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Yamada Lab
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A lab that deciphers the functions of microbes from genome information.
AboutAbout the lab
Deciphering vast amounts of biological data with computers.
Yamada Lab analyzes the wide variety of information obtained from biological experiments by computer, in order to discover biological knowledge that is not yet known.
This type of research is called bioinformatics.
Because a single experiment can now yield an enormous amount of information, the lab develops methods to analyze it quickly and techniques to visualize multidimensional information in an easy-to-read form.
With genome information at the core, the lab connects diverse kinds of information and carries out its research in collaboration with bioscience researchers in Japan and abroad.
Key terms
- Bioinformatics
- A research field that analyzes data obtained from biological experiments by computer to discover new insights
- Metagenome
- Gene sequences extracted all together, along with the microbes living there, from an environment such as soil or the gut
- Semantic Web
- A framework that describes the meaning of data in a form computers can process and links pieces of information together
NewsLab news
View More ↗ResearchResearch themes
Microbes live in every kind of environment, from the stratosphere to rock several kilometers underground, but we know little about which microbes with which functions are doing what. With genome information at the core, the lab uses bioinformatics to connect many different kinds of information and aims to derive new biological insights.
*Illustrative imageMetagenomic analysis
The lab analyzes large volumes of gene sequences obtained directly from environments such as soil, the ocean, and the human gut. It focuses in particular on the human gut microbiota and on soil.
*Illustrative imageComparative genomic analysis
By comparing the genomes of gut microbes, pathogenic microbes, algae, and others, the lab discovers metabolic functions found only in particular species, as well as insights into evolution.
*Illustrative imageDevelopment of knowledge databases
To discover new knowledge from the rapidly growing volume of genome and metagenome information, the lab develops knowledge databases that apply Semantic Web technology.
*Illustrative imageHigh-speed search tools
To quickly search large-scale data such as metagenomic sequences, the lab builds tools such as GPU-based gene similarity search tools.
MembersFaculty
The members of Yamada Lab are faculty, PhD, master's, and undergraduate students, researchers, secretaries, administrative assistants, and technical staff.As of 2026
- ProfessorTakuji YamadaPublications ↗
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Report an errorAbout the images
The top and research theme images are illustrative and were not taken at the lab. They are cropped from Wikimedia Commons images. Cropped CC BY-SA images are provided under the same CC BY-SA license as the original (version shown on each line).
- Top image: “E coli at 10000x, original” Photo by Eric Erbe, digital colorization by Christopher Pooley, both of USDA, ARS, EMU. / Public domain (cropped)
- Metagenomic analysis: “Colonie batteriche o vita marina?” Chiara.marraccini / CC BY-SA 4.0 (cropped)
- Comparative genomic analysis: “Methicillin-Resistant Staphylococcus Aureus (MRSA) Bacteria colorized scanning electron micrograph - 22” NIAID / CC BY 2.0 (cropped)
- Development of knowledge databases: “BalticServers data center” BalticServers.com / CC BY-SA 3.0 (cropped)
- High-speed search tools: “A Complex Graphics Card” Nick Stathas / CC BY-SA 4.0 (cropped)
- Related lab (伊藤研究室): “CSIRO ScienceImage 11313 The CSIRO GPU cluster at the data centre” division, CSIRO / CC BY 3.0 (cropped)
- Related lab (佐藤研究室): “Aminoacyl-tRNA synthetase in complex with cognate tRNA” Oleksandr V. Savytskyi, Yaroslav V. Katrich / CC BY 4.0 (cropped)
- Related lab (藤研究室): “Xenopus laevis nucleosome, Histone H3.3C (2) 1AOI” Luger K, Mäder AW, Richmond RK, Sargent DF, Richmond TJ / CC0 (cropped)
- Related lab (澤田研究室): “Bacteriophage T5 2024 ps” Dr. Victor Padilla-Sanchez, PhD / CC BY-SA 4.0 (cropped)
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