CisOrtho: A program pipeline for genome-wide identification of transcription factor target genes using phylogenetic footprinting. - Henry R. Bigelow; Adam S. Wenick; Allan Wong; Oliver Hobert (BMC Bioinform., 2004)

PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins. - Henry R. Bigelow; Burkhard Rost (Nucleic Acids Res., 2006)

Next-token pretraining implies in-context learning. - Paul M. Riechers; Henry R. Bigelow; Eric A. Alt; Adam S. Shai (CoRR, 2025)