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
Ava Amini
Principal Researcher
Publications
Publications by Year
-
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
Consequences of training data composition for deep learning models in single-cell biology
Ajay Nadig, Akshaya Thoutam, Madeline Hughes, Anay Gupta, Andrew W. Navia, Nicolo Fusi, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford
bioRxiv | February 2025
Benchmarking uncertainty quantification for protein engineering
Kevin P. Greenman, Ava P. Amini, Kevin Kaichuang Yang
PLOS Computational Biology | January 2025, Vol 21
-
Evaluating the role of pre-training dataset size and diversity on single-cell foundation model performance
Alan DenAdel, Madeline Hughes, Akshaya Thoutam, Anay Gupta, Nicolo Fusi, Andrew W. Navia, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford
bioRxiv | December 2024
Deeper evaluation of a single-cell foundation model
Rebecca Boiarsky, Nalini M. Singh, Alejandro Buendia, Ava P. Amini, Gad Getz, David Sontag
Nature Machine Intelligence | December 2024
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
Scalable, compressed phenotypic screening using pooled perturbations.
Nuo Liu, Walaa E. Kattan, Benjamin E. Mead, Conner Kummerlowe, Thomas Cheng, Sarah Ingabire, Jaime H Cheah, Christian K Soule, Anita Vrcic, Jane K. McIninch, Sergio Triana, Manuel Guzman, Tyler T. Dao, Joshua M. Peters, Kristen E. Lowder, Lorin Crawford, Ava P. Amini, Paul C. Blainey, William C. Hahn, Brian Cleary, Bryan D. Bryson, Peter S. Winter, Srivatsan Raghavan, Alex K. Shalek
Nature biotechnology | October 2024
Mutation and cell state compatibility is required and targetable in Ph+ acute lymphoblastic leukemia minimal residual disease
Peter S. Winter, Michelle L. Ramseier, Andrew W. Navia, Sachit D. Saksena, Haley Strouf, Nezha Senhaji, Alan DenAdel, Mahnoor Mirza, Hyun Hwan An, Laura L. Bilal, Peter Dennis, Catharine S. Leahy, Kay Shigemori, Jennyfer Galves-Reyes, Ye Zhang, Foster Powers, Nolawit Mulugeta, Alejandro J. Gupta, Nicholas L. Calistri, Alexandria van Scoyk, Kristen Jones, Huiyun Liu, Kristen Stevenson, S. Ren, M. Luskin, Charles P. Couturier, Ava P. Amini, Srivatsan Raghavan, Robert J. Kimmerling, Mark M. Stevens, Lorin Crawford, David M. Weinstock, Scott R. Manalis, Alex K. Shalek, Mark A. Murakami
bioRxiv | June 2024
A knockoff calibration method to avoid over-clustering in single-cell RNA-sequencing
Alan DenAdel, Michelle L. Ramseier, Andrew W. Navia, Alex K. Shalek, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford
bioRxiv | March 2024
Feature Reuse and Scaling: Understanding Transfer Learning with Protein Language Models
Francesca-Zhoufan Li, Ava P. Amini, Yisong Yue, Kevin Yang, Alex Lu
ICML 2024 | February 2024
Scalable nonparametric clustering with unified marker gene selection for single-cell RNA-seq data
Chibuikem Nwizu, Madeline Hughes, Michelle L. Ramseier, Andrew W. Navia, Alex K. Shalek, Nicolo Fusi, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford
bioRxiv | February 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
Priming agents transiently reduce the clearance of cell-free DNA to improve liquid biopsies
Carmen Martin-Alonso, Shervin Tabrizi, Kan Xiong, Timothy Blewett, Sainetra Sridhar, Andjela Crnjac, Sahil Patel, Zhenyi An, Ahmet Bekdemir, Douglas Shea, Shih-Ting Wang, Sergio A. Rodriguez-Aponte, Christopher A. Naranjo, Justin Rhoades, Jesse D. Kirkpatrick, Heather E. Fleming, Ava P. Amini, Todd R. Golub, J. C. Love, Sangeeta N. Bhatia, V. Adalsteinsson
Science | January 2024, Vol 383: pp. eadf2341-eadf2341
-
Assessing the limits of zero-shot foundation models in single-cell biology
Kasia Z. Kedzierska, Lorin Crawford, Ava P. Amini, Alex Lu
bioRxiv | November 2023
Continuous Time Evidential Distributions for Irregular Time Series
Taylor W. Killian, Haoran Zhang, Thomas Hartvigsen, Ava P. Amini
ArXiv | July 2023
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
Low protease activity in B cell follicles promotes retention of intact antigens after immunization
Aereas Aung, Ang Cui, Laura Maiorino, Ava P. Amini, Justin R. Gregory, Maurice Bukenya, Yiming Zhang, Heya Lee, Christopher A. Cottrell, Duncan M. Morgan, Murillo Silva, Heikyung Suh, Jesse D. Kirkpatrick, Parastoo Amlashi, Tanaka Remba, Leah M. Froehle, Shuhao Xiao, Wuhbet Abraham, Josetta Adams, J. Christopher Love, Phillip Huyett, Douglas S. Kwon, Nir Hacohen, William R. Schief, Sangeeta N. Bhatia, Darrell J. Irvine
Science | January 2023, Vol 379(379): pp. eabn8934
A nanoparticle priming agent reduces cellular uptake of cell-free DNA and enhances the sensitivity of liquid biopsies
Carmen Martin-Alonso, Shervin Tabrizi, Kan Xiong, Timothy Blewett, Sahil Patel, Zhenyi An, Sainetra Sridhar, Ahmet Bekdemir, Douglas Shea, Ava P. Amini, Shih-Ting Wang, Jesse Kirkpatrick, Justin Rhoades, Todd R. Golub, J. Christopher Love, Viktor A. Adalsteinsson, Sangeeta N. Bhatia
bioRxiv | January 2023
-
Multiscale profiling of protease activity in cancer
Ava P. Amini, Jesse D. Kirkpatrick, Cathy S. Wang, Alex M. Jaeger, Susan Su, Santiago Naranjo, Qian Zhong, Christina M. Cabana, Tyler Jacks, Sangeeta N. Bhatia
Nature Communications | October 2022, Vol 13(1)
Protease activity analysis: A toolkit for analyzing enzyme activity data
Ava P. Soleimany, Carmen Martin-Alonso, Melodi Anahtar, Cathy S. Wang, Sangeeta N. Bhatia
ACS Omega | July 2022, Vol 7(28): pp. 24292-24301
Host protease activity classifies pneumonia etiology
Melodi Anahtar, Leslie W. Chan, Henry Ko, Aditya Rao, Ava P. Soleimany, Purvesh Khatri, Sangeeta N. Bhatia
Proceedings of the National Academy of Sciences of the United States of America | June 2022, Vol 19(25)
Ionic Liquid‐Mediated Transdermal Delivery of Thrombosis‐Detecting Nanosensors
Ahmet Bekdemir, Eden E. L. Tanner, Jesse Kirkpatrick, Ava P. Soleimany, Samir Mitragotri, Sangeeta N. Bhatia
Advanced Healthcare Materials | February 2022, Vol 11(11)
-
Synthetic Circuit-Driven Expression of Heterologous Enzymes for Disease Detection
Jiang He, Lior Nissim, Ava P. Soleimany, Adina Binder-Nissim, Heather E. Fleming, Timothy K. Lu, Sangeeta N. Bhatia
ACS Synthetic Biology | August 2021, Vol 10(9): pp. 2231-2242
Evidential Deep Learning For Guided Molecular Property Prediction And Discovery
Ava P. Soleimany, Alexander Amini, Samuel Goldman, Daniela Rus, Sangeeta N. Bhatia, Connor W. Coley
ACS Central Science | July 2021, Vol 7(8): pp. 1356-1367
Activatable Zymography Probes Enable In Situ Localization of Protease Dysregulation in Cancer
Ava P. Soleimany, Jesse D. Kirkpatrick, Susan Su, Jaideep S. Dudani, Qian Zhong, Ahmet Bekdemir, Sangeeta N. Bhatia
Cancer Research | January 2021, Vol 81(1): pp. 213-224
-
Deep Evidential Regression
Alexander Amini, Wilko Schwarting, Ava Soleimany, Daniela Rus
2020 Neural Information Processing Systems | December 2020
Pharmacokinetic tuning of protein-antigen fusions enhances the immunogenicity of T-cell vaccines
Naveen K Mehta, Roma V Pradhan, Ava P. Soleimany, Kelly D Moynihan, Adrienne M Rothschilds, Noor Momin, Kavya Rakhra, Jordi Mata-Fink, Sangeeta N Bhatia, K Dane Wittrup, Darrell J Irvine
Nature Biomedical Engineering | May 2020, Vol 4(6): pp. 636-648
Activity-Based Diagnostics: An Emerging Paradigm for Disease Detection and Monitoring
Ava P. Soleimany, Sangeeta N. Bhatia
Trends in Molecular Medicine | April 2020, Vol 26(5): pp. 450-468
Urinary detection of lung cancer in mice via noninvasive pulmonary protease profiling
Jesse D. Kirkpatrick, Andrew D. Warren, Ava P. Soleimany, Peter M. K. Westcott, Justin C. Voog, Carmen Martin-Alonso, Heather E. Fleming, Tuomas Tammela, Tyler Jacks, Sangeeta N. Bhatia
Science Translational Medicine | March 2020, Vol 12(537)
-
Renal clearable catalytic gold nanoclusters for in vivo disease monitoring
Colleen N. Loynachan, Ava P. Soleimany, Jaideep S. Dudani, Yiyang Lin, Adrian Najer, Ahmet Bekdemir, Qu Chen, Sangeeta N. Bhatia, Molly M. Stevens
Nature Nanotechnology | August 2019, Vol 14(9): pp. 883-890
Uncovering and Mitigating Algorithmic Bias through Learned Latent Structure
Alexander Amini, Ava P. Soleimany, Wilko Schwarting, Sangeeta N. Bhatia, Daniela Rus
AAAI/ACM Conference on Artificial Intelligence, Ethics, and Society | January 2019
-
Synthetic recombinase-based state machines in living cells
Nathaniel Roquet, Ava P. Soleimany, Alyssa C. Ferris, Scott Aaronson, Timothy K. Lu
Science | July 2016, Vol 353(6297): pp. 363-363
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
Consequences of training data composition for deep learning models in single-cell biology
Ajay Nadig, Akshaya Thoutam, Madeline Hughes, Anay Gupta, Andrew W. Navia, Nicolo Fusi, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford
bioRxiv | February 2025
Benchmarking uncertainty quantification for protein engineering
Kevin P. Greenman, Ava P. Amini, Kevin Kaichuang Yang
PLOS Computational Biology | January 2025, Vol 21
Evaluating the role of pre-training dataset size and diversity on single-cell foundation model performance
Alan DenAdel, Madeline Hughes, Akshaya Thoutam, Anay Gupta, Nicolo Fusi, Andrew W. Navia, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford
bioRxiv | December 2024
Deeper evaluation of a single-cell foundation model
Rebecca Boiarsky, Nalini M. Singh, Alejandro Buendia, Ava P. Amini, Gad Getz, David Sontag
Nature Machine Intelligence | December 2024
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
Scalable, compressed phenotypic screening using pooled perturbations.
Nuo Liu, Walaa E. Kattan, Benjamin E. Mead, Conner Kummerlowe, Thomas Cheng, Sarah Ingabire, Jaime H Cheah, Christian K Soule, Anita Vrcic, Jane K. McIninch, Sergio Triana, Manuel Guzman, Tyler T. Dao, Joshua M. Peters, Kristen E. Lowder, Lorin Crawford, Ava P. Amini, Paul C. Blainey, William C. Hahn, Brian Cleary, Bryan D. Bryson, Peter S. Winter, Srivatsan Raghavan, Alex K. Shalek
Nature biotechnology | October 2024
Mutation and cell state compatibility is required and targetable in Ph+ acute lymphoblastic leukemia minimal residual disease
Peter S. Winter, Michelle L. Ramseier, Andrew W. Navia, Sachit D. Saksena, Haley Strouf, Nezha Senhaji, Alan DenAdel, Mahnoor Mirza, Hyun Hwan An, Laura L. Bilal, Peter Dennis, Catharine S. Leahy, Kay Shigemori, Jennyfer Galves-Reyes, Ye Zhang, Foster Powers, Nolawit Mulugeta, Alejandro J. Gupta, Nicholas L. Calistri, Alexandria van Scoyk, Kristen Jones, Huiyun Liu, Kristen Stevenson, S. Ren, M. Luskin, Charles P. Couturier, Ava P. Amini, Srivatsan Raghavan, Robert J. Kimmerling, Mark M. Stevens, Lorin Crawford, David M. Weinstock, Scott R. Manalis, Alex K. Shalek, Mark A. Murakami
bioRxiv | June 2024
A knockoff calibration method to avoid over-clustering in single-cell RNA-sequencing
Alan DenAdel, Michelle L. Ramseier, Andrew W. Navia, Alex K. Shalek, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford
bioRxiv | March 2024
Scalable nonparametric clustering with unified marker gene selection for single-cell RNA-seq data
Chibuikem Nwizu, Madeline Hughes, Michelle L. Ramseier, Andrew W. Navia, Alex K. Shalek, Nicolo Fusi, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford
bioRxiv | February 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
Priming agents transiently reduce the clearance of cell-free DNA to improve liquid biopsies
Carmen Martin-Alonso, Shervin Tabrizi, Kan Xiong, Timothy Blewett, Sainetra Sridhar, Andjela Crnjac, Sahil Patel, Zhenyi An, Ahmet Bekdemir, Douglas Shea, Shih-Ting Wang, Sergio A. Rodriguez-Aponte, Christopher A. Naranjo, Justin Rhoades, Jesse D. Kirkpatrick, Heather E. Fleming, Ava P. Amini, Todd R. Golub, J. C. Love, Sangeeta N. Bhatia, V. Adalsteinsson
Science | January 2024, Vol 383: pp. eadf2341-eadf2341
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
Low protease activity in B cell follicles promotes retention of intact antigens after immunization
Aereas Aung, Ang Cui, Laura Maiorino, Ava P. Amini, Justin R. Gregory, Maurice Bukenya, Yiming Zhang, Heya Lee, Christopher A. Cottrell, Duncan M. Morgan, Murillo Silva, Heikyung Suh, Jesse D. Kirkpatrick, Parastoo Amlashi, Tanaka Remba, Leah M. Froehle, Shuhao Xiao, Wuhbet Abraham, Josetta Adams, J. Christopher Love, Phillip Huyett, Douglas S. Kwon, Nir Hacohen, William R. Schief, Sangeeta N. Bhatia, Darrell J. Irvine
Science | January 2023, Vol 379(379): pp. eabn8934
A nanoparticle priming agent reduces cellular uptake of cell-free DNA and enhances the sensitivity of liquid biopsies
Carmen Martin-Alonso, Shervin Tabrizi, Kan Xiong, Timothy Blewett, Sahil Patel, Zhenyi An, Sainetra Sridhar, Ahmet Bekdemir, Douglas Shea, Ava P. Amini, Shih-Ting Wang, Jesse Kirkpatrick, Justin Rhoades, Todd R. Golub, J. Christopher Love, Viktor A. Adalsteinsson, Sangeeta N. Bhatia
bioRxiv | January 2023
Multiscale profiling of protease activity in cancer
Ava P. Amini, Jesse D. Kirkpatrick, Cathy S. Wang, Alex M. Jaeger, Susan Su, Santiago Naranjo, Qian Zhong, Christina M. Cabana, Tyler Jacks, Sangeeta N. Bhatia
Nature Communications | October 2022, Vol 13(1)
Protease activity analysis: A toolkit for analyzing enzyme activity data
Ava P. Soleimany, Carmen Martin-Alonso, Melodi Anahtar, Cathy S. Wang, Sangeeta N. Bhatia
ACS Omega | July 2022, Vol 7(28): pp. 24292-24301
Host protease activity classifies pneumonia etiology
Melodi Anahtar, Leslie W. Chan, Henry Ko, Aditya Rao, Ava P. Soleimany, Purvesh Khatri, Sangeeta N. Bhatia
Proceedings of the National Academy of Sciences of the United States of America | June 2022, Vol 19(25)
Ionic Liquid‐Mediated Transdermal Delivery of Thrombosis‐Detecting Nanosensors
Ahmet Bekdemir, Eden E. L. Tanner, Jesse Kirkpatrick, Ava P. Soleimany, Samir Mitragotri, Sangeeta N. Bhatia
Advanced Healthcare Materials | February 2022, Vol 11(11)
Synthetic Circuit-Driven Expression of Heterologous Enzymes for Disease Detection
Jiang He, Lior Nissim, Ava P. Soleimany, Adina Binder-Nissim, Heather E. Fleming, Timothy K. Lu, Sangeeta N. Bhatia
ACS Synthetic Biology | August 2021, Vol 10(9): pp. 2231-2242
Activatable Zymography Probes Enable In Situ Localization of Protease Dysregulation in Cancer
Ava P. Soleimany, Jesse D. Kirkpatrick, Susan Su, Jaideep S. Dudani, Qian Zhong, Ahmet Bekdemir, Sangeeta N. Bhatia
Cancer Research | January 2021, Vol 81(1): pp. 213-224
Pharmacokinetic tuning of protein-antigen fusions enhances the immunogenicity of T-cell vaccines
Naveen K Mehta, Roma V Pradhan, Ava P. Soleimany, Kelly D Moynihan, Adrienne M Rothschilds, Noor Momin, Kavya Rakhra, Jordi Mata-Fink, Sangeeta N Bhatia, K Dane Wittrup, Darrell J Irvine
Nature Biomedical Engineering | May 2020, Vol 4(6): pp. 636-648
Activity-Based Diagnostics: An Emerging Paradigm for Disease Detection and Monitoring
Ava P. Soleimany, Sangeeta N. Bhatia
Trends in Molecular Medicine | April 2020, Vol 26(5): pp. 450-468
Urinary detection of lung cancer in mice via noninvasive pulmonary protease profiling
Jesse D. Kirkpatrick, Andrew D. Warren, Ava P. Soleimany, Peter M. K. Westcott, Justin C. Voog, Carmen Martin-Alonso, Heather E. Fleming, Tuomas Tammela, Tyler Jacks, Sangeeta N. Bhatia
Science Translational Medicine | March 2020, Vol 12(537)
Renal clearable catalytic gold nanoclusters for in vivo disease monitoring
Colleen N. Loynachan, Ava P. Soleimany, Jaideep S. Dudani, Yiyang Lin, Adrian Najer, Ahmet Bekdemir, Qu Chen, Sangeeta N. Bhatia, Molly M. Stevens
Nature Nanotechnology | August 2019, Vol 14(9): pp. 883-890
Uncovering and Mitigating Algorithmic Bias through Learned Latent Structure
Alexander Amini, Ava P. Soleimany, Wilko Schwarting, Sangeeta N. Bhatia, Daniela Rus
AAAI/ACM Conference on Artificial Intelligence, Ethics, and Society | January 2019
Synthetic recombinase-based state machines in living cells
Nathaniel Roquet, Ava P. Soleimany, Alyssa C. Ferris, Scott Aaronson, Timothy K. Lu
Science | July 2016, Vol 353(6297): pp. 363-363
-
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
Feature Reuse and Scaling: Understanding Transfer Learning with Protein Language Models
Francesca-Zhoufan Li, Ava P. Amini, Yisong Yue, Kevin Yang, Alex Lu
ICML 2024 | February 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
Assessing the limits of zero-shot foundation models in single-cell biology
Kasia Z. Kedzierska, Lorin Crawford, Ava P. Amini, Alex Lu
bioRxiv | November 2023
Continuous Time Evidential Distributions for Irregular Time Series
Taylor W. Killian, Haoran Zhang, Thomas Hartvigsen, Ava P. Amini
ArXiv | July 2023
From noise to protein with image models
Ava P. Amini, Kevin Kaichuang Yang
Nature Computational Science | May 2023, Vol 3: pp. 366-367
Evidential Deep Learning For Guided Molecular Property Prediction And Discovery
Ava P. Soleimany, Alexander Amini, Samuel Goldman, Daniela Rus, Sangeeta N. Bhatia, Connor W. Coley
ACS Central Science | July 2021, Vol 7(8): pp. 1356-1367
Deep Evidential Regression
Alexander Amini, Wilko Schwarting, Ava Soleimany, Daniela Rus
2020 Neural Information Processing Systems | December 2020
Urinary detection of lung cancer in mice via noninvasive pulmonary protease profiling
Jesse D. Kirkpatrick, Andrew D. Warren, Ava P. Soleimany, Peter M. K. Westcott, Justin C. Voog, Carmen Martin-Alonso, Heather E. Fleming, Tuomas Tammela, Tyler Jacks, Sangeeta N. Bhatia
Science Translational Medicine | March 2020, Vol 12(537)
-
Synthetic recombinase-based state machines in living cells
Nathaniel Roquet, Ava P. Soleimany, Alyssa C. Ferris, Scott Aaronson, Timothy K. Lu
Science | July 2016, Vol 353(6297): pp. 363-363
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
Consequences of training data composition for deep learning models in single-cell biology
Ajay Nadig, Akshaya Thoutam, Madeline Hughes, Anay Gupta, Andrew W. Navia, Nicolo Fusi, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford
bioRxiv | February 2025
Benchmarking uncertainty quantification for protein engineering
Kevin P. Greenman, Ava P. Amini, Kevin Kaichuang Yang
PLOS Computational Biology | January 2025, Vol 21
Evaluating the role of pre-training dataset size and diversity on single-cell foundation model performance
Alan DenAdel, Madeline Hughes, Akshaya Thoutam, Anay Gupta, Nicolo Fusi, Andrew W. Navia, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford
bioRxiv | December 2024
Deeper evaluation of a single-cell foundation model
Rebecca Boiarsky, Nalini M. Singh, Alejandro Buendia, Ava P. Amini, Gad Getz, David Sontag
Nature Machine Intelligence | December 2024
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
Scalable, compressed phenotypic screening using pooled perturbations.
Nuo Liu, Walaa E. Kattan, Benjamin E. Mead, Conner Kummerlowe, Thomas Cheng, Sarah Ingabire, Jaime H Cheah, Christian K Soule, Anita Vrcic, Jane K. McIninch, Sergio Triana, Manuel Guzman, Tyler T. Dao, Joshua M. Peters, Kristen E. Lowder, Lorin Crawford, Ava P. Amini, Paul C. Blainey, William C. Hahn, Brian Cleary, Bryan D. Bryson, Peter S. Winter, Srivatsan Raghavan, Alex K. Shalek
Nature biotechnology | October 2024
Mutation and cell state compatibility is required and targetable in Ph+ acute lymphoblastic leukemia minimal residual disease
Peter S. Winter, Michelle L. Ramseier, Andrew W. Navia, Sachit D. Saksena, Haley Strouf, Nezha Senhaji, Alan DenAdel, Mahnoor Mirza, Hyun Hwan An, Laura L. Bilal, Peter Dennis, Catharine S. Leahy, Kay Shigemori, Jennyfer Galves-Reyes, Ye Zhang, Foster Powers, Nolawit Mulugeta, Alejandro J. Gupta, Nicholas L. Calistri, Alexandria van Scoyk, Kristen Jones, Huiyun Liu, Kristen Stevenson, S. Ren, M. Luskin, Charles P. Couturier, Ava P. Amini, Srivatsan Raghavan, Robert J. Kimmerling, Mark M. Stevens, Lorin Crawford, David M. Weinstock, Scott R. Manalis, Alex K. Shalek, Mark A. Murakami
bioRxiv | June 2024
A knockoff calibration method to avoid over-clustering in single-cell RNA-sequencing
Alan DenAdel, Michelle L. Ramseier, Andrew W. Navia, Alex K. Shalek, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford
bioRxiv | March 2024
Scalable nonparametric clustering with unified marker gene selection for single-cell RNA-seq data
Chibuikem Nwizu, Madeline Hughes, Michelle L. Ramseier, Andrew W. Navia, Alex K. Shalek, Nicolo Fusi, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford
bioRxiv | February 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
Priming agents transiently reduce the clearance of cell-free DNA to improve liquid biopsies
Carmen Martin-Alonso, Shervin Tabrizi, Kan Xiong, Timothy Blewett, Sainetra Sridhar, Andjela Crnjac, Sahil Patel, Zhenyi An, Ahmet Bekdemir, Douglas Shea, Shih-Ting Wang, Sergio A. Rodriguez-Aponte, Christopher A. Naranjo, Justin Rhoades, Jesse D. Kirkpatrick, Heather E. Fleming, Ava P. Amini, Todd R. Golub, J. C. Love, Sangeeta N. Bhatia, V. Adalsteinsson
Science | January 2024, Vol 383: pp. eadf2341-eadf2341
Assessing the limits of zero-shot foundation models in single-cell biology
Kasia Z. Kedzierska, Lorin Crawford, Ava P. Amini, Alex Lu
bioRxiv | November 2023
Continuous Time Evidential Distributions for Irregular Time Series
Taylor W. Killian, Haoran Zhang, Thomas Hartvigsen, Ava P. Amini
ArXiv | July 2023
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
Low protease activity in B cell follicles promotes retention of intact antigens after immunization
Aereas Aung, Ang Cui, Laura Maiorino, Ava P. Amini, Justin R. Gregory, Maurice Bukenya, Yiming Zhang, Heya Lee, Christopher A. Cottrell, Duncan M. Morgan, Murillo Silva, Heikyung Suh, Jesse D. Kirkpatrick, Parastoo Amlashi, Tanaka Remba, Leah M. Froehle, Shuhao Xiao, Wuhbet Abraham, Josetta Adams, J. Christopher Love, Phillip Huyett, Douglas S. Kwon, Nir Hacohen, William R. Schief, Sangeeta N. Bhatia, Darrell J. Irvine
Science | January 2023, Vol 379(379): pp. eabn8934
A nanoparticle priming agent reduces cellular uptake of cell-free DNA and enhances the sensitivity of liquid biopsies
Carmen Martin-Alonso, Shervin Tabrizi, Kan Xiong, Timothy Blewett, Sahil Patel, Zhenyi An, Sainetra Sridhar, Ahmet Bekdemir, Douglas Shea, Ava P. Amini, Shih-Ting Wang, Jesse Kirkpatrick, Justin Rhoades, Todd R. Golub, J. Christopher Love, Viktor A. Adalsteinsson, Sangeeta N. Bhatia
bioRxiv | January 2023
Multiscale profiling of protease activity in cancer
Ava P. Amini, Jesse D. Kirkpatrick, Cathy S. Wang, Alex M. Jaeger, Susan Su, Santiago Naranjo, Qian Zhong, Christina M. Cabana, Tyler Jacks, Sangeeta N. Bhatia
Nature Communications | October 2022, Vol 13(1)
Protease activity analysis: A toolkit for analyzing enzyme activity data
Ava P. Soleimany, Carmen Martin-Alonso, Melodi Anahtar, Cathy S. Wang, Sangeeta N. Bhatia
ACS Omega | July 2022, Vol 7(28): pp. 24292-24301
Host protease activity classifies pneumonia etiology
Melodi Anahtar, Leslie W. Chan, Henry Ko, Aditya Rao, Ava P. Soleimany, Purvesh Khatri, Sangeeta N. Bhatia
Proceedings of the National Academy of Sciences of the United States of America | June 2022, Vol 19(25)
Ionic Liquid‐Mediated Transdermal Delivery of Thrombosis‐Detecting Nanosensors
Ahmet Bekdemir, Eden E. L. Tanner, Jesse Kirkpatrick, Ava P. Soleimany, Samir Mitragotri, Sangeeta N. Bhatia
Advanced Healthcare Materials | February 2022, Vol 11(11)
Synthetic Circuit-Driven Expression of Heterologous Enzymes for Disease Detection
Jiang He, Lior Nissim, Ava P. Soleimany, Adina Binder-Nissim, Heather E. Fleming, Timothy K. Lu, Sangeeta N. Bhatia
ACS Synthetic Biology | August 2021, Vol 10(9): pp. 2231-2242
Evidential Deep Learning For Guided Molecular Property Prediction And Discovery
Ava P. Soleimany, Alexander Amini, Samuel Goldman, Daniela Rus, Sangeeta N. Bhatia, Connor W. Coley
ACS Central Science | July 2021, Vol 7(8): pp. 1356-1367
Activatable Zymography Probes Enable In Situ Localization of Protease Dysregulation in Cancer
Ava P. Soleimany, Jesse D. Kirkpatrick, Susan Su, Jaideep S. Dudani, Qian Zhong, Ahmet Bekdemir, Sangeeta N. Bhatia
Cancer Research | January 2021, Vol 81(1): pp. 213-224
Pharmacokinetic tuning of protein-antigen fusions enhances the immunogenicity of T-cell vaccines
Naveen K Mehta, Roma V Pradhan, Ava P. Soleimany, Kelly D Moynihan, Adrienne M Rothschilds, Noor Momin, Kavya Rakhra, Jordi Mata-Fink, Sangeeta N Bhatia, K Dane Wittrup, Darrell J Irvine
Nature Biomedical Engineering | May 2020, Vol 4(6): pp. 636-648
Activity-Based Diagnostics: An Emerging Paradigm for Disease Detection and Monitoring
Ava P. Soleimany, Sangeeta N. Bhatia
Trends in Molecular Medicine | April 2020, Vol 26(5): pp. 450-468
Urinary detection of lung cancer in mice via noninvasive pulmonary protease profiling
Jesse D. Kirkpatrick, Andrew D. Warren, Ava P. Soleimany, Peter M. K. Westcott, Justin C. Voog, Carmen Martin-Alonso, Heather E. Fleming, Tuomas Tammela, Tyler Jacks, Sangeeta N. Bhatia
Science Translational Medicine | March 2020, Vol 12(537)
Renal clearable catalytic gold nanoclusters for in vivo disease monitoring
Colleen N. Loynachan, Ava P. Soleimany, Jaideep S. Dudani, Yiyang Lin, Adrian Najer, Ahmet Bekdemir, Qu Chen, Sangeeta N. Bhatia, Molly M. Stevens
Nature Nanotechnology | August 2019, Vol 14(9): pp. 883-890
Synthetic recombinase-based state machines in living cells
Nathaniel Roquet, Ava P. Soleimany, Alyssa C. Ferris, Scott Aaronson, Timothy K. Lu
Science | July 2016, Vol 353(6297): pp. 363-363
-
Feature Reuse and Scaling: Understanding Transfer Learning with Protein Language Models
Francesca-Zhoufan Li, Ava P. Amini, Yisong Yue, Kevin Yang, Alex Lu
ICML 2024 | February 2024
Deep Evidential Regression
Alexander Amini, Wilko Schwarting, Ava Soleimany, Daniela Rus
2020 Neural Information Processing Systems | December 2020
Uncovering and Mitigating Algorithmic Bias through Learned Latent Structure
Alexander Amini, Ava P. Soleimany, Wilko Schwarting, Sangeeta N. Bhatia, Daniela Rus
AAAI/ACM Conference on Artificial Intelligence, Ethics, and Society | January 2019