Dear Editor, The accessible chromatin regions were enriched in regulatory elements in
human genome and many genetic variations associated with human diseases were …

Deciphering mechanisms in cell-fate decisions requires single-cell holistic reconstructions of
multidimensional epigenomic states in transcriptional regulation. Here we develop CoTECH …

The recent development of experimental methods for measuring chromatin state at single-
cell resolution has created a need for computational tools capable of analyzing these …

The assay for transposase-accessible chromatin using sequencing (ATAC-seq) provides a
simple and scalable way to detect the unique chromatin landscape associated with a cell …

Linking regulatory DNA elements to their target genes, which may be located hundreds of
kilobases away, remains challenging. Here, we introduce Cicero, an algorithm that identifies …

Abstract We present Model-based AnalysEs of Transcriptome and RegulOme (MAESTRO),
a comprehensive open-source computational workflow (http://github. com/liulab …

The recent development of experimental methods for measuring chromatin state at single-
cell resolution has created a need for computational tools capable of analyzing these …

Mammalian tissues are composed of highly specialized cell types defined by distinct gene
expression patterns. Identification of cis-regulatory elements responsible for cell-type …

An efficient, generalizable method for genome-wide mapping of single-cell histone
modifications or chromatin-binding proteins is lacking. Here, we develop CoBATCH …

Simultaneous profiling of transcriptome and chromatin accessibility within single cells is a
powerful approach to dissect gene regulatory programs in complex tissues. However …