Pavol Bokes

Event timing precision in stochastic gene expression withbursty production

The paper analyzes how degradation and bursty production affect the optimal feedback for minimizing timing variability in stochastic gene expression.

Modulation of noisy gene expression by general sequestration mechanisms

This paper develops a stochastic framework to quantify how sequestration mechanisms modulate cell-to-cell protein level variation by analyzing fluctuation attenuation regimes.

Gene Expression Variability with Feedback Regulation Implemented via Protein-Dependent Cell Growth

This study models gene expression variability in single cells and growing populations with feedback regulation, finding analytical solutions for protein concentration distributions and quantifying population growth parameters.

Postsynaptic integration of excitatory and inhibitory signals based on an adaptive firing threshold

The paper models postsynaptic firing dynamics with and without an adaptive threshold, showing how inhibitory inputs can increase firing frequency and characterizing ISI noise properties.

Stochastic Gene Expression under Sequestration: Noise Reduction and Emergent Distributions

The paper models how protein sequestration affects gene expression noise, showing that sequestration cooperativity and kinetics alter the distribution of free protein.

Stochastic Gene Expression in Proliferating Cells: Differing Noise Intensity in Single-Cell and Population Perspectives

The paper shows that noise in gene expression can differ between single-cell and population perspectives, with population-level noise being higher in some cases due to cell cycle dynamics and feedback loops.

Bursty Gene Expression in Single Cells and Expanding Populations: A Discrete Approach

This study analyzes bursty protein production in single cells and expanding populations using a Markovian model with feedback, showing differences in distribution patterns between single-cell and population-level dynamics.

Fluctuation Test with Phenotypic Switching: A Unified Stochastic Approximation Framework

The paper develops a stochastic framework for analyzing fluctuation tests with phenotypic switching, showing that stable distributions or large deviations theory can approximate the probability distribution of tolerant cells depending on switching frequency.

Hysteresis and noise floor in gene expression optimised for persistence against lethal events

This study identifies optimal protein expression strategies for bacterial survival under antibiotic stress, revealing hysteresis and a noise floor in gene expression.

Joint Distribution of Protein Concentration and Cell Volume Coupled by Feedback in Dilution

The paper models a feedback mechanism between protein concentration and cell volume in a growing population, finding an exact distribution and analyzing its effects on ergodicity and growth.

Reversibility of resistance in a fluctuation test experiment modifies the tail of the Luria-Delbrück distribution

The paper modifies the Luria-Delbrück distribution by allowing resistance reversibility, showing the tail deviates from the Landau distribution's power law decay.

Quantifying noise modulation from coupling of stochastic expression to cellular growth: An analytical approach

The paper analyzes how protein expression-growth coupling amplifies stochasticity in gene expression and quantifies the resulting noise and skewness in protein concentration.

Heavy-tailed distributions in a stochastic gene autoregulation model

The paper analyzes gene expression variability in a stochastic autoregulation model, showing that heavy-tailed distributions arise from burst dynamics and negative feedback.

A modified fluctuation test for elucidating drug resistance in microbial and cancer cells

The paper modifies the fluctuation test to estimate drug resistance emergence in microbial and cancer cells by analyzing colony size fluctuations.

Exact and WKB-approximate distributions in a gene expression model with feedback in burst frequency, burst size, and protein stability

The paper models gene expression with feedback in burst frequency, size, and protein stability, comparing exact and WKB-approximate distributions under different feedback assumptions.

Postponing production exponentially enhances the molecular memory of a stochastic switch

The paper analyzes how delayed production in a stochastic gene expression system can create a stable toggle switch with low molecule copy numbers.

Protein noise and distribution in a two-stage gene-expression model extended by an mRNA inactivation loop

The paper extends a two-stage gene-expression model with an mRNA inactivation loop, showing reduced protein noise and non-monotonic noise reduction with protein stability.

Mixture distributions in a stochastic gene expression model with delayed feedback

The paper analyzes a stochastic gene expression model with delayed feedback, showing that bistability leads to mixture distributions of protein levels.

The role of incoherent feedforward circuits in regulating precision of event timing

The paper investigates how an incoherent feedforward circuit involving holin and antiholin proteins regulates the precision of lysis timing in bacteriophage lambda.

Optimal bang--bang feedback for bursty gene expression

The paper analyzes optimal bang-bang feedback for bursty gene expression to minimize deviation from a target protein concentration.

Stationary distributions and metastable behaviour for self-regulating proteins with general lifetime distributions

The paper analyzes the stationary distributions and metastable behavior of self-regulating proteins with general lifetime distributions, showing invariance under certain conditions and exploring bistable switches.

Buffering gene expression noise by microRNA based feedforward regulation

The paper analyzes a microRNA-based feedforward regulatory motif to show it can reduce gene expression noise under specific conditions.

Noise induced bimodality in genetic circuits with monostable positive feedback

This study investigates how noncooperative positive feedback in burst frequency or size affects protein-level distributions and noise in genetic circuits.

Controlling noisy expression through auto regulation of burst frequency and protein stability

This paper compares feedback mechanisms in burst frequency and protein decay rate to control protein noise, showing decay rate feedback is more effective in reducing noise outside the small-noise regime.

Maintaining gene expression levels by positive feedback in burst size in the presence of infinitesimal delay

The paper analyzes how positive feedback in burst size affects gene expression levels with or without infinitesimal delay, showing both scenarios lead to a gamma distribution of protein levels.

Cell volume distributions in exponentially growing populations

The paper models cell volume dynamics in growing populations and shows that single-cell and population-level analyses yield different volume distribution results.

High Cooperativity In Negative Feedback Can Amplify Noisy Gene Expression

The paper analyzes how negative feedback in protein burst size affects gene expression noise, finding that high cooperativity feedbacks can amplify noise under certain conditions.