Rohs R - Search Results

1

TFBSshape: a motif database for DNA shape features of transcription factor binding sites.

Yang L, Zhou T, Dror I, Mathelier A, Wasserman WW, Gordân R, Rohs R. Yang L, et al. Among authors: rohs r. Nucleic Acids Res. 2014 Jan;42(Database issue):D148-55. doi: 10.1093/nar/gkt1087. Epub 2013 Nov 7. Nucleic Acids Res. 2014. PMID: 24214955 Free PMC article.

2

DrugHIVE: Target-specific spatial drug design and optimization with a hierarchical generative model.

Weller JA, Rohs R. Weller JA, et al. Among authors: rohs r. bioRxiv [Preprint]. 2024 Mar 17:2023.12.22.573155. doi: 10.1101/2023.12.22.573155. bioRxiv. 2024. Update in: J Chem Inf Model. 2024 Aug 26;64(16):6450-6463. doi: 10.1021/acs.jcim.4c01193. PMID: 38187658 Free PMC article. Updated. Preprint.

3

DeepPBS: Geometric deep learning for interpretable prediction of protein-DNA binding specificity.

Mitra R, Li J, Sagendorf JM, Jiang Y, Chiu TP, Rohs R. Mitra R, et al. Among authors: rohs r. bioRxiv [Preprint]. 2023 Dec 16:2023.12.15.571942. doi: 10.1101/2023.12.15.571942. bioRxiv. 2023. Update in: Nat Methods. 2024 Sep;21(9):1674-1683. doi: 10.1038/s41592-024-02372-w. PMID: 38293168 Free PMC article. Updated. Preprint.

4

Deep DNAshape: Predicting DNA shape considering extended flanking regions using a deep learning method.

Li J, Chiu TP, Rohs R. Li J, et al. Among authors: rohs r. bioRxiv [Preprint]. 2023 Oct 24:2023.10.22.563383. doi: 10.1101/2023.10.22.563383. bioRxiv. 2023. Update in: Nat Commun. 2024 Feb 9;15(1):1243. doi: 10.1038/s41467-024-45191-5. PMID: 37961633 Free PMC article. Updated. Preprint.

5

Hand2 represses non-cardiac cell fates through chromatin remodeling at cis- regulatory elements.

Komatsu V, Cooper B, Yim P, Chan K, Gong W, Wheatley L, Rohs R, Fraser SE, Trinh LA. Komatsu V, et al. Among authors: rohs r. bioRxiv [Preprint]. 2023 Sep 24:2023.09.23.559156. doi: 10.1101/2023.09.23.559156. bioRxiv. 2023. PMID: 37790542 Free PMC article. Preprint.

6

Targeting circadian transcriptional programs through a cis-regulatory mechanism in triple negative breast cancer.

Pan Y, Chiu TP, Zhou L, Chan P, Kuo TT, Battaglin F, Soni S, Jayachandran P, Li JJ, Lenz HJ, Mumenthaler SM, Rohs R, Torres ER, Kay SA. Pan Y, et al. Among authors: rohs r. bioRxiv [Preprint]. 2024 Oct 10:2024.04.26.590360. doi: 10.1101/2024.04.26.590360. bioRxiv. 2024. PMID: 38746115 Free PMC article. Preprint.

7

PNAbind: Structure-based prediction of protein-nucleic acid binding using graph neural networks.

Sagendorf JM, Mitra R, Huang J, Chen XS, Rohs R. Sagendorf JM, et al. Among authors: rohs r. bioRxiv [Preprint]. 2024 Mar 2:2024.02.27.582387. doi: 10.1101/2024.02.27.582387. bioRxiv. 2024. Update in: Biophys Rev. 2024 Jun 26;16(3):297-314. doi: 10.1007/s12551-024-01201-w. PMID: 38529493 Free PMC article. Updated. Preprint.

8

The role of DNA shape in protein-DNA recognition.

Rohs R, West SM, Sosinsky A, Liu P, Mann RS, Honig B. Rohs R, et al. Nature. 2009 Oct 29;461(7268):1248-53. doi: 10.1038/nature08473. Nature. 2009. PMID: 19865164 Free PMC article.

9

Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins.

Slattery M, Riley T, Liu P, Abe N, Gomez-Alcala P, Dror I, Zhou T, Rohs R, Honig B, Bussemaker HJ, Mann RS. Slattery M, et al. Among authors: rohs r. Cell. 2011 Dec 9;147(6):1270-82. doi: 10.1016/j.cell.2011.10.053. Cell. 2011. PMID: 22153072 Free PMC article.

10

DNA binding by GATA transcription factor suggests mechanisms of DNA looping and long-range gene regulation.

Chen Y, Bates DL, Dey R, Chen PH, Machado AC, Laird-Offringa IA, Rohs R, Chen L. Chen Y, et al. Among authors: rohs r. Cell Rep. 2012 Nov 29;2(5):1197-206. doi: 10.1016/j.celrep.2012.10.012. Epub 2012 Nov 8. Cell Rep. 2012. PMID: 23142663 Free PMC article.

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