1. Accurate and sensitive quantification of protein-DNA binding affinity Rastogi, Chaitanya; Rube, Hans Tomas; Kribelbauer, Judith Franziska; Crocker, Justin; Loker, Ryan Edmund; Martini, Gabriella D.; Laptenko, Oleg; Freed-Pastor, William Allen; Prives, Carol L.; Stern, David L.; Mann, Richard S.; Bussemaker, Harmen J. 2018 Articles Transcription factorsDNA-protein interactionsProtein bindingProbabilities--Mathematical models
2. Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein–DNA binding Rao, Satyanarayan; Chiu, Tsu-Pei; Kribelbauer, Judith F.; Mann, Richard S.; Bussemaker, Harmen J.; Rohs, Remo 2018 Articles DNA--MethylationEpigeneticsDNA-binding proteinsSystems biology
3. Quantitative Analysis of the DNA Methylation Sensitivity of Transcription Factor Complexes Kribelbauer, Judith F.; Laptenko, Oleg; Chen, Siying; Martini, Gabriella D.; Freed-Pastor, William Allen; Prives, Carol L.; Mann, Richard S.; Bussemaker, Harmen J. 2017 Articles DNA--MethylationTranscription factorsGenetic regulationDNA-protein interactionsEpigenetics
4. Characterizing a collective and dynamic component of chromatin immunoprecipitation enrichment profiles in yeast Ward, Lucas; Wang, Junbai; Bussemaker, Harmen J. 2014 Articles Protein bindingTranscription factorsGenetics
5. Dissecting complex transcriptional responses using pathway-level scores based on prior information Bussemaker, Harmen J.; Ward, Lucas; Boorsma, Andre 2007 Articles Messenger RNADNA microarraysBiologyGenetics
6. Detecting transcriptionally active regions using genomic tiling arrays Halasz, Gabor; van Batenburg, Marinus F.; Perusse, Joelle; Hua, Sujun; Lu, Xiang-Jun; White, Kevin P.; Bussemaker, Harmen J. 2006 Articles Genetic transcriptionDNA probesGenomicsDNA microarraysGeneticsBioinformatics
7. Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data Gao, Feng; Foat, Barrett; Bussemaker, Harmen J. 2004 Articles BioinformaticsGenetics
8. Hap4p overexpression in glucose-grown Saccharomyces cerevisiae induces cells to enter a novel metabolic state Lascaris, Romeo; Bussemaker, Harmen J.; Boorsma, André; Piper, Matt; van der Spek, Hans; Grivell, Les; Blom, Jolanda 2002 Articles Gene regulatory networksOverexpression (Genetics)MitochondriaSaccharomyces cerevisiae--GeneticsGeneticsCytology