M. Kimmel

Comparison of Tug-of-War Models Assuming Moran versus Branching Process Population Dynamics

The paper compares Tug-of-War models under Moran and branching process dynamics, showing similar statistics and inferring selection coefficients for breast cancer samples, supporting deleterious passenger mutations.

Evolutionary analysis of genomes of SARS-CoV-2-related bat viruses suggests old roots, constant effective population size, and possible increase of fitness

The paper analyzes SARS-CoV-2-related bat viruses to estimate their evolutionary history, finding old roots, constant population size, and possible fitness increase.

Mutation patterns in SARS-COV-2 Alpha and Beta variants indicate non-neutral evolution

The paper analyzes mutation patterns in SARS-CoV-2 Alpha and Beta variants to determine if their evolution was non-neutral, finding evidence of stronger selection and rapid genomic changes.

Moran Process Version of the Tug-of-War Model: Complex Behavior Revealed by Mathematical Analysis and Simulation Studies

The paper analyzes the Tug-of-War model of cancer evolution using a Moran process framework, showing complex stochastic behavior through mathematical proofs and simulations.

Heat Shock Factor 1 (HSF1) as a new tethering factor for ESR1 supporting its action in breast cancer.

This study shows HSF1 enhances ESR1's genomic action in breast cancer, increases transcriptome diversity, and together they predict poor prognosis in ER-negative cancers.

Predicting Minimal Residual Disease in Acute Myeloid Leukemia through Stochastic Modeling of Clonality

This paper develops a stochastic model to predict relapse in AML by analyzing MRD dynamics in a cohort of patients using whole genome sequencing data.

Heat shock response pathways regulate stimulus-specificity and sensitivity of NF-κB signalling to temperature stress

The paper shows that heat shock response pathways modulate NF-κB signaling specificity and sensitivity to temperature stress in breast cancer cells.

Statistical inference for the evolutionary history of cancer genomes

This paper compares SFS derived from birth-death processes and coalescent models in cancer evolution, showing they can be made comparable and presents a selective sweep model for tumor history analysis.