EvoAug: improving generalization and interpretability of genomic deep neural networks with evolution-inspired data augmentations von Lee, Nicholas Keone, Tang, Ziqi, Toneyan, Shushan, Koo, Peter K

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Evaluating deep learning for predicting epigenomic profiles von Toneyan, Shushan, Tang, Ziqi, Koo, Peter K.

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Interpreting cis-regulatory interactions from large-scale deep neural networks von Toneyan, Shushan, Koo, Peter K.

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Current approaches to genomic deep learning struggle to fully capture human genetic variation von Tang, Ziqi, Toneyan, Shushan, Koo, Peter K.

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Evaluating deep learning for predicting epigenomic profiles von Toneyan, Shushan, Tang, Ziqi, Koo, Peter K.

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Deconvolution of expression for nascent RNA-sequencing data (DENR) highlights pre-RNA isoform diversity in human cells von Zhao, Yixin, Dukler, Noah, Barshad, Gilad, Toneyan, Shushan, Danko, Charles G, Siepel, Adam

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ETV6 dependency in Ewing sarcoma by antagonism of EWS-FLI1-mediated enhancer activation von Gao, Yuan, He, Xue-Yan, Wu, Xiaoli S., Huang, Yu-Han, Toneyan, Shushan, Ha, Taehoon, Ipsaro, Jonathan J., Koo, Peter K., Joshua-Tor, Leemor, Bailey, Kelly M., Egeblad, Mikala, Vakoc, Christopher R.

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Analysis of single-cell CRISPR perturbations indicates that enhancers predominantly act multiplicatively von Zhou, Jessica L., Guruvayurappan, Karthik, Toneyan, Shushan, Chen, Hsiuyi V., Chen, Aaron R., Koo, Peter, McVicker, Graham

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Results from Interpreting Cis-Regulatory Interactions from Large-Scale Deep Neural Networks for Genomics von Toneyan, Shushan, Koo, Peter

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Interpreting Cis-Regulatory Interactions from Large-Scale Deep Neural Networks for Genomics von Toneyan, Shushan, Koo, Peter

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Evaluating deep learning for predicting epigenomic profiles von Toneyan Shushan, Ziqi, Tang, Peter, Koo

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EvoAug Model Weights and Code von Lee, Nicholas Keone, Ziqi Tang, Toneyan, Shushan, Koo, Peter K

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EvoAug Data von Lee, Nicholas Keone, Ziqi Tang, Toneyan, Shushan, Koo, Peter K

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Dataset from: Selecting deep neural networks that yield consistent attribution-based interpretations for genomics von Majdandzic, Antonio, Rajesh, Chandana, Tang, Amber, Toneyan, Shushan, Labelson, Ethan, Tripathy, Rohit, Koo, Peter

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