Mitra S and Hartemink AJ (2025) Inferring differential protein binding from time-series chromatin accessibility data. Bioinform Adv 5(1):vbaf080 PMID:40297777
Chen B, et al. (2023) Spatiotemporal kinetics of CAF-1-dependent chromatin maturation ensures transcription fidelity during S-phase. Genome Res 33(12):2108-2118 PMID:38081658
Mitra S, et al. (2020) RoboCOP: Multivariate State Space Model Integrating Epigenomic Accessibility Data to Elucidate Genome-Wide Chromatin Occupancy. Res Comput Mol Biol 12074:136-151 PMID:34386808
Guo X, et al. (2013) Branching process deconvolution algorithm reveals a detailed cell-cycle transcription program. Proc Natl Acad Sci U S A 110(10):E968-77 PMID:23388635
Luo K and Hartemink AJ (2013) Using DNase digestion data to accurately identify transcription factor binding sites. Pac Symp Biocomput 80-91 PMID:23424114
Mayhew MB, et al. (2011) A generalized model for multi-marker analysis of cell cycle progression in synchrony experiments. Bioinformatics 27(13):i295-303 PMID:21685084
Orlando DA, et al. (2009) A branching process model for flow cytometry and budding index measurements in cell synchrony experiments. Ann Appl Stat 3(4):1521-1541 PMID:21853014
Gordân R and Hartemink AJ (2008) Using DNA duplex stability information for transcription factor binding site discovery. Pac Symp Biocomput 453-64 PMID:18229707
Narlikar L, et al. (2006) Informative priors based on transcription factor structural class improve de novo motif discovery. Bioinformatics 22(14):e384-92 PMID:16873497
Bernard A and Hartemink AJ (2005) Informative structure priors: joint learning of dynamic regulatory networks from multiple types of data. Pac Symp Biocomput 459-70 PMID:15759651
Hartemink AJ, et al. (2002) Combining location and expression data for principled discovery of genetic regulatory network models. Pac Symp Biocomput 437-49 PMID:11928497
Hartemink AJ, et al. (2001) Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks. Pac Symp Biocomput 422-33 PMID:11262961