Journal of Theoretical Biology

Article	Citations
Resource budget model with Duffing oscillator for dynamics of synchronized biennial-bearing olives in the Levant	86
Modeling the influence of cell–cell contact and TGF-β signaling on the epithelial mesenchymal transition in MCF7 breast carcinoma cells	73
Learning to hunt: A data-driven stochastic feedback control model of predator–prey interactions	56
LRBmat: A novel gut microbial interaction and individual heterogeneity inference method for colorectal cancer	50
Evolution of mixed mating: Effects of among-parent variation in early-acting inbreeding depression coupled with overproduction of ovules	46
Topological early warning signals: Quantifying varying routes to extinction in a spatially distributed population model	43
An integrated vertex model of the mesoderm invagination during the embryonic development of Drosophila	35
Editorial Board	34
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
Cell size homeostasis under the circadian regulation of cell division in cyanobacteria	27
A mathematical model to evaluate the role of memory B and T cells in heterologous secondary dengue infection	27
A framework for relating natural movement to length and quality of life in human and non-human animals	26
Deciphering circulating tumor cells binding in a microfluidic system thanks to a parameterized mathematical model	25
Second compartment widens plasmid invasion conditions: Two-compartment pair-formation model of conjugation in the gut	24
Inter-city infections and the role of size heterogeneity in containment strategies	24
The effect of oxidative stress on the leading edge of the a-wave in retinitis pigmentosa	24
Social context modulates scale-free movements in a social insect	23
Stability and reactivity of food webs with trophic interactions	22
Lewy body radius growth: The hypothesis of the cube root of time dependency	20
Internal phosphorus recycling promotes rich and complex dynamics in an algae-phosphorus model: Implications for eutrophication management	19
Identifiability and inference of phylogenetic birth–death models	19
Extinctions as a vestige of instability: The geometry of stability and feasibility	18
Editorial Board	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	18
Editorial Board	18
A direct comparison of methods for assessing the threat from emerging infectious diseases in seasonally varying environments	17
Drug-loaded nanoparticles for cancer therapy: A high-throughput multicellular agent-based modeling study	17
Inference on the structure of gene regulatory networks	17
Peripheral straightness leads to shape diversification during formations of entire leaves	17
SIRS epidemics with individual heterogeneity of immunity waning	16
Computational modeling implicates protein scaffolding in p38 regulation of Akt	16
Separation of evolutionary timescales in coevolving species	16
The relative importance of social information use for population abundance in group-living and non-grouping prey	16
Network-based uncertainty quantification for mathematical models in epidemiology	16
Exploring COVID-19 transmission patterns and key factors during epidemics caused by three major strains in Asia	16
Pattern formation in marsh ecosystems modeled through the interaction of marsh vegetation, mussels and sediment	15
Editorial Board	15
Genomic compliance with Chargaff’s second parity rule may have originated non-adaptively, but stem-loops now function adaptively	15
Evolutionary game dynamics with non-uniform interaction rates in finite population	15
Humeri under external load: Mechanical implications of differing bone curvature in American otter and honey badger	15
Evolution of hunting efficiency of predator and hiding efficiency of prey in a stage-structured prey-predator model	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
A process-based life cycle model of the cabbage stem flea beetle on winter oilseed rape: Effects of temperature	15
Editorial Board	14
Estimating survival in continuous space from mark-dead-recovery data — Towards a continuous version of the multinomial dead recovery model	14
Editorial Board	14
Cargo transport properties are enhanced by cylindrical microtubule geometry and elliptical contact zone on cargo surface	14
Spatial dynamics of inflammation-causing and commensal bacteria in the gastrointestinal tract	14
A mathematical model of the within-host kinetics of SARS-CoV-2 neutralizing antibodies following COVID-19 vaccination	13
The long term effects of uncoupling interventions as a therapy for dementia in humans	13
A model of time-dependent macromolecular and elemental composition of phytoplankton	13
Multiple cohort study of hospitalized SARS-CoV-2 in-host infection dynamics: Parameter estimates, identifiability, sensitivity and the eclipse phase profile	13
Bounded environmental stochasticity generates secondary Allee thresholds	13
The influence of prey availability on behavioral decisions and reproductive success of a central-place forager during lactation	13
A novel cost framework reveals evidence for competitive selection in the evolution of complex traits during plant domestication	12
Data-informed model reduction for inference and prediction from non-identifiable models	12
Editorial Board	12
Bidirectional, unlike unidirectional transport, allows transporting axonal cargos against their concentration gradient	12
Branching architecture affects genetic diversity within an individual tree	12
Use of 3D chaos game representation to quantify DNA sequence similarity with applications for hierarchical clustering	12
Spatial Sucrose Sink Profiles Shape Phloem Transport Efficiency and Xylem-Phloem Water Exchange	12
Interrelating neuronal morphology by coincidence similarity networks	12
The nasal cavity of the bearded seal: An effective and robust organ for retaining body heat and water	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	11
Evolution of labor division in reproduction and multiple group tasks	11
Vaccination strategies in a pair formation model for human papillomavirus infection: An optimal control approach	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
On the Fourier transform of a quantitative trait: Implications for compressive sensing	11
The non-pharmaceutical interventions may affect the advantage in transmission of mutated variants during epidemics: A conceptual model for COVID-19	11
Rate-dependent effects of state-specific sodium channel blockers in cardiac tissue: Insights from idealized models	11
Bridging short- and long-distance dispersal in individual animal movement	11

A letter to the editor about the article “The modularity codes”	11
Genetic networks encode secrets of their past	11
Modelling female physiology from head to Toe: Impact of sex hormones, menstrual cycle, and pregnancy	10
The evolution of germ-soma specialization under different genetic and environmental effects	10
Pillars of biology: Boolean modeling of gene-regulatory networks	10
Computational model of articular cartilage regeneration induced by scaffold implantation in vivo	10
Optimization of antitumor radiotherapy fractionation via mathematical modeling with account of 4 R’s of radiobiology	10
Life history and deleterious mutation rate coevolution	10
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	10
Network reciprocity turns cheap talk into a force for cooperation	10
Artificial selection of communities drives the emergence of structured interactions	10
The effect of heterogeneity of relative vaccine costs on the mean population vaccination rate with mpox as an example	10
Modeling the effects of air pollutants and meteorological factors on scarlet fever in five provinces, Northwest China, 2013–2018	10
Uncertainty quantification for the random HIV dynamical model driven by drug adherence	10
Optimal control of pattern formations for an SIR reaction–diffusion epidemic model	10
A mathematical model to study the impact of intra-tumour heterogeneity on anti-tumour CD8+ T cell immune response	10
Dynamics and risk sharing in groups of selfish individuals	10
On minimising tumoural growth under treatment resistance	10
Noise-induced entrainment of the circadian clock by thermoperiods in tomato: A computational approach	9
Phenomenological modeling of gene transcription by approximating cooperativity of transcription factors improves prediction and reduces complexity in gene regulatory network models	9
Spreading speed of chronic wasting disease across deer groups with overlapping home ranges	9
Modeling transit time distributions in microvascular networks	9
HIV transactivation: Stochastic modeling for studying the effects of BET inhibitors on the modulation of P-TEFb levels	9
Role of coupling distances in a coupled thalamocortical network in the treatment of epilepsy	9
A simplified longitudinal model for the development of Type 2 Diabetes Mellitus	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
Hormonal regulation of ovarian follicle growth in humans: Model-based exploration of cycle variability and parameter sensitivities	9
How temporal environmental stochasticity affects species richness: Destabilization, neutralization and the storage effect	9
Editorial Board	9
Cell population growth kinetics in the presence of stochastic heterogeneity of cell phenotype	9
Chemotaxis in heterogeneous environments: A multi-agent model of decentralized gathering past obstacles	9
Kinetics, thresholds, and a comparison of mechanisms underlying systemic infection by Listeria monocytogenes	9
A phenotype-structured model to reproduce the avascular growth of a tumor and its interaction with the surrounding environment	9
Crick’s “Frozen accident theory” of the genetic code explored by Ising models	9
Evaluating the impact of human flow on the spread of infectious diseases	9
Revisiting a demographic model of pest infestation in farming	9
A cell model about symmetric and asymmetric stem cell division	9
Parameter identifiability and model selection for sigmoid population growth models	8
Model of drug delivery to populations composed of two cell types	8
Mathematical models of retinitis pigmentosa: The trophic factor hypothesis	8
An adaptive numerical method for multi-cellular simulations of tissue development and maintenance	8
A 3D mathematical model of coupled stem cell-nutrient dynamics in myocardial regeneration therapy	8
Downstream resource leakage a necessary condition for the stress-gradient hypothesis in processing chain commensalisms	8
Temperature variability regulates the interactive effects of warming and pharmaceutical on aquatic ecosystem dynamics	8
Approximating steady state distributions for household structured epidemic models	8
Exploring the role of the potential surface in the behaviour of early warning signals	8
Doubling time of infectious diseases	8
Multi-timescale analysis of midbrain dopamine neuronal firing activities	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
Ancestral process for infectious disease outbreaks with superspreading	8
Rankings of tuberculosis antibiotic treatment regimens are sensitive to spatial scale, detection limit, and initial host bacterial burden	8
On the onset of multicellular invasive behavior in hierarchical lineage: The role of inhibitory feedback and local fluctuations	8
A stochastic model for topographically influenced cell migration	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
Multi-scale model of lumen formation via inverse membrane blebbing mechanism during sprouting angiogenesis process	8
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
Mathematical modeling of the feather follicle morphogenetic wave in birds	7
Passive electrolocation in terrestrial arthropods: Theoretical modelling of location detection	7
Modelling the spread and management of Varroa Destructor in naive European Honeybee populations	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
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
The heterogeneous mixing model of COVID-19 with interventions	7
Using registry data to identify individual dairy cows with abnormal patterns in routinely recorded somatic cell counts	7
Adaptive dynamic resource allocation can cause tragedy of the commons in plants with nutrient competition	7
Evolutionary emergence of plant and pollinator polymorphisms in consumer-resource mutualisms	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
Evaluation of entropy and fractal dimension as biomarkers for tumor growth and treatment response using cellular automata	7
Disentangling the growth curve of microbial culture	7
A resource-based mechanistic framework for castration-resistant prostate cancer (CRPC)	7
Evolutionary coexistence in a metacommunity: Competition-colonization trade-off, ownership effects, environmental fluctuations	7
Editorial Board	7
Multiple colonies of cancer involved in mutual suppression with the immune system	7
Editorial Board	6
Propagation of an idealized infection in an airway tree, consequences of the inflammation on the oxygen transfer to blood	6

Optic flow enrichment via Drosophila head and retina motions to support inflight position regulation	6
Hot-topics cross-propagation and opinion-transfer dynamics in the Chinese Sina-microblog social media: A modeling study	6
Cell position-based evaluation of mechanical features of cells in multicellular systems	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
PD-based ADRC using time-varying gains: An application to microalgal-based bioprocess	6
Editorial Board	6
Corrigendum to “Multiscale numerical workflow describing microalgae motion and light pattern incidence towards population growth in a photobioreactor” [J. Theoret. Biol. 498 (2020) 110293]	6
Choice of spatial discretisation influences the progression of viral infection within multicellular tissues	6
Stochasticity-induced persistence in coupled social-ecological systems	6
A virtual host model of Mycobacterium tuberculosis infection identifies early immune events as predictive of infection outcomes	6
Local and systemic factors in the resolution of inflammation	6
Human papillomavirus driving cervical cancer: A mathematical model with persistent infection, cancer progression, and spontaneous remission	6
Geometrically balanced model of cell growth	6
Editorial Board	6
Optimal control of combination immunotherapy for a virtual murine cohort in a glioblastoma-immune dynamics model	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
Uncertainty and error in SARS-CoV-2 epidemiological parameters inferred from population-level epidemic models	6
Conformity and anti-conformity in a finite population	6
Modeling phyllotaxis: From the inhibition potential to the real plant	6
Computational model of the cancer necrotic core formation in a tumor-on-a-chip device	6
Flow modeling and structural characterization in fungal pellets	5
Mutant emergence timing and population immunisation status impact epidemiological dynamics	5
Editorial Board	5
Accounting for dimensional differences in stochastic domain invasion with applications to precancerous cell removal	5
Editorial Board	5
Tradeoffs in the energetic value of neuromodulation in a closed-loop neuromechanical system	5
Theoretical investigation of the dependence of population parameters on initial population size	5
Editorial Board	5
Boolean function metrics can assist modelers to check and choose logical rules	5
Numerical modeling of senile plaque development under conditions of limited diffusivity of amyloid-β monomers	5
Super-resolution ultrasound imaging of ischaemia flow: An in silico study	5
Editorial Board	5
Editorial Board	5
Establishment of risk classification index for animal brucellosis by stochastic models	5
Editorial Board	5
Revisiting the exclusion principle in epidemiology at the limit of a large competitive advantage	5
Pandemic modelling for regions implementing an elimination strategy	5
“Normal” phylogenetic networks may be emerging as the leading class	5
Pillars of theoretical biology: “Biochemical systems analysis, I, II and III”	5
Costly punishment sustains indirect reciprocity under low defection detectability	5
Flock2: A model for orientation-based social flocking	5
A multi-strain model with asymptomatic transmission: Application to COVID-19 in the US	5
The mechanism of pattern transitions between formation and dispersion	5
A note on metapopulation models	5
Comparing the biomechanics of triangular and cylindrical plant stems: When are triangular hollow structures mechanically superior to cylindrical ones?	5
Mathematical model suggests current CAR-macrophage dosage is efficient to low pre-infusion tumour burden but refractory to high tumour burden	5
Probability of extinction and peak time for multi-type epidemics with application to COVID-19 variants of concern	5
Bridging Wright–Fisher and Moran models	5
Distributions of 4-subtree patterns for uniform random unrooted phylogenetic trees	5
Pillars of Theoretical Biology: Airway stability and heterogeneity in the constricted lung	5
Inferring absolute cell numbers from relative proportion in stochastic models with cell plasticity	5
The importance of ecological dynamics in evolutionary processes: A host-bacteriophage model revisited	5
Biomechanics of transduction by mechanosensory cilia for prey detection in aquatic organisms	5
Predicting pathways for old and new metabolites through clustering	5
Representing stimulus information in an energy metabolism pathway	5
Enhanced precision of circadian rhythm by output system	5
Mechanisms of the end-plate potential noise and its implication for the neuromuscular junction anatomy	5
A PID controller for synchronization between master-slave neurons in fractional-order of neocortical network model	5
Estimating the basic reproduction number from noisy daily data	5
Optimal control applied to Zika virus epidemics in Colombia and Puerto Rico	5
Optimal spatial monitoring of populations described by reaction–diffusion models	5
Optimal targeted therapy for multiple cancers based on contrastive Notch signaling networks	5
Editorial Board	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
Editorial Board	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