Predicting the Beta-Helix Fold from Protein Sequence Data. - Lenore Cowen; Phil Bradley; Matthew Menke; Jonathan King; Bonnie Berger (J. Comput. Biol., 2002)

Wrap-and-pack: a new paradigm for beta structural motif recognition with application to recognizing beta trefoils. - Matthew Menke; Eben Scanlon; Jonathan King; Bonnie Berger; Lenore Cowen (RECOMB, 2004)

Wrap-and-Pack: A New Paradigm for Beta Structural Motif Recognition with Application to Recognizing Beta Trefoils. - Matthew Menke; Jonathan King; Bonnie Berger; Lenore Cowen (J. Comput. Biol., 2005)

Matt: Local Flexibility Aids Protein Multiple Structure Alignment. - Matthew Menke; Bonnie Berger; Lenore Cowen (PLoS Comput. Biol., 2008)

BETASCAN: Probable β-amyloids Identified by Pairwise Probabilistic Analysis. - Allen W. Bryan Jr.; Matthew Menke; Lenore J. Cowen; Susan Lindquist; Bonnie Berger (PLoS Comput. Biol., 2009)

Computational approaches to modeling the conserved structural core among distantly homologous proteins. - Matthew Menke (2009)

Touring Protein Space with Matt. - Noah M. Daniels; Anoop Kumar; Lenore Cowen; Matthew Menke (ISBRA, 2010)

Markov random fields reveal an N-terminal double beta-propeller motif as part of a bacterial hybrid two-component sensor system. - Matthew Menke; Bonnie Berger; Lenore Cowen (Proc. Natl. Acad. Sci. USA, 2010)

Molli: Interactive Visualization for Exploratory Protein Analysis. - Sara L. Su; Connor Gramazio; Daniela Extrum-Fernandez; Caitlin Crumm; Lenore J. Cowen; Matthew Menke; Megan Strait (IEEE Computer Graphics and Applications, 2012)