Epigenetic research aims to understand heritable gene regulation that is not directly
encoded in the DNA sequence. Epigenetic mechanisms such as DNA methylation and …

The MEME Suite is a powerful, integrated set of web-based tools for studying sequence
motifs in proteins, DNA and RNA. Such motifs encode many biological functions, and their …

Deep neural networks have been revolutionizing the field of machine learning for the past
several years. They have been applied with great success in many domains of the …

The regulation of DNA accessibility through nucleosome positioning is important for
transcription control. Computational models have been developed to predict genome-wide …

Background Position-specific priors have been shown to be a flexible and elegant way to
extend the power of Gibbs sampler-based motif discovery algorithms. Information of many …

Abstract cERMIT is a computationally efficient motif discovery tool based on analyzing
genome-wide quantitative regulatory evidence. Instead of pre-selecting promising candidate …

Finding functional DNA binding sites of transcription factors (TFs) throughout the genome is
a crucial step in understanding transcriptional regulation. Unfortunately, these binding sites …

Nucleosome positioning plays an essential role in cellular processes by modulating
accessibility of DNA to proteins. Many computational models have been developed to …

An important problem in molecular biology is to build a complete understanding of
transcriptional regulatory processes in the cell. We have developed a flexible, probabilistic …

As an increasing number of eukaryotic genomes are being sequenced, comparative studies
aimed at detecting regulatory elements in intergenic sequences are becoming more …