen; Aaron R. Quinlan (Nat. Comput. Sci., 2022)

Enriched phenotypes in rare variant carriers suggest pathogenic mechanisms in rare disease patients. - Lane Fitzsimmons; Maria T. Acosta; David R. Adams; Ben Afzali; Ali Al-Beshri; Eric Allenspach; Aimee Allworth; Raquel L. Alvarez; Justin Alvey; Ashley Andrews; Euan A. Ashley; Carlos A. Bacino; et al. (BioData Min., 2025)