The field of biology has expanded from the traditional approaches of focusing on specific organisms and phenomena to utilizing data science approaches in the pursuit of obtaining a comprehensive understanding of life. Under this context, our laboratory employs interdisciplinary approaches, including but not limited to: bioinformatics, laboratory experiments, mathematics, and field samplings to study evolution and ecology of diverse life forms, and to develop novel biotechnological methods.

• Evolutionary and ecological bioinformatics
• Evolution of genomes and life systems
• Microbial dark matter, non-model organisms
• Microbial ecology, metagenomics
• Environmental DNA

In particular, we are aiming at the following fundamental research questions:
(1) How have the elaborate and complex living systems evolved?
(2) How are the ecosystems stably maintained?
(3) What unknown gene functions have evolved in 4 billion years?
(4) What is the methodology to reveal unknown gene functions from big data?
(5) How many genes are being born on the earth?

Please refer to our Full Publication List.

Selected papers

• Mikami and Iwasaki. Methods in Ecology and Evolution (2021)
  The flipping t‐ratio test: phylogenetically informed assessment of the Pareto theory for phenotypic evolution.
• Matsui and Iwasaki. Systematic Biology (2020)
  Graph splitting: A graph-based approach for superfamily-scale phylogenetic tree reconstruction.
• Hiraoka, [...], and Iwasaki. Nature Communications (2019)
  Metaepigenomic analysis reveals the unexplored diversity of DNA methylation in an environmental prokaryotic community.
• Needham, Yoshizawa, Hosaka, [...], Iwasaki*, and Worden*. PNAS (2019)
  A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators.
• Cosentino and Iwasaki. Bioinformatics (2019)
  SonicParanoid: fast, accurate and easy orthology inference.
• Kumagai, [...], and Iwasaki. The ISME Journal (2018)
  Solar-panel and parasol strategies shape the proteorhodopsin distribution pattern in marine Flavobacteriia.
• Sato, [...], and Iwasaki. Molecular Biology and Evolution (2018)
  MitoFish and MiFish pipeline: a mitochondrial genome database of fish with an analysis pipeline for environmental DNA metabarcoding.
• Sriswasdi, Yang, and Iwasaki. Nature Communications (2017)
  Generalist species drive microbial dispersion and evolution.
• Sriswasdi, [...], and Iwasaki. Genome Research (2016)
  Global deceleration of gene evolution following recent genome hybridizations in fungi.
• Miya, [...], and Iwasaki. Royal Society Open Science (2015)
  MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species.
• Aoki, Ito, and Iwasaki. Molecular Biology and Evolution (2013)
  From beta- to alpha-proteobacteria: the origin and evolution of rhizobial nodulation genes nodIJ.
• Iwasaki et al. Molecular Biology and Evolution (2013)
  MitoFish and MitoAnnotator: A mitochondrial genome database of fish with an accurate and automatic annotation pipeline.
• Praneenararat, Takagi, and Iwasaki. Bioinformatics (2011)
  Interactive, multi-scale navigation of large and complicated biological networks.
• Iwasaki and Takagi. PLOS Genetics (2009)
  Rapid pathway evolution facilitated by horizontal gene transfers across prokaryotic lineages.
• Iwasaki and Takagi. Bioinformatics (2007)
  Reconstruction of highly heterogeneous gene-content evolution across the three domains of life.
• Iwasaki et al. Journal of Molecular Biology (2006)
  Structural basis of the water-assisted asparagine recognition by asparaginyl-tRNA synthetase.

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 by pursuing the research goals described above. If you are interested in joining our lab, please examine our publication list and email the Principal Investigator.

• Department of Integrated Biosciences (Graduate School of Frontier Sciences, UTokyo).
  • Graduate School of Frontier Sciences provides instructions for international students, as well as Summer Internship Program (UTSIP Kashiwa) for undergraduate students. Note that Iwasaki Lab is named as Laboratory of Computational Evolutionary Biology in Department of Integrated Biosciences.
• Department of Biological Sciences (Graduate School of Science, UTokyo).
  • Graduate School of Science provides admission, scholarship, and other information for international students.

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.

If you are interested in pursuing the research goals described above in our laboratory, please examine our publication list and email the Principal Investigator. 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 Research in Japan, 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.

Our laboratory is developing bioinformatic software and databases such as:

• MitoFish & MitoAnnotator: Fish mitochondrial genome database and annotator
• MiFish Pipeline: Pipeline for analyzing fish environmental DNA data
• SonicParanoid: Fast, accurate, and easy-to-use software tool for the identification of orthologs
• Graph Splitting: Phylogenetic tree reconstruction without multiple sequence alignment
• ProkAtlas: Inference of habitat environment of prokaryotes from 16S rRNA gene sequences.
• Logicome Profiler: Exhaustive detection of triplet logic relationships from a binary matrix dataset
• MetaMetaDB: Sequence database for revealing microbial habitats
• GroupTracker: Multiple animal tracking system
• MOCCS: Software to find all significant DNA-binding motifs based on ChIP-Seq data
• Image Manipulation Detector: Software for automatically detecting manipulated images in life science

For other software and databases, refer to Wataru Iwasaki's Webpage.

Our laboratory is located in GSFS Bioscience Building on the Kashiwa Campus of the University of Tokyo.
Address: Room 601, GSFS Bioscience Bldg, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-0882, JAPAN

Getting to the Kashiwa Campus (PDF)
UTokyo Shuttle Bus (Kashiwa Campus - Kashiwanoha Station) (page in Japanese)

GSFS Bioscience Building on Google Maps

Notes: If you use Tobu bus, please get off at either Todai-mae or Todai-nishi Stop. If you use UTokyo shuttle bus, please get off at the first stop (Kibantou-mae Stop). If you take a taxi from Kashiwanoha-campus station, it will take less than 10 minutes and cost about 1,000 JPY.