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Gene Regulation Lab
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The lab analyzes genome information to find useful genes.
AboutAbout the lab
Finding useful genes by advancing gene function information
The Gene Regulation Lab uses information science methods to analyze genome sequence data and gene expression data from a wide range of organisms, from microorganisms to humans.
The lab also comprehensively integrates data such as microRNA, peptides, proteins, and phenotypes, and uses bioinformatics to clarify the relationship between the phenotype and genotype of organisms.
It also works on developing methods for predicting gene function and on decoding genome sequences.
Key terms
- Bioinformatics
- A field that analyzes biological data, such as genome sequences and gene expression, using information science methods
- Phenotype
- The characteristics that appear in an organism, such as its form and traits; its relationship to differences in genome sequence (genotype) can be investigated
- Single nucleotide polymorphism (SNP)
- A polymorphism in the genome's nucleotide sequence in which only a single nucleotide differs between individuals or varieties
ResearchResearch themes
The lab aims to find useful genes by advancing gene function information. To do so, it works on collecting and analyzing gene function information, analyzing polymorphism information, developing knowledge discovery methods, and comprehensively analyzing transcripts.
*Illustrative imageCollecting gene function information to find useful genes
The lab collects information on gene function, performs secondary analysis, and develops methods for estimating the function of genes whose function is unknown. It clarifies the relationship between gene sequences and the characteristics of organisms (genotype and phenotype).
*Illustrative imageFinding useful genes from polymorphism information
The lab studies how genome sequence differences between individuals and varieties (polymorphisms) affect gene function. For single nucleotide polymorphisms (SNPs), it infers promoters and enhancers with deep learning and predicts three-dimensional structures with AlphaFold2 to search for "functional SNPs."
*Illustrative imageFinding useful genes with knowledge discovery methods
Using accumulated gene function information, the lab performs knowledge discovery with graph networks, deep learning, and Semantic Web technologies. It develops methods for searching for useful genes.
*Illustrative imageComprehensive analysis of transcripts and gene function
The lab analyzes comprehensive gene expression profile data for crops used in medicines, foods, and beverages. It aims to clarify gene regulation mechanisms and estimate functional genes, and for medicinal plants it also identifies the genes that produce medicinal compounds.
MembersFaculty
The Gene Regulation Lab consists of a professor, research fellows, technical staff, administrative staff, doctoral, master's, and undergraduate students, and research students.As of 2026
- ProfessorHideki Hirakawa
VoicesStudent voices
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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: “Genome Sequencer2” Database Center for Life Science (DBCLS) / CC BY 3.0 (cropped)
- Collecting gene function information to find useful genes: “DNA-Sequencers from Flickr 57080968” Flickr user jurvetson / CC BY 2.0 (cropped)
- Finding useful genes from polymorphism information: “Point-Mutation-Sickle-Cell-Normal and Mutated-Hemoglobin” Thomas Samuel for ACC-BioinnovationLab / CC BY-SA 4.0 (cropped)
- Finding useful genes with knowledge discovery methods: “Flow chart representation of Knowledge Discovery Process” Dipankar Sengupta, Meemansa Sood, Poorvika Vijayvargia, Sunil Hota, Pradeep K Naik / CC0 (cropped)
- Comprehensive analysis of transcripts and gene function: “Summary of RNA-Seq” Thomas Shafee / CC BY 4.0 (cropped)
- Related lab (Plant Production Physiology Lab): “Ice Plant ( )” dionysia / CC BY-SA 2.0 (cropped)
- Related lab (Water Environment Lab): “Flood under the Old Route 49 bridge crossing over the South Yuba River in Nevada City, California” Kelly M. Grow/ California Department of Water Resources / Public domain (cropped)
- Related lab (Food Chemistry Lab): “Vorspeise mit Dolma und Tzatziki” Kritzolina / CC BY-SA 4.0 (cropped)
- Related lab (Forest Ecosphere Environmental Resource Sciences Lab): “Lentinula edodes 20101113 a” Batholith (talk) / Public domain (cropped)
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