Ava Amini

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

DOI Publication

Assessing the limits of zero-shot foundation models in single-cell biology

Kasia Z. Kedzierska, Lorin Crawford, Ava P. Amini, Alex Lu

November 2023

Publication PDF

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

Publication

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

Preprint DOI

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)

Publication

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

DOI

Deep self-supervised learning for biosynthetic gene cluster detection and product classification

Carolina Rios-Martinez, Nicholas Bhattacharya, Ava P. Amini, Lorin Crawford, Kevin K. Yang

bioRxiv | July 2022

DOI

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

Publication

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)

Publication

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)

Publication

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

DOI Publication

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

Publication

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

DOI

Deep Evidential Regression

Alexander Amini, Wilko Schwarting, Ava Soleimany, Daniela Rus

2020 Neural Information Processing Systems | December 2020

PDF Publication

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

DOI Project

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

DOI

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)

DOI

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

DOI

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

DOI

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

DOI

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

DOI Publication

Assessing the limits of zero-shot foundation models in single-cell biology

Kasia Z. Kedzierska, Lorin Crawford, Ava P. Amini, Alex Lu

November 2023

Publication PDF

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

DOI

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

Publication

Deep Evidential Regression

Alexander Amini, Wilko Schwarting, Ava Soleimany, Daniela Rus

2020 Neural Information Processing Systems | December 2020

PDF Publication

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)

DOI

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

Publication

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

Preprint DOI

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)

Publication

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

DOI

Deep self-supervised learning for biosynthetic gene cluster detection and product classification

Carolina Rios-Martinez, Nicholas Bhattacharya, Ava P. Amini, Lorin Crawford, Kevin K. Yang

bioRxiv | July 2022

DOI

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

Publication

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)

Publication

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)

Publication

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

DOI Publication

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

DOI

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

DOI Project

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

DOI

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)

DOI

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

DOI

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

DOI

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

DOI

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

DOI

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

DOI Publication

Deep Evidential Regression

Alexander Amini, Wilko Schwarting, Ava Soleimany, Daniela Rus

2020 Neural Information Processing Systems | December 2020

PDF Publication

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

DOI

Assessing the limits of zero-shot foundation models in single-cell biology

Kasia Z. Kedzierska, Lorin Crawford, Ava P. Amini, Alex Lu

November 2023

Publication PDF

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

Publication

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

Preprint DOI

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)

Publication

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

DOI

Deep self-supervised learning for biosynthetic gene cluster detection and product classification

Carolina Rios-Martinez, Nicholas Bhattacharya, Ava P. Amini, Lorin Crawford, Kevin K. Yang

bioRxiv | July 2022

DOI

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

Publication

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)

Publication

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)

Publication

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

DOI Publication

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

Publication

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

DOI

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

DOI Project

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

DOI

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)

DOI

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

DOI

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

DOI