Journal of Theoretical Biology

Article	Citations
The eco-evolutionary modelling of populations and their traits using a measure of trait differentiation	78
Editorial Board	62
Editorial Board	53
Modeling the influence of cell–cell contact and TGF-β signaling on the epithelial mesenchymal transition in MCF7 breast carcinoma cells	46
A mathematical model to evaluate the role of memory B and T cells in heterologous secondary dengue infection	44
Editorial Board	44
Cell size homeostasis under the circadian regulation of cell division in cyanobacteria	43
Internal phosphorus recycling promotes rich and complex dynamics in an algae-phosphorus model: Implications for eutrophication management	41
An integrated vertex model of the mesoderm invagination during the embryonic development of Drosophila	40
Evolution of mixed mating: Effects of among-parent variation in early-acting inbreeding depression coupled with overproduction of ovules	38
Second compartment widens plasmid invasion conditions: Two-compartment pair-formation model of conjugation in the gut	34
Resource budget model with Duffing oscillator for dynamics of synchronized biennial-bearing olives in the Levant	33
A framework for relating natural movement to length and quality of life in human and non-human animals	31
Topological early warning signals: Quantifying varying routes to extinction in a spatially distributed population model	30
LRBmat: A novel gut microbial interaction and individual heterogeneity inference method for colorectal cancer	29
Linking the disease transmission to information dissemination dynamics: An insight from a multi-scale model study	28
Deciphering circulating tumor cells binding in a microfluidic system thanks to a parameterized mathematical model	28
Modelling uniaxial non-uniform yeast colony growth: Comparing an agent-based model and continuum approximations	27
In Remembrance: Professor Lewis Wolpert	27
Nonlinear thermodynamics of biological signal transduction for predicting conservation of entropy production rate	26
A model of tubulin removal and exchange caused by kinesin motor walking on microtubule lattices	25
Modeling the response of homogeneous and heterogeneous cerebral capillary networks to local changes in vessel diameters	23
Identifiability and inference of phylogenetic birth–death models	22
Using geometry to rank evenness measures: Towards a deeper understanding of divergence	22
Social context modulates scale-free movements in a social insect	22

Learning to hunt: A data-driven stochastic feedback control model of predator–prey interactions	21
Lewy body radius growth: The hypothesis of the cube root of time dependency	21
Computational modeling implicates protein scaffolding in p38 regulation of Akt	21
The impact of codon choice on translation process in Saccharomyces cerevisiae: folding class, protein function and secondary structure	21
Editorial Board	20
Editorial Board	20
The central role of host reproduction in determining the evolution of virulence in spatially structured populations	19
Genomic compliance with Chargaff’s second parity rule may have originated non-adaptively, but stem-loops now function adaptively	19
Impact of intervention on the spread of COVID-19 in India: A model based study	18
Exploring COVID-19 transmission patterns and key factors during epidemics caused by three major strains in Asia	18
Separation of evolutionary timescales in coevolving species	18
A direct comparison of methods for assessing the threat from emerging infectious diseases in seasonally varying environments	17
Inference on the structure of gene regulatory networks	17
Unraveling the origin of glucose mediated disparate proliferation dynamics of cancer stem cells	17
Network-based uncertainty quantification for mathematical models in epidemiology	17
Maintaining the proliferative cell niche in multicellular models of epithelia	17
The relative importance of social information use for population abundance in group-living and non-grouping prey	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
Peripheral straightness leads to shape diversification during formations of entire leaves	16
SIRS epidemics with individual heterogeneity of immunity waning	15
Branching architecture affects genetic diversity within an individual tree	15
Rules of nature’s Formula Run: Muscle mechanics during late stance is the key to explaining maximum running speed	15
Multiple cohort study of hospitalized SARS-CoV-2 in-host infection dynamics: Parameter estimates, identifiability, sensitivity and the eclipse phase profile	15
Extinctions as a vestige of instability: The geometry of stability and feasibility	15
Phenotypic variation modulates the growth dynamics and response to radiotherapy of solid tumours under normoxia and hypoxia	14
A mathematical model of the within-host kinetics of SARS-CoV-2 neutralizing antibodies following COVID-19 vaccination	14
Evolutionary game dynamics with non-uniform interaction rates in finite population	14
Editorial Board	14
A model of time-dependent macromolecular and elemental composition of phytoplankton	14
Editorial Board	14
Humeri under external load: Mechanical implications of differing bone curvature in American otter and honey badger	14
Data-informed model reduction for inference and prediction from non-identifiable models	14
The long term effects of uncoupling interventions as a therapy for dementia in humans	14
Spatial dynamics of inflammation-causing and commensal bacteria in the gastrointestinal tract	14
Pattern formation in marsh ecosystems modeled through the interaction of marsh vegetation, mussels and sediment	13
Calcium-dependent insulin resistance in hepatocytes: mathematical model	13
Editorial Board	13
Editorial Board	13
Coevolution of the reckless prey and the patient predator	13
Evaluation of innate and adaptive immune system interactions in the tumor microenvironment via a 3D continuum model	12
The influence of prey availability on behavioral decisions and reproductive success of a central-place forager during lactation	12
Cargo transport properties are enhanced by cylindrical microtubule geometry and elliptical contact zone on cargo surface	12
Editorial Board	12
A novel cost framework reveals evidence for competitive selection in the evolution of complex traits during plant domestication	12
Bidirectional, unlike unidirectional transport, allows transporting axonal cargos against their concentration gradient	12
Editorial Board	12
Estimating survival in continuous space from mark-dead-recovery data — Towards a continuous version of the multinomial dead recovery model	12
Bounded environmental stochasticity generates secondary Allee thresholds	12
A novel 3D atomistic-continuum cancer invasion model: In silico simulations of an in vitro organotypic invasion assay	11
Vaccination strategies in a pair formation model for human papillomavirus infection: An optimal control approach	11

Uncertainty quantification for the random HIV dynamical model driven by drug adherence	11
Evolution of labor division in reproduction and multiple group tasks	11
Computational model of articular cartilage regeneration induced by scaffold implantation in vivo	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 non-pharmaceutical interventions may affect the advantage in transmission of mutated variants during epidemics: A conceptual model for COVID-19	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
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
Genetic networks encode secrets of their past	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
Life history and deleterious mutation rate coevolution	11
The evolution of germ-soma specialization under different genetic and environmental effects	11
Editorial Board	10
Rate-dependent effects of state-specific sodium channel blockers in cardiac tissue: Insights from idealized models	10
Modelling female physiology from head to Toe: Impact of sex hormones, menstrual cycle, and pregnancy	10
Optimal control of pattern formations for an SIR reaction–diffusion epidemic model	10
Optimization of antitumor radiotherapy fractionation via mathematical modeling with account of 4 R’s of radiobiology	10
Bridging short- and long-distance dispersal in individual animal movement	10
Revisiting a demographic model of pest infestation in farming	10
Artificial selection of communities drives the emergence of structured interactions	10
Use of 3D chaos game representation to quantify DNA sequence similarity with applications for hierarchical clustering	10
Large connected components in sexual networks and their role in HIV transmission in Sub-Saharan Africa: A model-based analysis of HPTN 071(PopART) data	10
Dynamics of prion proliferation under combined treatment of pharmacological chaperones and interferons	10
Role of coupling distances in a coupled thalamocortical network in the treatment of epilepsy	10
Modeling the effects of air pollutants and meteorological factors on scarlet fever in five provinces, Northwest China, 2013–2018	10
On the Fourier transform of a quantitative trait: Implications for compressive sensing	10
Pillars of biology: Boolean modeling of gene-regulatory networks	10
A mathematical model to study the impact of intra-tumour heterogeneity on anti-tumour CD8+ T cell immune response	10
Chemotaxis in heterogeneous environments: A multi-agent model of decentralized gathering past obstacles	10
On minimising tumoural growth under treatment resistance	10
On the fitness of informative cues in complex environments	10
A stochastic model for topographically influenced cell migration	9
Cell population growth kinetics in the presence of stochastic heterogeneity of cell phenotype	9
Approximating steady state distributions for household structured epidemic models	9
Editorial Board	9
Model of drug delivery to populations composed of two cell types	9
A simplified longitudinal model for the development of Type 2 Diabetes Mellitus	9
How temporal environmental stochasticity affects species richness: Destabilization, neutralization and the storage effect	9
Mathematical models of retinitis pigmentosa: The trophic factor hypothesis	9
Stochastic simulation of a model for circadian rhythms in plants	9
Exploring the role of the potential surface in the behaviour of early warning signals	9
Editorial Board	9
Doubling time of infectious diseases	9
Ancestral process for infectious disease outbreaks with superspreading	9
A phenotype-structured model to reproduce the avascular growth of a tumor and its interaction with the surrounding environment	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
Noise-induced entrainment of the circadian clock by thermoperiods in tomato: A computational approach	9
Dynamics and risk sharing in groups of selfish individuals	9
Kinetics, thresholds, and a comparison of mechanisms underlying systemic infection by Listeria monocytogenes	9
HIV transactivation: Stochastic modeling for studying the effects of BET inhibitors on the modulation of P-TEFb levels	9
Hormonal regulation of ovarian follicle growth in humans: Model-based exploration of cycle variability and parameter sensitivities	9
Evaluating the impact of human flow on the spread of infectious diseases	9
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
PD-based ADRC using time-varying gains: An application to microalgal-based bioprocess	8
Effect of permeability on the initiation of Atherosclerosis modeled as an inflammatory process	8
A new real-time analog circuit of Ca2+ Li-Rinzel astrocyte model based on analytical method	8
A resource-based mechanistic framework for castration-resistant prostate cancer (CRPC)	8
Age-dependence of food allergy due to decreased supply of naïve T cells	8
Rankings of tuberculosis antibiotic treatment regimens are sensitive to spatial scale, detection limit, and initial host bacterial burden	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
The heterogeneous mixing model of COVID-19 with interventions	8
Passive electrolocation in terrestrial arthropods: Theoretical modelling of location detection	8
Multi-timescale analysis of midbrain dopamine neuronal firing activities	8
Application of growth rate from kinetic model to calculate stochastic growth of a bacteria population at low contamination level	8
Evolutionary coexistence in a metacommunity: Competition-colonization trade-off, ownership effects, environmental fluctuations	8
Modelling COVID-19 dynamics and potential for herd immunity by vaccination in Austria, Luxembourg and Sweden	8
On the onset of multicellular invasive behavior in hierarchical lineage: the role of inhibitory feedback and local fluctuations	8
Spreading speed of chronic wasting disease across deer groups with overlapping home ranges	8
Multi-scale model of lumen formation via inverse membrane blebbing mechanism during sprouting angiogenesis process	8
A cell model about symmetric and asymmetric stem cell division	8
An adaptive numerical method for multi-cellular simulations of tissue development and maintenance	8
Disentangling the growth curve of microbial culture	8
Temperature variability regulates the interactive effects of warming and pharmaceutical on aquatic ecosystem dynamics	8
Evolutionary emergence of plant and pollinator polymorphisms in consumer-resource mutualisms	8
Modeling transit time distributions in microvascular networks	8
Crick’s “Frozen accident theory” of the genetic code explored by Ising models	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
Editorial Board	7
Computational model of the cancer necrotic core formation in a tumor-on-a-chip device	7
A multiscale continuum model of the vertebrate outer retina: The temporal dynamics of background-induced flicker enhancement	7
Identifying critical regulatory interactions in cell fate decision and transition by systematic perturbation analysis	7
Cell orientation under stretch: A review of experimental findings and mathematical modelling	7
Editorial Board	7
Multiple colonies of cancer involved in mutual suppression with the immune system	7
Editorial Board	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
On the misuse of evolutionary theory to bolster the ‘scientific’ case for intelligent design: A cautionary note	7
The dynamics of relapses during treatment switch in relapsing-remitting multiple sclerosis	7
Geometrically balanced model of cell growth	7
Propagation of an idealized infection in an airway tree, consequences of the inflammation on the oxygen transfer to blood	7
Editorial Board	7
Phenomenological-based model of glucose transport from liver to abdominal subcutaneous adipose tissue	7
Analysis of phenotype-genotype associations using genomic informational field theory (GIFT)	7
Insights into the dynamics of ligand-induced dimerisation via mathematical modelling and analysis	7
Modeling long COVID dynamics: Impact of underlying health conditions	7
Optimal control of combination immunotherapy for a virtual murine cohort in a glioblastoma-immune dynamics model	7
Choice of spatial discretisation influences the progression of viral infection within multicellular tissues	7
Joint impacts of media, vaccination and treatment on an epidemic Filippov model with application to COVID-19	6
Representing stimulus information in an energy metabolism pathway	6
A phosphoinositide-based model of actin waves in frustrated phagocytosis	6
Autocatalytic-protection for an unknown locus CRISPR-Cas countermeasure for undesired mutagenic chain reactions	6
Optimal control applied to Zika virus epidemics in Colombia and Puerto Rico	6
Theoretical investigation of the dependence of population parameters on initial population size	6
Cell position-based evaluation of mechanical features of cells in multicellular systems	6
Hot-topics cross-propagation and opinion-transfer dynamics in the Chinese Sina-microblog social media: A modeling study	6
A process-based, stage-structured model of potato cyst nematode population dynamics: Effects of temperature and resistance	6
Modeling phyllotaxis: From the inhibition potential to the real plant	6
Optic flow enrichment via Drosophila head and retina motions to support inflight position regulation	6
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	6
Evolution of life cycle dimorphism: An example of sacoglossan sea slugs	6
Where do successful populations originate from?	6
Pillars of theoretical biology: “Biochemical systems analysis, I, II and III”	6
Boolean function metrics can assist modelers to check and choose logical rules	6
Accounting for dimensional differences in stochastic domain invasion with applications to precancerous cell removal	6
Enhanced precision of circadian rhythm by output system	6
Conformity and anti-conformity in a finite population	6
Pandemic modelling for regions implementing an elimination strategy	6
Data-driven models for the risk of infection and hospitalization during a pandemic: Case study on COVID-19 in Nepal	6
Editorial Board	6
Estimating the basic reproduction number from noisy daily data	6
A multi-strain model with asymptomatic transmission: Application to COVID-19 in the US	6
Editorial Board	6
Mathematical modeling of ventilator-induced lung inflammation	6
Effects of a differentiating therapy on cancer-stem-cell-driven tumors	6
Editorial Board	6
Flow modeling and structural characterization in fungal pellets	6
Modelling count data with partial differential equation models in biology	6
Editorial Board	6
Costly punishment sustains indirect reciprocity under low defection detectability	6
Editorial Board	6
The mechanism of pattern transitions between formation and dispersion	6
A virtual host model of Mycobacterium tuberculosis infection identifies early immune events as predictive of infection outcomes	6
Editorial Board	6
Predicting pathways for old and new metabolites through clustering	6
Uncertainty and error in SARS-CoV-2 epidemiological parameters inferred from population-level epidemic models	6
Editorial Board	6
A PID controller for synchronization between master-slave neurons in fractional-order of neocortical network model	6
Evaluation of entropy and fractal dimension as biomarkers for tumor growth and treatment response using cellular automata	6
Stochasticity-induced persistence in coupled social-ecological systems	6
Virulence management: Closing the feedback loop between healthcare interventions and virulence evolution	6
Distributions of 4-subtree patterns for uniform random unrooted phylogenetic trees	6
Evolution of enzyme levels in metabolic pathways: A theoretical approach. Part 2	5
Kinetic analysis of prothrombinase assembly and substrate delivery mechanisms	5
Revisiting the exclusion principle in epidemiology at the limit of a large competitive advantage	5
Optimal spatial monitoring of populations described by reaction–diffusion models	5
Model-based data analysis of tissue growth in thin 3D printed scaffolds	5
Co-inoculation with arbuscular mycorrhizal fungi differing in carbon sink strength induces a synergistic effect in plant growth	5
How do productivity gradient and diffusion shape patterns in a plant–herbivore grazing system?	5
Modified susceptible–exposed–infectious–recovered model for assessing the effectiveness of non-pharmaceutical interventions during the COVID-19 pandemic in Seoul	5
Causal theory on acceleration of seed germination in the vicinity of high voltage direct current transmission line	5
Beyond predation: Fish–coral interactions can tip the scales of coral disease	5
Corrigendum to “Bacterial resistance to antibodies: A model evolutionary study” [J. Theor. Biol. 417 (2017) 61–67]	5
Establishment of risk classification index for animal brucellosis by stochastic models	5
Mechanisms of the end-plate potential noise and its implication for the neuromuscular junction anatomy	5
Numerical modeling of senile plaque development under conditions of limited diffusivity of amyloid-β monomers	5
Biomechanics of transduction by mechanosensory cilia for prey detection in aquatic organisms	5
Mutant emergence timing and population immunisation status impact epidemiological dynamics	5
Optimal targeted therapy for multiple cancers based on contrastive Notch signaling networks	5
The effect of outcome choice on vaccine dose allocation: a modelling study	5
Lactate’s behavioral switch in the brain: An in-silico model	5
Runaway signals: Exaggerated displays of commitment may result from second-order signaling	5
Square root identities for harvested Beverton–Holt models	5
Synchronization transition in networks of Fractional-Order memristive Hindmarsh-Rose neurons	5
Circulating renin-angiotensin systems mediated feedback controls over the mean-arterial pressure	5
Hamilton’s rule and kin competition in a finite kin population	5
Inverted repeats in coronavirus SARS-CoV-2 genome manifest the evolution events	5
Probability of extinction and peak time for multi-type epidemics with application to COVID-19 variants of concern	5
Pillars of Theoretical Biology: Airway stability and heterogeneity in the constricted lung	5
Numerical investigation of the pharmacokinetics and pharmacodynamics of the chemotherapeutic drug in avascular and vascular stages of a brain tumor	5
Plant–pollinator interaction model with separate pollen and nectar dynamics	5
Spatially-dependent model for rods and cones in the retina	5