| Topsy-Turvy: integrating a global view into sequence-based PPI prediction R Singh, K Devkota, S Sledzieski, B Berger, L Cowen Bioinformatics 38 (Supplement_1), i264-i272, 2022 | 56 | 2022 |
| Current and future directions in network biology M Zitnik, MM Li, A Wells, K Glass, DM Gysi, A Krishnan, TM Murali, ... arXiv preprint arXiv:2309.08478, 2023 | 25 | 2023 |
| GLIDE: combining local methods and diffusion state embeddings to predict missing interactions in biological networks K Devkota, JM Murphy, LJ Cowen Bioinformatics 36 (Supplement_1), i464-i473, 2020 | 25 | 2020 |
| Bioengineered models of Parkinson’s disease using patient-derived dopaminergic neurons exhibit distinct biological profiles in a 3D microenvironment NJ Fiore, YM Ganat, K Devkota, R Batorsky, M Lei, K Lee, LJ Cowen, ... Cellular and Molecular Life Sciences 79 (2), 78, 2022 | 19 | 2022 |
| TT3D: Leveraging precomputed protein 3D sequence models to predict protein–protein interactions S Sledzieski, K Devkota, R Singh, L Cowen, B Berger Bioinformatics 39 (11), btad663, 2023 | 13 | 2023 |
| Diffusion state distances: multitemporal analysis, fast algorithms, and applications to biological networks L Cowen, K Devkota, X Hu, JM Murphy, K Wu SIAM Journal on Mathematics of Data Science 3 (1), 142-170, 2021 | 10 | 2021 |
| GLIDER: function prediction from GLIDE-based neighborhoods K Devkota, H Schmidt, M Werenski, JM Murphy, M Erden, V Arsenescu, ... Bioinformatics 38 (13), 3395-3406, 2022 | 8 | 2022 |
| MUNDO: protein function prediction embedded in a multispecies world V Arsenescu, K Devkota, M Erden, P Shpilker, M Werenski, LJ Cowen Bioinformatics Advances 2 (1), vbab025, 2022 | 5 | 2022 |
| Fast Approximate IsoRank for Scalable Global Alignment of Biological Networks K Devkota, A Blumer, X Hu, L Cowen International Conference on Research in Computational Molecular Biology, 1-16, 2024 | 3 | 2024 |
| Diffusion state distances: Multitemporal analysis, fast algorithms, and applications to biological networks L Cowen, K Devkota, X Hu, JM Murphy, K Wu arXiv preprint arXiv:2003.03616, 2020 | 3 | 2020 |
| Learning a CoNCISE language for small-molecule binding M Erden, K Devkota, L Varghese, L Cowen, R Singh bioRxiv, 2025.01. 08.632039, 2025 | | 2025 |
| Decoding the Functional Interactome of Non-Model Organisms with PHILHARMONIC S Sledzieski, C Versavel, R Singh, F Ocitti, K Devkota, L Kumar, ... bioRxiv, 2024.10. 25.620267, 2024 | | 2024 |
| Approximate IsoRank for Scalable and Functionally Meaningful Cross-Species Alignments of Protein Interaction Networks K Devkota, A Blumer, X Hu, L Cowen Journal of Computational Biology 31 (10), 990-1007, 2024 | | 2024 |
| Allo-Allo: Data-efficient prediction of allosteric sites T Dong, C Kan, K Devkota, R Singh bioRxiv, 2024.09. 28.615583, 2024 | | 2024 |
| Miniaturizing, Modifying, and Augmenting Nature's Proteins with Raygun K Devkota, D Shonai, J Mao, SH Soderling, R Singh bioRxiv, 2024.08. 13.607858, 2024 | | 2024 |
| Computational Methods for the Prediction and Analysis of Protein-Protein Interaction Networks K Devkota Tufts University, 2023 | | 2023 |
| Neighborhood embedding and re-ranking of disease genes with ADAGIO M Erden, M Gelement, S Hakimjee, K Levin, MJ Sidhom, K Devkota, ... Proceedings of the 13th ACM International Conference on Bioinformatics …, 2022 | | 2022 |
| Interactome-scale comparison of co-immunoprecipitation and yeast two-hybrid assays for protein interaction prediction K Devkota, L Cowen, R Singh ICML 2024 Workshop on Efficient and Accessible Foundation Models for …, 0 | | |