About Prof. Masao NAGASAKI

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Masao Nagasaki
Program-Specific Professor Ph.D
-Biomedical Information Analysis (Human Biosciences Unit for the Top Global Course Center for
the Promotion of Interdisciplinary Education and Research (CPIER)), Center for Genomic Medicine, Graduate School of Medicine, Kyoto University-

He was born at Osaka in 1976.

Educational Backgrounds
-April 1994 – Match 1998
BS: Department of Information Science, The University of Tokyo
-April 1998 – March 2000
MS: Graduate School of Information Science, The University of Tokyo
-April 2000 – March 2004
PhD (Science): Graduate School of Information Science, The University of Tokyo

Professional Backgrounds
-April 2001 – March 2003
Doctoral Fellow
Human Genome Center, Institute of Medical Science, The University of Tokyo
-April 2004 – March 2005
Post-Doctoral Fellow
Human Genome Center, Institute of Medical Science, The University of Tokyo
-April 2005 – Jan 2011
Assistant Professor
Human Genome Center, Institute of Medical Science, The University of Tokyo
-Jan 2011 – March 2012
Associate professor
Human Genome Center, Institute of Medical Science, The University of Tokyo
-April 2012 – March 2018
Professor
Department of Integrative Genomics,Tohoku Medical Megabank Organization Tohoku University
Group Leader of In Silico Analysis
-April 2019 –
Program-Specific Professor
Biomedical Information Analysis (Human Biosciences Unit for the Top Global Course Center for
the Promotion of Interdisciplinary Education and Research (CPIER)), Center for Genomic Medicine, Graduate School of Medicine, Kyoto University

Research Interest

His research interest is to develop algorithms and tools (software) that are really useful for biologists work in bench. The development of new algorithm and new statistical method just for writing paper is not the mission in this laboratory.

Research history

1999- To develop the modeling, simulation, and analysis software environment for biological pathways, e.g. metabolic pathway, gene regulatory network, signal transduction pathway, cell-cell interactions, and miRNA regulations by combining the literature driven approach and estimated approach by using statistical analysis. To achieve this, He promoted several projects http://www.csml.org/http://cionline.hgc.jp/ and developing application named Cell Illustrator.

2009-2012.3 In January 2009 his institute (IMS, UT) installed a new supercomputer environment called “Shirokane” with more than six thousands cores (=75Teraflops) and one Petabyte (=1024 Terabyte) storage. In January 2012, the computing power will be increased to 225TF and the storage capacity reached to 4 Petabyte. Next Generations Sequence (NGS) data from human patients and from cell lines were processed on a daily basis. The most frequently processed data was coming from the International Cancer Genome Consortium’s (ICGC, http://www.icgc.org/) liver cancer project, a collaboration among Riken, the National Cancer Center and our institute. The goal of the ICGC liver cancer project is to sequence the cancerous as well as the healthy cells of 500 patients and find the key genetic rate variants responsible for liver cancer from the resulting 1000 data sets.
Till 2012.3, 100 sets of deep sequenced data (30x to 40x coverage) were processed and analyzed on the supercomputer. If the mapping for 500 data sets would be calculated with the standard algorithm, but only on a single CPU, the computation would have to run for 1500 years. He built up a quick and stable management infrastructure and custom analysis pipeline on the “Shirokane” system. He also developed discovery using Bioinformatics approach, e.g. extract knowledge from large-scale publicly available sequencing data (http://www.ncbi.nlm.nih.gov/sra).
The earthquake on March 11th 2011 had a deep impact on the energy production and consumption in Japan. He also managed a new supercomputer energy saving system which drastically reduce the energy consumption. (2009-2012.3)

2012.4-2019.3 He moved to Tohoku University as full professor and took the responsibility of in silico data processing and analyzing massive NGS sequenced cohort data on super computer environment. He and his group will mainly focus on the downstream analyses on that environment using information science and statistical methods, especially combining other sequencing data, e.g. RNA-Seq, BS-Seq, ChIP-Seq and Exome-Seq, and medical diagnostics data. He already have the experiences to setup standard pipeline analysis on super computer environment (at IMS UT) and apply analyses to these multi-omics dataset [Nature, Yoshida et al 2011; Nature Genetics, Fujimoto et al 2010]. Recently, he is also taking the responsibility to reveal the direct-reprogramming mechanism using HiTSeq technology on supercomputer with the collaboration with Dr. Suzuki [Nature; Sekiya et al 2011].

2019.4- He moved to Center for Genomic Medicine, Graduate School of Medicine, Kyoto University as Program-Specific Professor. The main research topic is genomics, omics and integrated analysis of large-scale life science data on supercomputer environment to reveal the hidden relationships in the biomedical field.

Study Field / Current Study Theme / Keywords
Bioinformatics, Genome Informatics, Computational Biology, Computer Science, Statistics, Big Data, HiTSeq, Pathway Modeling, Pathway Simulation, Omics Data Analysis, Medical Informatics, Single cell analysis, Integrated Analysis, Population Genetics, High Performance Computing, Lifelog, Genetics