Journal of Theoretical Biology

Article	Citations
The eco-evolutionary modelling of populations and their traits using a measure of trait differentiation	74
Editorial Board	62
Editorial Board	49
Modeling the influence of cell–cell contact and TGF-β signaling on the epithelial mesenchymal transition in MCF7 breast carcinoma cells	46
Editorial Board	43
A mathematical model to evaluate the role of memory B and T cells in heterologous secondary dengue infection	42
Cell size homeostasis under the circadian regulation of cell division in cyanobacteria	42
Internal phosphorus recycling promotes rich and complex dynamics in an algae-phosphorus model: Implications for eutrophication management	39
A dynamical model for the origin of anisogamy	39
An integrated vertex model of the mesoderm invagination during the embryonic development of Drosophila	37
Evolution of mixed mating: Effects of among-parent variation in early-acting inbreeding depression coupled with overproduction of ovules	33
Second compartment widens plasmid invasion conditions: Two-compartment pair-formation model of conjugation in the gut	32
Resource budget model with Duffing oscillator for dynamics of synchronized biennial-bearing olives in the Levant	31
A framework for relating natural movement to length and quality of life in human and non-human animals	30
Topological early warning signals: Quantifying varying routes to extinction in a spatially distributed population model	29
The impact of codon choice on translation process in Saccharomyces cerevisiae: folding class, protein function and secondary structure	28
LRBmat: A novel gut microbial interaction and individual heterogeneity inference method for colorectal cancer	28
Deciphering circulating tumor cells binding in a microfluidic system thanks to a parameterized mathematical model	28
Linking the disease transmission to information dissemination dynamics: An insight from a multi-scale model study	25
Modelling uniaxial non-uniform yeast colony growth: Comparing an agent-based model and continuum approximations	24
Nonlinear thermodynamics of biological signal transduction for predicting conservation of entropy production rate	24
In Remembrance: Professor Lewis Wolpert	24
A model of tubulin removal and exchange caused by kinesin motor walking on microtubule lattices	22
Using geometry to rank evenness measures: Towards a deeper understanding of divergence	21
Identifiability and inference of phylogenetic birth–death models	21

Modeling the response of homogeneous and heterogeneous cerebral capillary networks to local changes in vessel diameters	21
Learning to hunt: A data-driven stochastic feedback control model of predator–prey interactions	20
Lewy body radius growth: The hypothesis of the cube root of time dependency	20
Social context modulates scale-free movements in a social insect	20
Computational modeling implicates protein scaffolding in p38 regulation of Akt	19
Editorial Board	18
The central role of host reproduction in determining the evolution of virulence in spatially structured populations	18
Editorial Board	18
Genomic compliance with Chargaff’s second parity rule may have originated non-adaptively, but stem-loops now function adaptively	18
Network-based uncertainty quantification for mathematical models in epidemiology	17
Exploring COVID-19 transmission patterns and key factors during epidemics caused by three major strains in Asia	17
Separation of evolutionary timescales in coevolving species	17
Peripheral straightness leads to shape diversification during formations of entire leaves	16
A direct comparison of methods for assessing the threat from emerging infectious diseases in seasonally varying environments	16
Unraveling the origin of glucose mediated disparate proliferation dynamics of cancer stem cells	16
An approximate solution of the SLIP model under the regime of linear angular dynamics during stance and the stability of symmetric periodic running gaits	16
Maintaining the proliferative cell niche in multicellular models of epithelia	16
Impact of intervention on the spread of COVID-19 in India: A model based study	15
A process-based life cycle of the cabbage stem flea beetle on winter oilseed rape: effects of temperature	15
Extinctions as a vestige of instability: The geometry of stability and feasibility	15
The long term effects of uncoupling interventions as a therapy for dementia in humans	15
SIRS epidemics with individual heterogeneity of immunity waning	15
The relative importance of social information use for population abundance in group-living and non-grouping prey	15
Rules of nature’s Formula Run: Muscle mechanics during late stance is the key to explaining maximum running speed	15
Inference on the structure of gene regulatory networks	15
Editorial Board	14
A model of time-dependent macromolecular and elemental composition of phytoplankton	14
Branching architecture affects genetic diversity within an individual tree	14
Cargo transport properties are enhanced by cylindrical microtubule geometry and elliptical contact zone on cargo surface	14
Bidirectional, unlike unidirectional transport, allows transporting axonal cargos against their concentration gradient	14
Editorial Board	14
Multiple cohort study of hospitalized SARS-CoV-2 in-host infection dynamics: Parameter estimates, identifiability, sensitivity and the eclipse phase profile	14
Evolutionary game dynamics with non-uniform interaction rates in finite population	13
Editorial Board	13
Calcium-dependent insulin resistance in hepatocytes: mathematical model	13
Editorial Board	13
Humeri under external load: Mechanical implications of differing bone curvature in American otter and honey badger	13
Pattern formation in marsh ecosystems modeled through the interaction of marsh vegetation, mussels and sediment	13
Editorial Board	13
Coevolution of the reckless prey and the patient predator	13
Spatial dynamics of inflammation-causing and commensal bacteria in the gastrointestinal tract	13
Editorial Board	13
Evaluation of innate and adaptive immune system interactions in the tumor microenvironment via a 3D continuum model	12
Sisyphus and his rock: Quasi-random walk inspired by the motion of a ball transported by a dung beetle on combined terrain	12
A mathematical model of the within-host kinetics of SARS-CoV-2 neutralizing antibodies following COVID-19 vaccination	12
Phenotypic variation modulates the growth dynamics and response to radiotherapy of solid tumours under normoxia and hypoxia	12
Estimating survival in continuous space from mark-dead-recovery data — Towards a continuous version of the multinomial dead recovery model	12
A novel cost framework reveals evidence for competitive selection in the evolution of complex traits during plant domestication	12
The influence of prey availability on behavioral decisions and reproductive success of a central-place forager during lactation	12
Computational model of articular cartilage regeneration induced by scaffold implantation in vivo	11

Optimal control of pattern formations for an SIR reaction–diffusion epidemic model	11
A novel 3D atomistic-continuum cancer invasion model: In silico simulations of an in vitro organotypic invasion assay	11
Genetic networks encode secrets of their past	11
Vaccination strategies in a pair formation model for human papillomavirus infection: An optimal control approach	11
The non-pharmaceutical interventions may affect the advantage in transmission of mutated variants during epidemics: A conceptual model for COVID-19	11
Interrelating neuronal morphology by coincidence similarity networks	11
The effect of heterogeneity of relative vaccine costs on the mean population vaccination rate with mpox as an example	11
Uncertainty quantification for the random HIV dynamical model driven by drug adherence	11
Mechanism of carbachol-induced 40 Hz gamma oscillations and the effects of NMDA activation on oscillatory dynamics in a model of the CA3 subfield of the hippocampus	11
Spatial scales in human movement between reservoirs of infection	11
The evolution of germ-soma specialization under different genetic and environmental effects	11
Life history and deleterious mutation rate coevolution	11
Artificial selection of communities drives the emergence of structured interactions	11
A mathematical model to study the impact of intra-tumour heterogeneity on anti-tumour CD8+ T cell immune response	11
The series of a four-node motif and coherent type-1 feed-forward loop can provide sensitive detection over arbitrary range of input signal, thereby explain Weber’s law in higher-order sensory processe	11
A letter to the editor about the article “The modularity codes”	11
The nasal cavity of the bearded seal: An effective and robust organ for retaining body heat and water	11
Cell population growth kinetics in the presence of stochastic heterogeneity of cell phenotype	10
Evolution of labor division in reproduction and multiple group tasks	10
Rate-dependent effects of state-specific sodium channel blockers in cardiac tissue: Insights from idealized models	10
On the fitness of informative cues in complex environments	10
Noise-induced entrainment of the circadian clock by thermoperiods in tomato: A computational approach	10
Stochastic simulation of a model for circadian rhythms in plants	10
Dynamics of prion proliferation under combined treatment of pharmacological chaperones and interferons	10
On the Fourier transform of a quantitative trait: Implications for compressive sensing	10
Pillars of biology: Boolean modeling of gene-regulatory networks	10
Optimization of antitumor radiotherapy fractionation via mathematical modeling with account of 4 R’s of radiobiology	10
Dynamics and risk sharing in groups of selfish individuals	10
Role of coupling distances in a coupled thalamocortical network in the treatment of epilepsy	10
Modelling female physiology from head to Toe: Impact of sex hormones, menstrual cycle, and pregnancy	10
Use of 3D chaos game representation to quantify DNA sequence similarity with applications for hierarchical clustering	10
Modeling the effects of air pollutants and meteorological factors on scarlet fever in five provinces, Northwest China, 2013–2018	10
Chemotaxis in heterogeneous environments: A multi-agent model of decentralized gathering past obstacles	10
Model of drug delivery to populations composed of two cell types	9
On minimising tumoural growth under treatment resistance	9
The influence of methylation status on a stochastic model of MGMT dynamics in glioblastoma: Phenotypic selection can occur with and without a downshift in promoter methylation status	9
How temporal environmental stochasticity affects species richness: Destabilization, neutralization and the storage effect	9
A stochastic model for topographically influenced cell migration	9
Evaluating the impact of human flow on the spread of infectious diseases	9
Hormonal regulation of ovarian follicle growth in humans: Model-based exploration of cycle variability and parameter sensitivities	9
Editorial Board	9
Exploring the role of the potential surface in the behaviour of early warning signals	9
A cell model about symmetric and asymmetric stem cell division	9
Doubling time of infectious diseases	9
A phenotype-structured model to reproduce the avascular growth of a tumor and its interaction with the surrounding environment	9
Ancestral process for infectious disease outbreaks with superspreading	9
Editorial Board	9
Kinetics, thresholds, and a comparison of mechanisms underlying systemic infection by Listeria monocytogenes	9
Approximating steady state distributions for household structured epidemic models	9
HIV transactivation: Stochastic modeling for studying the effects of BET inhibitors on the modulation of P-TEFb levels	9
Mathematical models of retinitis pigmentosa: The trophic factor hypothesis	9
Modelling how increased Cathepsin B/L and decreased TMPRSS2 usage for cell entry by the SARS-CoV-2 Omicron variant may affect the efficacy and synergy of TMPRSS2 and Cathepsin B/L inhibitors	9
A simplified longitudinal model for the development of Type 2 Diabetes Mellitus	9
Crick’s “Frozen accident theory” of the genetic code explored by Ising models	8
Modelling COVID-19 dynamics and potential for herd immunity by vaccination in Austria, Luxembourg and Sweden	8
Multi-scale model of lumen formation via inverse membrane blebbing mechanism during sprouting angiogenesis process	8
Age-dependence of food allergy due to decreased supply of naïve T cells	8
The heterogeneous mixing model of COVID-19 with interventions	8
Evolutionary emergence of plant and pollinator polymorphisms in consumer-resource mutualisms	8
Temperature variability regulates the interactive effects of warming and pharmaceutical on aquatic ecosystem dynamics	8
Effect of permeability on the initiation of Atherosclerosis modeled as an inflammatory process	8
Modeling transit time distributions in microvascular networks	8
Parameter identifiability and model selection for sigmoid population growth models	8
A 3D mathematical model of coupled stem cell-nutrient dynamics in myocardial regeneration therapy	8
An adaptive numerical method for multi-cellular simulations of tissue development and maintenance	8
Passive electrolocation in terrestrial arthropods: Theoretical modelling of location detection	8
Application of growth rate from kinetic model to calculate stochastic growth of a bacteria population at low contamination level	8
A new real-time analog circuit of Ca2+ Li-Rinzel astrocyte model based on analytical method	8
Comment on the article “Spatially-extended nucleation-aggregation-fragmentation models for the dynamics of prion-like neurodegenerative protein-spreading in the brain and its connectome 486 (2020) 110	8
Spreading speed of chronic wasting disease across deer groups with overlapping home ranges	8
Downstream resource leakage a necessary condition for the stress-gradient hypothesis in processing chain commensalisms	8
Using registry data to identify individual dairy cows with abnormal patterns in routinely recorded somatic cell counts	8
A resource-based mechanistic framework for castration-resistant prostate cancer (CRPC)	8
Evolutionary coexistence in a metacommunity: Competition-colonization trade-off, ownership effects, environmental fluctuations	8
Disentangling the growth curve of microbial culture	8
Multi-timescale analysis of midbrain dopamine neuronal firing activities	8
Optimal control of combination immunotherapy for a virtual murine cohort in a glioblastoma-immune dynamics model	7
Modeling long COVID dynamics: Impact of underlying health conditions	7
Identifying critical regulatory interactions in cell fate decision and transition by systematic perturbation analysis	7
Analysis of phenotype-genotype associations using genomic informational field theory (GIFT)	7

Computational model of the cancer necrotic core formation in a tumor-on-a-chip device	7
Editorial Board	7
Editorial Board	7
A multiscale continuum model of the vertebrate outer retina: The temporal dynamics of background-induced flicker enhancement	7
Propagation of an idealized infection in an airway tree, consequences of the inflammation on the oxygen transfer to blood	7
Cell orientation under stretch: A review of experimental findings and mathematical modelling	7
Effects of a differentiating therapy on cancer-stem-cell-driven tumors	7
Optic flow enrichment via Drosophila head and retina motions to support inflight position regulation	7
Evaluation of entropy and fractal dimension as biomarkers for tumor growth and treatment response using cellular automata	7
Corrigendum to “Multiscale numerical workflow describing microalgae motion and light pattern incidence towards population growth in a photobioreactor” [J. Theoret. Biol. 498 (2020) 110293]	7
Phenomenological-based model of glucose transport from liver to abdominal subcutaneous adipose tissue	7
Editorial Board	7
Editorial Board	7
The dynamics of relapses during treatment switch in relapsing-remitting multiple sclerosis	7
Geometrically balanced model of cell growth	7
Multiple colonies of cancer involved in mutual suppression with the immune system	7
Choice of spatial discretisation influences the progression of viral infection within multicellular tissues	7
Insights into the dynamics of ligand-induced dimerisation via mathematical modelling and analysis	7
Modeling phyllotaxis: From the inhibition potential to the real plant	7
PD-based ADRC using time-varying gains: An application to microalgal-based bioprocess	7
Modeling identifies variability in SARS-CoV-2 uptake and eclipse phase by infected cells as principal drivers of extreme variability in nasal viral load in the 48 h post infection	7
On the misuse of evolutionary theory to bolster the ‘scientific’ case for intelligent design: A cautionary note	7
Mechanisms of the end-plate potential noise and its implication for the neuromuscular junction anatomy	6
Data-driven models for the risk of infection and hospitalization during a pandemic: Case study on COVID-19 in Nepal	6
Where do successful populations originate from?	6
Predicting pathways for old and new metabolites through clustering	6
The importance of ecological dynamics in evolutionary processes: A host-bacteriophage model revisited	6
Representing stimulus information in an energy metabolism pathway	6
Conformity and anti-conformity in a finite population	6
Editorial Board	6
Virulence management: Closing the feedback loop between healthcare interventions and virulence evolution	6
A virtual host model of Mycobacterium tuberculosis infection identifies early immune events as predictive of infection outcomes	6
Inference on tissue transplantation experiments	6
Hot-topics cross-propagation and opinion-transfer dynamics in the Chinese Sina-microblog social media: A modeling study	6
Editorial Board	6
Optimal control applied to Zika virus epidemics in Colombia and Puerto Rico	6
Hamilton’s rule and kin competition in a finite kin population	6
Revisiting the exclusion principle in epidemiology at the limit of a large competitive advantage	6
Biomechanics of transduction by mechanosensory cilia for prey detection in aquatic organisms	6
Theoretical investigation of the dependence of population parameters on initial population size	6
Distributions of 4-subtree patterns for uniform random unrooted phylogenetic trees	6
Evolution of life cycle dimorphism: An example of sacoglossan sea slugs	6
Optimal spatial monitoring of populations described by reaction–diffusion models	6
Accounting for dimensional differences in stochastic domain invasion with applications to precancerous cell removal	6
Flow modeling and structural characterization in fungal pellets	6
Autocatalytic-protection for an unknown locus CRISPR-Cas countermeasure for undesired mutagenic chain reactions	6
The mechanism of pattern transitions between formation and dispersion	6
Pandemic modelling for regions implementing an elimination strategy	6
A phosphoinositide-based model of actin waves in frustrated phagocytosis	6
Editorial Board	6
A PID controller for synchronization between master-slave neurons in fractional-order of neocortical network model	6
Enhanced precision of circadian rhythm by output system	6
Cell position-based evaluation of mechanical features of cells in multicellular systems	6
Numerical modeling of senile plaque development under conditions of limited diffusivity of amyloid-β monomers	6
Inverted repeats in coronavirus SARS-CoV-2 genome manifest the evolution events	6
A process-based, stage-structured model of potato cyst nematode population dynamics: Effects of temperature and resistance	6
Pillars of theoretical biology: “Biochemical systems analysis, I, II and III”	6
Editorial Board	6
Uncertainty and error in SARS-CoV-2 epidemiological parameters inferred from population-level epidemic models	6
Joint impacts of media, vaccination and treatment on an epidemic Filippov model with application to COVID-19	6
Estimating the basic reproduction number from noisy daily data	6
Editorial Board	6
Mathematical modeling of ventilator-induced lung inflammation	6
Boolean function metrics can assist modelers to check and choose logical rules	6
Costly punishment sustains indirect reciprocity under low defection detectability	6
Editorial Board	6
Stochasticity-induced persistence in coupled social-ecological systems	6
Editorial Board	6
A multi-strain model with asymptomatic transmission: Application to COVID-19 in the US	6
Plant–pollinator interaction model with separate pollen and nectar dynamics	5
Tradeoffs in the energetic value of neuromodulation in a closed-loop neuromechanical system	5
Inferring absolute cell numbers from relative proportion in stochastic models with cell plasticity	5
Corrigendum to “Bacterial resistance to antibodies: A model evolutionary study” [J. Theor. Biol. 417 (2017) 61–67]	5
Kinetic analysis of prothrombinase assembly and substrate delivery mechanisms	5
Optimal dormancy strategies in fluctuating environments given delays in phenotypic switching	5
What does the tree of life look like as it grows? Evolution and the multifractality of time	5
Causal theory on acceleration of seed germination in the vicinity of high voltage direct current transmission line	5
Modified susceptible–exposed–infectious–recovered model for assessing the effectiveness of non-pharmaceutical interventions during the COVID-19 pandemic in Seoul	5
How do productivity gradient and diffusion shape patterns in a plant–herbivore grazing system?	5
Editorial Board	5
Flock2: A model for orientation-based social flocking	5
Editorial Board	5
Beyond predation: Fish–coral interactions can tip the scales of coral disease	5
A mathematical model for wound healing in the reef-building coral Pocillopora damicornis	5
A single-locus quantitative genetic model incorporating DNA methylation	5
Numerical investigation of the pharmacokinetics and pharmacodynamics of the chemotherapeutic drug in avascular and vascular stages of a brain tumor	5
Lactate’s behavioral switch in the brain: An in-silico model	5
Spatially-dependent model for rods and cones in the retina	5
Modelling count data with partial differential equation models in biology	5
Circulating renin-angiotensin systems mediated feedback controls over the mean-arterial pressure	5
Evolution of enzyme levels in metabolic pathways: A theoretical approach. Part 2	5
Square root identities for harvested Beverton–Holt models	5
Editorial Board	5
Antisocial peer exclusion does not eliminate the effectiveness of prosocial peer exclusion in structured populations	5
Runaway signals: Exaggerated displays of commitment may result from second-order signaling	5