Lorin Crawford

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

Multioviz: an interactive platform for in silico perturbation and interrogation of gene regulatory networks

Helen Xie, Lorin Crawford, Ashley Conard

October 2023

DOI Publication

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

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 Project

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

DOI

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, Vol 22(1): pp. 213

DOI

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, Vol 15(2): pp. 638-661

DOI

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

DOI

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

DOI

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, Vol 17(3)

DOI Publication

Generalizing Variational Autoencoders with Hierarchical Empirical Bayes.

Wei Cheng, Gregory Darnell, Sohini Ramachandran, Lorin Crawford

arXiv | July 2020

Publication

Multi-scale Genomic Inference using Biologically Annotated Neural Networks

Pinar Demetci, Wei Cheng, Gregory Darnell, Xiang Zhou, Sohini Ramachandran, Lorin Crawford

bioRxiv | July 2020

DOI PDF Publication

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, Vol 115(531): pp. 1139-1150

DOI

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, Vol 16(6): pp. 1139-1150

DOI

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

DOI

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, Vol 317(2)

DOI

Fast and flexible linear mixed models for genome-wide genetics.

Daniel E. Runcie, Lorin Crawford

PLOS Genetics | February 2019, Vol 15(2): pp. 1-24

DOI

Interpreting Deep Neural Networks Through Variable Importance.

Jonathan Ish-Horowicz, Dana Udwin, Seth R. Flaxman, Sarah Filippi, Lorin Crawford

arXiv | January 2019

Publication

Genome-wide Marginal Epistatic Association Mapping in Case-Control Studies

Lorin Crawford, Xiang Zhou

bioRxiv | July 2018

DOI

Bayesian Approximate Kernel Regression with Variable Selection

Lorin Crawford, Kris C. Wood, Xiang Zhou, Sayan Mukherjee

Journal of the American Statistical Association | June 2018, Vol 113(524): pp. 1710-1721

DOI

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, Vol 13(7)

DOI

Multioviz: an interactive platform for in silico perturbation and interrogation of gene regulatory networks

Helen Xie, Lorin Crawford, Ashley Conard

October 2023

DOI Publication

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

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 Project

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

DOI

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, Vol 22(1): pp. 213

DOI

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, Vol 15(2): pp. 638-661

DOI

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

DOI

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

DOI

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, Vol 17(3)

DOI Publication

Generalizing Variational Autoencoders with Hierarchical Empirical Bayes.

Wei Cheng, Gregory Darnell, Sohini Ramachandran, Lorin Crawford

arXiv | July 2020

Publication

Multi-scale Genomic Inference using Biologically Annotated Neural Networks

Pinar Demetci, Wei Cheng, Gregory Darnell, Xiang Zhou, Sohini Ramachandran, Lorin Crawford

bioRxiv | July 2020

DOI PDF Publication

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, Vol 115(531): pp. 1139-1150

DOI

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, Vol 16(6): pp. 1139-1150

DOI

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

DOI

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, Vol 317(2)

DOI

Fast and flexible linear mixed models for genome-wide genetics.

Daniel E. Runcie, Lorin Crawford

PLOS Genetics | February 2019, Vol 15(2): pp. 1-24

DOI

Interpreting Deep Neural Networks Through Variable Importance.

Jonathan Ish-Horowicz, Dana Udwin, Seth R. Flaxman, Sarah Filippi, Lorin Crawford

arXiv | January 2019

Publication

Genome-wide Marginal Epistatic Association Mapping in Case-Control Studies

Lorin Crawford, Xiang Zhou

bioRxiv | July 2018

DOI

Bayesian Approximate Kernel Regression with Variable Selection

Lorin Crawford, Kris C. Wood, Xiang Zhou, Sayan Mukherjee

Journal of the American Statistical Association | June 2018, Vol 113(524): pp. 1710-1721

DOI

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, Vol 13(7)

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

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

Multioviz: an interactive platform for in silico perturbation and interrogation of gene regulatory networks

Helen Xie, Lorin Crawford, Ashley Conard

October 2023

DOI Publication

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

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 Project

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

DOI

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, Vol 22(1): pp. 213

DOI

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, Vol 15(2): pp. 638-661

DOI

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

DOI

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

DOI

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, Vol 17(3)

DOI Publication

Generalizing Variational Autoencoders with Hierarchical Empirical Bayes.

Wei Cheng, Gregory Darnell, Sohini Ramachandran, Lorin Crawford

arXiv | July 2020

Publication

Multi-scale Genomic Inference using Biologically Annotated Neural Networks

Pinar Demetci, Wei Cheng, Gregory Darnell, Xiang Zhou, Sohini Ramachandran, Lorin Crawford

bioRxiv | July 2020

DOI PDF Publication

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, Vol 115(531): pp. 1139-1150

DOI

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, Vol 16(6): pp. 1139-1150

DOI

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

DOI

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, Vol 317(2)

DOI

Fast and flexible linear mixed models for genome-wide genetics.

Daniel E. Runcie, Lorin Crawford

PLOS Genetics | February 2019, Vol 15(2): pp. 1-24

DOI

Interpreting Deep Neural Networks Through Variable Importance.

Jonathan Ish-Horowicz, Dana Udwin, Seth R. Flaxman, Sarah Filippi, Lorin Crawford

arXiv | January 2019

Publication

Genome-wide Marginal Epistatic Association Mapping in Case-Control Studies

Lorin Crawford, Xiang Zhou

bioRxiv | July 2018

DOI

Bayesian Approximate Kernel Regression with Variable Selection

Lorin Crawford, Kris C. Wood, Xiang Zhou, Sayan Mukherjee

Journal of the American Statistical Association | June 2018, Vol 113(524): pp. 1710-1721

DOI

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, Vol 13(7)

DOI