Neighborhood embedding and re-ranking of disease genes with ADAGIO. - Mert Erden; Megan Gelement; Sarrah Hakimjee; Kyla Levin; Mary-Joy Sidhom; Kapil Devkota; Lenore J. Cowen (BCB, 2022)

GLIDER: function prediction from GLIDE-based neighborhoods. - Kapil Devkota; Henri Schmidt; Matthew Werenski; James M. Murphy; Mert Erden; Victor Arsenescu; Lenore J. Cowen (Bioinform., 2022)

Majority Vote Cascading: A Semi-Supervised Framework for Improving Protein Function Prediction. - John Lazarsfeld; Jonathan Rodríguez; Mert Erden; Yuelin Liu; Lenore J. Cowen (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Learning a CoNCISE Language for Small-Molecule Binding. - Mert Erden; Kapil Devkota; Lia Varghese; Lenore Cowen; Rohit Singh 001 (RECOMB, 2025)