Jue Wang
University of Washington
http://juewang.strikingly.com/
Accurate prediction of protein structures and interactions using a three-track neural network M Baek, F DiMaio, I Anishchenko, J Dauparas, S Ovchinnikov, GR Lee, … Science 373 (6557), 871-876, 2021 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=nU14GgkAAAAJ&citationforview=nU14GgkAAAAJ:CHSYGLWDkRkC
De novo design of protein structure and function with RFdiffusion JL Watson, D Juergens, NR Bennett, BL Trippe, J Yim, HE Eisenach, … Nature 620 (7976), 1089-1100, 2023 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=nU14GgkAAAAJ&citationforview=nU14GgkAAAAJ:UxriW0iASnsC
Scaffolding protein functional sites using deep learning J Wang, S Lisanza, D Juergens, D Tischer, JL Watson, KM Castro, … Science 377 (6604), 387-394, 2022 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=nU14GgkAAAAJ&citationforview=nU14GgkAAAAJ:nb7KW1ujOQ8C
Broadly applicable and accurate protein design by integrating structure prediction networks and diffusion generative models JL Watson, D Juergens, NR Bennett, BL Trippe, J Yim, HE Eisenach, … BioRxiv, 2022.12. 09.519842, 2022 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=nU14GgkAAAAJ&citationforview=nU14GgkAAAAJ:dshw04ExmUIC
Natural variation in preparation for nutrient depletion reveals a cost–benefit tradeoff J Wang, E Atolia, B Hua, Y Savir, R Escalante-Chong, M Springer PLoS biology 13 (1), e1002041, 2015 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=nU14GgkAAAAJ&citationforview=nU14GgkAAAAJ:yD5IFk8b50cC
Galactose metabolic genes in yeast respond to a ratio of galactose and glucose R Escalante-Chong, Y Savir, SM Carroll, JB Ingraham, J Wang, CJ Marx, … Proceedings of the National Academy of Sciences 112 (5), 1636-1641, 2015 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=nU14GgkAAAAJ&citationforview=nU14GgkAAAAJ:cFHS6HbyZ2cC
A chromatin-based mechanism for limiting divergent noncoding transcription S Marquardt, R Escalante-Chong, N Pho, J Wang, LS Churchman, … Cell 157 (7), 1712-1723, 2014 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=nU14GgkAAAAJ&citationforview=nU14GgkAAAAJ:u5HHmVD_uO8C
Generalized biomolecular modeling and design with RoseTTAFold All-Atom R Krishna, J Wang, W Ahern, P Sturmfels, P Venkatesh, I Kalvet, GR Lee, … Science 384 (6693), eadl2528, 2024 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=nU14GgkAAAAJ&citationforview=nU14GgkAAAAJ:SP6oXDckpogC
Large-effect beneficial synonymous mutations mediate rapid and parallel adaptation in a bacterium D Agashe, M Sane, K Phalnikar, GD Diwan, A Habibullah, … Molecular Biology and Evolution 33 (6), 1542-1553, 2016 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=nU14GgkAAAAJ&citationforview=nU14GgkAAAAJ:D03iK_w7-QYC
Design of proteins presenting discontinuous functional sites using deep learning D Tischer, S Lisanza, J Wang, R Dong, I Anishchenko, LF Milles, … Biorxiv, 2020.11. 29.402743, 2020 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=nU14GgkAAAAJ&citationforview=nU14GgkAAAAJ:abG-DnoFyZgC
Deep learning methods for designing proteins scaffolding functional sites J Wang, S Lisanza, D Juergens, D Tischer, I Anishchenko, M Baek, … BioRxiv, 2021.11. 10.468128, 2021 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=nU14GgkAAAAJ&citationforview=nU14GgkAAAAJ:1sJd4Hv_s6UC
Improving protein expression, stability, and function with ProteinMPNN KH Sumida, R Núñez-Franco, I Kalvet, SJ Pellock, BIM Wicky, LF Milles, … Journal of the American Chemical Society 146 (3), 2054-2061, 2024 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=nU14GgkAAAAJ&citationforview=nU14GgkAAAAJ:uWQEDVKXjbEC
Decoupling transcription factor expression and activity enables dimmer switch gene regulation C Ricci-Tam, I Ben-Zion, J Wang, J Palme, A Li, Y Savir, M Springer Science 372 (6539), 292-295, 2021 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=nU14GgkAAAAJ&citationforview=nU14GgkAAAAJ:_xSYboBqXhAC
Polymorphisms in the yeast galactose sensor underlie a natural continuum of nutrient-decision phenotypes KB Lee, J Wang, J Palme, R Escalante-Chong, B Hua, M Springer PLoS genetics 13 (5), e1006766, 2017 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=nU14GgkAAAAJ&citationforview=nU14GgkAAAAJ:pyW8ca7W8N0C
Enzyme engineering and in vivo testing of a formate reduction pathway J Wang, K Anderson, E Yang, L He, ME Lidstrom Synthetic Biology 6 (1), ysab020, 2021 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=nU14GgkAAAAJ&citationforview=nU14GgkAAAAJ:NhqRSupF_l8C
Protein sequence design by deep learning J Wang Nature Computational Science 2 (7), 416-417, 2022 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=nU14GgkAAAAJ&citationforview=nU14GgkAAAAJ:KxtntwgDAa4C
Variation in the modality of a yeast signaling pathway is mediated by a single regulator J Palme, J Wang, M Springer Elife 10, e69974, 2021 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=nU14GgkAAAAJ&citationforview=nU14GgkAAAAJ:b0M2c_1WBrUC
Giving E. coli a newfound appetite for formate ME Lidstrom, J Wang Nature Metabolism 2 (3), 219-220, 2020 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=nU14GgkAAAAJ&citationforview=nU14GgkAAAAJ:bFI3QPDXJZMC
Protein Design Using Structure-Prediction Networks: AlphaFold and RoseTTAFold as Protein Structure Foundation Models J Wang, JL Watson, SL Lisanza Cold Spring Harbor Perspectives in Biology, a041472, 2024 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=nU14GgkAAAAJ&citationforview=nU14GgkAAAAJ:OU6Ihb5iCvQC
Accurate single domain scaffolding of three non-overlapping protein epitopes using deep learning KM Castro, JL Watson, J Wang, J Southern, R Ayardulabi, S Georgeon, … bioRxiv, 2024.05. 07.592871, 2024 Link: https://scholar.google.com/citations?viewop=viewcitation&hl=en&user=nU14GgkAAAAJ&citationforview=nU14GgkAAAAJ:p2g8aNsByqUC
Michael Springer googlescholarauthorid michaelspringer.md:pJrcQwEAAAAJ
Christopher J. Marx googlescholarauthorid christopherj.marx.md:WM8A20AAAAJ
Sean Michael Carroll googlescholarauthorid seanmichael_carroll.md:DRqX9j8AAAAJ
John Ingraham googlescholarauthorid johningraham.md:qBarioAAAAAJ
Dr. Andreas Sebastian Marquardt googlescholarauthorid dr.andreassebastianmarquardt.md:_miZw7oAAAAJ
L. Stirling Churchman googlescholarauthorid l.stirling_churchman.md:Mufcdt0AAAAJ
Nam Pho googlescholarauthorid nampho.md:QHUk6wgAAAAJ
Deepa Agashe googlescholarauthorid deepaagashe.md:9zeR3CAAAAAJ
Lon Chubiz googlescholarauthorid lonchubiz.md:dFG263gAAAAJ
Renan Escalante-Chong googlescholarauthorid renanescalante-chong.md:dCwNRqoAAAAJ