Multimodal Alignment Improves Generalizability of Genomic Biomarker Prediction in Computational Pathology
Ekaterina Redekop, Eric Zimmermann, Ava P. Amini, Alex Lu, Neil Tenenholtz, Jimmy Hall, Lorin Crawford, Kristen Severson
February 2026
Lorin Crawford
Principal Researcher
출판물
-
-
-
-
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
-
-
-
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
-
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
-
-
-
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
-
Multioviz: an interactive platform for in silico perturbation and interrogation of gene regulatory networks
Helen Xie, Lorin Crawford, Ashley Conard
October 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, 제 19 권(5)
-
-
-
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, 제 184 권: pp. 6119-6137.e26
-
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
-
MegaLMM: Mega-scale linear mixed models for genomic predictions with thousands of traits.
Daniel E. Runcie, Jiayi Qu, Hao Cheng, Lorin Crawford
Genome Biology | July 2021, 제 22 권(1): pp. 213
-
A statistical pipeline for identifying physical features that differentiate classes of 3D shapes
Bruce Wang, Timothy Sudijono, Henry Kirveslahti, Tingran Gao, Douglas M. Boyer, Sayan Mukherjee, Lorin Crawford
The Annals of Applied Statistics | May 2021, 제 15 권(2): pp. 638-661
-
Redefining replication in multi-ancestry genome-wide association studies
Smith Sp, Shahamatdar S, Cheng W, Zhang S, Paik J, Graff M, Haiman C, Matise T, North Ke, Peters U, Kenny E, Gignoux C, Wojcik G, Lorin Crawford, Ramachandran S
bioRxiv | April 2021
-
The tumor microenvironment drives transcriptional phenotypes and their plasticity in metastatic pancreatic cancer
Srivatsan Raghavan, Peter S. Winter, Andrew W. Navia, Hannah L. Williams, Alan DenAdel, Radha L. Kalekar, Jennyfer Galvez-Reyes, Kristen E. Lowder, Nolawit Mulugeta, Manisha S. Raghavan, Ashir A. Borah, Kevin S. Kapner, Sara A. Väyrynen, Andressa Dias Costa, Raymond W.S. Ng, Junning Wang, Emma Reilly, Dorisanne Y. Ragon, Lauren K. Brais, Alex M. Jaeger, Liam F. Spurr, Yvonne Y. Li, Andrew D. Cherniack, Isaac Wakiro, Asaf Rotem, Bruce E. Johnson, James M. McFarland, Ewa T. Sicinska, Tyler E. Jacks, Thomas E. Clancy, Kimberly Perez, Douglas A. Rubinson, Kimmie Ng, James M. Cleary, Lorin Crawford, Scott R. Manalis, Jonathan A. Nowak, Brian M. Wolpin, William C. Hahn, Andrew J. Aguirre, Alex K. Shalek
bioRxiv | April 2021
-
Natural variation in the regulation of neurodevelopmental genes modifies flight performance in Drosophila.
Adam N. Spierer, Jim A. Mossman, Samuel Pattillo Smith, Lorin Crawford, Sohini Ramachandran, David M. Rand
PLOS Genetics | March 2021, 제 17 권(3)
-
-
-
Generalizing Variational Autoencoders with Hierarchical Empirical Bayes.
Wei Cheng, Gregory Darnell, Sohini Ramachandran, Lorin Crawford
arXiv | July 2020
-
Multi-scale Genomic Inference using Biologically Annotated Neural Networks
Pinar Demetci, Wei Cheng, Gregory Darnell, Xiang Zhou, Sohini Ramachandran, Lorin Crawford
bioRxiv | July 2020
-
Predicting Clinical Outcomes in Glioblastoma: An Application of Topological and Functional Data Analysis
Lorin Crawford, Anthea Monod, Andrew X. Chen, Sayan Mukherjee, Raúl Rabadán
Journal of the American Statistical Association | July 2020, 제 115 권(531): pp. 1139-1150
-
Estimation of non-null SNP effect size distributions enables the detection of enriched genes underlying complex traits.
Wei Cheng, Sohini Ramachandran, Lorin Crawford
PLOS Genetics | June 2020, 제 16 권(6): pp. 1139-1150
-
Convergent evolution of p38/MAPK activation in hormone resistant prostate cancer mediates pro-survival, immune evasive, and metastatic phenotypes
Kathryn E. Ware, Santosh Gupta, Jared Eng, Gabor Kemeny, Bhairavy J. Puviindran, Wen-Chi Foo, Lorin Crawford, R. Garland Almquist, Daniella Runyambo, Beatrice C. Thomas, Maya U. Sheth, Anika Agarwal, Mariaelena Pierobon, Emanuel F. Petricoin, David L. Corcoran, Jennifer Freedman, Steven R. Patierno, Tian Zhang, Simon Gregory, Zoi Sychev, Justin M. Drake, Andrew J. Armstrong, Jason A. Somarelli
bioRxiv | April 2020
-
-
-
Stem cells and extracellular vesicles: biological regulators of physiology and disease.
Theodor Borgovan, Lorin Crawford, Chibuikem Nwizu, Peter Quesenberry
American Journal of Physiology-cell Physiology | July 2019, 제 317 권(2)
-
Fast and flexible linear mixed models for genome-wide genetics.
Daniel E. Runcie, Lorin Crawford
PLOS Genetics | February 2019, 제 15 권(2): pp. 1-24
-
Interpreting Deep Neural Networks Through Variable Importance.
Jonathan Ish-Horowicz, Dana Udwin, Seth R. Flaxman, Sarah Filippi, Lorin Crawford
arXiv | January 2019
-
-
-
Genome-wide Marginal Epistatic Association Mapping in Case-Control Studies
Lorin Crawford, Xiang Zhou
bioRxiv | July 2018
-
Bayesian Approximate Kernel Regression with Variable Selection
Lorin Crawford, Kris C. Wood, Xiang Zhou, Sayan Mukherjee
Journal of the American Statistical Association | June 2018, 제 113 권(524): pp. 1710-1721
-
-
-
Detecting epistasis with the marginal epistasis test in genetic mapping studies of quantitative traits.
Lorin Crawford, Ping Zeng, Sayan Mukherjee, Xiang Zhou
PLOS Genetics | July 2017, 제 13 권(7)
-
-
-
Multimodal Alignment Improves Generalizability of Genomic Biomarker Prediction in Computational Pathology
Ekaterina Redekop, Eric Zimmermann, Ava P. Amini, Alex Lu, Neil Tenenholtz, Jimmy Hall, Lorin Crawford, Kristen Severson
February 2026
-
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
-
-
-
Multimodal Alignment Improves Generalizability of Genomic Biomarker Prediction in Computational Pathology
Ekaterina Redekop, Eric Zimmermann, Ava P. Amini, Alex Lu, Neil Tenenholtz, Jimmy Hall, Lorin Crawford, Kristen Severson
February 2026
-
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
-
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
-
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
-
Multioviz: an interactive platform for in silico perturbation and interrogation of gene regulatory networks
Helen Xie, Lorin Crawford, Ashley Conard
October 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, 제 19 권(5)
-
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, 제 184 권: pp. 6119-6137.e26
-
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
-
MegaLMM: Mega-scale linear mixed models for genomic predictions with thousands of traits.
Daniel E. Runcie, Jiayi Qu, Hao Cheng, Lorin Crawford
Genome Biology | July 2021, 제 22 권(1): pp. 213
-
A statistical pipeline for identifying physical features that differentiate classes of 3D shapes
Bruce Wang, Timothy Sudijono, Henry Kirveslahti, Tingran Gao, Douglas M. Boyer, Sayan Mukherjee, Lorin Crawford
The Annals of Applied Statistics | May 2021, 제 15 권(2): pp. 638-661
-
Redefining replication in multi-ancestry genome-wide association studies
Smith Sp, Shahamatdar S, Cheng W, Zhang S, Paik J, Graff M, Haiman C, Matise T, North Ke, Peters U, Kenny E, Gignoux C, Wojcik G, Lorin Crawford, Ramachandran S
bioRxiv | April 2021
-
The tumor microenvironment drives transcriptional phenotypes and their plasticity in metastatic pancreatic cancer
Srivatsan Raghavan, Peter S. Winter, Andrew W. Navia, Hannah L. Williams, Alan DenAdel, Radha L. Kalekar, Jennyfer Galvez-Reyes, Kristen E. Lowder, Nolawit Mulugeta, Manisha S. Raghavan, Ashir A. Borah, Kevin S. Kapner, Sara A. Väyrynen, Andressa Dias Costa, Raymond W.S. Ng, Junning Wang, Emma Reilly, Dorisanne Y. Ragon, Lauren K. Brais, Alex M. Jaeger, Liam F. Spurr, Yvonne Y. Li, Andrew D. Cherniack, Isaac Wakiro, Asaf Rotem, Bruce E. Johnson, James M. McFarland, Ewa T. Sicinska, Tyler E. Jacks, Thomas E. Clancy, Kimberly Perez, Douglas A. Rubinson, Kimmie Ng, James M. Cleary, Lorin Crawford, Scott R. Manalis, Jonathan A. Nowak, Brian M. Wolpin, William C. Hahn, Andrew J. Aguirre, Alex K. Shalek
bioRxiv | April 2021
-
Natural variation in the regulation of neurodevelopmental genes modifies flight performance in Drosophila.
Adam N. Spierer, Jim A. Mossman, Samuel Pattillo Smith, Lorin Crawford, Sohini Ramachandran, David M. Rand
PLOS Genetics | March 2021, 제 17 권(3)
-
Generalizing Variational Autoencoders with Hierarchical Empirical Bayes.
Wei Cheng, Gregory Darnell, Sohini Ramachandran, Lorin Crawford
arXiv | July 2020
-
Multi-scale Genomic Inference using Biologically Annotated Neural Networks
Pinar Demetci, Wei Cheng, Gregory Darnell, Xiang Zhou, Sohini Ramachandran, Lorin Crawford
bioRxiv | July 2020
-
Predicting Clinical Outcomes in Glioblastoma: An Application of Topological and Functional Data Analysis
Lorin Crawford, Anthea Monod, Andrew X. Chen, Sayan Mukherjee, Raúl Rabadán
Journal of the American Statistical Association | July 2020, 제 115 권(531): pp. 1139-1150
-
Estimation of non-null SNP effect size distributions enables the detection of enriched genes underlying complex traits.
Wei Cheng, Sohini Ramachandran, Lorin Crawford
PLOS Genetics | June 2020, 제 16 권(6): pp. 1139-1150
-
Convergent evolution of p38/MAPK activation in hormone resistant prostate cancer mediates pro-survival, immune evasive, and metastatic phenotypes
Kathryn E. Ware, Santosh Gupta, Jared Eng, Gabor Kemeny, Bhairavy J. Puviindran, Wen-Chi Foo, Lorin Crawford, R. Garland Almquist, Daniella Runyambo, Beatrice C. Thomas, Maya U. Sheth, Anika Agarwal, Mariaelena Pierobon, Emanuel F. Petricoin, David L. Corcoran, Jennifer Freedman, Steven R. Patierno, Tian Zhang, Simon Gregory, Zoi Sychev, Justin M. Drake, Andrew J. Armstrong, Jason A. Somarelli
bioRxiv | April 2020
-
Stem cells and extracellular vesicles: biological regulators of physiology and disease.
Theodor Borgovan, Lorin Crawford, Chibuikem Nwizu, Peter Quesenberry
American Journal of Physiology-cell Physiology | July 2019, 제 317 권(2)
-
Fast and flexible linear mixed models for genome-wide genetics.
Daniel E. Runcie, Lorin Crawford
PLOS Genetics | February 2019, 제 15 권(2): pp. 1-24
-
Interpreting Deep Neural Networks Through Variable Importance.
Jonathan Ish-Horowicz, Dana Udwin, Seth R. Flaxman, Sarah Filippi, Lorin Crawford
arXiv | January 2019
-
Genome-wide Marginal Epistatic Association Mapping in Case-Control Studies
Lorin Crawford, Xiang Zhou
bioRxiv | July 2018
-
Bayesian Approximate Kernel Regression with Variable Selection
Lorin Crawford, Kris C. Wood, Xiang Zhou, Sayan Mukherjee
Journal of the American Statistical Association | June 2018, 제 113 권(524): pp. 1710-1721
-
Detecting epistasis with the marginal epistasis test in genetic mapping studies of quantitative traits.
Lorin Crawford, Ping Zeng, Sayan Mukherjee, Xiang Zhou
PLOS Genetics | July 2017, 제 13 권(7)
-
-
-
Multimodal Alignment Improves Generalizability of Genomic Biomarker Prediction in Computational Pathology
Ekaterina Redekop, Eric Zimmermann, Ava P. Amini, Alex Lu, Neil Tenenholtz, Jimmy Hall, Lorin Crawford, Kristen Severson
February 2026
-
Multioviz: an interactive platform for in silico perturbation and interrogation of gene regulatory networks
Helen Xie, Lorin Crawford, Ashley Conard
October 2023
-
-
-
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
-
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
-
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
-
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
-
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, 제 19 권(5)
-
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, 제 184 권: pp. 6119-6137.e26
-
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
-
MegaLMM: Mega-scale linear mixed models for genomic predictions with thousands of traits.
Daniel E. Runcie, Jiayi Qu, Hao Cheng, Lorin Crawford
Genome Biology | July 2021, 제 22 권(1): pp. 213
-
A statistical pipeline for identifying physical features that differentiate classes of 3D shapes
Bruce Wang, Timothy Sudijono, Henry Kirveslahti, Tingran Gao, Douglas M. Boyer, Sayan Mukherjee, Lorin Crawford
The Annals of Applied Statistics | May 2021, 제 15 권(2): pp. 638-661
-
Redefining replication in multi-ancestry genome-wide association studies
Smith Sp, Shahamatdar S, Cheng W, Zhang S, Paik J, Graff M, Haiman C, Matise T, North Ke, Peters U, Kenny E, Gignoux C, Wojcik G, Lorin Crawford, Ramachandran S
bioRxiv | April 2021
-
The tumor microenvironment drives transcriptional phenotypes and their plasticity in metastatic pancreatic cancer
Srivatsan Raghavan, Peter S. Winter, Andrew W. Navia, Hannah L. Williams, Alan DenAdel, Radha L. Kalekar, Jennyfer Galvez-Reyes, Kristen E. Lowder, Nolawit Mulugeta, Manisha S. Raghavan, Ashir A. Borah, Kevin S. Kapner, Sara A. Väyrynen, Andressa Dias Costa, Raymond W.S. Ng, Junning Wang, Emma Reilly, Dorisanne Y. Ragon, Lauren K. Brais, Alex M. Jaeger, Liam F. Spurr, Yvonne Y. Li, Andrew D. Cherniack, Isaac Wakiro, Asaf Rotem, Bruce E. Johnson, James M. McFarland, Ewa T. Sicinska, Tyler E. Jacks, Thomas E. Clancy, Kimberly Perez, Douglas A. Rubinson, Kimmie Ng, James M. Cleary, Lorin Crawford, Scott R. Manalis, Jonathan A. Nowak, Brian M. Wolpin, William C. Hahn, Andrew J. Aguirre, Alex K. Shalek
bioRxiv | April 2021
-
Natural variation in the regulation of neurodevelopmental genes modifies flight performance in Drosophila.
Adam N. Spierer, Jim A. Mossman, Samuel Pattillo Smith, Lorin Crawford, Sohini Ramachandran, David M. Rand
PLOS Genetics | March 2021, 제 17 권(3)
-
Generalizing Variational Autoencoders with Hierarchical Empirical Bayes.
Wei Cheng, Gregory Darnell, Sohini Ramachandran, Lorin Crawford
arXiv | July 2020
-
Multi-scale Genomic Inference using Biologically Annotated Neural Networks
Pinar Demetci, Wei Cheng, Gregory Darnell, Xiang Zhou, Sohini Ramachandran, Lorin Crawford
bioRxiv | July 2020
-
Predicting Clinical Outcomes in Glioblastoma: An Application of Topological and Functional Data Analysis
Lorin Crawford, Anthea Monod, Andrew X. Chen, Sayan Mukherjee, Raúl Rabadán
Journal of the American Statistical Association | July 2020, 제 115 권(531): pp. 1139-1150
-
Estimation of non-null SNP effect size distributions enables the detection of enriched genes underlying complex traits.
Wei Cheng, Sohini Ramachandran, Lorin Crawford
PLOS Genetics | June 2020, 제 16 권(6): pp. 1139-1150
-
Convergent evolution of p38/MAPK activation in hormone resistant prostate cancer mediates pro-survival, immune evasive, and metastatic phenotypes
Kathryn E. Ware, Santosh Gupta, Jared Eng, Gabor Kemeny, Bhairavy J. Puviindran, Wen-Chi Foo, Lorin Crawford, R. Garland Almquist, Daniella Runyambo, Beatrice C. Thomas, Maya U. Sheth, Anika Agarwal, Mariaelena Pierobon, Emanuel F. Petricoin, David L. Corcoran, Jennifer Freedman, Steven R. Patierno, Tian Zhang, Simon Gregory, Zoi Sychev, Justin M. Drake, Andrew J. Armstrong, Jason A. Somarelli
bioRxiv | April 2020
-
Stem cells and extracellular vesicles: biological regulators of physiology and disease.
Theodor Borgovan, Lorin Crawford, Chibuikem Nwizu, Peter Quesenberry
American Journal of Physiology-cell Physiology | July 2019, 제 317 권(2)
-
Fast and flexible linear mixed models for genome-wide genetics.
Daniel E. Runcie, Lorin Crawford
PLOS Genetics | February 2019, 제 15 권(2): pp. 1-24
-
Interpreting Deep Neural Networks Through Variable Importance.
Jonathan Ish-Horowicz, Dana Udwin, Seth R. Flaxman, Sarah Filippi, Lorin Crawford
arXiv | January 2019
-
Genome-wide Marginal Epistatic Association Mapping in Case-Control Studies
Lorin Crawford, Xiang Zhou
bioRxiv | July 2018
-
Bayesian Approximate Kernel Regression with Variable Selection
Lorin Crawford, Kris C. Wood, Xiang Zhou, Sayan Mukherjee
Journal of the American Statistical Association | June 2018, 제 113 권(524): pp. 1710-1721
-
Detecting epistasis with the marginal epistasis test in genetic mapping studies of quantitative traits.
Lorin Crawford, Ping Zeng, Sayan Mukherjee, Xiang Zhou
PLOS Genetics | July 2017, 제 13 권(7)
-