AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis. - Thomas J. Boyle; Zhirong Bao; John I. Murray; Carlos L. Araya; Robert H. Waterston (BMC Bioinform., 2006)

Enrich: software for analysis of protein function by enrichment and depletion of variants. - Douglas M. Fowler; Carlos L. Araya; Wayne Gerard; Stanley Fields (Bioinform., 2011)

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)