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Wataru IWASAKI, Ph.D.
iwasaki AT bs.s.u-tokyo.ac.jp

  • Associate Professor at the University of Tokyo
  • - Department of Biological Sciences, Graduate School of Science
  • - Department of Bioinformatics and Systems Biology, Faculty of Science (adjunct)
  • - Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences (adjunct)
  • - Center for Earth Surface System Dynamics, Atmosphere and Ocean Research Institute (adjunct)
  • jsbi Lab Website

Research Topics

Our laboratory aims at providing new insights into life through bioinformatic approaches.

Technological innovations in the life science domain have enabled us to obtain and analyze massive amount of data that can unveil the underlying principles of life and its evolutionary history. While genomic data provide an overview of the history of life over hundreds of millions of years, other omic data illustrate how genomic sequences perform their functions about, for example, gene expression, regulation, and interactions. Pathway and network data represent diverse biological knowledge in a machine-understandable manner that permits large-scale computational analyses. Bioimaging and biologging data provide ways to quantitatively characterize phenotypes and behavior of organisms. Last but not least, metagenomic, ecogenomic, and environmental DNA data illustrate complex interactions between life and environments.

To understand life, it is fundamentally important to integrate and analyze these data comprehensively, not partially. In this context, utilizing deep understanding of both biology and informatics, we aim to uncover new concepts, insights, and laws behind life systems and ecosystems.

 Publications

Refer to Publication List in Brief.

 Joining Our Lab as a Graduate Student

We are accepting graduate students as faculty of the following departments in the University of Tokyo. We highly welcome those who majored bioinformatics and/or were involved in research projects related to bioinformatics during their undergraduate or master courses, and aim at earning a Ph.D. If you are interested in joining our lab, please email iwasaki AT bs.s.u-tokyo.ac.jp.

Department of Biological Sciences (Graduate School of Science, UTokyo)

  • Graduate School of Science provides admission, scholarship, and other information for international students. In addition, it provides several internship programs with financial aid (such as UTRIP) that should be helpful to prospective students.

Department of Computational Biology and Medical Sciences (Graduate School of Frontier Sciences, UTokyo)

Notes: We have experience in accepting students from outside of Japan. Japanese language is not mandatory if you have enough English skills; however, a will to learn Japanese would be necessary because it makes you enjoy Japan more and many optional classes are held in Japanese. As the University of Tokyo provides Japanese language classes, we usually encourage colleagues from abroad to take them. Also, we highly encourage international students to obtain scholarships because of financial support and credit for life in Japan. The best one would be Ministry of Education, Culture, Sports, Science and Technology (Monbukagakusho or "MEXT") Scholarship from the Japanese Government. Please consult with your local Japan Embassy for the selection information.

 Joining Our Lab as a Postdoctoral Fellow

If you are interested in pursuing research in our group, please email iwasaki AT bs.s.u-tokyo.ac.jp first. Information on our post-doc position availability may be posted in JREC-IN Portal, or we might have an open position even if there is no posted information. In addition, we may help you obtain fellowships such as Postdoctoral Fellowships for Overseas Researchers (Japan Society for the Promotion of Science) and Human Frontier Science Program Postdoctoral Fellowships.

Notes: We have experience in accepting Postdoctoral Fellows from outside of Japan. Japanese language is not mandatory if you have enough English skills; however, to enjoy life in Japan, a will to learn Japanese to some extent would be necessary. As the University of Tokyo provides Japanese language classes, we usually encourage colleagues from abroad to take them.

Profile (in 2017Apr)

2014Apr
Associate Professor at the University of Tokyo
- Department of Biological Sciences, Graduate School of Science
- Department of Bioinformatics and Systems Biology, Faculty of Science (adjunct)
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences (adjunct, reorganized from Department of Computational Biology in Apr 2015)
- Center for Earth Surface System Dynamics, Atmosphere and Ocean Research Institute (adjunct)
2011Jul
Assistant Professor (tenured, principal investigator position) at the University of Tokyo
- Center for Earth Surface System Dynamics, Atmosphere and Ocean Research Institute
- Department of Computational Biology, Graduate School of Frontier Sciences (adjunct)
2009Apr
Assistant Professor at the University of Tokyo
- Department of Computational Biology, Graduate School of Frontier Sciences
2007Apr
Research Fellow of the Japan Society for the Promotion of Science (DC1)

2009Mar Ph.D., Department of Computational Biology, the University of Tokyo
2007Mar Master of Science, Department of Computational Biology, the University of Tokyo
2005Mar Completed, Undergraduate Program for Bioinformatics and Systems Biology, the University of Tokyo
2005Mar Bachelor of Science, Department of Biophysics and Biochemistry, the University of Tokyo

 Professional Activities

Science Council of Japan

scj SCJ Website
Member

  • 2016Jan-2017Sep

Global Young Academy

gya GYA Website
Member

  • 2017May-

Institute for Chemical Research, Kyoto University

kuicr KUICR Website
Visiting Associate Professor

  • 2015Apr-2016Mar

Database Center for Life Science, Research Organization of Information and Systems

dbcls DBCLS Website
Project Collaborator

  • 2010Apr-

Japanese Society for Bioinformatics

jsbi JSBi Website
Vice President

  • 2017Apr-2018Mar

Board of Director (Councilor)

  • 2011Apr-2013Mar
  • 2013Apr-2015Mar
  • 2016Apr-2018Mar

Manager

  • 2014Apr-2015Mar
  • 2015Apr-2016Mar
  • 2016Apr-2017Mar
  • 2017Apr-2018Mar

Japanese Society of Microbial Ecology

jsme JSME Website
Councilor

  • 2015Apr-2016Dec
  • 2017Apr-2018Dec

Gender Equality and Diversity Committee

  • 2013Dec-

Gender Equality and Diversity Working Group

  • 2013Mar-2013Nov

The Molecular Biology Society of Japan

mbsj MBSJ Website
Career Path Committee Member

  • 2013Jan-2014Dec
  • 2015Jan-2016Dec

International Society for Computational Biology

sgmj ISCB Website

Society of Genome Microbiology, Japan

sgmj SGMJ Website

Society of Evolutionary Studies, Japan

sesj SESJ Website

Young Researchers Group for Computational/Omics/Systems Biology in Japan

bioinfowakate Bioinfowakate Website
President

  • 2009Feb-2011Mar

Board Member

  • 2009Feb-2015Mar

NGS-Field (Japanese Community for Researches Using NGS)

ngsfield NGS-Field Website
President

  • 2014Feb-2016May

Board Member

  • 2010Oct-

Scientific Reports

Scientific Reports Website
Editorial Board Member

  • 2017Feb-

Other Activities

2012Dec- Mendeley Advisor

 Conference Committees

Preparatory Committee, The Joint Meeting of Japanese Environmental Microbiology-related Associations 2017 (Aug 2017, Kawauchi Campus of Tohoku University, Sendai, Japan)

Conference Chair Advisor, The 5th Meeting of Japanese Community for Researches Using NGS (May 2017, Sendai International Center, Sendai, Japan)

Organizing Committee, The 10th Annual Meeting of Society of Genome Microbiology, Japan (Mar 2016, Ookayama Campus of Tokyo Institute of Technology, Tokyo, Japan)

Program Committee, The 4th Joint Conference on Informatics in Biology, Medicine, and Pharmacology. (The 2015 Annual Conference of the Japanese Society for Bioinformatics) (Oct 2015, Uji Campus of Kyoto University, Uji, Japan)

Conference Chair, The 4th Meeting of Japanese Community for Researches Using NGS (Jul 2015, Tsukuba International Congress Center, Tsukuba, Japan)

Program Committee, The 25th International Conference on Genome Informatics (GIW2014) (Dec 2014, Tokyo, Japan)

Organizing Committee, The 37th Annual Meeting of the Molecular Biology Society of Japan (Nov 2014, Pacifico Yokohama, Yokohama, Japan)

Organizing Member, The 5th Meeting of Young Researchers Group for Computational/Omics/Systems Biology in Japan (Feb 2014, Kemigawa Seminar House of the University of Tokyo, Chiba, Japan)

Organizing Committee, The 2nd Joint Conference on Informatics in Biology, Medicine, and Pharmacology. (The 2013 Annual Conference of the Japanese Society for Bioinformatics) (Oct 2013, Tower Hall Funabori, Tokyo, Japan)

Organizing Member, The 3rd Meeting of Japanese Community for Researches Using NGS (Sep 2013, Kobe International Conference Center, Kobe, Japan)

Organizing Member, The 4th Meeting of Young Researchers Group for Computational/Omics/Systems Biology in Japan (Mar 2013, National Institute for Basic Biology, Okazaki, Japan)

Organizing Committee and Program Committee, The 1st Joint Conference on Informatics in Biology, Medicine, and Pharmacology. (The 2012 Annual Conference of the Japanese Society for Bioinformatics) (Oct 2012, Tower Hall Funabori, Tokyo, Japan)

Program Committee, Recommender System Challenge (RecSysChallenge 2012), ACM Recommender Systems 2012 (Sep 2012, Dublin, Ireland)

Organizing Member, The 2nd Meeting of Japanese Community for Researches Using NGS (May 2012, Hotel Hankyu Expo Park, Suita, Japan)

Organizing Member, The 3rd Meeting of Young Researchers Group for Computational/Omics/Systems Biology in Japan (Oct 2011, National Institute for Basic Biology, Okazaki, Japan)

Organizing Member, The 1st Meeting of Japanese Community for Researches Using NGS (May 2011, Atami New Fujiya Hotel, Atami, Japan)

Advisory Committee, 4th Asian Young Researchers Conference on Computational and Omics Biology (Dec 2010, Biopolis, Singapore)

Organizing Member, The 2nd Meeting of Young Researchers Group for Computational/Omics/Systems Biology in Japan (Oct 2010, National Intitute of Genetics, Mishima, Japan)

Organizing Committee, 3rd Asian Young Researchers Conference on Computational and Omics Biology (Mar 2010, National Cheng Kung University, Tainan, Taiwan)

Organizing Member, The 1st Meeting of Young Researchers Group for Computational/Omics/Systems Biology in Japan (Apr 2009, National Intitute of Genetics, Mishima, Japan)

Conference Chair, The 2nd Taiwan-Japan Young Researchers Conference on Computational and Systems Biology (Nov 2008, Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan)

Organizing Committee, The 1st Japan-Taiwan Young Researchers Conference on Computational and Systems Biology (Mar 2008, National Tsing Hua University, Hsinchu, Taiwan)

Note: The general introduction to AYRCOB can be found here.

Tools and Databases

MitoFish & MitoAnnotator

MetaMetaDB

  • MetaMetaDB Website
  • MetaMetaDB is a 16S rRNA database for revealing which environments the species bearing the query 16S rRNA(s) can be found.

GroupTracker

  • GroupTracker Website
  • GroupTracker is a multiple animal tracking system that tracks individuals under severe occlusion.

TogoDoc Client

  • togodoc TogoDoc Client Website
  • Efficient management and smart recommendation of life science literature, for Windows and MacOSX.

TogoDoc Mobile

Wheel Tree

  • wheeltree Wheel Tree Website
  • Wheel Tree is an Intuitive, Informative, and Most Balanced representation of phylogenetic trees.

Arabimarklet: Useful Bookmarklets for Plant Researchers

NaviCluster

  • navicluster NaviCluster Website
  • Interactive navigation of large and complicated biological networks, in a Google-Maps like manner.

NaviClusterCS

MOCCS (Motif Centrality Analysis of ChIP-Seq)

  • MOCCS Website
  • A bioinformatic method that enumerates and evaluates all the significant DNA-binding motifs based on ChIP-Seq datasets.