Dantas Machado AC - Search Results

1

Crystal Structures of Ternary Complexes of MEF2 and NKX2-5 Bound to DNA Reveal a Disease Related Protein-Protein Interaction Interface.

Lei X, Zhao J, Sagendorf JM, Rajashekar N, Xu J, Dantas Machado AC, Sen C, Rohs R, Feng P, Chen L. Lei X, et al. Among authors: dantas machado ac. J Mol Biol. 2020 Sep 4;432(19):5499-5508. doi: 10.1016/j.jmb.2020.07.004. Epub 2020 Jul 15. J Mol Biol. 2020. PMID: 32681840 Free PMC article.

2

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: dantas machado ac. 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.

3

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: dantas machado ac. 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.

4

Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion.

Chen Y, Zhang X, Dantas Machado AC, Ding Y, Chen Z, Qin PZ, Rohs R, Chen L. Chen Y, et al. Among authors: dantas machado ac. Nucleic Acids Res. 2013 Sep;41(17):8368-76. doi: 10.1093/nar/gkt584. Epub 2013 Jul 8. Nucleic Acids Res. 2013. PMID: 23836939 Free PMC article.

5

Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling.

Zhang X, Dantas Machado AC, Ding Y, Chen Y, Lu Y, Duan Y, Tham KW, Chen L, Rohs R, Qin PZ. Zhang X, et al. Among authors: dantas machado ac. Nucleic Acids Res. 2014 Feb;42(4):2789-97. doi: 10.1093/nar/gkt1219. Epub 2013 Nov 30. Nucleic Acids Res. 2014. PMID: 24293651 Free PMC article.

6

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: dantas machado ac. 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.

7

Evolving insights on how cytosine methylation affects protein-DNA binding.

Dantas Machado AC, Zhou T, Rao S, Goel P, Rastogi C, Lazarovici A, Bussemaker HJ, Rohs R. Dantas Machado AC, et al. Brief Funct Genomics. 2015 Jan;14(1):61-73. doi: 10.1093/bfgp/elu040. Epub 2014 Oct 14. Brief Funct Genomics. 2015. PMID: 25319759 Free PMC article. Review.

8

Unraveling determinants of transcription factor binding outside the core binding site.

Levo M, Zalckvar E, Sharon E, Dantas Machado AC, Kalma Y, Lotam-Pompan M, Weinberger A, Yakhini Z, Rohs R, Segal E. Levo M, et al. Among authors: dantas machado ac. Genome Res. 2015 Jul;25(7):1018-29. doi: 10.1101/gr.185033.114. Epub 2015 Mar 11. Genome Res. 2015. PMID: 25762553 Free PMC article.

9

Structure of the Forkhead Domain of FOXA2 Bound to a Complete DNA Consensus Site.

Li J, Dantas Machado AC, Guo M, Sagendorf JM, Zhou Z, Jiang L, Chen X, Wu D, Qu L, Chen Z, Chen L, Rohs R, Chen Y. Li J, et al. Among authors: dantas machado ac. Biochemistry. 2017 Jul 25;56(29):3745-3753. doi: 10.1021/acs.biochem.7b00211. Epub 2017 Jul 11. Biochemistry. 2017. PMID: 28644006 Free PMC article.

10

Landscape of DNA binding signatures of myocyte enhancer factor-2B reveals a unique interplay of base and shape readout.

Dantas Machado AC, Cooper BH, Lei X, Di Felice R, Chen L, Rohs R. Dantas Machado AC, et al. Nucleic Acids Res. 2020 Sep 4;48(15):8529-8544. doi: 10.1093/nar/gkaa642. Nucleic Acids Res. 2020. PMID: 32738045 Free PMC article.

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