IQB Handbook

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27ACHIEVEMENT” Integrated analysis of gene expression and chromatin folding regulated by cohesin, cohesin loader and CTCF”, The 13th International Workshop on Advanced Genomics, 2019 JuneNakato R, Wada Y, Nakaki R, Nagae G, Katou Y, Tsutsumi S, Nakajima N, Fukuhara H, Iguchi A, Kohro T, Kanki Y, Saito Y, Kobayashi M, Izumi-Taguchi A, Osato N, Tatsuno K, Kamio A, Hayashi-Takanaka Y, Wada H, Ohta S, Aikawa M, Nakajima H, Nakamura M, McGee RC, Heppner KW, Kawakatsu T, Genno M, Yanase H, Kume H, Senbonmatsu T, Homma Y, Nishimura S, Mitsuyama T, Aburatani H, Kimura H, Shirahige K. Comprehensive epigenome characterization reveals diverse transcriptional regulation across human vascular endothelial cells. Epigenetics Chromatin. 2019 Dec 19;12(1):77. DOI:10.1186/s13072-019-0319-0Nakato R, Shirahige K. Sensitive and robust assessment of ChIP-seq read distribution using a strand-shift profile. Bioinformatics. 2018 Jul 15;34(14):2356-2363. DOI:10.1093/bioinformatics/bty137(1) Workflow of NGS analysis. Red rectangle indicates the computational part. (2) Visualization of multiple epigenome data by ChIP-seq analysis pipeline DROMPA (3) 3D genome modeling based on Hi-C data. (4) Gene co-expression network based on nine cell types of human vascular endothelial cells.NAKATO RYUICHIROPH.D. (2010) KYOTO UNIVERSITYRESEARCH ASSOCIATE (2010) INSTITUTE OF MOLECULAR AND CELLULAR BIOSCIENCES, THE UNIVERSITY OF TOKYORESEARCH ASSOCIATE (2018) IQB / INSTITUTE FOR QUANTITATIVE BIOSCIENCES, THE UNIVERSITY OF TOKYOLECTURER (2019) IQB / INSTITUTE FOR QUANTITATIVE BIOSCIENCES, THE UNIVERSITY OF TOKYO●MEMBER■ LECTURER :NAKATO RYUICHIRO■ TECHNICAL SPECIALIST :YOKOTA NAOKO■ TECHNICAL SPECIALIST : SAIJOU EIKO■ PROJECT RESEARCHER : NAKAJIMA NATSU■ PROJECT RESEARCHER : NAGAI LUIS AUGUSTO EIJYPUBLICATIONPUBLICATIONgenome of an organism contains all information for its biological activity and heredity, on which various events (e.g., gene activa-tion, DNA replication and chromatin folding) are cooperatively regulated. Genome-wide analyses with Next Generation Sequencer (NGS) is a mainstream method in computa-tional genomics and has led to important discoveries for dynamic regulation on the genome. We are interested in understanding the cooperative regulation of genomic events and its dysregulation in diseases by using computational genomics strategy. In collabo-ration with multiple wet labs, we have been investigating various cell-lines such as rare-disease patients and knockout mice by NGS assays including:- ChIP-seq: protein-DNA binding,- ATAC-seq: open chromatin,- RNA-seq: gene expression,- Exome-seq: gene mutation,- Hi-C: 3D genome folding,- ChIA-PET: chromatin looping, and- Single-cell analysis: cellular heterogeneity and differential analysis.Our research focus is "data-driven NGS analysis" that extracts important biological information from large NGS datasets (~hun-dreds of samples) without help from existing biological knowledge. We aim to develop a pipeline for multi-NGS omics that integrative-ly analyzes large datasets from multiple NGS assays and achieve an epoch-making discov-ery, e.g., higher-order coordination of multiple DNA-binding factors. We also put effort into cultivating next-gener-ation computational genomicists. We welcome enthusiastic and motivated students both of biology and of informatics who are interested in computational genomics.ASYMPOSIUM