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Current approaches to genomic deep learning struggle to fully capture human genetic variation.
Nat Genet. 2023 Dec;55(12):2021-2022. doi: 10.1038/s41588-023-01517-5.
Nat Genet. 2023.
PMID: 38036789
No abstract available.
Interpreting Cis-Regulatory Interactions from Large-Scale Deep Neural Networks for Genomics.
Toneyan S, Koo PK.
Toneyan S, et al.
bioRxiv [Preprint]. 2024 Mar 20:2023.07.03.547592. doi: 10.1101/2023.07.03.547592.
bioRxiv. 2024.
PMID: 37461616
Free PMC article.
Preprint.
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Evaluating deep learning for predicting epigenomic profiles.
Toneyan S, Tang Z, Koo PK.
Toneyan S, et al.
Nat Mach Intell. 2022 Dec;4(12):1088-1100. doi: 10.1038/s42256-022-00570-9. Epub 2022 Dec 5.
Nat Mach Intell. 2022.
PMID: 37324054
Free PMC article.
Item in Clipboard
Selecting deep neural networks that yield consistent attribution-based interpretations for genomics.
Majdandzic A, Rajesh C, Tang A, Toneyan S, Labelson E, Tripathy R, Koo PK.
Majdandzic A, et al. Among authors: toneyan s.
Proc Mach Learn Res. 2022 Nov;200:131-149.
Proc Mach Learn Res. 2022.
PMID: 37205975
Free PMC article.
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EvoAug: improving generalization and interpretability of genomic deep neural networks with evolution-inspired data augmentations.
Lee NK, Tang Z, Toneyan S, Koo PK.
Lee NK, et al. Among authors: toneyan s.
Genome Biol. 2023 May 5;24(1):105. doi: 10.1186/s13059-023-02941-w.
Genome Biol. 2023.
PMID: 37143118
Free PMC article.
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ETV6 dependency in Ewing sarcoma by antagonism of EWS-FLI1-mediated enhancer activation.
Gao Y, He XY, Wu XS, Huang YH, Toneyan S, Ha T, Ipsaro JJ, Koo PK, Joshua-Tor L, Bailey KM, Egeblad M, Vakoc CR.
Gao Y, et al. Among authors: toneyan s.
Nat Cell Biol. 2023 Feb;25(2):298-308. doi: 10.1038/s41556-022-01060-1. Epub 2023 Jan 19.
Nat Cell Biol. 2023.
PMID: 36658219
Free PMC article.
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Deconvolution of expression for nascent RNA-sequencing data (DENR) highlights pre-RNA isoform diversity in human cells.
Zhao Y, Dukler N, Barshad G, Toneyan S, Danko CG, Siepel A.
Zhao Y, et al. Among authors: toneyan s.
Bioinformatics. 2021 Dec 11;37(24):4727-4736. doi: 10.1093/bioinformatics/btab582.
Bioinformatics. 2021.
PMID: 34382072
Free PMC article.
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