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

Gobe: an interactive, web-based tool for comparative genomic visualization. - Brent S. Pedersen; Haibao Tang; Michael Freeling (Bioinform., 2011)

Screening synteny blocks in pairwise genome comparisons through integer programming. - Haibao Tang; Eric Lyons 002; Brent S. Pedersen; James C. Schnable; Andrew H. Paterson; Michael Freeling (BMC Bioinform., 2011)

BioStar: An Online Question & Answer Resource for the Bioinformatics Community. - Laurence D. Parnell; Pierre Lindenbaum; Khader Shameer; Giovanni Marco Dall'Olio; Daniel C. Swan; Lars Juhl Jensen; Simon J. Cockell; Brent S. Pedersen; Mary E. Mangan; Christopher A. Miller 002; István Albert (PLoS Comput. Biol., 2011)

Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values. - Brent S. Pedersen; David A. Schwartz; Ivana V. Yang; Katerina J. Kechris (Bioinform., 2012)

CruzDB: software for annotation of genomic intervals with UCSC genome-browser database. - Brent S. Pedersen; Ivana V. Yang; Subhajyoti De (Bioinform., 2013)

The dilemma of choosing the ideal permutation strategy while estimating statistical significance of genome-wide enrichment. - Subhajyoti De; Brent S. Pedersen; Katerina J. Kechris (Briefings Bioinform., 2014)

Efficient "pythonic" access to FASTA files using pyfaidx. - Matthew D. Shirley; Zhaorong Ma; Brent S. Pedersen; Sarah J. Wheelan (PeerJ Prepr., 2015)

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

bíogo/hts: high throughput sequence handling for the Go language. - R. Daniel Kortschak; Brent S. Pedersen; David L. Adelson (J. Open Source Softw., 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)

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)

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)

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)

A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar. - Erik Garrison; Zev N. Kronenberg; Eric T. Dawson; Brent S. Pedersen; Pjotr Prins (PLoS Comput. Biol., 2022)