1. Genomics and Epigenomics

 We are studying a wide range of genomic and epigenomic data in various biological contexts. First of all, we have analyzed the exome and transcriptome of tissues, cell lines, and organoids in human cancers and mouse cancer models. In particular, genomic analysis of pancreatic adenocarcinoma has been one of our main focuses (DOI: 10.1038/s43018-022-00479-7), revealing the diverse cellular composition and subtypes related to prognosis. We are expanding our expertise to pan-cancer studies and cancer diagnosis by sequencing cell-free DNA. Second, we are analyzing epigenomic data such as Chromatin Immunoprecipitation followed by sequencing (ChIP-seq) and Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq). Recently, we uncovered the epigenetic regulatory mechanism during autophagy upon glucose starvation through categorizing chromatin states based on a large number of ChIP-seq and ATAC-seq data (DOI: 10.1093/nar/gkac584). Moreover, epigenetic responses by inflammation and stem cell differentiation were investigated at a genome-wide scale(DOI: 10.1093/nar/gkaa626, 10.1073/pnas.1907595116). Third, we are utilizing genomic approaches to examine the evolution of genome and nucleic acids. For example, whole genome sequencing and single cell sequencing were performed for the cell line with damaged genomes in the absence of telomerase activity (DOI: 10.1038/s41467-021-21341-x). Independently, we have also reported the sequence pattern of the self-growing / self-evolving genome (DOI: 10.1093/nar/gkz044). Taken together, we are interested in all kinds of the state-of-art genomic analyses based on high throughput sequencing technologies.