List of works - Tomasz Lipniacki

A computational model for early events in B cell antigen receptor signaling: analysis of the roles of Lyn and Fyn.

scientific article

A shear stress micromodel of urinary tract infection by the Escherichia coli producing Dr adhesin

scientific article published on 09 January 2020

Accounting for super-spreading gives the basic reproduction number R0 of COVID-19 that is higher than initially estimated

scientific article published on 01 May 2020

Adjoint systems for models of cell signaling pathways and their application to parameter fitting.

scientific article published in July 2007

Asymptotic behavior of distributions of mRNA and protein levels in a model of stochastic gene expression

article

B cell activation triggered by the formation of the small receptor cluster: a computational study

scientific article

Cascade of vortex loops initiated by a single reconnection of quantum vortices

scientific article

Cell fate in antiviral response arises in the crosstalk of IRF, NF-κB and JAK/STAT pathways

scientific article

Chemically driven traveling waves in DNA.

scientific article published in December 1999

Clustering reveals limits of parameter identifiability in multi-parameter models of biochemical dynamics.

scientific article published on 29 September 2015

Computation and measurement of cell decision making errors using single cell data

scientific article published on 5 April 2017

Computational analysis of an autophagy/translation switch based on mutual inhibition of MTORC1 and ULK1

scientific article

Crosstalk between p53 and nuclear factor-B systems: pro- and anti-apoptotic functions of NF-B

scientific article published on 01 September 2009

Deterministic and stochastic models of NFkappaB pathway

scientific article published on 18 October 2007

Digital signaling decouples activation probability and population heterogeneity.

scientific article

Dynamic cross talk model of the epithelial innate immune response to double-stranded RNA stimulation: coordinated dynamics emerging from cell-level noise.

scientific article

Dynamics of COVID-19 pandemic at constant and time-dependent contact rates

scholarly article by Tomasz Lipniacki published in 2020

Dynamics of a stochastic spatially extended system predicted by comparing deterministic and stochastic attractors of the corresponding birth-death process

scientific article published on 25 September 2012

Effective reaction rates for diffusion-limited reaction cycles

scientific article published in December 2015

Effective reaction rates in diffusion-limited phosphorylation-dephosphorylation cycles

scientific article published on 3 February 2015

Electrochemical Immunosensors Based on Screen-Printed Gold and Glassy Carbon Electrodes: Comparison of Performance for Respiratory Syncytial Virus Detection

scientific article published on 13 November 2020

Exact solutions to a spatially extended model of kinase-receptor interaction

scientific article published on 10 August 2011

Exploring mechanisms of oscillations in p53 and nuclear factor-B systems

scientific article published on 01 September 2009

Feedbacks, Bifurcations, and Cell Fate Decision-Making in the p53 System

scientific article

Genetic toggle switch controlled by bacterial growth rate

scientific article published on 2 December 2017

Guidelines for visualizing and annotating rule-based models

scientific article

Homoclinic solutions in mechanical systems with small dissipation. Application to DNA dynamics.

scientific article published in April 2002

Importins promote high-frequency NF-κB oscillations increasing information channel capacity

scientific article

Information processing in the NF-κB pathway.

scientific article published on 21 November 2017

Levels of pro-apoptotic regulator Bad and anti-apoptotic regulator Bcl-xL determine the type of the apoptotic logic gate

scientific article

Limits to the rate of information transmission through the MAPK pathway

article

MEK1 and MEK2 differentially control the duration and amplitude of the ERK cascade response

scientific article published on 4 June 2013

Mathematical model of NF-kappaB regulatory module

scientific article

Model-based optimization of combination protocols for irradiation-insensitive cancers

scientific article published on 28 July 2020

Modeling and measurement of signaling outcomes affecting decision making in noisy intracellular networks using machine learning methods

scientific article published on 01 May 2020

Oscillations and bistability in the stochastic model of p53 regulation.

scientific article published on 4 June 2008

Polarization of concave domains by traveling wave pinning

scientific article

RAF1/BRAF dimerization integrates the signal from RAS to ERK and ROKα.

scientific article published on 7 March 2017

Regulation of kinase activity by diffusion and feedback.

scientific article published on 21 March 2009

Relaxation oscillations and hierarchy of feedbacks in MAPK signaling

scientific article

SPATKIN: a simulator for rule-based modeling of biomolecular site dynamics on surfaces.

scientific article published on 17 July 2017

Sampling rare events in stochastic reaction-diffusion systems within trajectory looping

scientific article published on 01 August 2018

Single TNFalpha trimers mediating NF-kappaB activation: stochastic robustness of NF-kappaB signaling.

scientific article

Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing.

scientific article published on 27 June 2010

Slow nucleosome dynamics set the transcriptional speed limit and induce RNA polymerase II traffic jams and bursts

scientific article published on 10 February 2022

Spatial gradients in kinase cascade regulation.

scientific article published in November 2010

Spontaneous NF-κB activation by autocrine TNFα signaling: a computational analysis

scientific article published on 11 November 2013

Stability of bacterial toggle switches is enhanced by cell-cycle lengthening by several orders of magnitude.

scientific article published on 11 February 2014

Stochastic effects and bistability in T cell receptor signaling

scientific article published on 10 May 2008

Stochastic effects of multiple regulators on expression profiles in eukaryotes.

scientific article published on 8 December 2004

Stochastic regulation in early immune response

scientific article

Stochastic transitions in a bistable reaction system on the membrane

scientific article

Super-spreading events initiated the exponential growth phase of COVID-19 with ℛ0 higher than initially estimated

scientific article published on 23 September 2020

The interplay of double phosphorylation and scaffolding in MAPK pathways

scientific article

Thermodynamics of local DNA openings

scientific article published on 29 October 2001

Toggle switch: noise determines the winning gene

scientific article published on 4 June 2013

Transcriptional stochasticity in gene expression.

scientific article published on 21 July 2005

Traveling and standing fronts on curved surfaces

Type of noise defines global attractors in bistable molecular regulatory systems

scientific article published on 11 October 2012

Vortex loops cascade as a channel of quantum turbulence decay

scientific article

List of works by Tomasz Lipniacki

A computational model for early events in B cell antigen receptor signaling: analysis of the roles of Lyn and Fyn.

A shear stress micromodel of urinary tract infection by the Escherichia coli producing Dr adhesin

Accounting for super-spreading gives the basic reproduction number R0 of COVID-19 that is higher than initially estimated

Adjoint systems for models of cell signaling pathways and their application to parameter fitting.

Asymptotic behavior of distributions of mRNA and protein levels in a model of stochastic gene expression

B cell activation triggered by the formation of the small receptor cluster: a computational study

Cascade of vortex loops initiated by a single reconnection of quantum vortices

Cell fate in antiviral response arises in the crosstalk of IRF, NF-κB and JAK/STAT pathways

Chemically driven traveling waves in DNA.

Clustering reveals limits of parameter identifiability in multi-parameter models of biochemical dynamics.

Computation and measurement of cell decision making errors using single cell data

Computational analysis of an autophagy/translation switch based on mutual inhibition of MTORC1 and ULK1

Crosstalk between p53 and nuclear factor-B systems: pro- and anti-apoptotic functions of NF-B

Deterministic and stochastic models of NFkappaB pathway

Digital signaling decouples activation probability and population heterogeneity.

Dynamic cross talk model of the epithelial innate immune response to double-stranded RNA stimulation: coordinated dynamics emerging from cell-level noise.

Dynamics of COVID-19 pandemic at constant and time-dependent contact rates

Dynamics of a stochastic spatially extended system predicted by comparing deterministic and stochastic attractors of the corresponding birth-death process

Effective reaction rates for diffusion-limited reaction cycles

Effective reaction rates in diffusion-limited phosphorylation-dephosphorylation cycles

Electrochemical Immunosensors Based on Screen-Printed Gold and Glassy Carbon Electrodes: Comparison of Performance for Respiratory Syncytial Virus Detection

Exact solutions to a spatially extended model of kinase-receptor interaction

Exploring mechanisms of oscillations in p53 and nuclear factor-B systems

Feedbacks, Bifurcations, and Cell Fate Decision-Making in the p53 System

Genetic toggle switch controlled by bacterial growth rate

Guidelines for visualizing and annotating rule-based models

Homoclinic solutions in mechanical systems with small dissipation. Application to DNA dynamics.

Importins promote high-frequency NF-κB oscillations increasing information channel capacity

Information processing in the NF-κB pathway.

Levels of pro-apoptotic regulator Bad and anti-apoptotic regulator Bcl-xL determine the type of the apoptotic logic gate

Limits to the rate of information transmission through the MAPK pathway

MEK1 and MEK2 differentially control the duration and amplitude of the ERK cascade response

Mathematical model of NF-kappaB regulatory module

Model-based optimization of combination protocols for irradiation-insensitive cancers

Modeling and measurement of signaling outcomes affecting decision making in noisy intracellular networks using machine learning methods

Oscillations and bistability in the stochastic model of p53 regulation.

Polarization of concave domains by traveling wave pinning

RAF1/BRAF dimerization integrates the signal from RAS to ERK and ROKα.

Regulation of kinase activity by diffusion and feedback.

Relaxation oscillations and hierarchy of feedbacks in MAPK signaling

SPATKIN: a simulator for rule-based modeling of biomolecular site dynamics on surfaces.

Sampling rare events in stochastic reaction-diffusion systems within trajectory looping

Single TNFalpha trimers mediating NF-kappaB activation: stochastic robustness of NF-kappaB signaling.

Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing.

Slow nucleosome dynamics set the transcriptional speed limit and induce RNA polymerase II traffic jams and bursts

Spatial gradients in kinase cascade regulation.

Spontaneous NF-κB activation by autocrine TNFα signaling: a computational analysis

Stability of bacterial toggle switches is enhanced by cell-cycle lengthening by several orders of magnitude.

Stochastic effects and bistability in T cell receptor signaling

Stochastic effects of multiple regulators on expression profiles in eukaryotes.

Stochastic regulation in early immune response

Stochastic transitions in a bistable reaction system on the membrane

Super-spreading events initiated the exponential growth phase of COVID-19 with ℛ0 higher than initially estimated

The interplay of double phosphorylation and scaffolding in MAPK pathways

Thermodynamics of local DNA openings

Toggle switch: noise determines the winning gene

Transcriptional stochasticity in gene expression.

Traveling and standing fronts on curved surfaces

Type of noise defines global attractors in bistable molecular regulatory systems

Vortex loops cascade as a channel of quantum turbulence decay