Hideyuki Doi

Graduate School of Informatics

Kyoto University


Laboratory of Biosphere Informatics, Department of Social Informatics, Graduate School of Informatics, Kyoto University

Yoshidahonmachi, Sakyo-ku, Kyoto 606-8501 JAPAN


E-mail: hideyuki.doi (at) icloud.com





  • 1 Oct.  We moved to Graduate School of Informatics, Kyoto University
  • 19 Jan. We published a new paper for global lockdown effects on global SDG attainment.We revealed a drastic reduction in human movement and NO2 emissions and showed that many SDGs were influenced due to the global lockdown of COVID-19. LINK



  • 21 July We published a new paper for causal analysis of the temperature impact on deep-sea biodiversity using CCM analysis for the time-series data. LINK
  • 20 June We published a new paper for rapid on-site eDNA methods with ~30 mins for eDNA detection using ultrarapid mobile PCR. LINK
  • 1 Apr. We welcome Yurie Otake as a new post-doc.
  • 1 Apr.  "Graduate School of Information Science" has been established, and our affiliation has been changed to "Graduate School of Information Science".
  • 25 Mar. A PhD student, Tatsuya Saito, published two papers: We demonstrated the decay of environmental DNA in water using the experiments with isolated cells and DNA fragments, and analyzed using three decay modelsLINK , and simulation of eDNA decay prediction using a meta-analysis from 28 published articlesLINK.



  • 20 Oct. NEW PAPER: Our new paper is out in PNAS. We estimated global diversity of microbial communities and in marine sediment. I mainly contributed to estimate the data analysis, especially for global bacteria richness. LINK
  • 9 Oct. NEW PAPER: We published the eDNA paper in Communications Biology. We can track decadal-centennial dynamics of fish abundance in the last 300 years using sedimentary DNA. LINK
  • 4 Aug. NEW PAPER: Our new review paper was published. The review synthesized ecological and evolutionary factors of intraspecific variation in inducible defenses, insights gained from Daphnia experiments LINK
  • 3 Aug. Our lab. twitter started! https://twitter.com/Doi_Lab
  • 12 Jan. NEW PAPERS: We published two papers for developing the eDNA methods of the rare freshwater mussel (Sinanodonta spp.) LINK and the invasive red-eared sliders (Trachemy scripta elegans) in  Japanese ponds.  LINK 


  • 23 Jul. NEW PAPER: Our global project was published a math-analysis paper in Nature Communications. Our global meta-analysis found adaptive phenological responses of animals, mainly birds, against global warming, but did not find the sufficient morphological responses to warming. LINK
  • 11 Jul. NEW PAPER: Using eDNA metabarcoding, we implied that information on the terrestrial and aquatic fungal compositions of watersheds, and therefore their spatial structure, can be obtained by investigating the fungal DNA assemblages in river water. LINK
  • 28 Jan. NEW PAPER: Our food-chain length paper was published in Communications Biology. We investigated how the sequence of species immigration affects food-chain length and whether the effect depends on productivity using microcosm experiments. LINK


  • 30 Sep. We had the first annual meeting of The eDNA Society (https://ednasociety.org).
  • 4 Jul. Our perspective paper "A macroecological perspective for phenological research under climate change" was nominated a groundbreaking article for Change the World 2018. LINK 


Research overview

Our research objective is to understand ecosystem and community dynamics in ecosystems. We are broadly interested in the ecology, especially, trophic interactions in food web and phenological dynamics of community. Also, we are interested in general biology and sciences, such as metabolic theory and biological stoichiometry, environmental pollution. Currently, our research themes are follows.


1) Food webs: spatial patterns of food webs, production, material cycling in aquatic ecosystems, food web analysis using multiple stable isotopes, food-chain length theory


2) Prey-predator interactions: microalgal communities and grazers interaction, habitat use of aquatic grazers, interactions between hosts and parasites


3) Environmental DNA: estimation of species distribution by eDNA,  biomass/abundance estimation by eDNA, high-thoughput sequencing for eDNA meta-barcording


4) Phenology and climate change: recent climate changes and the phenological timings of the organisms, mismatching in trophic interactions in response to climate change


5) Meta-analysis and big data analysis to synthesize ecological and biological themes: metabolic scaling and grow rate of organisms, predator effect on ecosystems, food-chain lengths and ecosystem history