Bussemaker HJ - Search Results

1

Context-Dependent Gene Regulation by Homeodomain Transcription Factor Complexes Revealed by Shape-Readout Deficient Proteins.

Kribelbauer JF, Loker RE, Feng S, Rastogi C, Abe N, Rube HT, Bussemaker HJ, Mann RS. Kribelbauer JF, et al. Among authors: bussemaker hj. Mol Cell. 2020 Apr 2;78(1):152-167.e11. doi: 10.1016/j.molcel.2020.01.027. Epub 2020 Feb 12. Mol Cell. 2020. PMID: 32053778 Free PMC article.

2

Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences.

Ward LD, Bussemaker HJ. Ward LD, et al. Among authors: bussemaker hj. Bioinformatics. 2008 Jul 1;24(13):i165-71. doi: 10.1093/bioinformatics/btn154. Bioinformatics. 2008. PMID: 18586710 Free PMC article.

3

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: bussemaker hj. Cell. 2011 Dec 9;147(6):1270-82. doi: 10.1016/j.cell.2011.10.053. Cell. 2011. PMID: 22153072 Free PMC article.

4

Nuclear pore component Nup98 is a potential tumor suppressor and regulates posttranscriptional expression of select p53 target genes.

Singer S, Zhao R, Barsotti AM, Ouwehand A, Fazollahi M, Coutavas E, Breuhahn K, Neumann O, Longerich T, Pusterla T, Powers MA, Giles KM, Leedman PJ, Hess J, Grunwald D, Bussemaker HJ, Singer RH, Schirmacher P, Prives C. Singer S, et al. Among authors: bussemaker hj. Mol Cell. 2012 Dec 14;48(5):799-810. doi: 10.1016/j.molcel.2012.09.020. Epub 2012 Oct 24. Mol Cell. 2012. PMID: 23102701 Free PMC article.

5

SELEX-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes.

Riley TR, Slattery M, Abe N, Rastogi C, Liu D, Mann RS, Bussemaker HJ. Riley TR, et al. Among authors: bussemaker hj. Methods Mol Biol. 2014;1196:255-78. doi: 10.1007/978-1-4939-1242-1_16. Methods Mol Biol. 2014. PMID: 25151169 Free PMC article.

6

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. Among authors: bussemaker hj. 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.

7

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: bussemaker hj. 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.

8

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: bussemaker hj. 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.

9

Building accurate sequence-to-affinity models from high-throughput in vitro protein-DNA binding data using FeatureREDUCE.

Riley TR, Lazarovici A, Mann RS, Bussemaker HJ. Riley TR, et al. Among authors: bussemaker hj. Elife. 2015 Dec 23;4:e06397. doi: 10.7554/eLife.06397. Elife. 2015. PMID: 26701911 Free PMC article.

10

Quantitative Analysis of the DNA Methylation Sensitivity of Transcription Factor Complexes.

Kribelbauer JF, Laptenko O, Chen S, Martini GD, Freed-Pastor WA, Prives C, Mann RS, Bussemaker HJ. Kribelbauer JF, et al. Among authors: bussemaker hj. Cell Rep. 2017 Jun 13;19(11):2383-2395. doi: 10.1016/j.celrep.2017.05.069. Cell Rep. 2017. PMID: 28614722 Free PMC article.

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