Data scientist at Biome Inc., Kyoto, Japan

Email: k.atsumi115_at_gmail.com

Introduction

In my childhood I wanted to be a shark taxonomist that would allow me to see various kinds of fishes and roam across the world. Yet, in doing undergraduate study I faced lot of difficulty to do so and I became more interested in evolutionary biology.

In the PhD course at Hokkaido University, Japan, I decided to work on freshwater fish to investigate how female ornamentation works and why interspecific mating happens. While I did behavioral experiment/field survey/citizen science for the fish, I also conducted meta-analysis to uncover general pattens of F1 hybrids’ phenotypic distribution.

In the late years of my PhD I became interested in ecology as well. To understand how the strength of predator-prey interaction between larvae of salamander and frog are determined, I did lots of experiments (sadly they are not published yet).

On 2021, thanks to JSPS, I got a chance to be a postdoc at the United States/Italy. However, due to covid-19 pandemic, I could not move to US and start the planned study. During the desperate period, I became interested in connecting evolutionary biology/ecology to society/economy because I watched NIKKEI TV everyday.

Now I came back to Japan and became a data scientist at a startup company Biome Inc.. While I keep my interest in evolutionary biology/ecology, I set connecting biology with society through citizen science as one of my career goals.

Here I note that contents of this website does not relate with any organizations I am involved.

Experience

Education

2016 - 2020 Ph.D. Grad. Environmental Earth Science, Hokkaido Univ., Japan
Supervisor, Dr. Itsuro Koizumi
2014 - 2016 M.Sc. Grad. Agricultural and Life Sciences, Univ. Tokyo, Japan
2010 - 2014 B.Sc. Fac. Fisheries Science, Hokkaido Univ., Japan

Work experience

2022.4- Data scientist at Biome Inc.
2021.7-2022.3 Postdoctoral fellow at University of Padova - Gil Rosenthal lab, supported by JSPS
2021.3-7 Postdoctoral fellow at Texas A&M University - Gil Rosenthal lab, supported by JSPS
2021.5-6 Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, Mexico
2017.10-12
2019.10-12		 Visiting scholar at University of New South Wales - Shinichi Nakagawa lab, Sydney, to conduct meta-analysis of phenotypic distribution of F1 hybrids
2018.4 - 2020.3 JSPS research fellow at Hokkaido University (DC2, doctoral students)
2016.5 - 2017.2 Research assistant for the experiment investigating trigger of ocean-migration of masu trout, Hokkaido University
2016.5 - 2017.2 Teaching assistant, Hokkaido University
2015 - 2016 Research assistant at National Museum of Nature and Science, Tsukuba (maintain fish specimens)
2013 - 2014 Volunteer as a curator of Hokkaido University Museum, Hakodate (make, maintain and exhibit fish specimens)

Research output

Research funding

2020.4 - 2022.3 JSPS Overseas Research Fellow (JSPS)
2018.4 - 2020.3 Grant in Aid for JSPS Research Fellow (JSPS)
2017.4 - 2018.3 Grant for Zoological Research (Fujiwara Natural History Foundation)
2017.4 - 2018.3 Sasakawa Scientific Research Grant (The Japan Science Society)

Awards

2018.3 Best paper award of Ecological research
2017.3 Best Research Award, Poster Presentation Session, Grad. Environmental Science, Hokkaido Univ.
2016 JASSO Repayment Exemption for Students with Particularly Outstanding Results (half exemption)
2011 Nitobe Award for outstanding freshman, Hokkaido University

Skills

Computer (Software)

  • Statistical analyses (e.g. phylogenetic meta analysis and Bayesian models) using R

  • Systematic review using Rayyan

  • Semi-automated biodiversity monitoring using computer vision and deep learning

  • Genome analysis using plink

  • Image processing using inkscape, gimp and sai

  • CUI operation on Linux

Field survey

  • Collected fishes using an electric shocker and cast net for behavioral experiments

  • Collected amphibians using large traps

  • Tracked migration of fish by using bio logging techniques

Experiments

  • Behavioral experiments: measuring personalities and mate preferences in fish

  • Field/laboratory experiments for predator-prey interaction in amphibians

  • DNA experiments: designing primer; microsatellite analysis; RFLP analysis; sanger sequencing

  • Specimen dissection: musculoskeletal structure; gut parasite infection status

Organize meetings

2016-2020 EZO zemi - Cross-disciplinary seminar series for ecologists/evolutionary biologists at Hokkaido Univ
2018.3 Organized symposium For interpretation of animal personality and its implications for ecology at Annual Meetings of the Ecological Society of Japan. This symposium was compiled as the special feature of Japanese journal of ecology