151 citations · 956 across the 18 of their papers we have counts for
19 papers
Encounter networks from collective mitochondrial dynamics support the emergence of effective mtDNA genomes in plant cells
Konstantinos Giannakis, Joanna M. Chustecki, Iain G. Johnston
Mitochondria in plant cells form strikingly dynamic populations of largely individual organelles. Each mitochondrion contains on average less than a full copy of the mitochondrial…
Data-driven modelling and characterisation of task completion sequences in online courses
Robert L. Peach, Sam F. Greenbury, Iain G. Johnston +3
The intrinsic temporality of learning demands the adoption of methodologies capable of exploiting time-series information. In this study we leverage the sequence data framework and…
Intracellular Energy Variability Modulates Cellular Decision-Making Capacity
Ryan Kerr, Sara Jabbari, Iain G. Johnston
Cells are able to generate phenotypic diversity both during development and in response to stressful and changing environments, aiding survival. The biologically and medically vita…
HyperTraPS: Inferring probabilistic patterns of trait acquisition in evolutionary and disease progression pathways
Sam F. Greenbury, Mauricio Barahona, Iain G. Johnston
The explosion of data throughout the biomedical sciences provides unprecedented opportunities to learn about the dynamics of evolution and disease progression, but harnessing these…
Mitochondrial network state scales mtDNA genetic dynamics
Juvid Aryaman, Charlotte Bowles, Nick S. Jones +1
Mitochondrial DNA (mtDNA) mutations cause severe congenital diseases but may also be associated with healthy aging. MtDNA is stochastically replicated and degraded, and exists with…
Mitochondrial heterogeneity
Juvid Aryaman, Iain G. Johnston, Nick S. Jones
Cell-to-cell heterogeneity drives a range of (patho)physiologically important phenomena, such as cell fate and chemotherapeutic resistance. The role of metabolism, and particularly…
Stochastic modelling, Bayesian inference, and new in vivo measurements elucidate the debated mtDNA bottleneck mechanism
Iain G. Johnston, Joerg P. Burgstaller, Vitezslav Havlicek +5
Dangerous damage to mitochondrial DNA (mtDNA) can be ameliorated during mammalian development through a highly debated mechanism called the mtDNA bottleneck. Uncertainty surroundin…
Closed-form stochastic solutions for non-equilibrium dynamics and inheritance of cellular components over many cell divisions
Iain G. Johnston, Nick S. Jones
Stochastic dynamics govern many important processes in cellular biology, and an underlying theoretical approach describing these dynamics is desirable to address a wealth of questi…
Explicit tracking of uncertainty increases the power of quantitative rule-of-thumb reasoning in cell biology
Iain G. Johnston, Benjamin C. Rickett, Nick S. Jones
"Back-of-the-envelope" or "rule-of-thumb" calculations involving rough estimates of quantities play a central scientific role in developing intuition about the structure and behavi…
Phenotypic landscape inference reveals multiple evolutionary paths to C photosynthesis
Ben P. Williams, Iain G. Johnston, Sarah Covshoff +1
C photosynthesis has independently evolved from the ancestral C pathway in at least 60 plant lineages, but, as with other complex traits, how it evolved is unclear. Here we…
Efficient parametric inference for stochastic biological systems with measured variability
Iain G. Johnston
Stochastic systems in biology often exhibit substantial variability within and between cells. This variability, as well as having dramatic functional consequences, provides informa…
A tractable genotype-phenotype map for the self-assembly of protein quaternary structure
Sam F. Greenbury, Iain G. Johnston, Ard A. Louis +1
The mapping between biological genotypes and phenotypes is central to the study of biological evolution. Here we introduce a rich, intuitive, and biologically realistic genotype-ph…
The chaos within: exploring noise in cellular biology
Iain G. Johnston
Cellular biology exists embedded in a world dominated by random dynamics and chance. Many vital molecules and pieces of cellular machinery diffuse within cells, moving along random…
Epistasis can lead to fragmented neutral spaces and contingency in evolution
Steffen Schaper, Iain G. Johnston, Ard A. Louis
In evolution, the effects of a single deleterious mutation can sometimes be compensated for by a second mutation which recovers the original phenotype. Such epistatic interactions…
Mitochondrial Variability as a Source of Extrinsic Cellular Noise
Iain G. Johnston, Bernadett Gaal, Ricardo Pires das Neves +3
We present a study investigating the role of mitochondrial variability in generating noise in eukaryotic cells. Noise in cellular physiology plays an important role in many fundame…
Evolutionary Dynamics in a Simple Model of Self-Assembly
Iain G. Johnston, Sebastian A. Ahnert, Jonathan P. K. Doye +1
We investigate the evolutionary dynamics of an idealised model for the robust self-assembly of two-dimensional structures called polyominoes. The model includes rules that encode i…
The effect of scale-free topology on the robustness and evolvability of genetic regulatory networks
Sam F. Greenbury, Iain G. Johnston, Matthew A. Smith +2
We investigate how scale-free (SF) and Erdos-Renyi (ER) topologies affect the interplay between evolvability and robustness of model gene regulatory networks with Boolean threshold…
Modelling the Self-Assembly of Virus Capsids
Iain G. Johnston, Ard A. Louis, Jonathan P. K. Doye
We use computer simulations to study a model, first proposed by Wales [1], for the reversible and monodisperse self-assembly of simple icosahedral virus capsid structures. The succ…
The self-assembly of DNA Holliday junctions studied with a minimal model
Thomas E. Ouldridge, Iain G. Johnston, Ard A. Louis +1
In this paper, we explore the feasibility of using coarse-grained models to simulate the self-assembly of DNA nanostructures. We introduce a simple model of DNA where each nucleoti…