Z. Kilic

Single-Molecule Reaction-Diffusion

This paper introduces Bayes-smRD, a method to analyze single-molecule reaction-diffusion using photon arrival data, revealing molecule-specific properties with reduced data and photodamage.

BNP-Track: A framework for multi-particle superresolved tracking

BNP-Track is a framework for superresolved tracking of fluorescent molecules that uses Bayesian nonparametrics to infer emitter numbers and tracks, outperforming conventional methods in crowded environments.

Inferring gene expression models from snapshot RNA data

The paper introduces a Bayesian nonparametric method to infer gene networks from single-cell RNA data by simultaneously learning gene states, connectivities, and rate parameters.

A Continuous Time Representation of smFRET for the Extraction of Rapid Kinetics

This paper develops a continuous-time hidden Markov jump process to learn kinetic rates from smFRET data beyond acquisition rates, validated on simulated and experimental data.

Generalizing HMMs to Continuous Time for Fast Kinetics: Hidden Markov Jump Processes

This paper generalizes hidden Markov models to continuous time for analyzing single molecule kinetics, introducing hidden Markov jump processes to handle fast transitions without discrete time assumptions.

Residence Time Analysis of RNA Polymerase Transcription Dynamics: A Bayesian Sticky HMM Approach

This paper introduces a Bayesian sticky HMM approach to analyze RNA polymerase residence times without distinguishing between long and short events, revealing force-dependent dynamics and limited effects of GreB.