F-Seq: a feature density estimator for high-throughput sequence tags. - Alan P. Boyle; Justin Guinney; Gregory E. Crawford; Terrence S. Furey (Bioinform., 2008)

Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures. - Douglas H. Phanstiel; Alan P. Boyle; Carlos L. Araya; Michael P. Snyder (Bioinform., 2014)

Comparative analysis of regulatory information and circuits across distant species Open. - Alan P. Boyle; Carlos L. Araya; Cathleen Brdlik; Philip Cayting; Chao Cheng; Yong Cheng; Kathryn Gardner; LaDeana W. Hillier; Judith Janette; Lixia Jiang; Dionna Kasper; Trupti Kawli; et al. (Nat., 2014)

Mango: a bias-correcting ChIA-PET analysis pipeline. - Douglas H. Phanstiel; Alan P. Boyle; Nastaran Heidari; Michael P. Snyder (Bioinform., 2015)

A proximity-based graph clustering method for the identification and application of transcription factor clusters. - Maxwell T. Spadafore; Kayvan Najarian; Alan P. Boyle (BMC Bioinform., 2017)

CGIMP: Real-time exploration and covariate projection for self-organizing map datasets. - Adam Diehl; Alan P. Boyle (J. Open Source Softw., 2019)

Predicting the effects of SNPs on transcription factor binding affinity. - Sierra S. Nishizaki; Natalie Ng; Shengcheng Dong; Robert S. Porter; Cody Morterud; Colten Williams; Courtney Asman; Jessica A Switzenberg; Alan P. Boyle (Bioinform., 2020)

MapGL: inferring evolutionary gain and loss of short genomic sequence features by phylogenetic maximum parsimony. - Adam Diehl; Alan P. Boyle (BMC Bioinform., 2020)

SEMplMe: a tool for integrating DNA methylation effects in transcription factor binding affinity predictions. - Sierra S. Nishizaki; Alan P. Boyle (BMC Bioinform., 2022)