Pavel Kravchenko

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.

ArChIPelago combines multiple PWMs using classic machine learning to improve TFBS prediction, outperforming individual PWMs and other models across species.

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 systematically determines the sequence specificity of 332 poorly characterized human transcription factors, identifying over 4,000 experiments and revealing tens of thousands of new TF binding sites.

This study identifies Nr5a2 as a key activator of zygotic genome activation in mouse embryos, showing it regulates 72% of ZGA genes and is essential for development beyond the 2-cell stage.