James Holehouse

The paper uses metagenomic data to show microbial ecosystems follow unique ecological assembly patterns distinct from other complex systems.

The paper argues that subpopulations in single-cell data may not reflect distinct behavioral modes and shows that noise can create false subpopulations from a single mode.

This study provides an exact time-dependent solution for the CME of a gene circuit with autoregulation and bursty expression using spectral decomposition.

The paper shows that some fission yeast cell division genes exhibit sub-Poissonian mRNA noise, below the classical Poissonian limit, due to specific transcription and degradation mechanisms.

The paper compares two-state (telegraph-like) and mechanistic models of mammalian gene expression, showing they can produce similar transcript number distributions but differ in waiting time distributions.

The paper derives a closed-form solution for stochastic enzyme kinetics and shows transient bimodality in substrate distribution under specific conditions.

The paper shows that standard stochastic models with Hill-type propensities are inaccurate for gene regulatory networks with fast promoter switching, especially when protein-DNA binding rates are high.