Yang Shen
Yang Shen
Associate Professor, ECE + CSE @ Texas A&M University ; Research Affiliate, CSAIL + BE @ MIT
Verified email at - Homepage
Cited by
Cited by
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
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
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
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
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
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
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,, 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
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
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
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
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
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
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
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, 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
Graph Contrastive Learning Automated
Y You, T Chen, Y Shen, Z Wang
arXiv preprint arXiv:2106.07594 and International Conference on Machine …, 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
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
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
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