{"id":209,"date":"2025-02-14T11:44:39","date_gmt":"2025-02-14T19:44:39","guid":{"rendered":"https:\/\/dornsife.usc.edu\/kribelbauer\/?page_id=209"},"modified":"2026-03-24T14:36:30","modified_gmt":"2026-03-24T21:36:30","slug":"publications","status":"publish","type":"page","link":"https:\/\/dornsife.usc.edu\/kribelbauer\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"\n    \n  \n    \n\n\n\n\n\n\n<div\n  class=\"cc--component-container cc--link-list \"\n\n  \n  \n  \n  \n  \n  \n  >\n  <div class=\"c--component c--link-list\"\n    \n      >\n\n    \n      <div class=\"header-container\">\n\n                  \n<div class=\"f--field f--section-title\">\n\n    \n  <h2>\n          Full List of Publications\n      <\/h2>\n\n\n<\/div>\n                <\/div>\n  \n      <div class=\"links-container\">\n\n                        \n        \n          \n            <div class=\"column\">\n                <ul>\n                                                                  <li>\n                                \n<div class=\"f--field f--link\">\n\n    \n    \n  \n<a \n  class=\"link\"\n  href= https:\/\/scholar.google.com\/citations?user=E-3i3ikAAAAJ&#038;hl=en\n    aria-label=\"Read more about Google Scholar\"  \n>\n    Google Scholar \n  <svg version=\"1.1\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" x=\"0px\" y=\"0px\" viewBox=\"0 0 35 35\" enable-background=\"new 0 0 35 35\" width=\"25\" height=\"25\" xml:space=\"preserve\"><polygon fill-rule=\"evenodd\" clip-rule=\"evenodd\" fill=\"#000\" points=\"19.3,27.5 29.3,17.5,19.3,7.5 16.3,10.4 21.4,15.4 6.7,15.4 6.7,19.6 21.4,19.6 16.3,24.6 \"\/><\/svg>\n<\/a>\n\n\n<\/div>\n\n                                                    <\/li>\n                                                          <\/ul>\n            <\/div>\n\n          \n          \n        \n          \n            <div class=\"column\">\n                <ul>\n                                                                  <li>\n                                \n<div class=\"f--field f--link\">\n\n    \n    \n  \n<a \n  class=\"link\"\n  href= https:\/\/orcid.org\/0000-0002-8072-7773\n    aria-label=\"Read more about ORCID\"  \n>\n    ORCID \n  <svg version=\"1.1\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" x=\"0px\" y=\"0px\" viewBox=\"0 0 35 35\" enable-background=\"new 0 0 35 35\" width=\"25\" height=\"25\" xml:space=\"preserve\"><polygon fill-rule=\"evenodd\" clip-rule=\"evenodd\" fill=\"#000\" points=\"19.3,27.5 29.3,17.5,19.3,7.5 16.3,10.4 21.4,15.4 6.7,15.4 6.7,19.6 21.4,19.6 16.3,24.6 \"\/><\/svg>\n<\/a>\n\n\n<\/div>\n\n                                                    <\/li>\n                                                          <\/ul>\n            <\/div>\n\n          \n          \n        \n\n\n\n    <\/div>\n  \n\n  <\/div><\/div>\n\n\n\n\n  \n    \n\n\n\n\n\n\n<div\n  class=\"cc--component-container cc--rich-text \"\n\n  \n  \n  \n  \n  \n  \n  >\n  <div class=\"c--component c--rich-text\"\n    \n      >\n\n    \n      \n<div class=\"f--field f--wysiwyg\">\n\n    \n  <table style=\"font-weight: 400; height: 1280px;\">\n<tbody>\n<tr>\n<td style=\"width: 766px;\">\n<h2><strong>Select Publications<\/strong><\/h2>\n<\/td>\n<\/tr>\n<tr style=\"height: 80px;\">\n<td style=\"height: 80px; width: 766px;\">\n<h2><strong><u>Research articles:<\/u><\/strong><\/h2>\n<p>DaSilva LF, Senan S, <strong>Kribelbauer-Swietek JF<\/strong>, Patel ZM, Louis LK, Reddy AJ, et al. Designing synthetic regulatory elements using the generative AI framework DNA-Diffusion. Nat Genet [Internet]. 2025 Dec 23]; Available from: <a href=\"https:\/\/www.nature.com\/articles\/s41588-025-02441-6\">https:\/\/www.nature.com\/articles\/s41588-025-02441-6<\/a><\/p>\n<p><strong>Kribelbauer-Swietek, J. F.<\/strong> <em>et al., <\/em>2024. EXTRA-seq: a genome-integrated extended massively parallel reporter assay to quantify enhancer-promoter communication. <em><span style=\"text-decoration: underline;\">Preprint BioRxiv<\/span><\/em> (<a href=\"https:\/\/doi.org\/10.1101\/2024.12.08.627402\">https:\/\/doi.org\/10.1101\/2024.12.08.627402<\/a>)<\/p>\n<p style=\"font-weight: 400;\">Jolma, A., Laverty, K., Fathi, A., Yang, A., Yellan, I., Vorontsov, I.E., <strong>Kribelbauer-Swietek, J.F.\u00a0<\/strong>et al. 2024. Perspectives on Codebook: sequence specificity of uncharacterized human transcription factors. <em><span style=\"text-decoration: underline;\">Preprint BioRxiv<\/span><\/em> <a href=\"https:\/\/doi.org\/10.1101\/2024.11.11.622097\">https:\/\/doi.org\/10.1101\/2024.11.11.622097<\/a> .<\/p>\n<p><strong>Kribelbauer-Swietek, J.F.<sup>#<\/sup>,<\/strong> Pushkarev, O., Gardeux, V., Russeil, J., Van Mierlo, G., Deplancke, B.<sup>#<\/sup>, 2024. Context transcription factors establish cooperative environments and mediate enhancer communication. <span style=\"text-decoration: underline;\"><em>Nature\u00a0<\/em><em>Genetics<\/em><\/span><em>.<\/em> 56, 2199\u20132212 (# co-correspondence)<\/p>\n<p>Rube, H.T., Rastogi, C., Feng, S., <strong>Kribelbauer, J.F.,<\/strong> 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\u2013ligand binding affinity from sequencing data with interpretable machine learning. <span style=\"text-decoration: underline;\"><em>Nature Biotechnology<\/em><\/span> 40, 1520\u20131527. https:\/\/doi.org\/10.1038\/s41587-022-01307-0<\/p>\n<p>Llimos, G., Gardeux, V., Koch, U., <strong>Kribelbauer, J.F., <\/strong>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. <span style=\"text-decoration: underline;\"><em>Nature Communication<\/em><\/span> 13, 2022. https:\/\/doi.org\/10.1038\/s41467-022-29625-6<\/p>\n<p><strong>Kribelbauer, J.F., <\/strong>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. <span style=\"text-decoration: underline;\"><em>Molecular Cell<\/em><\/span> 78, 152-167.e11. https:\/\/doi.org\/10.1016\/j.molcel.2020.01.027<\/p>\n<p>Rastogi, C., Rube, H.T., <strong>Kribelbauer, J.F.,<\/strong> 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. <span style=\"text-decoration: underline;\"><em>Proc. Natl. Acad. Sci<\/em>.<\/span> U.S.A. 115. https:\/\/doi.org\/10.1073\/pnas.1714376115<\/p>\n<p>Rao, S., Chiu, T.-P., <strong>Kribelbauer, J.F.,<\/strong> Mann, R.S., Bussemaker, H.J., Rohs, R., 2018. Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein\u2013DNA binding. <span style=\"text-decoration: underline;\"><em>Epigenetics &amp; Chromatin<\/em><\/span> 11, 6. https:\/\/doi.org\/10.1186\/s13072-018-0174-4<\/p>\n<p><strong>Kribelbauer, J.F.,<\/strong> 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. <span style=\"text-decoration: underline;\"><em>Cell Reports<\/em><\/span> 19, 2383\u20132395. https:\/\/doi.org\/10.1016\/j.celrep.2017.05.069<\/td>\n<\/tr>\n<tr style=\"height: 184px;\">\n<td style=\"width: 766px; height: 184px;\">\n<h2><strong><u>Review articles:<\/u><\/strong><\/h2>\n<p>&nbsp;<\/p>\n<p>Van Mierlo, G., Pushkarev, O., <strong>Kribelbauer, J.F.,<\/strong> Deplancke, B., 2023. Chromatin modules and their implication in genomic organization and gene regulation. <span style=\"text-decoration: underline;\"><em>Trends in Genetics<\/em><\/span> 39, 140\u2013153. https:\/\/doi.org\/10.1016\/j.tig.2022.11.003<\/p>\n<p><strong>Kribelbauer, J.F.,<\/strong> Lu, X.-J., Rohs, R., Mann, R.S., Bussemaker, H.J., 2020b. Toward a Mechanistic Understanding of DNA Methylation Readout by Transcription Factors. <span style=\"text-decoration: underline;\"><em>Journal of Molecular Biology<\/em><\/span> 432, 1801\u20131815. https:\/\/doi.org\/10.1016\/j.jmb.2019.10.021<\/p>\n<p><strong>Kribelbauer, J.F.,<\/strong> Rastogi, C., Bussemaker, H.J., Mann, R.S., 2019. Low-Affinity Binding Sites and the Transcription Factor Specificity Paradox in Eukaryotes. <span style=\"text-decoration: underline;\"><em>Annu. Rev. Cell Dev. Biol<\/em>.<\/span> 35, 357\u2013379. https:\/\/doi.org\/10.1146\/annurev-cellbio-100617-062719<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n\n\n\n<\/div>\n\n\n  <\/div><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":919,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"class_list":["post-209","page","type-page","status-publish","hentry"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.1.1 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Publications - Kribelbauer Lab<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/dornsife.usc.edu\/kribelbauer\/publications\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Publications - 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