Faculty at School of Natural Sciences

Koichi Kawakami

Koichi Kawakami

Distinguished Professor

School of Natural Sciences


Contact Information

Koichi Kawakami is a developmental biologist and geneticist specializing in zebrafish genetics, transgenesis, and neuroscience. He served for many years at the National Institute of Genetics (Japan), where he developed the Tol2 transposon-mediated transgenesis system and established extensive gene trap and enhancer trap resources for zebrafish. His research has focused on functional genomics, neural circuits, developmental biology, and disease models using zebrafish. He is currently a Distinguished Professor at Shiv Nadar Institution of Eminence, India, and continues to promote international collaborative research in zebrafish biology.

My research focuses on the development and application of innovative genetic technologies in zebrafish to advance our understanding of vertebrate biology and human disease.

A major area of interest is the development of useful transgenic fish through transposon-mediated and CRISPR/Cas9-mediated genome engineering. I am committed to generating and disseminating valuable transgenic zebrafish resources and promoting international collaborative research by making these resources widely available to the scientific community.

My research also aims to elucidate the neuronal circuits and cellular mechanisms that regulate complex vertebrate behaviors, including learning, memory, feeding, and social behavior. By combining transgenic technologies, genome editing, functional imaging, and cell-specific manipulation, I seek to reveal the organization and function of neural circuits and to investigate the evolutionary conservation and diversification of vertebrate brain structures.

Another important research interest is the application of transgenic zebrafish to biomedical research, including high-throughput screening of small molecules that regulate gene expression, disease modeling, regenerative biology, and drug discovery. Through these studies, I aim to bridge basic developmental biology with translational research.

Ultimately, my goal is to establish next-generation functional genomic platforms that integrate advanced genetic technologies, quantitative phenotyping, and international collaboration to uncover fundamental principles of vertebrate biology and contribute to improvements in human health.

Degree

Year

Subject

University/Institution

% of marks

 B. Sc.

 1982

 Biology

 Univ of Tokyo

 N/A

 M. Sc.

 1984

 Biology

 Univ of Tokyo

 N/A

 Ph. D.

 1987

 Biology

 Univ of Tokyo

 N/A

S.No.

Positions held

Name of the Institute

From

To

Pay Scale

 1

Assistant Professor

Univ of Tokyo

1987

1994

 N/A

 2

Postdoctoral Fellow

Massachusetts Institute of Technology

1994

1996

 N/A

3

Postdoctoral Associate

Massachusetts Institute of Technology

1996

1997

N/A

4

Assistant Professor

Univ of Tokyo

1997

2002

N/A

5

Associate Professor

National Institute of Genetics

2002

2006

N/A

 

6

Professor

National Institute of Genetics

2006

2025

N/A

7

Researcher

Choju Medical Institute

2025

2026

N/A

8

Distinguished Visiting Professor

Shiv Nadar Institution of Eminence

2025-

 

N/A

S.No

Name of Award

Awarding Agency

Year

1

Christiane Nüsslein-Volhard Award

European Zebrafish Society

2021

2

Commendation for Science and Technology

The Minister of Education, Culture, Sports, Science and Technology, Japan

2023

Koichi Kawakami is internationally recognized for developing the Tol2 transposon-mediated transgenesis system, which has become one of the standard tools for vertebrate functional genomics, particularly in zebrafish. He has established extensive gene trap and enhancer trap resources and the publicly available zTrap database, which are widely used by researchers worldwide. He served as a Founding Board Member of the International Zebrafish Society (IZFS) and the Zebrafish Disease Models Society (ZDMS) from 2014 to 2021. Nationally, his work has played a leading role in advancing zebrafish genetics and functional genomics in Japan through the development and distribution of research resources and collaborative research.

International Zebrafish Society (IZFS)

Zebrafish Disease Models Society (ZDMS)

  1. Kawakami, K., and Hopkins, N.* Rapid identification of transgenic zebrafish. Trends in Genetics 12, 9-10 (1996).
  1. Gaiano, N., Allende, M., Amsterdam, A., Kawakami, K., and Hopkins, N.* Highly efficient germ-line transmission of proviral insertions in zebrafish. Natl. Acad. Sci. USA 93, 7777-7782 (1996).
  1. Gaiano, N., Amsterdam, A., Kawakami, K., Allende, M., Becker, T., and Hopkins, N.* Insertional mutagenesis and rapid cloning of essential genes in zebrafish. Nature 383, 829-832 (1996).
  1. Kawakami, K.*, Koga, K., Hori, H., and Shima, A. Excision of the Tol2 transposable element of the medaka fish, Oryzias latipes, in zebrafish, Danio rerio. Gene 225, 17-22 (1998).
  1. Kawakami, K.*, and Shima, A. Identification of the Tol2 transposase of the medaka fish Oryzias latipes that catalyzes excision of a nonautonomous Tol2 element in zebrafish Danio rerio. Gene 240, 239-244 (1999).
  1. Kawakami , K.*, Amsterdam, A., Shimoda, N., Becker,T., Mugg, J., Shima, A., and Hopkins, N. Proviral insertions in the zebrafish hagoromo gene, encoding an F-box/WD40-repeat protein, cause stripe pattern anomalies. Current Biology 10, 463-466 (2000).
  1. Kawakami, K.*, Shima, A., and Kawakami, N. Identification of a functional transposase of the Tol2 element, an Ac-like element from the Japanese medaka fish, and its transposition in the zebrafish germ lineage. Natl. Acad. Sci. USA 97, 11403-11408 (2000).
  1. Kawakami, K.*, and Noda, T. Transposition of the Tol2 element, an Ac-like element from the Japanese medaka fish Oryzias latipes, in mouse embryonic stem cells. Genetics 166, 895-899 (2004).
  1. Kawakami, K.*, Takeda, H., Kawakami, N., Kobayashi, M., Matsuda, N., and Mishina, M. A transposon-mediated gene trap approach identifies developmentally regulated genes in zebrafish. Developmental Cell 7, 133-144 (2004).
  1. Urasaki, A., Morvan, G., and Kawakami, K.* Functional dissection of the Tol2 transposable element identified the minimal cis-sequence and a highly repetitive sequence in the subterminal region essential for transposition. Genetics 174, 639-649 (2006).
  1. Fisher, S., Grice, E.A., Vinton, R.M., Bessling, S.L., Urasaki, A., Kawakami, K., and McCallion, A.S.* Evaluating the biological relevance of putative enhancers using Tol2 transposon-mediated transgenesis in zebrafish. Nature Protocols 1, 1297-1305 (2006).
  1. Kawakami, K.* Tol2: a versatile gene transfer vector in vertebrates. Genome Biology 8, Suppl 1:S7 (2007).
  1. Nagayoshi, S., Hayashi, E., Abe, G., Osato, N., Asakawa, K., Urasaki, A., Horikawa, K., Ikeo, K., Takeda, H., and Kawakami, K.* Insertional mutagenesis by the Tol2 transposon-mediated enhancer trap approach generated mutations in two developmental genes: tcf7 and synembryn-like. Development 135, 159-169 (2008).
  1. Asakawa, K., Suster, M.L., Mizusawa, K., Nagayoshi, S., Kotani, T., Urasaki, A., Kishimoto, Y., Hibi, M., and Kawakami, K.* Genetic dissection of neural circuits by Tol2 transposon-mediated Gal4 gene and enhancer trapping in zebrafish. Natl. Acad. Sci. USA 105, 1255-1260 (2008).
  1. Urasaki, A., Asakawa, K., and Kawakami, K.* Efficient transposition of the Tol2 transposable element from a single copy donor in zebrafish. Natl. Acad. Sci. USA 105, 19827-19832 (2008).
  1. Muto, A., Ohkura, M., Kotani, T., Higashijima, S.-i., Nakai, J., and Kawakami, K.* Genetic visualization with an improved GCaMP calcium indicator reveals spatiotemporal activation of the spinal motor neurons in zebrafish. Natl. Acad. Sci. USA 108, 5425-5430 (2011).
  1. Suster, M.L., Abe, G., Schouw, A., and Kawakami, K.* Transposon-mediated BAC transgenesis in zebrafish. Nature Protocols 6, 1998-2021 (2011).
  1. Muto, A., Ohkura, M., Abe, G., Nakai, J.*, and Kawakami, K.* Real-time visualizationof neuronal activity during perception. Current Biology 23, 307–311 (2013).
  1. Kawakami, K.*, Asakawa, K., Hibi, M., Itoh, M., Muto, A., and Wada, H. Gal4 driver transgenic zebrafish: powerful tools to study developmental biology, organogenesis, and neuroscience. Advances in Genetics 95, 65-87 (2016).
  1. Sternberg, J.R., Severi, K.E., Fidelin, K., Gomez, J., Ihara, H., Alcheikh, Y., Hubbard, J. M., Kawakami, K. *, Suster, M., and Wyatt, C.* Optimization of a neurotoxin to investigate the contribution of excitatory interneurons to speed modulation in vivo. Current Biology 17, 2319-2328 (2016).
  1. Muto, A.*, Lal, P., Ailani, D., Abe, G., Itoh, M., and Kawakami, K.* Activation of the hypothalamic feeding centre upon visual prey detection. Nature Communications 8, 15029 (2017).
  1. Kawakami, K., Largaespada, D.A., and Ivics, Z.* Transposons as tools for functional genomics in vertebrate models. Trends in Genetics 33, 784-801 (2017).
  1. Lal, P., Tanabe, H., Suster, M.L., Ailani, D., Kotani, Y., Muto, A., Itoh, M., Iwasaki, M., Wada, H., Yaksi, E., and Kawakami, K.* Identification of a neuronal population in the telencephalon essential for fear conditioning in zebrafish. BMC Biology 16, 45 (2018).
  1. Asakawa, K.*, and Kawakami, K.* Protocadherin-mediated cell repulsion controls the central topography and efferent projections of the abducens nucleus. Cell Reports 24, 1562-1572 (2018).
  1. Asakawa, K.*, Handa, H., and Kawakami, K.* Optogenetic modulation of TDP-43 oligomerization accelerates ALS-related pathologies in the spinal motor neurons. Nature Communications 11:1004 (2020).
  1. Huang, K.-H., Rupprecht, P., Frank, T., Kawakami, K., Bouwmeester, T., and Friedrich, R.W.* A virtual reality system to analyze neural activity and behavior in adult zebrafish. Nature Methods 17, 343-351 (2020).
     
  2. Asakawa, K.*, Tomita, T., Shioya, S., Handa, H., Saeki, Y., and Kawakami, K. Intrinsically accelerated cellular degradation is amplified by TDP-43 loss in ALS-vulnerable motor neurons in a zebrafish model. Nature Communications 16:9213 (2025).

 

 

  1. Lieschke, G.J., Oates, A.C., Kawakami, K. (eds) Zebrafish: Methods and Protocols. Methods in Molecular Biology 546, Humana Press, New York (2009).
  1. Kawakami, K., Patton, E.E., Orger, M. (eds) Zebrafish: Methods and Protocols: Second Edition. Methods in Molecular Biology 1451, Humana Press, New York (2016).
  1. Amatruda, J.F., Houart, C., Kawakami, K., Poss, K.D. (eds) Zebrafish: Methods and Protocols: Third Edition. Methods in Molecular Biology 2707, Humana, New York (2023).

Year Conference / Workshop / Lecture
2001 Aquarama 2001 World Conference on Ornamental Fish, Singapore
2003 The 1st Annual International Conference on Transposition, Minneapolis, MN
2005 The 3rd Annual International Conference on Transposition, Minneapolis, MN
2005 FASEB summer research Conference "Mammalian Mobile Elements", Tucson, Arizona.
2005 EMBO Practical Course: Enhancer Detection, Gene Trapping, and Tilling in Zebrafish, Bergen, Norway
2005 Lecture @Peking University, Beijing, China
2007 The International KOGO Conference, Seoul, Korea
2008 6th Annual International Conference on Transposition & Animal Biotechnology, Berlin, Germany
2009 International Symposium Marine Genomics, Okinawa, Japan
2010 11th Australia & New Zealand Zebrafish Workshop, Sydney, Australia
2010 2010 Taiwan Zebrafish Developmental Biology Meeting, Taipei, Taiwan
2010 Lecture @ National Health Research Institutes, Miaoli country, Taiwan
2010 Workshop "Imaging Structure and Function in the Zebrafish Brain", Lisbon, Portugal
2012 Janelia Workshop on Zebrafish Genetics, Transgenesis, and Systems Biology, Ashburn, VA
2012 Asia-Pacific Developmental Biology Conference 2012, Taipei, Taiwan
2012 Lecture @ National Taiwan University, Taipei, Taiwan
2013 3rd Chinese Zebrafish Meeting, Suzou, China
2014 ISTT 2014 Zebrafish Transgenesis workshop, Edinburgh, UK
2014 12th Transgenic Technology Meeting 2014, Edinburgh, UK
2014 7th Model Organism Symposium at KRIBB, Daejeon, Korea
2015 Imaging the nervous system (Univ of Cambridge), Cambridge, UK
2016 International FishMed Conference on Zebrafish Research (Fishmed2016), Warsaw, Poland
2017 2nd Malaysia Zebrafish Disease Model Workshop, Kuala Lumpur, Malaysia
2017 The 5th Zebrafish Research Conference of China, Wu Zhen, China
2017 IMB symposium at Academia Sinica, Taipei, Taiwan
2018 Lecture @ Kangwon National University, Chuncheon, Korea
2018 IJCGM International Joint Conference on Genetics & Medicine, Seoul, Korea
2019 The First International Zebrafish Workshop in Qatar, Doha, Qatar
2019 Lecture @ Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, China
2019 4th Zebrafish for Personalized/Precision Medicine Conference & 3rd Zebrafish Neuroscience Workshop, Toronto, Canada
2020 Lecture @ Southern Medical University, Guangzhou, China
2021 2021 Korean Zebrafish Symposium, Korea (on-line)
2022 Webinar 2022: “Zebrafish as experimental model for research" University of São Paulo
2022 IBRO-APRC Advanced School of Neuroscience 2022: Monash University Malaysia (on-line).
2023 Human Genetics Asia 2023, Tokyo, Japan
2024 5th Indian Zebrafish Investigators Meeting
2025 Symposium “Biology Across Scales”, Shiv Nadar Univ, India
2025 Symposium “Zebrafish & the Art of Fear”, Montclair State Univ, USA
2025 Model organisms in Inherited Metabolic Disease Research Symposium @International Congress on Inborn Errors of Metabolism 2025, Kyoto, Japan
2026 Symposium “Cellular & Molecular Mechanisms of Development and Regeneration”, Shiv Nadar Univ, India

Year Editorial Board / Membership
2009–2018 Editorial Board Member, Mobile DNA
2009–present Editorial Board Member, Zebrafish
2020–present Member, Board of Reviewing Editors, eLife
2014–2021 Founding Board Member, International Zebrafish Society (IZFS)
2014–2021 Founding Board Member, Zebrafish Disease Models Society (ZDMS)
2026–present Specialty Chief Editor, Frontiers in Physiology

 

Meeting organizer

 

Year Meeting / Role
2008 8th International Conference on Zebrafish Development and Genetics/organizer
2012 5th Annual Zebrafish Disease Models Meeting/organizer
2013 8th European Zebrafish Meeting/advisory committee member
2014 6th Asia Oceania Zebrafish Meeting/organizer
2014 Cold Spring Harbor Asia Meeting “Genetics, Genomics & Phenomics of Fish/organizer
2017 7th Strategic Conference of Zebrafish Investigators/organizer
2018 NIG International Symposium 2018 “Genome Editing and Functional Genomics”/organizer
2023 12th European Zebrafish Meeting/international advisory board member
2023 NIG International Symposium 2023 “Toward Understanding of Mechanisms of Human Diseases: Challenges Using Model Organisms”/organizer
2025 19th International Conference on Zebrafish Development and Genetics/organizer
2026 13th European Zebrafish Meeting/scientific committee member