Subfamily HMMS in Functional Genomics. - Duncan P. Brown; Nandini Krishnamurthy; Joseph M. Dale; Wayne Christopher; Kimmen Sjölander (Pacific Symposium on Biocomputing, 2005)

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. - Peter D. Karp; Suzanne M. Paley; Markus Krummenacker; Mario Latendresse; Joseph M. Dale; Thomas J. Lee; Pallavi Kaipa; Fred Gilham; Aaron Spaulding; Liviu Popescu; Tomer Altman; Ian T. Paulsen; et al. (Briefings Bioinform., 2010)

Machine learning methods for metabolic pathway prediction. - Joseph M. Dale; Liviu Popescu; Peter D. Karp (BMC Bioinform., 2010)

A systematic study of genome context methods: calibration, normalization and combination. - Luciana Ferrer; Joseph M. Dale; Peter D. Karp (BMC Bioinform., 2010)

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. - Ron Caspi; Tomer Altman; Joseph M. Dale; Kate Dreher; Carol A. Fulcher; Fred Gilham; Pallavi Kaipa; Athikkattuvalasu S. Karthikeyan; Anamika Kothari; Markus Krummenacker; Mario Latendresse; Lukas A. Mueller; et al. (Nucleic Acids Res., 2010)