IJ
Iain G. Johnston
mitochondriamtDNAevolutionary biologyq-bio.PEq-bio.QMEvolution, MoleculargeneticsbioinformaticsBiological Evolutionbottleneck
On Valency
published · living versionsW_fgs3n2ts·v1 · currentpublished
Stochastic modelling, Bayesian inference, and new in vivo measurements elucidate the debated mtDNA bottleneck mechanism
with Joerg P. Burgstaller, Vitezslav Havlicek, Thomas Kolbe, Thomas Rulicke +3
1 version
Preprints & journals
119 papers in the corpus · 2008–2026Mitochondrial dynamics can resolve stoichiometric challenges in plant mtDNA repair.42926698 · Johnston, Iain G, Sloan, Daniel B, Møller, Ian Max2026 · 0 citationsbioRxiv : the preprint server for biology. 2026
Mitochondrial dynamics resolve physical-social tensions and challenges through adaptable multi-objective optimisation.42818170 · Chustecki, Joanna M, Johnston, Iain G2026 · 0 citationsbioRxiv : the preprint server for biology. 2026
A method for comparing inferred evolutionary accumulation dynamics across covariates and model structures2608.02781v1 · Jakob Fernø, Michelle B. Verstraaten, Lila Gravellier et al.2026 · 0 citationsarXiv
Identifying parsimonious pathways of accumulation and convergent evolution from binary data.42429475 · Giannakis, Konstantinos, Aga, Olav N L, Moen, Marcus T et al.2026 · 4 citationsSystematic biology. 2026
Optimal Organelle Inheritance Strategies Under Different Changing Environments and Mutational Pressures.42363700 · García-Pascual, Belén, Nordbotten, Jan M, Johnston, Iain G2026 · 0 citationsGenome biology and evolution. 2026;18(7)
Evolutionary inference reveals global natural histories and predicted pathways of antimicrobial resistance in Klebsiella pneumoniae.42284356 · Aga, Olav N L, Moyo, Sabrina J, Manyahi, Joel et al.2026 · 0 citationsPLoS biology. 2026;24(6):e3003848
A structural causal framework for interventions on evolutionary accumulation models2606.12597v2 · Ramon Diaz-Uriarte, 'Inigo R'ios-Arroyo, Iain G. Johnston2026 · 0 citationsarXiv
The hypercubic Mk model in reduced state space for the coupled, reversible coevolution of multiple binary characters10.64898/2026.06.01.729317v1 · Johnston, I., Diaz-Uriarte, R., Boyko, J.2026 · 1 citationbioRxiv
Antimicrobial resistance in paediatric bloodstream infections in Tanzania: a longitudinal comparison of two cohort studies.41981461 · Kristiansen, Trygve, Moyo, Sabrina John, Manyahi, Joel et al.2026 · 0 citationsBMC microbiology. 2026;26(1)
Segregation of mtDNA mutations protects mitochondria across kingdoms, with impacts from longevity to agriculture and evolvability.41923598 · Johnston, Iain G2026 · 1 citationPhilosophical transactions of the Royal Society of London. Series B, Biological sciences. 2026;381(1947)
Extracting useful information about reversible evolutionary processes from irreversible evolutionary accumulation models2601.13010v2 · Iain G. Johnston2026 · 1 citationarXiv
Convergent pathways of reductive mitochondrial evolution characterized with hypercubic inference.40990941 · Glastad, Robert C, Johnston, Iain G2025 · 1 citationJournal of evolutionary biology. 2025;38(12):1590-1600
An Algebraic Approach to Evolutionary Accumulation Models2511.06999v2 · Jessica Renz, Frederik Witt, Iain G. Johnston2025 · 0 citationsarXiv
A natural history of AMR in Klebsiella pneumoniae: Global diversity, predictors, and predictions of evolutionary pathways10.1101/2025.09.20.677523v3 · Aga, O. N. L., Moyo, S. J., Manyahi, J. et al.2025 · 2 citationsbioRxiv
Estimating physical conditions supporting gradients of ATP concentration in the eukaryotic cell.40528343 · Kumar, Rajneesh, Johnston, Iain G2026 · 4 citationsBiophysical journal. 2026;125(2):377-386
Evolutionary accumulation modeling in AMR: machine learning to infer and predict evolutionary dynamics of multi-drug resistance.40396716 · Renz, Jessica, Dauda, Kazeem A, Aga, Olav N L et al.2025 · 14 citationsmBio. 2025;16(6):e0048825
Convergent pathways of reductive mitochondrial evolution characterised with hypercubic inference10.1101/2025.04.29.651065v1 · Glastad, R. C., Johnston, I.2025 · 0 citationsbioRxiv
Flexible inference of evolutionary accumulation dynamics using uncertain observational data2502.05872v4 · Jessica Renz, Morten Brun, Iain G. Johnston2025 · 1 citationarXiv
A hypercubic Mk model framework for capturing reversibility in disease, cancer, and evolutionary accumulation modelling.39666947 · Johnston, Iain G, Diaz-Uriarte, Ramon2024 · 12 citationsBioinformatics (Oxford, England). 2024;41(1)
Modelling benefits and costs of decision making and feedback control for organisms in changing environments10.1101/2024.11.30.626137v1 · Kumar, R., Johnston, I.2024 · 0 citationsbioRxiv
Evolutionary accumulation modelling in AMR: machine learning to infer and predict evolutionary dynamics of multi-drug resistance2411.00219v2 · Jessica Renz, Kazeem A. Dauda, Olav N. L. Aga et al.2024 · 7 citationsarXiv
Clustering large-scale biomedical data to model dynamic accumulation processes in disease progression and anti-microbial resistance evolution10.1101/2024.09.19.613871v1 · Dauda, K. A., Aga, O. N., Johnston, I.2024 · 9 citationsbioRxiv
HyperTraPS-CT: Inference and prediction for accumulation pathways with flexible data and model structures.39231165 · Aga, Olav N L, Brun, Morten, Dauda, Kazeem A et al.2024 · 15 citationsPLoS computational biology. 2024;20(9):e1012393
Evolution and maintenance of mtDNA gene content across eukaryotes.39101615 · Veeraragavan, Shibani, Johansen, Maria, Johnston, Iain G2024 · 15 citationsThe Biochemical journal. 2024;481(15):1015-1042
Ecological Predictors of Organelle Genome Evolution: Phylogenetic Correlations with Taxonomically Broad, Sparse, Unsystematized Data.38459872 · Giannakis, Konstantinos, Richards, Luke, Johnston, Iain G2024 · 9 citationsSystematic biology. 2024;73(2):419-433
The cellular basis of feeding-dependent body size plasticity in sea anemones.38980277 · Garschall, Kathrin, Pascual-Carreras, Eudald, García-Pascual, Belén et al.2024 · 12 citationsDevelopment (Cambridge, England). 2024;151(20)
The Nitroplast and Its Relatives Support a Universal Model of Features Predicting Gene Retention in Endosymbiont and Organelle Genomes.38900924 · Johnston, Iain G2024 · 1 citationGenome biology and evolution. 2024;16(7)
Connecting Species-Specific Extents of Genome Reduction in Mitochondria and Plastids.38758976 · Giannakis, Konstantinos, Richards, Luke, Dauda, Kazeem A et al.2024 · 5 citationsMolecular biology and evolution. 2024;41(6)
Stromule Geometry Allows Optimal Spatial Regulation of Organelle Interactions in the Quasi-2D Cytoplasm.37658689 · Erickson, Jessica Lee, Prautsch, Jennifer, Reynvoet, Frisine et al.2024 · 12 citationsPlant & cell physiology. 2024;65(4):618-630
Nucleoside supplements as treatments for mitochondrial DNA depletion syndrome.38665433 · Dombi, Eszter, Marinaki, Tony, Spingardi, Paolo et al.2024 · 15 citationsFrontiers in cell and developmental biology. 2024;12:1260496
Comparing structure and dynamics of transition graphs by the symmetric difference metric over an edge-filtration10.1101/2024.01.29.577802v1 · Garcia Pascual, B., Salbu, L. M., Renz, J. et al.2024 · 5 citationsbioRxiv
A picture guide to cancer progression and monotonic accumulation models: evolutionary assumptions, plausible interpretations, and alternative uses2312.06824v5 · Ramon Diaz-Uriarte, Iain G. Johnston2023 · 12 citationsIEEE Access 13 (2025) 62306 - 62340
Collective mitochondrial dynamics resolve conflicting cellular tensions: From plants to general principles.38043948 · Chustecki, Joanna M, Johnston, Iain G2023 · 10 citationsSeminars in cell & developmental biology. 2024;156:253-265
Fine-grained modelling of ATP dependence of decision-making capacity in genetic regulatory networks10.1101/2023.11.16.567352v1 · Kumar, R., Johnston, I.2023 · 1 citationbioRxiv
Stochastic organelle genome segregation through Arabidopsis development and reproduction.37925790 · Broz, Amanda K, Sloan, Daniel B, Johnston, Iain G2023 · 20 citationsThe New phytologist. 2024;241(2):896-910
Avoiding misleading estimates using mtDNA heteroplasmy statistics to study bottleneck size and selection.36951404 · Giannakis, Konstantinos, Broz, Amanda K, Sloan, Daniel B et al.2023 · 10 citationsG3 (Bethesda, Md.). 2023;13(6)
Metabolic role of the hepatic valine/3-hydroxyisobutyrate (3-HIB) pathway in fatty liver disease.37084480 · Bjune, Mona Synnøve, Lawrence-Archer, Laurence, Laupsa-Borge, Johnny et al.2023 · 32 citationsEBioMedicine. 2023;91:104569
Mitochondrial network structure controls cell-to-cell mtDNA variability generated by cell divisions.36952562 · Glastad, Robert C, Johnston, Iain G2023 · 17 citationsPLoS computational biology. 2023;19(3):e1010953
Cellular and environmental dynamics influence species-specific extents of organelle gene retention.36883279 · García Pascual, Belén, Nordbotten, Jan M, Johnston, Iain G2023 · 12 citationsProceedings. Biological sciences. 2023;290(1994):20222140
Data science approaches provide a roadmap to understanding the role of abscisic acid in defence.37077700 · Stevens, Katie, Johnston, Iain G, Luna, Estrella2023 · 5 citationsQuantitative plant biology. 2023;4:e2
HyperHMM: efficient inference of evolutionary and progressive dynamics on hypercubic transition graphs.36511587 · Moen, Marcus T, Johnston, Iain G2023 · 22 citationsBioinformatics (Oxford, England). 2023;39(1)
Dynamics of organelle DNA segregation in Arabidopsis development and reproduction revealed with tissue-specific heteroplasmy profiling and stochastic modelling10.1101/2022.11.07.515340v2 · Broz, A. K., Sloan, D. B., Johnston, I.2022 · 1 citationbioRxiv
Organelle bottlenecks facilitate evolvability by traversing heteroplasmic fitness valleys.36386853 · Radzvilavicius, Arunas L, Johnston, Iain G2024 · 11 citationsFrontiers in genetics. 2022;13:974472
Evolutionary inference across eukaryotes identifies universal features shaping organelle gene retention.36115336 · Giannakis, Konstantinos, Arrowsmith, Samuel J, Richards, Luke et al.2022 · 28 citationsCell systems. 2022;13(11):874-884.e5
Altered collective mitochondrial dynamics in the Arabidopsis msh1 mutant compromising organelle DNA maintenance.35662332 · Chustecki, Joanna M, Etherington, Ross D, Gibbs, Daniel J et al.2022 · 25 citationsJournal of experimental botany. 2022;73(16):5428-5439
Quantification and uncertainty of root growth stimulation by elevated CO2 in a mature temperate deciduous forest.36096230 · Ziegler, Clare, Kulawska, Aleksandra, Kourmouli, Angeliki et al.2023 · 24 citationsThe Science of the total environment. 2023;854:158661
Exchange on dynamic encounter networks allows plant mitochondria to collect complete sets of mitochondrial DNA products despite their incomplete genomes.37077986 · Giannakis, Konstantinos, Chustecki, Joanna M, Johnston, Iain G2023 · 23 citationsQuantitative plant biology. 2022;3:e18
Sorting of mitochondrial and plastid heteroplasmy in Arabidopsis is extremely rapid and depends on MSH1 activity.35969753 · Broz, Amanda K, Keene, Alexandra, Fernandes Gyorfy, Matheus et al.2022 · 57 citationsProceedings of the National Academy of Sciences of the United States of America. 2022;119(34):e2206973119
Reply to Ocklenburg and Mundorf: The interplay of developmental bias and natural selection.35787035 · Johnston, Iain G, Dingle, Kamaludin, Greenbury, Sam F et al.2022 · 6 citationsProceedings of the National Academy of Sciences of the United States of America. 2022;119(28):e2205299119
Efficient inference of evolutionary and progressive dynamics on hypercubic transition graphs10.1101/2022.05.09.491130v1 · Moen, M., Johnston, I.2022 · 4 citationsbioRxiv
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