Graduate School of Science, Nagoya City University
Our goal
How do "brain functions"—such as perception, memory, emotion, and decision-making—arise from a network of nerve cells? To reveal its basic principle, we study the nematode C. elegance, the roundworm with a simple brain.
Our strategy
To understand how the brain functions, it is critical to rigorously quantify sensory stimuli, behavioral responses triggered by the stimuli, and neural activities in between, and to reveal the relationships among them. We measure and analyze those multiple aspects of worm's sensory behavior with the robot and machine learning technologies through collaborations with researchers in the fields.
・Measuring dynamic odor gradient formed by volatilization and diffusion in a plate: Yamazoe-Umemoto et al., Bio-protocol 2018
・Simultaneous measurement of behavior and neural activity of a freely behaving worm in a virtual odor gradient: Tanimoto et al., eLife 2017 [F1000Prime] [EurekAlert]
・Single cell-targeted regulation of neural activity of a freely behaving worm by optogenetics: Tanimoto et al., Sci Rep 2016
・A versatile method for analyzing animal trajectory by a hybrid machine learning technique: Yamazaki et al., Front Neurosci 2019 [EurekAlert]
・Imaging whole brain activities of a worm by deep learning-based 3D cell tracking algorithm: Wen et al., eLife 2021 [eLife digest]
・Analyzing whole brain activities with machine learning-based modeling: Wen and Kimura, Jpn J Appl Phys 2020
Using the methods above, we have found the mechanisms of brain functions that can be conserved in higher animals.
・Odor learning modulated by dopamine signaling: Kimura et al., J Neurosci 2010
・Neuropeptide signaling for memory acquisition and dopamine signaling for memory execution: Yamazoe-Umemoto et al., NSR 2015
・Functional diversification of dopamine neurons: Tanimoto et al., Sci Rep 2016
・Cellular and molecular mechanisms for decision-making: Tanimoto et al., eLife 2017 [F1000Prime]
For all the publications by the PI, please see Google Scholar and Publons.com.
Collaborators
We are conducting joint research with various research institutes.
Overseas: Columbia University (USA), University of Edinburg (UK), etc.
Domestic: Osaka University, Nagoya University, Nagoya Institute of Technology, Tohoku University, National Institute for Physiological Sciences, National Institute for Basic Biology, RIKEN, etc.
Our education
・ Original research themes using various methods, such as molecular genetics, imaging, programming, electronic circuit
・ Bi-weekly 1:1 meetings
・ Joint meeting with other labs in Nagoya Univ.
Our team
Would you like to join our team with state-of-the-art technologies, such as robotic microscopes, whole brain imaging, and machine learning techniques, at Nagoya, one of the biggest cities in Japan? Please send an email to the PI!
Our achievement
News
2025/10/1
Two B3 students have joined us! And another is currently visiting for some experiments...
Dr. Jang promoted as a Specially Appointed Assistant Professor.
2025/8/21
At nFuture2025, Ryoga Suzuki (D2) received the Oral Presentation Award, and Kaho Ieda (D1) received the Poster Presentation Award❗️
2025/7/31
Dr Aoki has been selected for the JSPS Research Fellowship for Postdoctoral Researchers (RPD) in 2026‼️🎉
2025/7/24-27
Kimura (M2), Butsugan (M1), and Mashiat (M1) attended the 48th Annual Meeting of the Japanese Neuroscience Society held in Niigata.
2025/7/16-18
Ieda (D1) attended the 58th Joint Meeting of the Japanese Society for Developmental Biology held in Aichi.
20256/28-7/2
Kimura (D2), Suzuki (D1), and Ieda (D1) attended the International Worm Meeting held in the US.
2025/6/23
Our second paper this year on cutting-edge microscopy technology—measuring neural activity across the entire nematode brain and mapping it to neural circuit structures—has been published❗️The first paper was a collaboration with researchers in the US and elsewhere; the second is from the Kimura Lab. [First Paper][Second Paper]
2025/4/1
This year, one member graduated in March, and one new member joined us in April.
2024/10/7
Professor Gary Ruvkun (Harvard University, USA), who was Kimura's PI during his study abroad, won the Nobel Prize in Physiology or Medicine‼️🎉🏆
2024/10/1
One M1 (Japanese Government Scholarship student) and two undergraduate 3rd-year students joined our lab❗️
2024/9/4-5
We hosted the NIPS Research Seminar: “Large-Scale Brain Activity Measurement - What Are We Measuring and Where Are We Going?”
2024/8/24
At the 26th Workshop on Active Amines, Kimura gave an invited lecture.
2024/7/25-26
At Neuro2024, Dr. Ikejiri (alumnus) received the 2024 NSR Best Paper Award, and D1 Suzuki and M1 Butsugan presented posters.
2024/6/22
M2 Ieda presented a poster at the 57th Annual Meeting of the Japanese Society for Developmental Biology and received the Outstanding Poster Award. 🏆🎉 [Link]
2024/4/1
This year, four members graduated in March, and four new members joined in April, resulting in about a 30% change in our team. Is this the beginning of Season 2 for the Kimura Lab at NCU⁉️
2024/3/12
Dr. Yosuke Ikejiri's PhD thesis paper, published in Neuroscience Research, was selected for the 2024 Best Paper Award❗️ (We didn't even submit it, and it was completely unexpected, so we were truly shocked...) [Link]
2024/2/20
We held WorMING (Worm Meeting of Innovative Neuroscience Groups in Japan) and the subsequent social gathering at TAKI Teria on campus.
2024/2/19
Kimura was selected for the Development Research Grant from the Nakatani Medical Engineering and Measurement Technology Promotion Foundation. [Link]
2024/2/16
M2 student Suzuki received the Outstanding Presentation Award at the Graduate School's Master's Thesis Presentation Session. 🏆🎉
2023/10/2
Two B3 students have joined us. Please give them a warm welcome!
2023/9/25
Ling Fei Tee, who was a graduate student until last year, presented her doctoral thesis on August 29 and was awarded her PhD on September 25. 👩🏻🎓 🎉
2023/9/22
We hosted WorMING (Worm Meeting of Innovative Neuroscience Groups in Japan) at Nagoya City University. After the meeting, we held a social gathering at TAKI Teria on campus.
2023/9/19
Kimura was selected as the principal investigator for the JST CREST “Cell Manipulation” project. [Related Page]
August 31, 2023
The “Intestinal and Extramural Tissue Communication” workshop was held at Nagoya University.
August 22-24, 2023
Kimura revisited the Hillman Lab at Columbia University, USA, as part of the MEXT International Collaborative Research Enhancement (B) program.
August 18, 2023
It was known that the nematode C. elegans can sense stimuli, remember them, and select appropriate actions (“decision-making”). This time, we have discovered for the first time that C. elegans may also possess a prototype of “emotion”!❗️ This is the result of collaborative research led by Tee, an international student from Malaysia, along with graduate students from our lab and Professor Young from Northeastern University in the USA. [Paper]
August 1-4, 2023
At the 46th Annual Meeting of the Japanese Neuroscience Society, M2 Suzuki gave an oral presentation, while M2 Aihara and M1 Kimura presented posters.
August 7, 2023
Kimura delivered an intensive lecture titled “Redefining Model Organisms 2023” for undergraduate and graduate students at the University of Tokyo's Graduate School of Arts and Sciences.
2023/7/23
At the 56th Annual Meeting of the Japanese Society for Developmental Biology, M1 student Ieda presented a poster.
2023/5/22
We announced “Seg2Link,” software designed to efficiently delineate cell regions by combining artificial intelligence techniques like U-Net for processing 3D image data. This is a result of collaborative research between former researcher Wen, who transferred to RIKEN BDR, and Professor Sawamoto's group at our university's Graduate School of Medicine. [Paper]
May 14, 2023
Following the paper by Ikejiri published in February, our laboratory's activities were featured in the Nikkei newspaper.
February 1, 2023
When nematode odor receptor neurons experience an unpleasant odor, their activity pattern changes as a “gain adjustment.” Analysis using a mathematical model revealed that this change can be explained solely by the “elimination of the second derivative term of odor concentration.” Furthermore, genes likely involved in this “term elimination” were identified. This is graduate student Ikejiri's research result, a collaborative effort with Professor Yasushi Iwatani of Hirosaki University (with whom we worked on “Biological Mobility Informatics”) and Professor Koichi Fujimoto, who was Kimura's neighbor when he had a lab at Osaka University. [Paper]
2023/1/11
Kimura gave a talk at the Nagoya City University Brain Science Institute IBS Seminar.
2022/12/12
Kimura gave a talk at a mini-session of the ExCELLS Symposium.
2022/10/7
We secured international collaborative research funding for a “microscope capable of ultra-high-speed 3D imaging while automatically tracking moving nematodes.”
2022/10/1
Three new undergraduate students joined our lab.
2022/8/8
Kimura delivered an intensive lecture titled “Redefining Model Organisms 2022” for undergraduate and graduate students at the University of Tokyo's Graduate School of Arts and Sciences.
2022/4/15
Invited by Professor Etsuo Suzaki of Juntendo University Graduate School of Medicine, we conducted a lab tour and seminar.
2022/3/31
Dr. Wen Chentao, who brought DX to our lab as a Super Postdoctoral Fellow for five years, has transferred to Kobe as an SPDR at RIKEN. Thank you so much for everything. We look forward to your continued support.
2021/12/13
Kimura gave an invited talk at the Osaka University Protein Research Institute Seminar “Exploring the Brain through Diverse Dopamine Neurotransmission”.
2021/10/1
New undergraduate students have joined, bringing our group to a total of 13 members.
September 17, 2021
New collaborative research with Associate Professor Takuya Maekawa from Osaka University's Information Science: Using the “attention” mechanism of deep learning, we discovered common behavioral abnormalities across humans (Parkinson's disease patients), mice, beetles, and nematodes with abnormal dopamine transmission, transcending evolutionary boundaries. [Link]
2021/9/9
NHK-BS “Humanience” featured research results from Tanimoto, Zheng et al. (Sci Rep 2016).
