Journal of Theoretical Biology

Article	Citations
Resource budget model with Duffing oscillator for dynamics of synchronized biennial-bearing olives in the Levant	86
The eco-evolutionary modelling of populations and their traits using a measure of trait differentiation	71
Learning to hunt: A data-driven stochastic feedback control model of predator–prey interactions	52
LRBmat: A novel gut microbial interaction and individual heterogeneity inference method for colorectal cancer	48
Using geometry to rank evenness measures: Towards a deeper understanding of divergence	46
Evolution of mixed mating: Effects of among-parent variation in early-acting inbreeding depression coupled with overproduction of ovules	43
Topological early warning signals: Quantifying varying routes to extinction in a spatially distributed population model	37
Editorial Board	33
An integrated vertex model of the mesoderm invagination during the embryonic development of Drosophila	33
Modeling the response of homogeneous and heterogeneous cerebral capillary networks to local changes in vessel diameters	32
Editorial Board	30
A model of tubulin removal and exchange caused by kinesin motor walking on microtubule lattices	28
A mathematical model to evaluate the role of memory B and T cells in heterologous secondary dengue infection	28
Second compartment widens plasmid invasion conditions: Two-compartment pair-formation model of conjugation in the gut	27
Inter-city infections and the role of size heterogeneity in containment strategies	26
Stability and reactivity of food webs with trophic interactions	26
A framework for relating natural movement to length and quality of life in human and non-human animals	25
Deciphering circulating tumor cells binding in a microfluidic system thanks to a parameterized mathematical model	24
Internal phosphorus recycling promotes rich and complex dynamics in an algae-phosphorus model: Implications for eutrophication management	24
Cell size homeostasis under the circadian regulation of cell division in cyanobacteria	24
Lewy body radius growth: The hypothesis of the cube root of time dependency	22
Identifiability and inference of phylogenetic birth–death models	21
Social context modulates scale-free movements in a social insect	20
Modeling the influence of cell–cell contact and TGF-β signaling on the epithelial mesenchymal transition in MCF7 breast carcinoma cells	19
Extinctions as a vestige of instability: The geometry of stability and feasibility	19

Editorial Board	18
Editorial Board	18
Peripheral straightness leads to shape diversification during formations of entire leaves	17
Computational modeling implicates protein scaffolding in p38 regulation of Akt	17
Exploring COVID-19 transmission patterns and key factors during epidemics caused by three major strains in Asia	17
The relative importance of social information use for population abundance in group-living and non-grouping prey	17
A direct comparison of methods for assessing the threat from emerging infectious diseases in seasonally varying environments	17
A process-based life cycle model of the cabbage stem flea beetle on winter oilseed rape: Effects of temperature	17
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
Humeri under external load: Mechanical implications of differing bone curvature in American otter and honey badger	16
Genomic compliance with Chargaff’s second parity rule may have originated non-adaptively, but stem-loops now function adaptively	16
Inference on the structure of gene regulatory networks	16
Editorial Board	16
Separation of evolutionary timescales in coevolving species	16
Network-based uncertainty quantification for mathematical models in epidemiology	16
SIRS epidemics with individual heterogeneity of immunity waning	16
Evolutionary game dynamics with non-uniform interaction rates in finite population	15
Editorial Board	15
Editorial Board	15
Evaluation of innate and adaptive immune system interactions in the tumor microenvironment via a 3D continuum model	15
Editorial Board	15
Editorial Board	15
Pattern formation in marsh ecosystems modeled through the interaction of marsh vegetation, mussels and sediment	15
Coevolution of the reckless prey and the patient predator	15
Multiple cohort study of hospitalized SARS-CoV-2 in-host infection dynamics: Parameter estimates, identifiability, sensitivity and the eclipse phase profile	14
Spatial dynamics of inflammation-causing and commensal bacteria in the gastrointestinal tract	14
Estimating survival in continuous space from mark-dead-recovery data — Towards a continuous version of the multinomial dead recovery model	14
Data-informed model reduction for inference and prediction from non-identifiable models	14
Cargo transport properties are enhanced by cylindrical microtubule geometry and elliptical contact zone on cargo surface	14
A mathematical model of the within-host kinetics of SARS-CoV-2 neutralizing antibodies following COVID-19 vaccination	13
The influence of prey availability on behavioral decisions and reproductive success of a central-place forager during lactation	13
The long term effects of uncoupling interventions as a therapy for dementia in humans	13
Branching architecture affects genetic diversity within an individual tree	13
A novel cost framework reveals evidence for competitive selection in the evolution of complex traits during plant domestication	13
Bounded environmental stochasticity generates secondary Allee thresholds	13
Bidirectional, unlike unidirectional transport, allows transporting axonal cargos against their concentration gradient	13
A model of time-dependent macromolecular and elemental composition of phytoplankton	13
The nasal cavity of the bearded seal: An effective and robust organ for retaining body heat and water	12
The effect of heterogeneity of relative vaccine costs on the mean population vaccination rate with mpox as an example	12
On the Fourier transform of a quantitative trait: Implications for compressive sensing	12
Interrelating neuronal morphology by coincidence similarity networks	12
Bridging short- and long-distance dispersal in individual animal movement	12
Use of 3D chaos game representation to quantify DNA sequence similarity with applications for hierarchical clustering	12
Editorial Board	12
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	12
Vaccination strategies in a pair formation model for human papillomavirus infection: An optimal control approach	11
Rate-dependent effects of state-specific sodium channel blockers in cardiac tissue: Insights from idealized models	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
Life history and deleterious mutation rate coevolution	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
The non-pharmaceutical interventions may affect the advantage in transmission of mutated variants during epidemics: A conceptual model for COVID-19	11
A mathematical model to study the impact of intra-tumour heterogeneity on anti-tumour CD8+ T cell immune response	11
Modelling female physiology from head to Toe: Impact of sex hormones, menstrual cycle, and pregnancy	11
Uncertainty quantification for the random HIV dynamical model driven by drug adherence	11
A letter to the editor about the article “The modularity codes”	11
Genetic networks encode secrets of their past	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
The evolution of germ-soma specialization under different genetic and environmental effects	11
Pillars of biology: Boolean modeling of gene-regulatory networks	11
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
Modeling the effects of air pollutants and meteorological factors on scarlet fever in five provinces, Northwest China, 2013–2018	10
Role of coupling distances in a coupled thalamocortical network in the treatment of epilepsy	10
HIV transactivation: Stochastic modeling for studying the effects of BET inhibitors on the modulation of P-TEFb levels	10
Optimal control of pattern formations for an SIR reaction–diffusion epidemic model	10
Dynamics and risk sharing in groups of selfish individuals	10
On minimising tumoural growth under treatment resistance	10
Chemotaxis in heterogeneous environments: A multi-agent model of decentralized gathering past obstacles	10
Artificial selection of communities drives the emergence of structured interactions	10
Revisiting a demographic model of pest infestation in farming	10
Cell population growth kinetics in the presence of stochastic heterogeneity of cell phenotype	10
Editorial Board	9
Doubling time of infectious diseases	9
Modeling transit time distributions in microvascular networks	9
Modelling COVID-19 dynamics and potential for herd immunity by vaccination in Austria, Luxembourg and Sweden	9
Exploring the role of the potential surface in the behaviour of early warning signals	9
Approximating steady state distributions for household structured epidemic models	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
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	9
A phenotype-structured model to reproduce the avascular growth of a tumor and its interaction with the surrounding environment	9
Parameter identifiability and model selection for sigmoid population growth models	9
Mathematical models of retinitis pigmentosa: The trophic factor hypothesis	9
A stochastic model for topographically influenced cell migration	9
Evaluating the impact of human flow on the spread of infectious diseases	9
How temporal environmental stochasticity affects species richness: Destabilization, neutralization and the storage effect	9
A cell model about symmetric and asymmetric stem cell division	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
Ancestral process for infectious disease outbreaks with superspreading	9
On the onset of multicellular invasive behavior in hierarchical lineage: The role of inhibitory feedback and local fluctuations	9
Rankings of tuberculosis antibiotic treatment regimens are sensitive to spatial scale, detection limit, and initial host bacterial burden	9
Model of drug delivery to populations composed of two cell types	9
Kinetics, thresholds, and a comparison of mechanisms underlying systemic infection by Listeria monocytogenes	9
Temperature variability regulates the interactive effects of warming and pharmaceutical on aquatic ecosystem dynamics	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
The heterogeneous mixing model of COVID-19 with interventions	8
Evolutionary emergence of plant and pollinator polymorphisms in consumer-resource mutualisms	8
Disentangling the growth curve of microbial culture	8
Multi-timescale analysis of midbrain dopamine neuronal firing activities	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
A resource-based mechanistic framework for castration-resistant prostate cancer (CRPC)	8
Editorial Board	8
Downstream resource leakage a necessary condition for the stress-gradient hypothesis in processing chain commensalisms	8
Mathematical modeling of the feather follicle morphogenetic wave in birds	8
Effect of permeability on the initiation of Atherosclerosis modeled as an inflammatory process	8
Age-dependence of food allergy due to decreased supply of naïve T cells	8
Evolutionary coexistence in a metacommunity: Competition-colonization trade-off, ownership effects, environmental fluctuations	8
Using registry data to identify individual dairy cows with abnormal patterns in routinely recorded somatic cell counts	8
Multi-scale model of lumen formation via inverse membrane blebbing mechanism during sprouting angiogenesis process	8
Optimal control of combination immunotherapy for a virtual murine cohort in a glioblastoma-immune dynamics model	7
Geometrically balanced model of cell growth	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
Modeling long COVID dynamics: Impact of underlying health conditions	7
On the misuse of evolutionary theory to bolster the ‘scientific’ case for intelligent design: A cautionary note	7
Phenomenological-based model of glucose transport from liver to abdominal subcutaneous adipose tissue	7
Editorial Board	7
Stochasticity-induced persistence in coupled social-ecological systems	7
Cell orientation under stretch: A review of experimental findings and mathematical modelling	7
Computational model of the cancer necrotic core formation in a tumor-on-a-chip device	7
Propagation of an idealized infection in an airway tree, consequences of the inflammation on the oxygen transfer to blood	7
Editorial Board	7
Insights into the dynamics of ligand-induced dimerisation via mathematical modelling and analysis	7
Effects of a differentiating therapy on cancer-stem-cell-driven tumors	7
Editorial Board	7

Choice of spatial discretisation influences the progression of viral infection within multicellular tissues	7
PD-based ADRC using time-varying gains: An application to microalgal-based bioprocess	7
Modeling phyllotaxis: From the inhibition potential to the real plant	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
Multiple colonies of cancer involved in mutual suppression with the immune system	7
The dynamics of relapses during treatment switch in relapsing-remitting multiple sclerosis	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
Optic flow enrichment via Drosophila head and retina motions to support inflight position regulation	7
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
The mechanism of pattern transitions between formation and dispersion	6
Optimal control applied to Zika virus epidemics in Colombia and Puerto Rico	6
Data-driven models for the risk of infection and hospitalization during a pandemic: Case study on COVID-19 in Nepal	6
Conformity and anti-conformity in a finite population	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
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
Uncertainty and error in SARS-CoV-2 epidemiological parameters inferred from population-level epidemic models	6
Editorial Board	6
Pandemic modelling for regions implementing an elimination strategy	6
Revisiting the exclusion principle in epidemiology at the limit of a large competitive advantage	6
Editorial Board	6
Theoretical investigation of the dependence of population parameters on initial population size	6
Costly punishment sustains indirect reciprocity under low defection detectability	6
Editorial Board	6
A virtual host model of Mycobacterium tuberculosis infection identifies early immune events as predictive of infection outcomes	6
Virulence management: Closing the feedback loop between healthcare interventions and virulence evolution	6
Predicting pathways for old and new metabolites through clustering	6
Flow modeling and structural characterization in fungal pellets	6
Boolean function metrics can assist modelers to check and choose logical rules	5
Corrigendum to “An optimal network that promotes the spread of an advantageous variant in an SIR epidemic”. [J. Theor. Biol. 605 (2025) 112095]	5
Biomechanics of transduction by mechanosensory cilia for prey detection in aquatic organisms	5
“Normal” phylogenetic networks may be emerging as the leading class	5
Editorial Board	5
The importance of ecological dynamics in evolutionary processes: A host-bacteriophage model revisited	5
Plant–pollinator interaction model with separate pollen and nectar dynamics	5
Spatially-dependent model for rods and cones in the retina	5
A single-locus quantitative genetic model incorporating DNA methylation	5
Modelling count data with partial differential equation models in biology	5
Corrigendum to “Bacterial resistance to antibodies: A model evolutionary study” [J. Theor. Biol. 417 (2017) 61–67]	5
Representing stimulus information in an energy metabolism pathway	5
Super-resolution ultrasound imaging of ischaemia flow: An in silico study	5
Numerical modeling of senile plaque development under conditions of limited diffusivity of amyloid-β monomers	5
Editorial Board	5
Editorial Board	5
Bridging Wright–Fisher and Moran models	5
Circulating renin-angiotensin systems mediated feedback controls over the mean-arterial pressure	5
Editorial Board	5
A note on metapopulation models	5
Establishment of risk classification index for animal brucellosis by stochastic models	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
Editorial Board	5
Mechanisms of the end-plate potential noise and its implication for the neuromuscular junction anatomy	5
Synchronization transition in networks of Fractional-Order memristive Hindmarsh-Rose neurons	5
Pillars of theoretical biology: “Biochemical systems analysis, I, II and III”	5
Probability of extinction and peak time for multi-type epidemics with application to COVID-19 variants of concern	5
Accounting for dimensional differences in stochastic domain invasion with applications to precancerous cell removal	5
Editorial Board	5
Inverted repeats in coronavirus SARS-CoV-2 genome manifest the evolution events	5
Inferring absolute cell numbers from relative proportion in stochastic models with cell plasticity	5
Distributions of 4-subtree patterns for uniform random unrooted phylogenetic trees	5
Tradeoffs in the energetic value of neuromodulation in a closed-loop neuromechanical system	5
Co-inoculation with arbuscular mycorrhizal fungi differing in carbon sink strength induces a synergistic effect in plant growth	5
Editorial Board	5
Lactate’s behavioral switch in the brain: An in-silico model	5
Optimal spatial monitoring of populations described by reaction–diffusion models	5
Beyond predation: Fish–coral interactions can tip the scales of coral disease	5
Flock2: A model for orientation-based social flocking	5
Optimal targeted therapy for multiple cancers based on contrastive Notch signaling networks	5
Mutant emergence timing and population immunisation status impact epidemiological dynamics	5
Pillars of Theoretical Biology: Airway stability and heterogeneity in the constricted lung	5
Enhanced species coexistence in Lotka-Volterra competition models due to nonlocal interactions	4
Pillars of theoretical biology: ‘Mathematical models for cellular interaction in development, I and II’	4
Editorial Board	4
RSC-based differential model with correlation removal for improving multi-omics clustering	4
Incorporating adult age into mosquito population models: Implications for predicting abundances in changing climates	4
A Boolean network model of the double-strand break repair pathway choice	4
Tumor microenvironment as a metapopulation model: The effects of angiogenesis, emigration and treatment modalities	4
Mathematical consideration of massive estimation of dissociation rate constant for genotype–phenotype linking molecules bound to targets through washing/selection and next-generation sequencing	4
Decoding cancer dynamics: The role of miRNA in E2F/Myc networks and bifurcation points	4
A geometric approach to the evolution of altruism	4
Powered-gliding/climbing flight	4
Mathematical models of long term evolution of blue whale song types’ frequencies	4
Phase synchronization analysis of EEG functional connectivity in Parkinson’s disease	4
Infections are not alike: The effects of covariation between individual susceptibility and transmissibility on epidemic dynamics	4
Mathematical modelling of autoimmune myocarditis and the effects of immune checkpoint inhibitors	4
Modeling alternative strategies of male emergence timing	4
Structural patterns of SARS-CoV-2 variants of concern (alpha, beta, gamma, delta) spike protein are influenced by variant-specific amino acid mutations: A computational study with implications on vira	4
Perivascular pumping in the mouse brain: Improved boundary conditions reconcile theory, simulation, and experiment	4
A mathematical model of cell movement and clustering due to chemotaxis	4
Unification of alpha, mu, and tau rhythms and their beta-band harmonics via eigenmodes: spectral peaks, topography, and reactivity	4