| 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 9 (1), 96-113, 2019 | 351 | 2019 |
| ICAM1 initiates CTC cluster formation and trans-endothelial migration in lung metastasis of breast cancer R Taftaf, X Liu, S Singh, Y Jia, NK Dashzeveg, AD Hoffmann, ... Nature communications 12 (1), 4867, 2021 | 171 | 2021 |
| 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 | 128 | 2019 |
| De novo protein design for novel folds using guided conditional wasserstein generative adversarial networks M Karimi, S Zhu, Y Cao, Y Shen Journal of chemical information and modeling 60 (12), 5667-5681, 2020 | 99 | 2020 |
| TALE: Transformer-based protein function Annotation with joint sequence–Label Embedding Y Cao, Y Shen Bioinformatics 37 (18), 2825-2833, 2021 | 97 | 2021 |
| Learning to optimize in swarms Y Cao, T Chen, Z Wang, Y Shen Advances in neural information processing systems 32, 2019 | 62 | 2019 |
| Energy‐based graph convolutional networks for scoring protein docking models Y Cao, Y Shen Proteins: Structure, Function, and Bioinformatics 88 (8), 1091-1099, 2020 | 53 | 2020 |
| Extracellular Domains I and II of cell-surface glycoprotein CD44 mediate its trans-homophilic dimerization and tumor cluster aggregation M Kawaguchi, N Dashzeveg, Y Cao, Y Jia, X Liu, Y Shen, H Liu Journal of Biological Chemistry 295 (9), 2640-2649, 2020 | 34 | 2020 |
| Bayesian active learning for optimization and uncertainty quantification in protein docking Y Cao, Y Shen Journal of chemical theory and computation 16 (8), 5334-5347, 2020 | 29 | 2020 |
| Fold2Seq: A joint sequence (1D)-Fold (3D) embedding-based generative model for protein design Y Cao, P Das, V Chenthamarakshan, PY Chen, I Melnyk, Y Shen International Conference on Machine Learning, 1261-1271, 2021 | 25 | 2021 |
| Machine learning-assisted elucidation of CD81–CD44 interactions in promoting cancer stemness and extracellular vesicle integrity EK Ramos, CF Tsai, Y Jia, Y Cao, M Manu, R Taftaf, AD Hoffmann, ... Elife 11, e82669, 2022 | 20 | 2022 |
| Assessment of blind predictions of the clinical significance of BRCA1 and BRCA2 variants MS Cline, G Babbi, S Bonache, Y Cao, R Casadio, X de la Cruz, O Díez, ... Human Mutation 40 (9), 1546-1556, 2019 | 18 | 2019 |
| Assessing the performance of in silico methods for predicting the pathogenicity of variants in the gene CHEK2, among Hispanic females with breast cancer A Voskanian, P Katsonis, O Lichtarge, V Pejaver, P Radivojac, ... Human mutation 40 (9), 1612-1622, 2019 | 11 | 2019 |
| Predicting pathogenicity of missense variants with weakly supervised regression Y Cao, Y Sun, M Karimi, H Chen, O Moronfoye, Y Shen Human mutation 40 (9), 1579-1592, 2019 | 9 | 2019 |
| De novo protein design for novel folds using guided conditional wasserstein generative adversarial networks (gcwgan). bioRxiv M Karimi, S Zhu, Y Cao, Y Shen | 6 | 2019 |
| Bayesian modeling and uncertainty quantification for learning to optimize: What, why, and how Y You, Y Cao, T Chen, Z Wang, Y Shen International Conference on Learning Representations, 2022 | 2 | 2022 |
| CD81 partners with CD44 in promoting exosome biogenesis, tumor cluster formation, and lung metastasis in triple negative breast cancer EK Ramos, CF Tsai, NK Dashzeveg, Y Jia, Y Cao, M Manu, R Taftaf, ... bioRxiv, 2022.02. 23.481674, 2022 | | 2022 |
| Single cell RNA sequencing-based identification of molecular drivers in circulating tumor cell cluster formation and lung metastasis R Taftaf, X Liu, S Singh, Y Jia, D Scholten, Y Zhang, A Davis, C Reduzzi, ... Cancer Research 80 (16_Supplement), 2603-2603, 2020 | | 2020 |
| Supporting Information TALE: Transformer-based protein function Annotation through joint sequence-Label Embedding Y Cao, Y Shen | | |
| CD81 Facilitates Tumor Cell Clustering and Metastasis in Triple Negative Breast Cancer E Ramos, N Dashzeveg, Y Jia, M Manu, R Taftaf, Y Cao, A Hoffmann, ... | | |
