Supporting research to uncover many 'differences' with programs designed to find them.
The complete set of genetic information in an organism is called the genome.
It consists of DNA, and differences in the sequence of four bases determine the differences among species.
Within the genome, there are tens of thousands of regions called genes in mammals, including humans, and thousands in bacteria such as lactic acid bacteria.
The activity of genes in the genome varies depending on the person, tissue, condition, or cell.
Even within the same individual, gene activity differs between organs, and within the same tissue, it differs between states such as cancerous and normal.
For example, muscular dystrophy is a disease caused by abnormalities in the dystrophin gene, which produces a protein essential for maintaining muscle function.
It is known that this gene is less active in diseased tissue than in normal tissue (this is referred to as reduced expression).
In life sciences, studies called transcriptome analyses, which examine such differences in gene activity, are actively conducted.
We are developing methods and software to efficiently detect these kinds of 'differences.'
Many research findings using our programs have been published in academic papers.
Educational approach
Conducting theoretical research gracefully while contributing to advancing research across Japan.
Our laboratory was established in 2022 as the Laboratory of Bioinformatics Analysis in collaboration with the Department of Applied Biological Chemistry.
There are no positions for undergraduates; only graduate students are accepted.
It is a laboratory that values independence, allowing research to be conducted at one’s own pace with just a laptop.
As we are theory-oriented, it is desirable to have at least one 'yes' to being good at computers, enjoying programming, excelling in statistics, or understanding mathematical formulas.
Of course, our graduate school welcomes students from diverse backgrounds, and we work together to choose research themes suited to each student's skills and interests.
Experimental techniques to comprehensively examine gene expression have existed for over 20 years and continue to evolve.
However, even today, the overall framework of identifying genes with expression differences between conditions such as cancerous and normal remains unchanged.
We have engaged in diverse activities, including developing methodologies and GUIs for better detection of such 'differences,' publishing textbooks in related fields, and providing web-based materials that allow genome and transcriptome analysis using the R environment with simple copy-paste commands.
We will continue to respond to needs from various places and aim to foster individuals who can empathize with those who do not understand.
Vision for industry-academia collaboration
Remaining unique through our strengths in bioinformatics education and support.
Agricultural Bioinformatics Research Unit, to which I belong, is a facility in our graduate school with a primary mission of education in bioinformatics.
Bioinformatics can be regarded as a life science-specialized version of data science, which has recently become a buzzword.
I have conducted many large-scale training sessions open to corporate researchers, and my strength lies in extensive experience and achievements in recurrent education.
Of course, nowadays, one can Google the wealth of data analysis know-how accumulated on platforms like Qiita, so I believe the educational needs are also changing.
Precisely because we live in an era where pressing a run button yields results, there may be a growing need to revisit and understand the formula-heavy algorithms that once frustrated us as students.
In our recently published textbook, we provide detailed explanations of formulas in accompanying web materials, and we hope these will be put to good use.
I have also served as a go-to consultant for researchers without nearby data analysis experts.
I will continue to contribute behind the scenes to advancing research throughout Japan.
