Ally W. H. Yang

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 identifies two distinct DNA-binding domains in Zelda that regulate its tissue-specific chromatin occupancy in Drosophila embryos and neuroblasts.

The paper identifies genomic binding sites of 166 poorly characterized human transcription factors, revealing that some bind to dark matter DNA and others to regulatory regions.

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.

The paper uses deep learning to analyze chromatin accessibility in Drosophila embryos, revealing a two-phase process driven by pioneer TFs and enhancer-activating TFs.