Browse by CSHL Author

Paper

Zhou, Jessica L, Guruvayurappan, Karthik, Toneyan, Shushan, Chen, Hsiuyi V, Chen, Aaron R, Koo, Peter, McVicker, Graham (October 2024) Analysis of single-cell CRISPR perturbations indicates that enhancers predominantly act multiplicatively. Cell Genomics. p. 100672. ISSN 2666-979X (Public Dataset)

Toneyan, Shushan, Koo, Peter K (September 2024) Interpreting cis-regulatory interactions from large-scale deep neural networks. Nature Genetics. ISSN 1546-1718 (Public Dataset)

Zhou, Jessica, Guruvayurappan, Karthik, Toneyan, Shushan, Chen, Hsiuyi V, Chen, Aaron R, Koo, Peter, McVicker, Graham (July 2024) Analysis of single-cell CRISPR perturbations indicates that enhancers act multiplicatively and provides limited evidence for epistatic-like interactions. bioRxiv. (Public Dataset) (Submitted)

Tang, Ziqi, Toneyan, Shushan, Koo, Peter K (December 2023) Current approaches to genomic deep learning struggle to fully capture human genetic variation. Nature Genetics, 55 (12). pp. 2021-2022. ISSN 1061-4036

Toneyan, Shushan, Koo, Peter K (July 2023) Interpreting Cis -Regulatory Interactions from Large-Scale Deep Neural Networks for Genomics. bioRxiv. (Submitted)

Lee, Nicholas Keone, Tang, Ziqi, Toneyan, Shushan, Koo, Peter K (May 2023) EvoAug: improving generalization and interpretability of genomic deep neural networks with evolution-inspired data augmentations. Genome Biology, 24 (1). p. 105. ISSN 1474-760X

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 (January 2023) ETV6 dependency in Ewing sarcoma by antagonism of EWS-FLI1-mediated enhancer activation. Nature Cell Biology. ISSN 1465-7392 (Public Dataset)

Toneyan, Shushan, Tang, Ziqi, Koo, Peter K (December 2022) Evaluating deep learning for predicting epigenomic profiles. Nature Machine Intelligence, 4 (12). pp. 1088-1100. ISSN 2522-5839

Majdandzic, Antonio, Rajesh, Chandana, Tang, Amber, Toneyan, Shushan, Labelson, Ethan, Tripathy, Rohit, Koo, Peter K (November 2022) Selecting deep neural networks that yield consistent attribution-based interpretations for genomics. Proc Mach Learn Res, 200. pp. 131-149. ISSN 2640-3498

Toneyan, Shushan, Tang, Ziqi, Koo, Peter K (May 2022) Evaluating deep learning for predicting epigenomic profiles. bioRxiv. (Unpublished)

Lee, Nicholas Keone, Tang, Ziqi, Toneyan, Shushan, Koo, Peter (2022) EvoAug: improving generalization and interpretability of genomic deep neural networks with evolution-inspired data augmentations. bioRxiv. (Submitted)

Zhao, Yixin, Dukler, Noah, Barshad, Gilad, Toneyan, Shushan, Danko, Charles G, Siepel, Adam (August 2021) Deconvolution of Expression for Nascent RNA sequencing data (DENR) highlights pre-RNA isoform diversity in human cells. Bioinformatics. ISSN 1367-4803

Zhao, Yixin, Dukler, Noah, Barshad, Gilad, Toneyan, Shushan, Danko, Charles, Siepel, Adam (March 2021) Deconvolution of Expression for Nascent RNA Sequencing Data (DENR) Highlights Pre-RNA Isoform Diversity in Human Cells. BioRxiv. (Unpublished)

Thesis

Toneyan, Shushan (May 2024) Evaluating and interpreting genomic insights from sequence-based deep learning for regulatory genomics. PhD thesis, Cold Spring Harbor Laboratory.