Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms. - Daniel I. Speiser; M. Sabrina Pankey; Alexander K. Zaharoff; Barbara A. Battelle; Heather D. Bracken-Grissom; Jesse W. Breinholt; Seth M. Bybee; Thomas W. Cronin; Anders Garm; Annie R. Lindgren; Nipam H. Patel; Megan L. Porter; et al. (BMC Bioinform., 2014)

Detecting false positive sequence homology: a machine learning approach. - M. Stanley Fujimoto; Anton Suvorov; Nicholas O. Jensen; Mark J. Clement; Seth M. Bybee (BMC Bioinform., 2016)

Genome Polymorphism Detection Through Relaxed de Bruijn Graph Construction. - M. Stanley Fujimoto; Cole A. Lyman; Anton Suvorov; Paul M. Bodily; Quinn Snell; Keith A. Crandall; Seth M. Bybee; Mark J. Clement (BIBE, 2017)

Whole Genome Phylogenetic Tree Reconstruction Using Colored de Bruijn Graphs. - Cole A. Lyman; M. Stanley Fujimoto; Anton Suvorov; Paul M. Bodily; Quinn Snell; Keith A. Crandall; Seth M. Bybee; Mark J. Clement (BIBE, 2017)

The OGCleaner: filtering false-positive homology clusters. - M. Stanley Fujimoto; Anton Suvorov; Nicholas O. Jensen; Mark J. Clement; Quinn Snell; Seth M. Bybee (Bioinform., 2017)