Kateřina Faltejsková

This study identifies DNA binding motifs for 98 human transcription factors using meSMiLE-seq, revealing methylation-sensitive binding preferences for some TFs.

The paper uses GHT-SELEX to show many human TFs have high intrinsic sequence specificity and complex DNA binding, often matching in vivo ChIP-seq results.

The paper evaluates cross-platform DNA motif discovery tools using 4,237 experiments to identify reliable transcription factor binding motifs and highlights challenges in motif detection.

The paper shows that GC content increases around transcription factor binding sites across cell lines and proposes that this reflects a scanning mechanism for DNA binding.

EXTRA-seq quantifies enhancer-promoter communication in endogenous contexts, revealing the TATA-box's role in modulating expression and improving gene expression prediction when integrated with deep learning models.