| Structure-based protein function prediction using graph convolutional networks V Gligorijević, PD Renfrew, T Kosciolek, JK Leman, D Berenberg, ... Nature communications 12 (1), 3168, 2021 | 804 | 2021 |
| The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens N Zhou, Y Jiang, TR Bergquist, AJ Lee, BZ Kacsoh, AW Crocker, ... Genome biology 20, 1-23, 2019 | 448 | 2019 |
| Methods for biological data integration: perspectives and challenges V Gligorijević, N Pržulj Journal of the Royal Society Interface 12 (112), 20150571, 2015 | 345 | 2015 |
| Integrative methods for analyzing big data in precision medicine V Gligorijević, N Malod‐Dognin, N Pržulj Proteomics 16 (5), 741-758, 2016 | 234 | 2016 |
| deepNF: deep network fusion for protein function prediction V Gligorijević, M Barot, R Bonneau Bioinformatics 34 (22), 3873-3881, 2018 | 230 | 2018 |
| Non-negative matrix factorizations for multiplex network analysis V Gligorijević, Y Panagakis, S Zafeiriou IEEE transactions on pattern analysis and machine intelligence 41 (4), 928-940, 2018 | 99 | 2018 |
| Protein remote homology detection and structural alignment using deep learning T Hamamsy, JT Morton, R Blackwell, D Berenberg, N Carriero, ... Nature biotechnology 42 (6), 975-985, 2024 | 68 | 2024 |
| Co-evolutionary mechanisms of emotional bursts in online social dynamics and networks B Tadić, V Gligorijević, M Mitrović, M Šuvakov Entropy 15 (12), 5084-5120, 2013 | 67 | 2013 |
| Fuse: multiple network alignment via data fusion V Gligorijević, N Malod-Dognin, N Pržulj Bioinformatics 32 (8), 1195-1203, 2016 | 63 | 2016 |
| Patient-specific data fusion for cancer stratification and personalised treatment V Gligorijević, N Malod-Dognin, N Pržulj Biocomputing 2016: Proceedings of the Pacific Symposium, 321-332, 2016 | 62 | 2016 |
| Sequence-structure-function relationships in the microbial protein universe J Koehler Leman, P Szczerbiak, PD Renfrew, V Gligorijevic, D Berenberg, ... Nature communications 14 (1), 2351, 2023 | 54 | 2023 |
| How the online social networks are used: dialogues-based structure of MySpace M Šuvakov, M Mitrović, V Gligorijević, B Tadić Journal of the Royal Society Interface 10 (79), 20120819, 2013 | 50 | 2013 |
| Abdiffuser: full-atom generation of in-vitro functioning antibodies K Martinkus, J Ludwiczak, WC Liang, J Lafrance-Vanasse, I Hotzel, ... Advances in Neural Information Processing Systems 36, 40729-40759, 2023 | 48 | 2023 |
| Equifold: Protein structure prediction with a novel coarse-grained structure representation JH Lee, P Yadollahpour, A Watkins, NC Frey, A Leaver-Fay, S Ra, K Cho, ... Biorxiv, 2022.10. 07.511322, 2022 | 46 | 2022 |
| Function-guided protein design by deep manifold sampling V Gligorijević, D Berenberg, S Ra, A Watkins, S Kelow, K Cho, R Bonneau bioRxiv, 2021.12. 22.473759, 2021 | 45 | 2021 |
| Integration of molecular network data reconstructs Gene Ontology V Gligorijević, V Janjić, N Pržulj Bioinformatics 30 (17), i594-i600, 2014 | 42 | 2014 |
| Protein discovery with discrete walk-jump sampling NC Frey, D Berenberg, K Zadorozhny, J Kleinhenz, J Lafrance-Vanasse, ... arXiv preprint arXiv:2306.12360, 2023 | 36 | 2023 |
| TCRconv: predicting recognition between T cell receptors and epitopes using contextualized motifs E Jokinen, A Dumitrescu, J Huuhtanen, V Gligorijević, S Mustjoki, ... Bioinformatics 39 (1), btac788, 2023 | 26 | 2023 |
| NetQuilt: deep multispecies network-based protein function prediction using homology-informed network similarity M Barot, V Gligorijević, K Cho, R Bonneau Bioinformatics 37 (16), 2414-2422, 2021 | 23 | 2021 |
| Protein structural alignments from sequence JT Morton, CEM Strauss, R Blackwell, D Berenberg, V Gligorijevic, ... BioRxiv, 2020.11. 03.365932, 2020 | 20 | 2020 |
Richard BonneauGenentechVerified email at gene.com
