| Global alignment of multiple protein interaction networks with application to functional orthology detection R Singh, J Xu, B Berger Proceedings of the National Academy of Sciences 105 (35), 12763-12768, 2008 | 854 | 2008 |
| IsoRankN: spectral methods for global alignment of multiple protein networks CS Liao, K Lu, M Baym, R Singh, B Berger Bioinformatics 25 (12), i253-i258, 2009 | 511 | 2009 |
| Pairwise global alignment of protein interaction networks by matching neighborhood topology R Singh, J Xu, B Berger Annual international conference on research in computational molecular …, 2007 | 405 | 2007 |
| D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions S Sledzieski, R Singh, L Cowen, B Berger Cell Systems 12 (10), 969-982. e6, 2021 | 168* | 2021 |
| Struct2Net: a web service to predict protein–protein interactions using a structure-based approach R Singh, D Park, J Xu, R Hosur, B Berger Nucleic acids research 38 (suppl_2), W508-W515, 2010 | 149 | 2010 |
| Contrastive learning in protein language space predicts interactions between drugs and protein targets R Singh, S Sledzieski, B Bryson, L Cowen, B Berger Proceedings of the National Academy of Sciences 120 (24), e2220778120, 2023 | 144 | 2023 |
| IsoBase: a database of functionally related proteins across PPI networks D Park, R Singh, M Baym, CS Liao, B Berger Nucleic acids research 39 (suppl_1), D295-D300, 2010 | 142 | 2010 |
| Proteomic and functional genomic landscape of receptor tyrosine kinase and ras to extracellular signal–regulated kinase signaling AA Friedman, G Tucker, R Singh, D Yan, A Vinayagam, Y Hu, R Binari, ... Science signaling 4 (196), rs10-rs10, 2011 | 109 | 2011 |
| Classification of music signals in the visual domain H Deshpande, R Singh, U Nam Proceedings of the COST-G6 conference on digital audio effects 1 (3), 1-4, 2001 | 108 | 2001 |
| Global alignment of multiple protein interaction networks R Singh, J Xu, B Berger Biocomputing 2008, 303-314, 2008 | 91 | 2008 |
| Struct2net: integrating structure into protein-protein interaction prediction R Singh, J Xu, B Berger Biocomputing 2006, 403-414, 2006 | 84 | 2006 |
| 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 | 67 | 2022 |
| Schema: metric learning enables interpretable synthesis of heterogeneous single-cell modalities R Singh, BL Hie, A Narayan, B Berger Genome biology 22 (1), 131, 2021 | 49 | 2021 |
| RNAiCut: automated detection of significant genes from functional genomic screens IM Kaplow, R Singh, A Friedman, C Bakal, N Perrimon, B Berger Nature methods 6 (7), 476-477, 2009 | 33 | 2009 |
| Active learning for sampling in time-series experiments with application to gene expression analysis R Singh, N Palmer, D Gifford, B Berger, Z Bar-Joseph Proceedings of the 22nd international conference on Machine learning, 832-839, 2005 | 32 | 2005 |
| Predicting and annotating catalytic residues: an information theoretic approach B Sterner, R Singh, B Berger Journal of Computational Biology 14 (8), 1058-1073, 2007 | 26 | 2007 |
| Mugec: Automatic music genre classification H Deshpande, U Nam, R Singh Technical Report, Stanford University, 2001 | 23 | 2001 |
| Identifying structural motifs in proteins R Singh, M Saha Biocomputing 2003, 228-239, 2002 | 22 | 2002 |
| Learning the language of antibody hypervariability R Singh, C Im, Y Qiu, B Mackness, A Gupta, T Joren, S Sledzieski, ... Proceedings of the National Academy of Sciences 122 (1), e2418918121, 2025 | 19 | 2025 |
| 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 | 19 | 2023 |
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