Tsu-Pei Chiu

Contribution of DNA breathing to physical interactions with transcription factors

The paper investigates DNA breathing's role in TF-DNA interactions using in vitro and in vivo data, finding correlations between breathing features near motifs and binding affinity across multiple TFs.

DeepPBS: Geometric deep learning for interpretable prediction of protein-DNA binding specificity

DeepPBS predicts protein-DNA binding specificity using geometric deep learning, showing alignment with experimental mutagenesis data and enabling analysis of molecular dynamics simulations.

DNA sequence context and the chromatin landscape differentiate sequence-specific transcription factor binding in the human malaria parasite, Plasmodium falciparum

The paper investigates how DNA sequence and chromatin context influence transcription factor binding in Plasmodium falciparum, showing that both factors contribute to differential binding site selection.

Targeting circadian transcriptional programs in triple negative breast cancer through a cis-regulatory mechanism

This paper identifies a cis-regulatory mechanism in triple-negative breast cancer where targeting circadian transcription factors with small molecules represses a circadian transcriptional program, offering a new therapeutic strategy.

Deep DNAshape: Predicting DNA shape considering extended flanking regions using a deep learning method

This paper introduces Deep DNAshape, a deep learning method that predicts DNA shape by considering extended flanking regions, improving prediction accuracy and providing insights into protein-DNA binding mechanisms.