Publications

Select Publications

Research articles:

Kribelbauer-Swietek, J. F. et al., 2024. EXTRA-seq: a genome-integrated extended massively parallel reporter assay to quantify enhancer-promoter communication. Preprint BioRxiv (https://doi.org/10.1101/2024.12.08.627402)

Jolma, A., Laverty, K., Fathi, A., Yang, A., Yellan, I., Vorontsov, I.E., Kribelbauer-Swietek, J.F. et al. 2024. Perspectives on Codebook: sequence specificity of uncharacterized human transcription factors. Preprint BioRxiv https://doi.org/10.1101/2024.11.11.622097 .

Kribelbauer-Swietek, J.F.^#, Pushkarev, O., Gardeux, V., Russeil, J., Van Mierlo, G., Deplancke, B.^#, 2024. Context transcription factors establish cooperative environments and mediate enhancer communication. Nature Genetics. 56, 2199–2212 (# co-correspondence)

Rube, H.T., Rastogi, C., Feng, S., Kribelbauer, J.F., Li, A., Becerra, B., Melo, L.A.N., Do, B.V., Li, X., Adam, H.H., Shah, N.H., Mann, R.S., Bussemaker, H.J., 2022. Prediction of protein–ligand binding affinity from sequencing data with interpretable machine learning. Nature Biotechnology 40, 1520–1527. https://doi.org/10.1038/s41587-022-01307-0

Llimos, G., Gardeux, V., Koch, U., Kribelbauer, J.F., Hafner, A., Alpern, D., Pezoldt, J., Litovchenko, M., Russeil, J., Dainese, R., Moia, R., Mahmoud, A.M., Rossi, D., Gaidano, G., Plass, C., Lutsik, P., Gerhauser, C., Waszak, S.M., Boettiger, A., Radtke, F., Deplancke, B., 2022. A leukemia-protective germline variant mediates chromatin module formation via transcription factor nucleation. Nature Communication 13, 2022. https://doi.org/10.1038/s41467-022-29625-6

Kribelbauer, J.F., Loker, R.E., Feng, S., Rastogi, C., Abe, N., Rube, H.T., Bussemaker, H.J., Mann, R.S., 2020a. Context-Dependent Gene Regulation by Homeodomain Transcription Factor Complexes Revealed by Shape-Readout Deficient Proteins. Molecular Cell 78, 152-167.e11. https://doi.org/10.1016/j.molcel.2020.01.027

Rastogi, C., Rube, H.T., Kribelbauer, J.F., Crocker, J., Loker, R.E., Martini, G.D., Laptenko, O., Freed-Pastor, W.A., Prives, C., Stern, D.L., Mann, R.S., Bussemaker, H.J., 2018. Accurate and sensitive quantification of protein-DNA binding affinity. Proc. Natl. Acad. Sci. U.S.A. 115. https://doi.org/10.1073/pnas.1714376115

Rao, S., Chiu, T.-P., Kribelbauer, J.F., Mann, R.S., Bussemaker, H.J., Rohs, R., 2018. Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein–DNA binding. Epigenetics & Chromatin 11, 6. https://doi.org/10.1186/s13072-018-0174-4

Kribelbauer, J.F., Laptenko, O., Chen, S., Martini, G.D., Freed-Pastor, W.A., Prives, C., Mann, R.S., Bussemaker, H.J., 2017. Quantitative Analysis of the DNA Methylation Sensitivity of Transcription Factor Complexes. Cell Reports 19, 2383–2395. https://doi.org/10.1016/j.celrep.2017.05.069

Review articles:

Van Mierlo, G., Pushkarev, O., Kribelbauer, J.F., Deplancke, B., 2023. Chromatin modules and their implication in genomic organization and gene regulation. Trends in Genetics 39, 140–153. https://doi.org/10.1016/j.tig.2022.11.003

Kribelbauer, J.F., Lu, X.-J., Rohs, R., Mann, R.S., Bussemaker, H.J., 2020b. Toward a Mechanistic Understanding of DNA Methylation Readout by Transcription Factors. Journal of Molecular Biology 432, 1801–1815. https://doi.org/10.1016/j.jmb.2019.10.021

Kribelbauer, J.F., Rastogi, C., Bussemaker, H.J., Mann, R.S., 2019. Low-Affinity Binding Sites and the Transcription Factor Specificity Paradox in Eukaryotes. Annu. Rev. Cell Dev. Biol. 35, 357–379. https://doi.org/10.1146/annurev-cellbio-100617-062719