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Nucleic Acids Research|July 18, 2015
DSSR: an integrated software tool for dissecting the spatial structure of RNAXiang-Jun Lu, Harmen J Bussemaker, Wilma K Olson
Bioinformatics (Oxford, England)|July 29, 2006
Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCEBarrett C Foat, Alexandre V Morozov, Harmen J Bussemaker
Trends in Cell Biology|August 28, 2014
In search of the determinants of enhancer-promoter interaction specificityJoris van Arensbergen, Bas van Steensel, Harmen J Bussemaker
Genome Biology|November 1, 2024
Benchmarking and building DNA binding affinity models using allele-specific and allele-agnostic transcription factor binding dataXiaoting Li, Lucas A N Melo, Harmen J Bussemaker
Nucleic Acids Research|March 13, 2010
The RNA backbone plays a crucial role in mediating the intrinsic stability of the GpU dinucleotide platform and the GpUpA/GpA miniduplexXiang-Jun Lu, Wilma K Olson, Harmen J Bussemaker
Annual Review of Biophysics and Biomolecular Structure|February 22, 2007
Predictive modeling of genome-wide mRNA expression: from modules to moleculesHarmen J Bussemaker, Barrett C Foat, Lucas D Ward
Biorxiv : the Preprint Server for Biology|January 3, 2024
Benchmarking DNA binding affinity models using allele-specific transcription factor binding dataXiaoting Li, Lucas A N Melo, Harmen J Bussemaker
Molecular Systems Biology|February 24, 2018
A unified approach for quantifying and interpreting DNA shape readout by transcription factorsH Tomas Rube, Chaitanya Rastogi, Judith F Kribelbauer, et al.
Elife|December 25, 2015
Building accurate sequence-to-affinity models from high-throughput in vitro protein-DNA binding data using FeatureREDUCETodd R Riley, Allan Lazarovici, Richard S Mann, et al.
Annual Review of Cell and Developmental Biology|July 9, 2019
Low-Affinity Binding Sites and the Transcription Factor Specificity Paradox in EukaryotesJudith F Kribelbauer, Chaitanya Rastogi, Harmen J Bussemaker, et al.
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