Computational Biology Research Center[CBRC]

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Voice of a Researcher

Hear from our researchers about the type of research activities they participate in, and reasons why they work at the Computational Biology Research Center.

Kana SHIMIZU Kana SHIMIZU
Born in Tokyo, 1978.
Senior Research Scientist, RNA Informatics Team
Computational Biology Research Center (CBRC)
Doctorate received from the Graduate School of Science and Engineering, Waseda University
The joint research during my student days was a big motivation.
− First, please talk a little about your background and what led you to CBRC.

I majored in computer science at university. I was in a research lab that respected the independence of students, so students each had their own research themes and subjects. We conducted research in various fields ?image processing, music information retrievaloverlay network, etc. I chose DNA analysis as my research subject. This was just when the deciphering of the human genome sequence was a big topic. That got me interested in biology, which was a big reason why I chose DNA analysis.

When I told the lab professor that I wanted to move ahead into the field of bioinformatics, he recommended that I participate at RIKEN. There, I was able to do research on analyzing the protein coding region of mouse DNA, and my interest in bioinformatics continued to grow. After that, when I was doing research for my doctorate, I was introduced to CBRC, where I came up doing joint research. And afterwards I stayed on at CBRC, where I've been continuing my research ever since. That's my background.

Excitement in new discoveries that arise from the analysis of information
− Did you feel any resistance or disinclination about going from computer science to biology?

When I thought of biology as being just another application, I didn't have much resistance to it. Of course, my overall knowledge of biology is much less than that of those who have specialized in the field. However, when it comes to solving particular problems, such as predicting the location of exon-intron structures of genes, or predicting the three-dimensional structure of proteins, you can succeed to a certain extent if you acquire the specific knowledge around the problem. But if you want to go further and do more than just simple data mining, then, I think, you have to have deeper knowledge and sensibility about biology. Bioinformatics is an interdisciplinary field among many disciplines including biology and computer science. So, I think it's very important to have a balanced approach: to conduct research without relying overly much on analytical tools (computer science), and with an awareness of the objective (biology). I haven't yet been able to master that approach. To do so, I strongly feel that daily effort is necessary.

Bioinformatics, like research focused on graphics, music and other such information, is a form of data mining. But, unlike those other fields, bioinformatics is not particularly glamorous and might even seem a little austere. However, the areas where research results are linked to discoveries of new knowledge are extremely fascinating.

Our goal is to contribute to the field of biology
− What subjects have you researched since you joined CBRC?

The first research I did was for the CASP6 of 2004. It involved creating a program for predicting protein disorder regions. The results I achieved were rather mediocre (laughs). But the experience in CASP6 served to motivate me, so I put a lot of energy into producing a program (POODLE) for CASP7, the continuation of CASP6. That was very rewarding. Our team's efforts were highly regarded, and I was able to experience a sense of achievement. I felt that I was able to contribute to research in biology by creating a tool that many biologists could use.

Since then, I've been continuing my research with the aim of obtaining new biological knowledge, because I didn't want to end our study with just development of program, but I wanted to make use of the program to find new biological knowledge which can contribute to the research community. One achievement that resulted from this was our latest paper which was selected for Faculty of 1000 Biology*1. In that paper, we reported how we were able to determine that the interactions between disordered proteins were significantly frequent. I was gratified that specialists active in the field of biology were interested in our findings.

*1: Faculty of 1000 Biology is an online system, used by research institutions worldwide, that evaluates papers published in the biological sciences. It divides biology into 70 fields, and a few dozen leading researchers in each field choose and recommend the best of the latest papers in that field.

The high degree of freedom in choosing research subjects is a big advantage.
− What are the advantages of conducting research at CBRC?

First and foremost, I would say, is the high degree of freedom that we have in choosing research subjects. Having a boss and then conducting research based on his instructionsthere is almost none of that. This research is important. I'd like to do it. If you can show that kind of conviction, then, with the environment at CBRC, you can pursue your research quite freely, and you'll also be able to obtain various kinds of support necessary for achieving your goal.

Another virtue of CBRC is that it's a place where there are numerous specialists from the fields of both biology and computer science. As you pursue your research, you can get advice about it from a lot of people. Every time I talk with researchers working at CBRC, I come away with new knowledge and a sense of amazement.

A wonderful environment for self-reliant researchers who enjoy a sense of tension
− What kind of people would you prefer to participate at CBRC?

CBRC is a place where you can pursue research freely. On the other hand, it's a place where nothing gets started if you don't have a clear sense of purpose. If you don't have your own goals and aren't self-reliant, you might not be able to appreciate CBRC's virtues. But if you're a self-starter rather than someone who waits to be given instructions, you can use the environment at CBRC to enormous advantage.

CBRC is also a place where you're asked to produce results in a relatively short period of time. To grapple for decades with accomplishing a single purpose is one way of doing research. But setting a big goal that is decades in the future while producing certain interim results in a span of one to two years and making them public for others to use, is what I feel is asked of us at CBRC. I think other research institutions are probably the same, but at CBRC we go about our research feeling a certain amount of tension. I would like people who can enjoy the tension, one who can convert the tension to a challenge, to participate at CBRC.

(Note: This interview was conducted in December 2009.)
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