Topic 38

systems model mathematical dynamics parameters models framework experimental stochastic biophysics theoretical theory modeling computational simulations parameter how biological can networks network such time simple dynamical simulation based it system equations processes general paper problem noise experimentally properties numerical equation number nonlinear principles different find between predictions modelling author propose state space work experiments show approach linear distributions underlying describe perturbations develop reaction rate kinetic feedback derive growth analytical understanding be interactions reproduce steady account fundamental set diffusion information process complex optimal conditions this dimensional allows where biology predicts on constraints way introduce proposed states level scales robustness complexity understand fitting

860 items. Top items listed below.

Predicting global dynamics of spatial microbial communities from local interaction rules 158 99 38 17 5

Biological network growth in complex environments - a computational framework 38 18 4

Uncovering modeling features of viral replication dynamics from high-throughput single-cell virology experiments 38 21 4

The Roles of Space and Stochasticity in Computational Simulations of Cellular Biochemistry: Quantitative Analysis and Qualitative Insights 38 4

HippoUnit: A software tool for the automated testing and systematic comparison of detailed models of hippocampal neurons based on electrophysiological data 62 4 2

Local homeostatic regulation of the spectral radius of echo-state networks 38 2

A model of the PI cycle reveals the regulating roles of lipid-binding proteins and pitfalls of using mosaic biological data 38 8

A Spiking Neuron and Population Model based on the Growth Transform Dynamical System 38 2

Novel tunable spatio-temporal patterns from a simple genetic oscillator circuit 38 18

The covariance perceptron: A new paradigm for classification and processing of time series in recurrent neuronal networks 100 50 38 23 2

A stochastic model of gene expression with polymerase recruitment and pause release 127 38

First-principles prediction of the information processing capacity of a simple genetic circuit 38 4

Overlaid positive and negative feedback loops shape dynamical properties of PhoPQ two-component system 38

Graph neural fields: a framework for spatiotemporal dynamical models on the human connectome 22 2

Analysis of single-cell gene pair coexpression landscapes by stochastic kinetic modeling reveals gene-pair interactions in development 43 38 4

Optimal Design of Single-Cell Experiments within Temporally Fluctuating Environments 38 4

DNN-Assisted Statistical Analysis of a Model of Local Cortical Circuits 38 26 4 2

New mathematical modelling tools for co-culture experiments: when do we need to explicitly account for signalling molecules? 127 38 18 4

Phenotypic delay in the evolution of bacterial antibiotic resistance: mechanistic models and their implications 185 21 5

Robust point-process Granger causality analysis in presence of exogenous temporal modulations and trial-by-trial variability in spike trains. 123 38 2

Understanding biochemical design principles with ensembles of canonical non-linear models 38 26 4

Systems biology informed deep learning for inferring parameters and hidden dynamics 38 26 4

Representing Organic Matter Thermodynamics in Biogeochemical Reactions via Substrate-Explicit Modeling 38 4

Using optimal control to understand complex metabolic pathways 38 4

Learning receptive field properties of complex cells in V1 100 50 38 23 2

The Design Principles of Discrete Turing Patterning Systems 38

Dynamic bistable switches enhance robustness and accuracy of cell cycle transitions 38 8

Effects of spatial heterogeneity on bacterial genetic circuits 7

Connecting actin polymer dynamics across multiple scales 127 38 8

A theoretical framework to study the influence of electrical fields on mesenchymal stem cells 172 127 38 18

Identification of multiple noise sources improves estimation of neural responses across stimulus conditions 72 38 2

The shape of density dependence and the relationship between population growth, intraspecific competition and equilibrium population density 99 38 17 5

Programming cell growth into different cluster shapes using diffusible signals 38 18

Transcriptional kinetic synergy: a complex landscape revealed by integrating modelling and synthetic biology 31 8

Denoising large-scale biological data using network filters 26 4

Development of an objective index, neural activity score (NAS), reveals neural network ontogeny and treatment effects on microelectrode arrays 4 2

A computational framework for a Lyapunov-enabled analysis of biochemical reaction networks 38 4

An active inference approach to modeling structure learning: concept learning as an example case 157 38 26 4 2

Neural Circuit Dynamics for Sensory Detection 50 38 2

Stochastic synchronization of dynamics on the human connectome 38 2

From graph topology to ODE models for gene regulatory networks 38 4

Constrained proteome allocation affects coexistence inmodels of competitive microbial communities 99 38 17 5

Estimating RNA dynamics using one time point for one sample in a single-pulse metabolic experiment 83 4

Machine Learning and Optimal Control of Enzyme Activities to Preserve Solvent Capacity in the Cell 67 38 26 4

Modeling microbial cross-feeding at intermediate scale portrays community dynamics and species coexistence 158 99 38 29 17 5 4

Towards an evolutionarily appropriate null model: jointly inferring demography and purifying selection 83 21 5 4

Transfer function for YAP/TAZ nuclear translocation revealed through spatial systems modeling 38 18 8

Exploring the Sequence Fitness Landscape of a Bridge Between Protein Folds 149 91 38 8 4

Investigation of Inter-Individual Variability in CD8 T Cell Responses with Nonlinear Mixed Effects Models 38 4

Testing structural identifiability by a simple scaling method 38 4

Computational study on ratio-sensing in yeast galactose utilization pathway 158 38

A Parallel Ratchet-Stroke Mechanism Leads to an Optimum Force for Molecular Motor Function. 127 38 8

Bayesian Connective Field Modeling: a Markov Chain Monte Carlo approach. 38 2

Robust coding with spiking networks: a geometric perspective 38 2

MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics 62 38 4

Engineering recurrent neural networks from task-relevant manifolds and dynamics 100 38 2

A spatial model of the plant circadian clock reveals design principles for coordinated timing under noisy environments 155 38

Adaptation is influenced by the complexity of environmental change during evolution in a dynamic environment 21 5

Emergence and Propagation of Epistasis in Metabolic Networks 38 21 5

A hybrid stochastic-deterministic approach to explore multiple infection and evolution in HIV 38 21

Raman spectroscopy-based measurements of single-cell phenotypic diversity in microbial communities 158 38 18 17 5

Model Reduction Tools For Phenomenological Modeling of Input-Controlled Biological Circuits 38 4

Macroscale network feedback structure of transcriptome during cell fate transition 7

Ecological consequences of intraspecific variation in coevolutionary systems 99 21 5 4

On the automatic annotation of gene functions using observational data and phylogenetic trees 162 13 4

Personalized logical models to investigate cancer response to BRAF treatments in melanomas and colorectal cancers 112 38 26 4

A network model of the barrel cortex combined with a differentiator detector reproduces features of the behavioral response to single-neuron stimulation. 50 11 2

Synaptic dynamics as convolutional units 38 26 2

Fractional diffusion theory of balanced heterogeneous neural networks 38 2

Resilience and evolvability of protein-protein interaction networks 38 21 5

Optimal transcriptional regulation of cellular responses to sudden environmental shifts 192 38 31 21

A predictive model of gene expression reveals the role of regulatory motifs in the mating response of yeast 7

Cell size statistics in cell lineages and population snapshots with different growth regimes and division strategies. 127 38 5

Training and inferring neural network function with multi-agent reinforcement learning 38 2

How well do crop modeling groups predict wheat phenology, given calibration data from the target population? 182 83 38 4

A minimal yet flexible likelihood framework to assess correlated evolution 83 21 4

Dynamics of chromosomal target search by a membrane-integrated one-component receptor 127 8 3

Complementary effects of adaptation and gain control on sound encoding in primary auditory cortex 23 2

Role of cell polarity dynamics and motility in pattern formation due to contact dependent signalling 55 38 8

Multi-Approach and Multi-Scale Model of CD4+ T Cells Predicts Switch-Like and Oscillatory Emergent Behaviors in Inflammatory Response to Infection 38 4

Quantifying the dynamics of viral recombination during free virus and cell-to-cell transmission in HIV-1 infection 41 21

Event-based pattern detection in active dendrites 38 2

Generative modeling of single-cell population time series for inferring cell differentiation landscapes 38 4

A novel single-cell based method for breast cancer prognosis 43 26 4

Mathematical modeling of plant cell fate transitions controlled by hormonal signals 38 16

Social networks with strong spatial embedding generate non-standard epidemic dynamics driven by higher-order clustering 38

Benchmarking kinetic models of Escherichia coli metabolism 38 4

Diverse cell stimulation kinetics identify predictive signal transduction models 38 18 4

Constrained brain volume in an efficient coding model explains the fraction of excitatory and inhibitory neurons in sensory cortices 50 2

Division stochasticity can be transmitted to protein expression through chromosome replication 127 38 21 5

Four different mechanisms for switching cell polarity 127 38 8

Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments 158 112 4

Model guided trait-specific co-expression network estimation as a new perspective for identifying molecular interactions and pathways 112 4

Detection of the changes in dynamical structures insynchronous neural oscillations from a viewpoint of probabilistic inference 123 38 2

Population codes of prior knowledge learned through environmental regularities 157 58 23 2

Elucidating relationships between P.falciparum prevalence and measures of genetic diversity with a combined genetic-epidemiological model of malaria 155 83 38 21 5 4

Efficient search for informational cores in complex systems: Application to brain networks 38 4 2

Structure-informed functional connectivity driven by identifiable and state-specific control regions 38 22 2

Generating Synthetic Signaling Networks for in Silico Modeling Studies 38 26 4

An organ-based multi-level model for glucose homeostasis: organ distributions, timing, and impact of blood flow 38