| ESR1 ligand-binding domain mutations in hormone-resistant breast cancer W Toy, Y Shen, H Won, B Green, RA Sakr, M Will, Z Li, K Gala, S Fanning, ... Nature Genetics 45 (12), 1439–1445, 2013 | 974 | 2013 |
| Genomic and molecular landscape of DNA damage repair deficiency across The Cancer Genome Atlas TA Knijnenburg, L Wang, MT Zimmermann, N Chambwe, GF Gao, ... Cell reports 23 (1), 239-254.e6, 2018 | 511 | 2018 |
| Overcoming mutation-based resistance to antiandrogens with rational drug design MD Balbas, MJ Evans, DJ Hosfield, J Wongvipat, VK Arora, PA Watson, ... eLife 2, e00499, 2013 | 398 | 2013 |
| Graph Contrastive Learning with Augmentations Y You, T Chen, Y Sui, T Chen, Z Wang, Y Shen Advances in Neural Information Processing Systems 33, 5812-5823, 2020 | 298 | 2020 |
| Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13–19 D Kozakov, DR Hall, D Beglov, R Brenke, SR Comeau, Y Shen, K Li, ... Proteins: Structure, Function, and Bioinformatics 78 (15), 3124-3130, 2010 | 262 | 2010 |
| Estrogen receptor alpha somatic mutations Y537S and D538G confer breast cancer endocrine resistance by stabilizing the activating function-2 binding conformation SW Fanning, CG Mayne, V Dharmarajan, KE Carlson, TA Martin, ... Elife 5, e12792, 2016 | 190 | 2016 |
| Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen MP Menden, D Wang, MJ Mason, B Szalai, KC Bulusu, Y Guan, T Yu, ... Nature Communications 10, https://doi.org/10.1038/s41467-019-09799, 2019 | 186* | 2019 |
| Homophilic CD44 interactions mediate tumor cell aggregation and polyclonal metastasis in patient-derived breast cancer models X Liu, R Taftaf, M Kawaguchi, YF Chang, W Chen, D Entenberg, Y Zhang, ... Cancer Discovery, CD-18-0065, 2018 | 162 | 2018 |
| DeepAffinity: Interpretable Deep Learning of Compound-Protein Affinity through Unified Recurrent and Convolutional Neural Networks M Karimi, D Wu, Z Wang, Y Shen arXiv preprint arXiv:1806.07537 and Bioinformatics 2019 Feb 2. pii: btz111 …, 2018 | 157 | 2018 |
| Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: A CASP‐CAPRI experiment MF Lensink, S Velankar, A Kryshtafovych, SY Huang, ... Proteins: Structure, Function, and Bioinformatics 84, 323-348, 2016 | 140 | 2016 |
| ClusPro: performance in CAPRI rounds 6–11 and the new server SR Comeau, D Kozakov, R Brenke, Y Shen, D Beglov, S Vajda Proteins: Structure, Function, and Bioinformatics 69 (4), 781-785, 2007 | 98 | 2007 |
| When does self-supervision help graph convolutional networks? Y You, T Chen, Z Wang, Y Shen International Conference on Machine Learning 119, 10871-10880, 2020 | 91 | 2020 |
| Blind prediction of homo‐and hetero‐protein complexes: The CASP13‐CAPRI experiment MF Lensink, G Brysbaert, N Nadzirin, S Velankar, RAG Chaleil, T Gerguri, ... Proteins: Structure, Function, and Bioinformatics 87 (12), 1200-1221, 2019 | 71 | 2019 |
| Blind Prediction of Interfacial Water Positions in CAPRI MF Lensink, IH Moal, PA Bates, PL Kastritis, AS Melquiond, E Karaca, ... Proteins: Structure, Function and Bioinformatics, 2014 | 55 | 2014 |
| The SERM/SERD Bazedoxifene Disrupts ESR1 Helix 12 to Overcome Acquired Hormone Resistance in Breast Cancer Cells SW Fanning, R Jeselsohn, V Dharmarajan, CG Mayne, M Karimi, ... eLife 7, e37161 https://doi.org/10.7554/eLife.371, 2018 | 49 | 2018 |
| Protein docking by the underestimation of free energy funnels in the space of encounter complexes Y Shen, IC Paschalidis, P Vakili, S Vajda PLoS Computational Biology 4 (10), e1000191, 2008 | 45 | 2008 |
| Graph Contrastive Learning Automated Y You, T Chen, Y Shen, Z Wang arXiv preprint arXiv:2106.07594 and International Conference on Machine …, 2021 | 41 | 2021 |
| Engineering a HER2-specific antibody–drug conjugate to increase lysosomal delivery and therapeutic efficacy JC Kang, W Sun, P Khare, M Karimi, X Wang, Y Shen, RJ Ober, ES Ward Nature biotechnology, 2019 | 41 | 2019 |
| Identification of YbeY-Protein Interactions Involved in 16S rRNA Maturation and Stress Regulation in Escherichia coli M Vercruysse, C Köhrer, Y Shen, S Proulx, A Ghosal, BW Davies, ... mBio 7 (6), e01785-16, 2016 | 39 | 2016 |
| A genetically encoded, phage‐displayed cyclic‐peptide library XS Wang, PHC Chen, JT Hampton, JM Tharp, CA Reed, SK Das, ... Angewandte Chemie 131 (44), 16051-16056, 2019 | 37 | 2019 |
