Koo PK - Search Results

1

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: koo pk. 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.

2

ZBED2 is an antagonist of interferon regulatory factor 1 and modifies cell identity in pancreatic cancer.

Somerville TDD, Xu Y, Wu XS, Maia-Silva D, Hur SK, de Almeida LMN, Preall JB, Koo PK, Vakoc CR. Somerville TDD, et al. Among authors: koo pk. Proc Natl Acad Sci U S A. 2020 May 26;117(21):11471-11482. doi: 10.1073/pnas.1921484117. Epub 2020 May 8. Proc Natl Acad Sci U S A. 2020. PMID: 32385160 Free PMC article.

3

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: koo pk. Genome Biol. 2023 May 5;24(1):105. doi: 10.1186/s13059-023-02941-w. Genome Biol. 2023. PMID: 37143118 Free PMC article.

4

Current approaches to genomic deep learning struggle to fully capture human genetic variation.

Tang Z, Toneyan S, Koo PK. Tang Z, et al. Among authors: koo pk. Nat Genet. 2023 Dec;55(12):2021-2022. doi: 10.1038/s41588-023-01517-5. Nat Genet. 2023. PMID: 38036789 No abstract available.

5

Interpreting cis-regulatory interactions from large-scale deep neural networks.

Toneyan S, Koo PK. Toneyan S, et al. Among authors: koo pk. Nat Genet. 2024 Nov;56(11):2517-2527. doi: 10.1038/s41588-024-01923-3. Epub 2024 Sep 16. Nat Genet. 2024. PMID: 39284975

6

Correcting gradient-based interpretations of deep neural networks for genomics.

Majdandzic A, Rajesh C, Koo PK. Majdandzic A, et al. Among authors: koo pk. Genome Biol. 2023 May 9;24(1):109. doi: 10.1186/s13059-023-02956-3. Genome Biol. 2023. PMID: 37161475 Free PMC article.

7

Improving representations of genomic sequence motifs in convolutional networks with exponential activations.

Koo PK, Ploenzke M. Koo PK, et al. Nat Mach Intell. 2021 Mar;3(3):258-266. doi: 10.1038/s42256-020-00291-x. Epub 2021 Feb 8. Nat Mach Intell. 2021. PMID: 34322657 Free PMC article.

8

Interpreting cis-regulatory mechanisms from genomic deep neural networks using surrogate models.

Seitz EE, McCandlish DM, Kinney JB, Koo PK. Seitz EE, et al. Among authors: koo pk. bioRxiv [Preprint]. 2024 Mar 2:2023.11.14.567120. doi: 10.1101/2023.11.14.567120. bioRxiv. 2024. PMID: 38013993 Free PMC article. Preprint.

9

Deep learning for inferring transcription factor binding sites.

Koo PK, Ploenzke M. Koo PK, et al. Curr Opin Syst Biol. 2020 Feb;19:16-23. doi: 10.1016/j.coisb.2020.04.001. Epub 2020 Jun 11. Curr Opin Syst Biol. 2020. PMID: 32905524 Free PMC article.

10

WASP family proteins regulate the mobility of the B cell receptor during signaling activation.

Rey-Suarez I, Wheatley BA, Koo P, Bhanja A, Shu Z, Mochrie S, Song W, Shroff H, Upadhyaya A. Rey-Suarez I, et al. Nat Commun. 2020 Jan 23;11(1):439. doi: 10.1038/s41467-020-14335-8. Nat Commun. 2020. PMID: 31974357 Free PMC article.

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