Toward deep learning sequence–structure co-generation for protein design
Chentong Wang, Sarah Alamdari, Carles Domingo-Enrich, Ava P. Amini, Kevin Kaichuang Yang
Current Opinion in Structural Biology | March 2025
Kevin Kaichuang Yang
Senior Researcher
Publications
Publications by Year
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Deep learning guided design of protease substrates
Carmen Martin-Alonso, Sarah Alamdari, Tahoura S. Samad, Kevin Kaichuang Yang, Sangeeta N. Bhatia, Ava P. Amini
bioRxiv | March 2025
Benchmarking uncertainty quantification for protein engineering
Kevin P. Greenman, Ava P. Amini, Kevin Kaichuang Yang
PLOS Computational Biology | January 2025, Vol 21
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Protein generation with evolutionary diffusion: sequence is all you need
Sarah Alamdari, Nitya Thakkar, Rianne van den Berg, Neil Tenenholtz, Robert Strome, Alan M. Moses, Alex Lu, Nicolo Fusi, Ava P. Amini, Kevin Kaichuang Yang
bioRxiv | November 2024
ProtNote: a multimodal method for protein-function annotation
Samir Char, Nathaniel Corley, Sarah Alamdari, Kevin Kaichuang Yang, Ava P. Amini
bioRxiv | October 2024
Protein structure generation via folding diffusion
Kevin E. Wu, Kevin Kaichuang Yang, Rianne van den Berg, Sarah Alamdari, James Zou, Alex Lu, Ava P. Amini
Nature Communications | February 2024, Vol 15
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Deep self-supervised learning for biosynthetic gene cluster detection and product classification
Carolina Rios-Martinez, Nicholas Bhattacharya, Ava P. Amini, Lorin Crawford, Kevin Kaichuang Yang
PLOS Computational Biology | May 2023, Vol 19(5)
From noise to protein with image models
Ava P. Amini, Kevin Kaichuang Yang
Nature Computational Science | May 2023, Vol 3: pp. 366-367
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Protein structure generation via folding diffusion
Kevin E. Wu, Kevin K. Yang, Rianne van den Berg, James Y. Zou, Alex X. Lu, Ava P. Amini
arXiv | September 2022
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A Topological Data Analytic Approach for Discovering Biophysical Signatures in Protein Dynamics
W. S. Tang, G. M. da Silva, H. Kirveslahti, E. Skeens, B. Feng, T. Sudijono, Kevin Kaichuang Yang, S. Mukherjee, B. Rubenstein, Lorin Crawford
bioRxiv | July 2021
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Machine learning-guided channelrhodopsin engineering enables minimally invasive optogenetics.
Claire N. Bedbrook, Kevin Kaichuang Yang, J. Elliott Robinson, Elisha D. Mackey, Viviana Gradinaru, Frances H. Arnold
Nature Methods | October 2019, Vol 16(11): pp. 1176-1184
Machine-learning-guided directed evolution for protein engineering.
Kevin Kaichuang Yang, Zachary Wu, Frances H Arnold
Nature Methods | July 2019, Vol 16(8): pp. 687-694
Publications by Research Area
-
Toward deep learning sequence–structure co-generation for protein design
Chentong Wang, Sarah Alamdari, Carles Domingo-Enrich, Ava P. Amini, Kevin Kaichuang Yang
Current Opinion in Structural Biology | March 2025
Deep learning guided design of protease substrates
Carmen Martin-Alonso, Sarah Alamdari, Tahoura S. Samad, Kevin Kaichuang Yang, Sangeeta N. Bhatia, Ava P. Amini
bioRxiv | March 2025
Benchmarking uncertainty quantification for protein engineering
Kevin P. Greenman, Ava P. Amini, Kevin Kaichuang Yang
PLOS Computational Biology | January 2025, Vol 21
Protein generation with evolutionary diffusion: sequence is all you need
Sarah Alamdari, Nitya Thakkar, Rianne van den Berg, Neil Tenenholtz, Robert Strome, Alan M. Moses, Alex Lu, Nicolo Fusi, Ava P. Amini, Kevin Kaichuang Yang
bioRxiv | November 2024
ProtNote: a multimodal method for protein-function annotation
Samir Char, Nathaniel Corley, Sarah Alamdari, Kevin Kaichuang Yang, Ava P. Amini
bioRxiv | October 2024
Protein structure generation via folding diffusion
Kevin E. Wu, Kevin Kaichuang Yang, Rianne van den Berg, Sarah Alamdari, James Zou, Alex Lu, Ava P. Amini
Nature Communications | February 2024, Vol 15
Deep self-supervised learning for biosynthetic gene cluster detection and product classification
Carolina Rios-Martinez, Nicholas Bhattacharya, Ava P. Amini, Lorin Crawford, Kevin Kaichuang Yang
PLOS Computational Biology | May 2023, Vol 19(5)
From noise to protein with image models
Ava P. Amini, Kevin Kaichuang Yang
Nature Computational Science | May 2023, Vol 3: pp. 366-367
Protein structure generation via folding diffusion
Kevin E. Wu, Kevin K. Yang, Rianne van den Berg, James Y. Zou, Alex X. Lu, Ava P. Amini
arXiv | September 2022
A Topological Data Analytic Approach for Discovering Biophysical Signatures in Protein Dynamics
W. S. Tang, G. M. da Silva, H. Kirveslahti, E. Skeens, B. Feng, T. Sudijono, Kevin Kaichuang Yang, S. Mukherjee, B. Rubenstein, Lorin Crawford
bioRxiv | July 2021
Machine learning-guided channelrhodopsin engineering enables minimally invasive optogenetics.
Claire N. Bedbrook, Kevin Kaichuang Yang, J. Elliott Robinson, Elisha D. Mackey, Viviana Gradinaru, Frances H. Arnold
Nature Methods | October 2019, Vol 16(11): pp. 1176-1184
Machine-learning-guided directed evolution for protein engineering.
Kevin Kaichuang Yang, Zachary Wu, Frances H Arnold
Nature Methods | July 2019, Vol 16(8): pp. 687-694
-
Toward deep learning sequence–structure co-generation for protein design
Chentong Wang, Sarah Alamdari, Carles Domingo-Enrich, Ava P. Amini, Kevin Kaichuang Yang
Current Opinion in Structural Biology | March 2025
Benchmarking uncertainty quantification for protein engineering
Kevin P. Greenman, Ava P. Amini, Kevin Kaichuang Yang
PLOS Computational Biology | January 2025, Vol 21
Protein generation with evolutionary diffusion: sequence is all you need
Sarah Alamdari, Nitya Thakkar, Rianne van den Berg, Neil Tenenholtz, Robert Strome, Alan M. Moses, Alex Lu, Nicolo Fusi, Ava P. Amini, Kevin Kaichuang Yang
bioRxiv | November 2024
ProtNote: a multimodal method for protein-function annotation
Samir Char, Nathaniel Corley, Sarah Alamdari, Kevin Kaichuang Yang, Ava P. Amini
bioRxiv | October 2024
Protein structure generation via folding diffusion
Kevin E. Wu, Kevin Kaichuang Yang, Rianne van den Berg, Sarah Alamdari, James Zou, Alex Lu, Ava P. Amini
Nature Communications | February 2024, Vol 15
From noise to protein with image models
Ava P. Amini, Kevin Kaichuang Yang
Nature Computational Science | May 2023, Vol 3: pp. 366-367
Protein structure generation via folding diffusion
Kevin E. Wu, Kevin K. Yang, Rianne van den Berg, James Y. Zou, Alex X. Lu, Ava P. Amini
arXiv | September 2022
Publications by Type
-
Toward deep learning sequence–structure co-generation for protein design
Chentong Wang, Sarah Alamdari, Carles Domingo-Enrich, Ava P. Amini, Kevin Kaichuang Yang
Current Opinion in Structural Biology | March 2025
Deep learning guided design of protease substrates
Carmen Martin-Alonso, Sarah Alamdari, Tahoura S. Samad, Kevin Kaichuang Yang, Sangeeta N. Bhatia, Ava P. Amini
bioRxiv | March 2025
Benchmarking uncertainty quantification for protein engineering
Kevin P. Greenman, Ava P. Amini, Kevin Kaichuang Yang
PLOS Computational Biology | January 2025, Vol 21
Protein generation with evolutionary diffusion: sequence is all you need
Sarah Alamdari, Nitya Thakkar, Rianne van den Berg, Neil Tenenholtz, Robert Strome, Alan M. Moses, Alex Lu, Nicolo Fusi, Ava P. Amini, Kevin Kaichuang Yang
bioRxiv | November 2024
ProtNote: a multimodal method for protein-function annotation
Samir Char, Nathaniel Corley, Sarah Alamdari, Kevin Kaichuang Yang, Ava P. Amini
bioRxiv | October 2024
Protein structure generation via folding diffusion
Kevin E. Wu, Kevin Kaichuang Yang, Rianne van den Berg, Sarah Alamdari, James Zou, Alex Lu, Ava P. Amini
Nature Communications | February 2024, Vol 15
Deep self-supervised learning for biosynthetic gene cluster detection and product classification
Carolina Rios-Martinez, Nicholas Bhattacharya, Ava P. Amini, Lorin Crawford, Kevin Kaichuang Yang
PLOS Computational Biology | May 2023, Vol 19(5)
From noise to protein with image models
Ava P. Amini, Kevin Kaichuang Yang
Nature Computational Science | May 2023, Vol 3: pp. 366-367
Protein structure generation via folding diffusion
Kevin E. Wu, Kevin K. Yang, Rianne van den Berg, James Y. Zou, Alex X. Lu, Ava P. Amini
arXiv | September 2022
A Topological Data Analytic Approach for Discovering Biophysical Signatures in Protein Dynamics
W. S. Tang, G. M. da Silva, H. Kirveslahti, E. Skeens, B. Feng, T. Sudijono, Kevin Kaichuang Yang, S. Mukherjee, B. Rubenstein, Lorin Crawford
bioRxiv | July 2021
Machine learning-guided channelrhodopsin engineering enables minimally invasive optogenetics.
Claire N. Bedbrook, Kevin Kaichuang Yang, J. Elliott Robinson, Elisha D. Mackey, Viviana Gradinaru, Frances H. Arnold
Nature Methods | October 2019, Vol 16(11): pp. 1176-1184
Machine-learning-guided directed evolution for protein engineering.
Kevin Kaichuang Yang, Zachary Wu, Frances H Arnold
Nature Methods | July 2019, Vol 16(8): pp. 687-694