Tomasz Lipniacki

The paper develops a rule-based computational model of the MAPK/ERK pathway to account for isoform-specific regulation and interactions, revealing how differential RAF-14-3-3 interactions influence signaling behavior.

The paper applies a Neyman-Pearson framework to single-cell TNF-NF-κB signaling data to quantify decision-making performance and detect pathway failures.

The paper quantifies how cancer and drug treatments affect the information capacity of RTK signaling pathways using optogenetic stimulation and information theory.

The paper uses a numerical model to study information transmission in cell monolayers, identifying stochastic factors that affect wave propagation and determining optimal channel widths and wave frequencies for effective communication.

This study shows that type III interferons suppress viral infections by promoting rapid cell death in infected epithelial cells, unlike type I interferons which mainly induce ISG expression.

The paper models and computes decision making errors in a molecular signaling system with two outputs using single cell measurements of NFκB and ATF-2 concentrations.

The paper models the antagonism between viral infection and innate immunity at the single-cell level using an agent-based stochastic approach, revealing three levels of viral interference with the immune response.

The paper demonstrates that non-identifiable models can still have predictive power when measured with appropriate stimulation protocols and iterative variable measurements.

The paper quantifies the information transmission rate of the MAPK/ERK pathway, finding it can transmit at least 6 bits per hour.

The paper reduces a complex NF-kB pathway model to a simpler identifiable model that retains key dynamics and can be used for further studies.

This paper introduces decision-theoretic and statistical methods to model signaling outcomes in cells, using single-cell data to analyze decision accuracy and dynamics in biological systems.

The paper shows that the MAPK/ERK pathway can transmit up to 1.86 bits of information per hour by encoding temporal patterns of EGF pulses into ERK activity pulses.