Journal of Theoretical Biology

Article	Citations
The eco-evolutionary modelling of populations and their traits using a measure of trait differentiation	80
Editorial Board	68
Editorial Board	55
Editorial Board	46
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	43
Cell size homeostasis under the circadian regulation of cell division in cyanobacteria	41
Internal phosphorus recycling promotes rich and complex dynamics in an algae-phosphorus model: Implications for eutrophication management	39
An integrated vertex model of the mesoderm invagination during the embryonic development of Drosophila	35
Evolution of mixed mating: Effects of among-parent variation in early-acting inbreeding depression coupled with overproduction of ovules	34
Second compartment widens plasmid invasion conditions: Two-compartment pair-formation model of conjugation in the gut	31
Resource budget model with Duffing oscillator for dynamics of synchronized biennial-bearing olives in the Levant	30
A framework for relating natural movement to length and quality of life in human and non-human animals	30
LRBmat: A novel gut microbial interaction and individual heterogeneity inference method for colorectal cancer	29
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
Deciphering circulating tumor cells binding in a microfluidic system thanks to a parameterized mathematical model	28
A model of tubulin removal and exchange caused by kinesin motor walking on microtubule lattices	26
Using geometry to rank evenness measures: Towards a deeper understanding of divergence	25
Modeling the response of homogeneous and heterogeneous cerebral capillary networks to local changes in vessel diameters	25
Identifiability and inference of phylogenetic birth–death models	22
Learning to hunt: A data-driven stochastic feedback control model of predator–prey interactions	22
Linking the disease transmission to information dissemination dynamics: An insight from a multi-scale model study	22
Social context modulates scale-free movements in a social insect	22
Lewy body radius growth: The hypothesis of the cube root of time dependency	22

Computational modeling implicates protein scaffolding in p38 regulation of Akt	21
Editorial Board	21
Editorial Board	21
Genomic compliance with Chargaff’s second parity rule may have originated non-adaptively, but stem-loops now function adaptively	20
Separation of evolutionary timescales in coevolving species	20
Inference on the structure of gene regulatory networks	19
Exploring COVID-19 transmission patterns and key factors during epidemics caused by three major strains in Asia	19
Unraveling the origin of glucose mediated disparate proliferation dynamics of cancer stem cells	18
Maintaining the proliferative cell niche in multicellular models of epithelia	18
Network-based uncertainty quantification for mathematical models in epidemiology	18
A direct comparison of methods for assessing the threat from emerging infectious diseases in seasonally varying environments	18
An approximate solution of the SLIP model under the regime of linear angular dynamics during stance and the stability of symmetric periodic running gaits	17
SIRS epidemics with individual heterogeneity of immunity waning	17
Peripheral straightness leads to shape diversification during formations of entire leaves	17
The relative importance of social information use for population abundance in group-living and non-grouping prey	17
Branching architecture affects genetic diversity within an individual tree	16
A process-based life cycle model of the cabbage stem flea beetle on winter oilseed rape: Effects of temperature	16
Multiple cohort study of hospitalized SARS-CoV-2 in-host infection dynamics: Parameter estimates, identifiability, sensitivity and the eclipse phase profile	16
Extinctions as a vestige of instability: The geometry of stability and feasibility	16
A mathematical model of the within-host kinetics of SARS-CoV-2 neutralizing antibodies following COVID-19 vaccination	15
Evolutionary game dynamics with non-uniform interaction rates in finite population	15
Editorial Board	15
Humeri under external load: Mechanical implications of differing bone curvature in American otter and honey badger	15
The long term effects of uncoupling interventions as a therapy for dementia in humans	15
A model of time-dependent macromolecular and elemental composition of phytoplankton	15
Editorial Board	15
Coevolution of the reckless prey and the patient predator	14
Editorial Board	14
Pattern formation in marsh ecosystems modeled through the interaction of marsh vegetation, mussels and sediment	14
Spatial dynamics of inflammation-causing and commensal bacteria in the gastrointestinal tract	14
Editorial Board	14
Editorial Board	14
Editorial Board	14
Estimating survival in continuous space from mark-dead-recovery data — Towards a continuous version of the multinomial dead recovery model	13
Evaluation of innate and adaptive immune system interactions in the tumor microenvironment via a 3D continuum model	13
Cargo transport properties are enhanced by cylindrical microtubule geometry and elliptical contact zone on cargo surface	13
A novel cost framework reveals evidence for competitive selection in the evolution of complex traits during plant domestication	13
Data-informed model reduction for inference and prediction from non-identifiable models	13
The influence of prey availability on behavioral decisions and reproductive success of a central-place forager during lactation	12
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	12
Vaccination strategies in a pair formation model for human papillomavirus infection: An optimal control approach	12
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	12
Bidirectional, unlike unidirectional transport, allows transporting axonal cargos against their concentration gradient	12
Genetic networks encode secrets of their past	12
Spatial scales in human movement between reservoirs of infection	12
Phenotypic variation modulates the growth dynamics and response to radiotherapy of solid tumours under normoxia and hypoxia	12
A letter to the editor about the article “The modularity codes”	12
The non-pharmaceutical interventions may affect the advantage in transmission of mutated variants during epidemics: A conceptual model for COVID-19	12
The evolution of germ-soma specialization under different genetic and environmental effects	11
Optimal control of pattern formations for an SIR reaction–diffusion epidemic model	11

A mathematical model to study the impact of intra-tumour heterogeneity on anti-tumour CD8+ T cell immune response	11
Dynamics of prion proliferation under combined treatment of pharmacological chaperones and interferons	11
Computational model of articular cartilage regeneration induced by scaffold implantation in vivo	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
Use of 3D chaos game representation to quantify DNA sequence similarity with applications for hierarchical clustering	11
Artificial selection of communities drives the emergence of structured interactions	11
On the fitness of informative cues in complex environments	11
Life history and deleterious mutation rate coevolution	11
The effect of heterogeneity of relative vaccine costs on the mean population vaccination rate with mpox as an example	11
Editorial Board	11
Modelling female physiology from head to Toe: Impact of sex hormones, menstrual cycle, and pregnancy	11
Pillars of biology: Boolean modeling of gene-regulatory networks	11
Rate-dependent effects of state-specific sodium channel blockers in cardiac tissue: Insights from idealized models	11
On the Fourier transform of a quantitative trait: Implications for compressive sensing	11
Interrelating neuronal morphology by coincidence similarity networks	11
The nasal cavity of the bearded seal: An effective and robust organ for retaining body heat and water	11
Role of coupling distances in a coupled thalamocortical network in the treatment of epilepsy	10
On minimising tumoural growth under treatment resistance	10
Stochastic simulation of a model for circadian rhythms in plants	10
Kinetics, thresholds, and a comparison of mechanisms underlying systemic infection by Listeria monocytogenes	10
Editorial Board	10
Noise-induced entrainment of the circadian clock by thermoperiods in tomato: A computational approach	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
Revisiting a demographic model of pest infestation in farming	10
Editorial Board	10
HIV transactivation: Stochastic modeling for studying the effects of BET inhibitors on the modulation of P-TEFb levels	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
Cell population growth kinetics in the presence of stochastic heterogeneity of cell phenotype	10
Exploring the role of the potential surface in the behaviour of early warning signals	10
Model of drug delivery to populations composed of two cell types	10
Downstream resource leakage a necessary condition for the stress-gradient hypothesis in processing chain commensalisms	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
A stochastic model for topographically influenced cell migration	9
A simplified longitudinal model for the development of Type 2 Diabetes Mellitus	9
A cell model about symmetric and asymmetric stem cell division	9
Modeling transit time distributions in microvascular networks	9
Crick’s “Frozen accident theory” of the genetic code explored by Ising models	9
Parameter identifiability and model selection for sigmoid population growth models	9
Ancestral process for infectious disease outbreaks with superspreading	9
How temporal environmental stochasticity affects species richness: Destabilization, neutralization and the storage effect	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
Mathematical models of retinitis pigmentosa: The trophic factor hypothesis	9
Modelling COVID-19 dynamics and potential for herd immunity by vaccination in Austria, Luxembourg and Sweden	9
Multi-scale model of lumen formation via inverse membrane blebbing mechanism during sprouting angiogenesis process	9
A 3D mathematical model of coupled stem cell-nutrient dynamics in myocardial regeneration therapy	9
Rankings of tuberculosis antibiotic treatment regimens are sensitive to spatial scale, detection limit, and initial host bacterial burden	9
Approximating steady state distributions for household structured epidemic models	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
Spreading speed of chronic wasting disease across deer groups with overlapping home ranges	9
Evolutionary emergence of plant and pollinator polymorphisms in consumer-resource mutualisms	8
Effect of permeability on the initiation of Atherosclerosis modeled as an inflammatory process	8
Disentangling the growth curve of microbial culture	8
Insights into the dynamics of ligand-induced dimerisation via mathematical modelling and analysis	8
Analysis of phenotype-genotype associations using genomic informational field theory (GIFT)	8
PD-based ADRC using time-varying gains: An application to microalgal-based bioprocess	8
A new real-time analog circuit of Ca2+ Li-Rinzel astrocyte model based on analytical method	8
The heterogeneous mixing model of COVID-19 with interventions	8
Application of growth rate from kinetic model to calculate stochastic growth of a bacteria population at low contamination level	8
Age-dependence of food allergy due to decreased supply of naïve T cells	8
Multi-timescale analysis of midbrain dopamine neuronal firing activities	8
Computational model of the cancer necrotic core formation in a tumor-on-a-chip device	8
Editorial Board	8
Passive electrolocation in terrestrial arthropods: Theoretical modelling of location detection	8
Mathematical modeling of the feather follicle morphogenetic wave in birds	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
Evolutionary coexistence in a metacommunity: Competition-colonization trade-off, ownership effects, environmental fluctuations	8
Temperature variability regulates the interactive effects of warming and pharmaceutical on aquatic ecosystem dynamics	8
A resource-based mechanistic framework for castration-resistant prostate cancer (CRPC)	8
Corrigendum to “Multiscale numerical workflow describing microalgae motion and light pattern incidence towards population growth in a photobioreactor” [J. Theoret. Biol. 498 (2020) 110293]	8
Phenomenological-based model of glucose transport from liver to abdominal subcutaneous adipose tissue	8
Editorial Board	8
Editorial Board	8
Using registry data to identify individual dairy cows with abnormal patterns in routinely recorded somatic cell counts	8
An adaptive numerical method for multi-cellular simulations of tissue development and maintenance	8
Modeling phyllotaxis: From the inhibition potential to the real plant	7

The dynamics of relapses during treatment switch in relapsing-remitting multiple sclerosis	7
Optic flow enrichment via Drosophila head and retina motions to support inflight position regulation	7
Identifying critical regulatory interactions in cell fate decision and transition by systematic perturbation analysis	7
Mathematical modeling of ventilator-induced lung inflammation	7
A multiscale continuum model of the vertebrate outer retina: The temporal dynamics of background-induced flicker enhancement	7
Geometrically balanced model of cell growth	7
Effects of a differentiating therapy on cancer-stem-cell-driven tumors	7
Choice of spatial discretisation influences the progression of viral infection within multicellular tissues	7
Propagation of an idealized infection in an airway tree, consequences of the inflammation on the oxygen transfer to blood	7
On the misuse of evolutionary theory to bolster the ‘scientific’ case for intelligent design: A cautionary note	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
Stochasticity-induced persistence in coupled social-ecological systems	7
Multiple colonies of cancer involved in mutual suppression with the immune system	7
Editorial Board	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
A PID controller for synchronization between master-slave neurons in fractional-order of neocortical network model	7
Evaluation of entropy and fractal dimension as biomarkers for tumor growth and treatment response using cellular automata	7
Cell orientation under stretch: A review of experimental findings and mathematical modelling	7
Biomechanics of transduction by mechanosensory cilia for prey detection in aquatic organisms	6
Pillars of theoretical biology: “Biochemical systems analysis, I, II and III”	6
Distributions of 4-subtree patterns for uniform random unrooted phylogenetic trees	6
Pandemic modelling for regions implementing an elimination strategy	6
Boolean function metrics can assist modelers to check and choose logical rules	6
Cell position-based evaluation of mechanical features of cells in multicellular systems	6
Editorial Board	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
A phosphoinositide-based model of actin waves in frustrated phagocytosis	6
Editorial Board	6
Uncertainty and error in SARS-CoV-2 epidemiological parameters inferred from population-level epidemic models	6
The mechanism of pattern transitions between formation and dispersion	6
Mechanisms of the end-plate potential noise and its implication for the neuromuscular junction anatomy	6
Inverted repeats in coronavirus SARS-CoV-2 genome manifest the evolution events	6
Editorial Board	6
Hamilton’s rule and kin competition in a finite kin population	6
Conformity and anti-conformity in a finite population	6
Editorial Board	6
Editorial Board	6
Autocatalytic-protection for an unknown locus CRISPR-Cas countermeasure for undesired mutagenic chain reactions	6
Virulence management: Closing the feedback loop between healthcare interventions and virulence evolution	6
Estimating the basic reproduction number from noisy daily data	6
Costly punishment sustains indirect reciprocity under low defection detectability	6
A multi-strain model with asymptomatic transmission: Application to COVID-19 in the US	6
Editorial Board	6
Revisiting the exclusion principle in epidemiology at the limit of a large competitive advantage	6
Optimal spatial monitoring of populations described by reaction–diffusion models	6
Where do successful populations originate from?	6
A virtual host model of Mycobacterium tuberculosis infection identifies early immune events as predictive of infection outcomes	6
Modelling count data with partial differential equation models in biology	6
Flow modeling and structural characterization in fungal pellets	6
Representing stimulus information in an energy metabolism pathway	6
Predicting pathways for old and new metabolites through clustering	6
Editorial Board	6
Enhanced precision of circadian rhythm by output system	6
Hot-topics cross-propagation and opinion-transfer dynamics in the Chinese Sina-microblog social media: A modeling study	6
Evolution of life cycle dimorphism: An example of sacoglossan sea slugs	6
Data-driven models for the risk of infection and hospitalization during a pandemic: Case study on COVID-19 in Nepal	6
Numerical modeling of senile plaque development under conditions of limited diffusivity of amyloid-β monomers	6
Causal theory on acceleration of seed germination in the vicinity of high voltage direct current transmission line	5
Co-inoculation with arbuscular mycorrhizal fungi differing in carbon sink strength induces a synergistic effect in plant growth	5
Beyond predation: Fish–coral interactions can tip the scales of coral disease	5
Pillars of Theoretical Biology: Airway stability and heterogeneity in the constricted lung	5
Tradeoffs in the energetic value of neuromodulation in a closed-loop neuromechanical system	5
Flock2: A model for orientation-based social flocking	5
Optimal targeted therapy for multiple cancers based on contrastive Notch signaling networks	5
The importance of ecological dynamics in evolutionary processes: A host-bacteriophage model revisited	5
Editorial Board	5
What does the tree of life look like as it grows? Evolution and the multifractality of time	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
Synchronization transition in networks of Fractional-Order memristive Hindmarsh-Rose neurons	5
Kinetic analysis of prothrombinase assembly and substrate delivery mechanisms	5
Probability of extinction and peak time for multi-type epidemics with application to COVID-19 variants of concern	5
Runaway signals: Exaggerated displays of commitment may result from second-order signaling	5
Super-resolution ultrasound imaging of ischaemia flow: An in silico study	5
Editorial Board	5
Circulating renin-angiotensin systems mediated feedback controls over the mean-arterial pressure	5
Editorial Board	5
Square root identities for harvested Beverton–Holt models	5
A mathematical model for wound healing in the reef-building coral Pocillopora damicornis	5
Editorial Board	5
A single-locus quantitative genetic model incorporating DNA methylation	5
Plant–pollinator interaction model with separate pollen and nectar dynamics	5
Establishment of risk classification index for animal brucellosis by stochastic models	5
Spatially-dependent model for rods and cones in the retina	5
Model-based data analysis of tissue growth in thin 3D printed scaffolds	5
Mutant emergence timing and population immunisation status impact epidemiological dynamics	5
Accounting for dimensional differences in stochastic domain invasion with applications to precancerous cell removal	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
Evolution of enzyme levels in metabolic pathways: A theoretical approach. Part 2	5
How do productivity gradient and diffusion shape patterns in a plant–herbivore grazing system?	5
The effect of outcome choice on vaccine dose allocation: a modelling study	5
Modified susceptible–exposed–infectious–recovered model for assessing the effectiveness of non-pharmaceutical interventions during the COVID-19 pandemic in Seoul	5