GLIDE: combining local methods and diffusion state embeddings to predict missing interactions in biological networks. - Kapil Devkota; James M. Murphy; Lenore J. Cowen (Bioinform., 2020)

Diffusion State Distances: Multitemporal Analysis, Fast Algorithms, and Applications to Biological Networks. - Lenore Cowen; Kapil Devkota; Xiaozhe Hu; James M. Murphy; Kaiyi Wu (SIAM J. Math. Data Sci., 2021)

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)

Topsy-Turvy: integrating a global view into sequence-based PPI prediction. - Rohit Singh 001; Kapil Devkota; Samuel Sledzieski; Bonnie Berger; Lenore Cowen (Bioinform., 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)

TT3D: Leveraging precomputed protein 3D sequence models to predict protein-protein interactions. - Samuel Sledzieski; Kapil Devkota; Rohit Singh 001; Lenore Cowen; Bonnie Berger (Bioinform., 2023)

Fast Approximate IsoRank for Scalable Global Alignment of Biological Networks. - Kapil Devkota; Anselm Blumer; Xiaozhe Hu; Lenore Cowen (RECOMB, 2024)

Approximate IsoRank for Scalable and Functionally Meaningful Cross-Species Alignments of Protein Interaction Networks. - Kapil Devkota; Anselm Blumer; Xiaozhe Hu; Lenore Cowen (J. Comput. Biol., 2024)

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

Decoding the Functional Interactome of Non-model Organisms with PHILHARMONIC. - Samuel Sledzieski; Charlotte Versavel; Rohit Singh 001; Faith Ocitti; Kapil Devkota; Lokender Kumar; Polina Shpilker; Liza Roger; Jinkyu Yang; Nastassja Lewinski; Hollie Putnam; Bonnie Berger; et al. (RECOMB, 2025)