We greatly welcome collaborations!
If you have any interests in collaborations and co-writing papers/proposals, please, send an email to K. Inomura (inomura@uri.edu). The common types of collaborations are as follows but any types of collaborative suggestions are welcomed:
1. Interpretation of experimental and observational data of biological, ecological, and biogeochemical sciences:
We have a unique set of quantitative/computational tools for the growth and metabolisms of microbial cells to interpret laboratory and observational data. The models are useful in providing quantitative interpretations to the observation and make data-and-theory based predictions. Please, take a look at the “Model list” below as well as our recent review paper (Inomura et al., 2020a PDF ). Even if you do not see a model you would like, we are happy to revise/develop a new model in collaboration with experimental and observational scientists.
2. Providing tools for representing cellular metabolisms in ecological and biogeochemical models:
Our models are kept simple and computationally efficient, allowing their incorporation into different model frameworks. The incorporated model will provide addtional layers of physiological details such as intracellular metabolic networks, macromolecular allocations and elemental ratios of the cells PDF .
Model list:
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Growth and metabolism of heterotrophic nitrogen fixing bacteria (Inomura et al., 2017,
PDF , 2018 PDF ) -
Growth and metabolism of Trichodesmium, marine multi-cellular photoautotrophic nitrogen fixers (Inomura et al., 2019a PDF )
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Growth, metabolism and molecular allocation of Crocosphaera, marine unicellular photoautotrophic nitrogen fixers (Inomura et al., 2019b PDF , 2019c PDF )
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Metabolisms of the heterogeneous population of microorganisms (Masuda, Inomura et al., 2020b PDF )
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Growth, metabolism, and molecular allocation of phytoplankton (Inomura et al., 2020
PDF ) -
Growth, metabolism and molecular exchange in microbial symbiosis (Inomura et al., 2020c PDF , Gao et al., 2022 PDF )
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Growth and metabolism of general heterotrophic bacteria (based on Rittmann and McCarty 2001)
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Simple model of microbial ecosystems (Inomura et al., 2019c PDF )
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Computation of carbon chemistry (based on Emerson and Hedges 2008, e.g., Masuda et al., 2021 PDF )
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Temperature dependencies of macromolecular allocation and elemental ratios in phytoplankton (Armin and Inomura., 2021 PDF )
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Growth of Cyanothece under CO2 limitation (Inomura et al., 2021 PDF )
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A simple nutrient uptake model of Crocosphaera (Masuda and Inomura et al., 2022 PDF )
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A simple metabolic model of Crocosphaera and Cyanothece (Masuda et al., 2022 PDF )
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A macromolecular model of phytoplankton embedded in a ocean ecological simulation (Inomura et al., 2022 PDF )