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
Return to Microsoft Research Lab – New England
Biomedical ML
출판물
연도별 간행물
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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, 제 21 권
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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
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
Virchow2: Scaling Self-Supervised Mixed Magnification Models in Pathology
Eric Zimmermann, Eugene Vorontsov, Julian Viret, Adam Casson, Michal Zelechowski, George Shaikovski, Neil Tenenholtz, Jimmy Hall, Thomas J. Fuchs, Nicolo Fusi, Siqi Liu, Kristen Severson
July 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, 제 15 권
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, 제 383 권: pp. eadf2341-eadf2341
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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)
From noise to protein with image models
Ava P. Amini, Kevin Kaichuang Yang
Nature Computational Science | May 2023, 제 3 권: pp. 366-367
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Discovering molecular features of intrinsically disordered regions by using evolution for contrastive learning
Alex X. Lu, Amy X. Lu, Iva Pritišanac, Taraneh Zarin, Julie D. Forman-Kay, Alan M. Moses
PLOS Computational Biology | July 2022, 제 18 권(6)
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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
Discovery of Parkinson’s disease states and disease progression modelling: a longitudinal data study using machine learning
Kristen Severson, Lana M Chahine, Luba A Smolensky, Murtaza Dhuliawala, Mark Frasier, Kenney Ng, Soumya Ghosh, Jianying Hu
July 2021
Evidential Deep Learning for Guided Molecular Property Prediction and Discovery
Ava P. Amini, Alexander Amini, Samuel Goldman, Daniela Rus, Sangeeta N. Bhatia, Connor W. Coley
ACS central science | 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)
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, 제 81 권(1): pp. 213-224
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Deep Evidential Regression
Alexander Amini, Wilko Schwarting, Ava Soleimany, Daniela Rus
2020 Neural Information Processing Systems | December 2020
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
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, 제 4 권(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, 제 26 권(5): pp. 450-468
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
DPVis: Visual Analytics With Hidden Markov Models for Disease Progression Pathways.
Bum Chul Kwon, Vibha Anand, Kristen Severson, Soumya Ghosh, Zhaonan Sun, Brigitte I Frohnert, Markus Lundgren, Kenney Ng
IEEE Transactions on Visualization and Computer Graphics | April 2020, 제 27 권(9): pp. 3685-3700
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, 제 12 권(537)
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Personalized Input-Output Hidden Markov Models for Disease Progression Modeling.
Kristen Severson, Lana M. Chahine, Luba Smolensky, Kenney Ng, Jianying Hu, Soumya Ghosh
December 2019
Machine learning-guided channelrhodopsin engineering enables minimally invasive optogenetics.
Claire N. Bedbrook, Kevin Kaichuang Yang, J. Elliott Robinson, Elisha D. Mackey, Viviana Gradinaru, Frances H. Arnold
Nature Methods | October 2019, 제 16 권(11): pp. 1176-1184
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, 제 14 권(9): pp. 883-890
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)
Unsupervised Learning with Contrastive Latent Variable Models
Kristen Severson, Soumya Ghosh, Kenney Ng
2019 National Conference on Artificial Intelligence | July 2019
Machine-learning-guided directed evolution for protein engineering.
Kevin Kaichuang Yang, Zachary Wu, Frances H Arnold
Nature Methods | July 2019, 제 16 권(8): pp. 687-694
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
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
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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
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Orthologous CRISPR–Cas9 enzymes for combinatorial genetic screens
Nicolo Fusi, et al
nature biotechnology | October 2017, 제 36 권: pp. 179-189
On the challenges of learning with inference networks on sparse, high-dimensional data
Rahul Gopalkrishnan, Dawen Liang, Matthew D. Hoffman
International Conference on Artificial Intelligence and Statistics | October 2017
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)
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Synthetic recombinase-based state machines in living cells
Nathaniel Roquet, Ava P. Soleimany, Alyssa C. Ferris, Scott Aaronson, Timothy K. Lu
Science | July 2016, 제 353 권(6297): pp. 363-363
Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9
John G. Doench, Nicolo Fusi, Meagan Sullender, Mudra Hegde, Emma W. Vaimberg, Katherine F. Donovan, Ian Smith, Zuzana Tothova, Craig Wilen, Robert Orchard, Herbert W. Virgin, Jennifer Listgarten, David E. Root
nature biotechnology | January 2016, pp. 184-191
연구분야별 간행물
-
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
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, 제 21 권
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
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
Virchow2: Scaling Self-Supervised Mixed Magnification Models in Pathology
Eric Zimmermann, Eugene Vorontsov, Julian Viret, Adam Casson, Michal Zelechowski, George Shaikovski, Neil Tenenholtz, Jimmy Hall, Thomas J. Fuchs, Nicolo Fusi, Siqi Liu, Kristen Severson
July 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, 제 15 권
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, 제 383 권: 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, 제 19 권(5)
From noise to protein with image models
Ava P. Amini, Kevin Kaichuang Yang
Nature Computational Science | May 2023, 제 3 권: pp. 366-367
Discovering molecular features of intrinsically disordered regions by using evolution for contrastive learning
Alex X. Lu, Amy X. Lu, Iva Pritišanac, Taraneh Zarin, Julie D. Forman-Kay, Alan M. Moses
PLOS Computational Biology | July 2022, 제 18 권(6)
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
Discovery of Parkinson’s disease states and disease progression modelling: a longitudinal data study using machine learning
Kristen Severson, Lana M Chahine, Luba A Smolensky, Murtaza Dhuliawala, Mark Frasier, Kenney Ng, Soumya Ghosh, Jianying Hu
July 2021
Evidential Deep Learning for Guided Molecular Property Prediction and Discovery
Ava P. Amini, Alexander Amini, Samuel Goldman, Daniela Rus, Sangeeta N. Bhatia, Connor W. Coley
ACS central science | 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)
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, 제 81 권(1): pp. 213-224
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
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, 제 4 권(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, 제 26 권(5): pp. 450-468
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
DPVis: Visual Analytics With Hidden Markov Models for Disease Progression Pathways.
Bum Chul Kwon, Vibha Anand, Kristen Severson, Soumya Ghosh, Zhaonan Sun, Brigitte I Frohnert, Markus Lundgren, Kenney Ng
IEEE Transactions on Visualization and Computer Graphics | April 2020, 제 27 권(9): pp. 3685-3700
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, 제 12 권(537)
Personalized Input-Output Hidden Markov Models for Disease Progression Modeling.
Kristen Severson, Lana M. Chahine, Luba Smolensky, Kenney Ng, Jianying Hu, Soumya Ghosh
December 2019
Machine learning-guided channelrhodopsin engineering enables minimally invasive optogenetics.
Claire N. Bedbrook, Kevin Kaichuang Yang, J. Elliott Robinson, Elisha D. Mackey, Viviana Gradinaru, Frances H. Arnold
Nature Methods | October 2019, 제 16 권(11): pp. 1176-1184
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, 제 14 권(9): pp. 883-890
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)
Unsupervised Learning with Contrastive Latent Variable Models
Kristen Severson, Soumya Ghosh, Kenney Ng
2019 National Conference on Artificial Intelligence | July 2019
Machine-learning-guided directed evolution for protein engineering.
Kevin Kaichuang Yang, Zachary Wu, Frances H Arnold
Nature Methods | July 2019, 제 16 권(8): pp. 687-694
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
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
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
Orthologous CRISPR–Cas9 enzymes for combinatorial genetic screens
Nicolo Fusi, et al
nature biotechnology | October 2017, 제 36 권: pp. 179-189
On the challenges of learning with inference networks on sparse, high-dimensional data
Rahul Gopalkrishnan, Dawen Liang, Matthew D. Hoffman
International Conference on Artificial Intelligence and Statistics | October 2017
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)
Synthetic recombinase-based state machines in living cells
Nathaniel Roquet, Ava P. Soleimany, Alyssa C. Ferris, Scott Aaronson, Timothy K. Lu
Science | July 2016, 제 353 권(6297): pp. 363-363
Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9
John G. Doench, Nicolo Fusi, Meagan Sullender, Mudra Hegde, Emma W. Vaimberg, Katherine F. Donovan, Ian Smith, Zuzana Tothova, Craig Wilen, Robert Orchard, Herbert W. Virgin, Jennifer Listgarten, David E. Root
nature biotechnology | January 2016, pp. 184-191
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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, 제 21 권
ProtNote: a multimodal method for protein-function annotation
Samir Char, Nathaniel Corley, Sarah Alamdari, Kevin Kaichuang Yang, Ava P. Amini
bioRxiv | October 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, 제 15 권
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
From noise to protein with image models
Ava P. Amini, Kevin Kaichuang Yang
Nature Computational Science | May 2023, 제 3 권: pp. 366-367
Discovering molecular features of intrinsically disordered regions by using evolution for contrastive learning
Alex X. Lu, Amy X. Lu, Iva Pritišanac, Taraneh Zarin, Julie D. Forman-Kay, Alan M. Moses
PLOS Computational Biology | July 2022, 제 18 권(6)
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, 제 12 권(537)
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Virchow2: Scaling Self-Supervised Mixed Magnification Models in Pathology
Eric Zimmermann, Eugene Vorontsov, Julian Viret, Adam Casson, Michal Zelechowski, George Shaikovski, Neil Tenenholtz, Jimmy Hall, Thomas J. Fuchs, Nicolo Fusi, Siqi Liu, Kristen Severson
July 2024
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Synthetic recombinase-based state machines in living cells
Nathaniel Roquet, Ava P. Soleimany, Alyssa C. Ferris, Scott Aaronson, Timothy K. Lu
Science | July 2016, 제 353 권(6297): pp. 363-363
유형별 출판물
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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
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, 제 21 권
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
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, 제 15 권
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, 제 383 권: 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
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)
From noise to protein with image models
Ava P. Amini, Kevin Kaichuang Yang
Nature Computational Science | May 2023, 제 3 권: pp. 366-367
Discovering molecular features of intrinsically disordered regions by using evolution for contrastive learning
Alex X. Lu, Amy X. Lu, Iva Pritišanac, Taraneh Zarin, Julie D. Forman-Kay, Alan M. Moses
PLOS Computational Biology | July 2022, 제 18 권(6)
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
Evidential Deep Learning for Guided Molecular Property Prediction and Discovery
Ava P. Amini, Alexander Amini, Samuel Goldman, Daniela Rus, Sangeeta N. Bhatia, Connor W. Coley
ACS central science | 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)
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, 제 81 권(1): pp. 213-224
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
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, 제 4 권(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, 제 26 권(5): pp. 450-468
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
DPVis: Visual Analytics With Hidden Markov Models for Disease Progression Pathways.
Bum Chul Kwon, Vibha Anand, Kristen Severson, Soumya Ghosh, Zhaonan Sun, Brigitte I Frohnert, Markus Lundgren, Kenney Ng
IEEE Transactions on Visualization and Computer Graphics | April 2020, 제 27 권(9): pp. 3685-3700
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, 제 12 권(537)
Machine learning-guided channelrhodopsin engineering enables minimally invasive optogenetics.
Claire N. Bedbrook, Kevin Kaichuang Yang, J. Elliott Robinson, Elisha D. Mackey, Viviana Gradinaru, Frances H. Arnold
Nature Methods | October 2019, 제 16 권(11): pp. 1176-1184
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, 제 14 권(9): pp. 883-890
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)
Machine-learning-guided directed evolution for protein engineering.
Kevin Kaichuang Yang, Zachary Wu, Frances H Arnold
Nature Methods | July 2019, 제 16 권(8): pp. 687-694
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
Orthologous CRISPR–Cas9 enzymes for combinatorial genetic screens
Nicolo Fusi, et al
nature biotechnology | October 2017, 제 36 권: pp. 179-189
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)
Synthetic recombinase-based state machines in living cells
Nathaniel Roquet, Ava P. Soleimany, Alyssa C. Ferris, Scott Aaronson, Timothy K. Lu
Science | July 2016, 제 353 권(6297): pp. 363-363
Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9
John G. Doench, Nicolo Fusi, Meagan Sullender, Mudra Hegde, Emma W. Vaimberg, Katherine F. Donovan, Ian Smith, Zuzana Tothova, Craig Wilen, Robert Orchard, Herbert W. Virgin, Jennifer Listgarten, David E. Root
nature biotechnology | January 2016, pp. 184-191
-
Virchow2: Scaling Self-Supervised Mixed Magnification Models in Pathology
Eric Zimmermann, Eugene Vorontsov, Julian Viret, Adam Casson, Michal Zelechowski, George Shaikovski, Neil Tenenholtz, Jimmy Hall, Thomas J. Fuchs, Nicolo Fusi, Siqi Liu, Kristen Severson
July 2024
Discovery of Parkinson’s disease states and disease progression modelling: a longitudinal data study using machine learning
Kristen Severson, Lana M Chahine, Luba A Smolensky, Murtaza Dhuliawala, Mark Frasier, Kenney Ng, Soumya Ghosh, Jianying Hu
July 2021
Personalized Input-Output Hidden Markov Models for Disease Progression Modeling.
Kristen Severson, Lana M. Chahine, Luba Smolensky, Kenney Ng, Jianying Hu, Soumya Ghosh
December 2019
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Deep Evidential Regression
Alexander Amini, Wilko Schwarting, Ava Soleimany, Daniela Rus
2020 Neural Information Processing Systems | December 2020
Unsupervised Learning with Contrastive Latent Variable Models
Kristen Severson, Soumya Ghosh, Kenney Ng
2019 National Conference on Artificial Intelligence | July 2019
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
On the challenges of learning with inference networks on sparse, high-dimensional data
Rahul Gopalkrishnan, Dawen Liang, Matthew D. Hoffman
International Conference on Artificial Intelligence and Statistics | October 2017