Project Ex Vivo

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

Publication DOI

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

Preprint

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

DOI Publication

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

Preprint

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

Preprint

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

Preprint

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

Preprint PDF

Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer

Srivatsan Raghavan, Peter S. Winter, Andrew W Navia, Hannah L. Williams, Alan DenAdel, Kristen E. Lowder, Jennyfer Galvez-Reyes, R. Kalekar, Nolawit Mulugeta, Kevin S. Kapner, M. Raghavan, Ashir A. Borah, Nuo Liu, Sara A. Väyrynen, Andressa Dias Costa, R. Ng, Junning Wang, Emma K. Hill, Dorisanne Y. Ragon, L. Brais, Alex M. Jaeger, Liam F. Spurr, Yvonne Y. Li, A. Cherniack, M. Booker, Elizabeth F Cohen, M. Tolstorukov, Isaac Wakiro, Asaf Rotem, B. Johnson, James M. McFarland, E. Sicinska, T. Jacks, R. Sullivan, G. Shapiro, T. Clancy, Kimberly Perez, D. Rubinson, K. Ng, J. Cleary, Lorin Crawford, S. Manalis, J. Nowak, B. Wolpin, William C. Hahn, A. Aguirre, A. Shalek

PubMed Cell | November 2021, Vol 184: pp. 6119-6137.e26

DOI Publication Publication

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

Publication DOI

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

Preprint

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

DOI Publication

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

Preprint

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

Preprint

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

Preprint

Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer

Srivatsan Raghavan, Peter S. Winter, Andrew W Navia, Hannah L. Williams, Alan DenAdel, Kristen E. Lowder, Jennyfer Galvez-Reyes, R. Kalekar, Nolawit Mulugeta, Kevin S. Kapner, M. Raghavan, Ashir A. Borah, Nuo Liu, Sara A. Väyrynen, Andressa Dias Costa, R. Ng, Junning Wang, Emma K. Hill, Dorisanne Y. Ragon, L. Brais, Alex M. Jaeger, Liam F. Spurr, Yvonne Y. Li, A. Cherniack, M. Booker, Elizabeth F Cohen, M. Tolstorukov, Isaac Wakiro, Asaf Rotem, B. Johnson, James M. McFarland, E. Sicinska, T. Jacks, R. Sullivan, G. Shapiro, T. Clancy, Kimberly Perez, D. Rubinson, K. Ng, J. Cleary, Lorin Crawford, S. Manalis, J. Nowak, B. Wolpin, William C. Hahn, A. Aguirre, A. Shalek

PubMed Cell | November 2021, Vol 184: pp. 6119-6137.e26

DOI Publication Publication

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

Preprint PDF

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

Publication DOI

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

Preprint

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

DOI Publication

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

Preprint

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

Preprint

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

Preprint

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

Preprint PDF

Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer

Srivatsan Raghavan, Peter S. Winter, Andrew W Navia, Hannah L. Williams, Alan DenAdel, Kristen E. Lowder, Jennyfer Galvez-Reyes, R. Kalekar, Nolawit Mulugeta, Kevin S. Kapner, M. Raghavan, Ashir A. Borah, Nuo Liu, Sara A. Väyrynen, Andressa Dias Costa, R. Ng, Junning Wang, Emma K. Hill, Dorisanne Y. Ragon, L. Brais, Alex M. Jaeger, Liam F. Spurr, Yvonne Y. Li, A. Cherniack, M. Booker, Elizabeth F Cohen, M. Tolstorukov, Isaac Wakiro, Asaf Rotem, B. Johnson, James M. McFarland, E. Sicinska, T. Jacks, R. Sullivan, G. Shapiro, T. Clancy, Kimberly Perez, D. Rubinson, K. Ng, J. Cleary, Lorin Crawford, S. Manalis, J. Nowak, B. Wolpin, William C. Hahn, A. Aguirre, A. Shalek

PubMed Cell | November 2021, Vol 184: pp. 6119-6137.e26

DOI Publication Publication