Iain's research group is interested in combining mathematical, statistical, and experimental approaches to learn about the biological world, and how we can interact with it to improve human lives. We often work on questions where "blue skies" biological knowledge can be translated into strategies to address disease and crop production. We're particularly interested in the bioenergetic organelles (mitochondria and chloroplasts) that provide the energy that powers complex life.

One major current focus of the group is EvoConBiO -- an ERC-funded project exploring the evolution and cellular control of mitochondria and chloroplasts, using approaches from stochastic modelling, bioinformatics, and molecular biology.

You can read more at the research group website, and find non-technical summaries of research papers here.

Some keywords related to our research -- mathematical: stochastic modelling, discrete population processes, inference and model selection, uncertainty quantification, pathway inference; biological: stochastic biology, cell heterogeneity, mitochondria, chloroplasts, mtDNA, cpDNA, evolution, disease progression, bioinformatics, plant systems biology. 

Academic article

• Giannakis, Konstantinos; Richards, Luke; Dauda, Kazeem Adesina et al. (2024). Connecting Species-Specific Extents of Genome Reduction in Mitochondria and Plastids. (external link)
• Garschall, Kathrin; Pascual Carreras, Eudald; Pascual, Belen Garcia et al. (2024). The cellular basis of feeding-dependent body size plasticity in sea anemones. (external link)
• Aga, Olav Nicolay Larsson; Brun, Morten; Dauda, Kazeem Adesina et al. (2024). HyperTraPS-CT: Inference and prediction for accumulation pathways with flexible data and model structures. (external link)
• Giannakis, Konstantinos; Richards, Luke; Johnston, Iain (2024). Ecological Predictors of Organelle Genome Evolution: Phylogenetic Correlations with Taxonomically Broad, Sparse, Unsystematized Data. (external link)
• Kumar, Rajneesh; Johnston, Iain (2024). ATP dependence of decision-making capacity in a fine-grained model of gene regulatory networks. (external link)
• Pascual, Belen Garcia; Salbu, Lars Moberg; Renz, Jessica et al. (2024). Comparing Structure and Dynamics of Transition Graphs by the Symmetric Difference Metric Over an Edge-Filtration. (external link)
• Johnston, Iain (2024). The Nitroplast and Its Relatives Support a Universal Model of Features Predicting Gene Retention in Endosymbiont and Organelle Genomes. (external link)
• Dombi, Eszter; Marinaki, Tony; Spingardi, Paolo et al. (2024). Nucleoside supplements as treatments for mitochondrial DNA depletion syndrome. (external link)
• Erickson, Jennifer Lee; Prautsch, Jennifer; Reynvoet, Frisine et al. (2023). Stromule Geometry Allows Optimal Spatial Regulation of Organelle Interactions in the Quasi-2D Cytoplasm. (external link)
• Stevens, Katie; Johnston, Iain; Luna, Estrella (2023). Data science approaches provide a roadmap to understanding the role of abscisic acid in defence. (external link)
• Glastad, Robert Clay; Johnston, Iain (2023). Mitochondrial network structure controls cell-to-cell mtDNA variability generated by cell divisions. (external link)
• Garcia Pascual, Belen; Nordbotten, Jan Martin; Johnston, Iain (2023). Cellular and environmental dynamics influence species-specific extents of organelle gene retention. (external link)
• Giannakis, Konstantinos; Broz, Amanda K.; Sloan, Daniel B. et al. (2023). Avoiding misleading estimates using mtDNA heteroplasmy statistics to study bottleneck size and selection. (external link)
• Bjune, Mona Synnøve; Dyer, Laurence; Laupsa-Borge, Johnny et al. (2023). Metabolic role of the hepatic valine/3-hydroxyisobutyrate (3-HIB) pathway in fatty liver disease. (external link)
• Broz, Amanda K.; Sloan, Daniel B.; Johnston, Iain (2023). Stochastic organelle genome segregation through Arabidopsis development and reproduction. (external link)
• Johnston, Iain George (2022). Optimal strategies in the Fighting Fantasy gaming system: influencing stochastic dynamics by gambling with limited resource. (external link)
• Kerr, Ryan; Jabbari, Sara; Blair, Jessica et al. (2022). Dynamic Boolean modelling reveals the influence of energy supply on bacterial efflux pump expression. (external link)
• Johnston, Iain; Slater, Mark; Cazier, Jean-Baptiste (2022). Interdisciplinary and Transferable Concepts in Bioinformatics Education: Observations and Approaches From a UK MSc Course. (external link)
• Johnston, Iain; Dingle, Kamaludin; Greenbury, Sam et al. (2022). Symmetry and simplicity spontaneously emerge from the algorithmic nature of evolution. (external link)
• Giannakis, Konstantinos; Chustecki, Joanna M.; Johnston, Iain George (2022). Exchange on dynamic encounter networks allows plant mitochondria to collect complete sets of mitochondrial DNA products despite their incomplete genomes. (external link)
• Moen, Marcus Theodor; Johnston, Iain George (2022). HyperHMM: efficient inference of evolutionary and progressive dynamics on hypercubic transition graphs. (external link)
• Chustecki, Joanna M.; Etherington, Ross D; Gibbs, Daniel J. et al. (2022). Altered collective mitochondrial dynamics in the Arabidopsis msh1 mutant compromising organelle DNA maintenance. (external link)
• Ziegler, Clare; Kulawska, Aleksandra; Kourmouli, Angeliki et al. (2022). Quantification and uncertainty of root growth stimulation by elevated CO<inf>2</inf> in a mature temperate deciduous forest. (external link)
• Giannakis, Konstantinos; Arrowsmith, Samuel J.; Richards, Luke et al. (2022). Evolutionary inference across eukaryotes identifies universal features shaping organelle gene retention. (external link)
• Radzvilavicius, Arunas; Johnston, Iain (2022). Organelle bottlenecks facilitate evolvability by traversing heteroplasmic fitness valleys. (external link)
• Broz, Amanda K.; Keene, Alexandra; Gyorfy, Matheus Fernandes et al. (2022). Sorting of mitochondrial and plastid heteroplasmy in Arabidopsis is extremely rapid and depends on MSH1 activity. (external link)
• Edwards, David; Røyrvik, Ellen Christine; Chustecki, Joanne et al. (2021). Avoiding organelle mutational meltdown across eukaryotes with or without a germline bottleneck. (external link)
• Chustecki, Joanna M.; Gibbs, Daniel J.; Bassel, George W. et al. (2021). Network analysis of Arabidopsis mitochondrial dynamics reveals a resolved tradeoff between physical distribution and social connectivity. (external link)
• Radzvilavicius, Arunas; Layh, Sean; Hall, Matthew D. et al. (2021). Sexually antagonistic evolution of mitochondrial and nuclear linkage. (external link)
• Pantic, Boris; Ives, Daniel; Mennuni, Mara et al. (2021). 2-Deoxy-D-glucose couples mitochondrial DNA replication with mitochondrial fitness and promotes the selection of wild-type over mutant mitochondrial DNA. (external link)
• Peach, Robert; Greenbury, Sam; Johnston, Iain George et al. (2021). Understanding learner behaviour in online courses with Bayesian modelling and time series characterisation. (external link)
• Duran-Nebreda, Salva; Johnston, Iain George; Bassel, George (2020). Efficient vasculature investment in tissues can be determined without global information. (external link)
• Athanasiou, Angelos-Theodoros; Nussbaumer, T; Kummer, Stefan et al. (2020). S100A4 mRNA-protein relationship uncovered by measurement noise reduction. (external link)
• Johnston, Iain George; Røyrvik, Ellen Christine (2020). Data-Driven Inference Reveals Distinct and Conserved Dynamic Pathways of Tool Use Emergence across Animal Taxa. (external link)
• Lechuga-Vieco, Ana Victoria; Latorre-Pellicer, Ana; Johnston, Iain et al. (2020). Cell identity and nucleo-mitochondrial genetic context modulate OXPHOS performance and determine somatic heteroplasmy dynamics. (external link)
• Røyrvik, Ellen Christine; Johnston, Iain (2020). MtDNA sequence features associated with 'selfish genomes' predict tissue-specific segregation and reversion. (external link)
• Johnston, Iain (2019). Tension and resolution: dynamic, evolving populations of organelle genomes within plant cells. (external link)
• Ziegler, Clare; Dyson, Rosemary; Johnston, Iain George (2019). Model selection and parameter estimation for root architecture models using likelihood-free inference. (external link)
• Johnston, Iain George; Hoffmann, Till; Greenbury, Sam et al. (2019). Precision identification of high-risk phenotypes and progression pathways in severe malaria without requiring longitudinal data. (external link)
• Aryaman, Juvid; Bowles, Charlotte; Jones, Nick et al. (2019). Mitochondrial network state scales mtDNA genetic dynamics. (external link)
• Johnston, Iain George (2019). Varied mechanisms and models for the varying mitochondrial bottleneck. (external link)
• Johnston, Iain George; Burgstaller, Joerg (2019). Evolving mtDNA populations within cells. (external link)
• Kerr, Ryan; Jabbari, Sara; Johnston, Iain (2019). Intracellular Energy Variability Modulates Cellular Decision-Making Capacity. (external link)
• Greenbury, Sam; Barahona, Mauricio; Johnston, Iain (2019). HyperTraPS: Inferring probabilistic patterns of trait acquisition in evolutionary and disease progression pathways. (external link)
• Hoitzing, Hanne; Gammage, Payam; van Haute, Lindsey et al. (2019). Energetic costs of cellular and therapeutic control of stochastic mitochondrial DNA populations. (external link)
• Johnston, Iain George (2019). Regulation of Mother-to-Offspring Transmission of mtDNA Heteroplasmy. (external link)
• Johnston, Iain; Bassel, George (2018). Identification of a bet-hedging network motif generating noise in hormone concentrations and germination propensity in Arabidopsis. (external link)

Academic literature review

• Veeraragavan, Shibani; Johansen, Maria; Johnston, Iain (2024). Evolution and maintenance of mtDNA gene content across eukaryotes. (external link)
• Chustecki, Joanna M.; Johnston, Iain George (2023). Collective mitochondrial dynamics resolve conflicting cellular tensions: From plants to general principles. (external link)
• Autran, Daphné; Bassel, George W.; Chae, Eunyoung et al. (2021). What is quantitative plant biology?. (external link)

Poster

• Kumar, Rajneesh; Johnston, Iain George (2023). Population Dynamics in Response to Environmental Stimuli. (external link)
• Kumar, Rajneesh; Johnston, Iain George (2023). Stochastic and Deterministic Computation in the regulation of Decision – Making Genetic circuits by Energy Availability.. (external link)

Letter to the editor

• Johnston, Iain; Dingle, Kamaludin; Greenbury, Sam F. et al. (2022). Reply to Ocklenburg and Mundorf: The interplay of developmental bias and natural selection. (external link)

See a complete overview of publications in Cristin.

Iain's publications can be found on Google Scholar here or ORCID here .

The CRIStin profile below is currently being updated.

EvoConBiO (ERC StG) -- evolution and control of bioenergetic organelles

CAMRIA (Trond Mohn) -- combatting antimicrobial resistance with interdisciplinary approaches

QUINTUS (UK NERC) -- responses of forest ecosystems to elevated CO2

HyperTraPS (Alan Turing Institute) -- inferring pathways of evolution and disease progression

Iain also supervises researchers on projects funded by the UK BBSRC and Wellcome Trust, working on plant mitochondria, seed germination, and antimicrobial resistance.