Rohs R - Search Results

1

Absence of a simple code: how transcription factors read the genome.

Slattery M, Zhou T, Yang L, Dantas Machado AC, Gordân R, Rohs R. Slattery M, et al. Among authors: rohs r. Trends Biochem Sci. 2014 Sep;39(9):381-99. doi: 10.1016/j.tibs.2014.07.002. Epub 2014 Aug 14. Trends Biochem Sci. 2014. PMID: 25129887 Free PMC article. Review.

2

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. PMID: 37961633 Free PMC article. Updated. Preprint.

3

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.

4

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. PMID: 38293168 Free PMC article. Preprint.

5

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. PMID: 38187658 Free PMC article. Preprint.

6

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.

7

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.

8

Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape.

Gordân R, Shen N, Dror I, Zhou T, Horton J, Rohs R, Bulyk ML. Gordân R, et al. Among authors: rohs r. Cell Rep. 2013 Apr 25;3(4):1093-104. doi: 10.1016/j.celrep.2013.03.014. Epub 2013 Apr 4. Cell Rep. 2013. PMID: 23562153 Free PMC article.

9

Probing DNA shape and methylation state on a genomic scale with DNase I.

Lazarovici A, Zhou T, Shafer A, Dantas Machado AC, Riley TR, Sandstrom R, Sabo PJ, Lu Y, Rohs R, Stamatoyannopoulos JA, Bussemaker HJ. Lazarovici A, et al. Among authors: rohs r. Proc Natl Acad Sci U S A. 2013 Apr 16;110(16):6376-81. doi: 10.1073/pnas.1216822110. Epub 2013 Apr 1. Proc Natl Acad Sci U S A. 2013. PMID: 23576721 Free PMC article.

10

DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale.

Zhou T, Yang L, Lu Y, Dror I, Dantas Machado AC, Ghane T, Di Felice R, Rohs R. Zhou T, et al. Among authors: rohs r. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W56-62. doi: 10.1093/nar/gkt437. Epub 2013 May 22. Nucleic Acids Res. 2013. PMID: 23703209 Free PMC article.

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