Yang L - Search Results

1

Coregulation of transcription factor binding and nucleosome occupancy through DNA features of mammalian enhancers.

Barozzi I, Simonatto M, Bonifacio S, Yang L, Rohs R, Ghisletti S, Natoli G. Barozzi I, et al. Among authors: yang l. Mol Cell. 2014 Jun 5;54(5):844-857. doi: 10.1016/j.molcel.2014.04.006. Epub 2014 May 8. Mol Cell. 2014. PMID: 24813947 Free PMC article.

2

DNA Shape Features Improve Transcription Factor Binding Site Predictions In Vivo.

Mathelier A, Xin B, Chiu TP, Yang L, Rohs R, Wasserman WW. Mathelier A, et al. Among authors: yang l. Cell Syst. 2016 Sep 28;3(3):278-286.e4. doi: 10.1016/j.cels.2016.07.001. Epub 2016 Aug 18. Cell Syst. 2016. PMID: 27546793 Free PMC article.

3

Transcription factor family-specific DNA shape readout revealed by quantitative specificity models.

Yang L, Orenstein Y, Jolma A, Yin Y, Taipale J, Shamir R, Rohs R. Yang L, et al. Mol Syst Biol. 2017 Feb 6;13(2):910. doi: 10.15252/msb.20167238. Mol Syst Biol. 2017. PMID: 28167566 Free PMC article.

4

DNA sequence+shape kernel enables alignment-free modeling of transcription factor binding.

Ma W, Yang L, Rohs R, Noble WS. Ma W, et al. Among authors: yang l. Bioinformatics. 2017 Oct 1;33(19):3003-3010. doi: 10.1093/bioinformatics/btx336. Bioinformatics. 2017. PMID: 28541376 Free PMC article.

5

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. 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.

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: yang l. 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

GBshape: a genome browser database for DNA shape annotations.

Chiu TP, Yang L, Zhou T, Main BJ, Parker SC, Nuzhdin SV, Tullius TD, Rohs R. Chiu TP, et al. Among authors: yang l. Nucleic Acids Res. 2015 Jan;43(Database issue):D103-9. doi: 10.1093/nar/gku977. Epub 2014 Oct 17. Nucleic Acids Res. 2015. PMID: 25326329 Free PMC article.

8

Genome-wide features of neuroendocrine regulation in Drosophila by the basic helix-loop-helix transcription factor DIMMED.

Hadžić T, Park D, Abruzzi KC, Yang L, Trigg JS, Rohs R, Rosbash M, Taghert PH. Hadžić T, et al. Among authors: yang l. Nucleic Acids Res. 2015 Feb 27;43(4):2199-215. doi: 10.1093/nar/gku1377. Epub 2015 Jan 29. Nucleic Acids Res. 2015. PMID: 25634895 Free PMC article.

9

Quantitative modeling of transcription factor binding specificities using DNA shape.

Zhou T, Shen N, Yang L, Abe N, Horton J, Mann RS, Bussemaker HJ, Gordân R, Rohs R. Zhou T, et al. Among authors: yang l. Proc Natl Acad Sci U S A. 2015 Apr 14;112(15):4654-9. doi: 10.1073/pnas.1422023112. Epub 2015 Mar 9. Proc Natl Acad Sci U S A. 2015. PMID: 25775564 Free PMC article.

10

Deconvolving the recognition of DNA shape from sequence.

Abe N, Dror I, Yang L, Slattery M, Zhou T, Bussemaker HJ, Rohs R, Mann RS. Abe N, et al. Among authors: yang l. Cell. 2015 Apr 9;161(2):307-18. doi: 10.1016/j.cell.2015.02.008. Epub 2015 Apr 2. Cell. 2015. PMID: 25843630 Free PMC article.

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