Kribelbauer JF, Lu XJ, Rohs R, Mann RS, Bussemaker HJ. Toward a Mechanistic Understanding of DNA Methylation Readout by Transcription Factors. J Mol Biol. 2019 Nov 2. pii: S0022-2836(19)30617-5. doi: 10.1016/j.jmb.2019.10.021.

Sánchez-Higueras C, Rastogi C, Voutev R, Bussemaker HJ, Mann RS, Hombría JC. In vivo Hox binding specificity revealed by systematic changes to a single cis regulatory module. Nat Commun. 2019 Aug 9;10(1):3597. doi: 10.1038/s41467-019-11416-1.

Rube HT, Rastogi C, Kribelbauer JF, Bussemaker HJ. A unified approach for quantifying and interpreting DNA shape readout by transcription factors. Mol Syst Biol. 2018 Feb 22; 14(2): e7902.

Rao S, Chiu TP, Kribelbauer JF, Mann RS, Bussemaker HJ, Rohs R. Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein-DNA binding. Epigenetics Chromatin. 2018 Feb 6;11(1):6.

Zhang L, Martini GD, Rube HT, Kribelbauer JF, Rastogi C, FitzPatrick VD, Houtman JC,Bussemaker HJ, Pufall MA. SelexGLM differentiates androgen and glucocorticoid receptor DNA-binding preference over an extended binding site. Genome Res. 2018 Jan;28(1):111-121. Epub 2017 Dec 1.

Kribelbauer JF, Laptenko O, Chen S, Martini GD, Freed-Pastor WA, Prives C, Mann RS,Bussemaker HJ. Quantitative Analysis of the DNA Methylation Sensitivity of Transcription Factor Complexes. Cell Rep. 2017 Jun 13;19(11):2383-2395.

Bussemaker HJ, Causton HC, Fazlollahi M, Lee E, Muroff I. Network-based approaches that exploit inferred transcription factor activity to analyze the impact of genetic variation on gene expression. Curr Opin Syst Biol. 2017 Apr;2:98-102. Epub 2017 Apr 17.

Tepper RG, Ashraf J, Kaletsky R, Kleemann G, Murphy CT, Bussemaker HJ. PQM-1 complements DAF-16 as a key transcriptional regulator of DAF-2-mediated development and longevity . Cell. 2013 Aug 1;154(3):676-90.

Lazarovici A, Zhou T, Shafer A, Dantas Machado AC, Riley TR, Sandstrom R, Sabo PJ, Lu Y, Rohs R, Stamatoyannopoulos JA, Bussemaker HJ. Probing DNA shape and methylation state on a genomic scale with DNase I . Proc Natl Acad Sci U S A. 2013 Apr 16;110(16):6376-81.

Slattery M, Riley T, Liu P, Abe N, Gomez-Alcala P, Dror I, Zhou T, Rohs R, Honig B, Bussemaker HJ, Mann RS. Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins . Cell. 2011 Dec 9;147(6):1270-82.

Filion GJ, van Bemmel JG, Braunschweig U, Talhout W, Kind J, Ward LD, Brugman W, de Castro IJ, Kerkhoven RM, Bussemaker HJ, van Steensel B. Systematic protein location mapping reveals five principal chromatin types in Drosophila cells . Cell. 2010 Oct 15;143(2):212-24. Erratum in: Cell. 2011 Apr 1;145(1):160.

Lee E, Bussemaker HJ. Identifying the genetic determinants of transcription factor activity . Mol Syst Biol. 2010 Sep 21;6:412.

Bussemaker HJ, Li H, Siggia ED. Regulatory element detection using correlation with expression . Nat Genet. 2001 Feb;27(2):167-71.