Michael Saint-Antoine

Defining and detecting global transcriptional amplitude in circadian gene expression

The paper analyzes circadian gene expression amplitude across multiple human tissues and finds that global transcriptional amplitude varies by individual and tissue, but is not strongly correlated with core clock gene metrics.

Comparative circadian transcriptome analysis reveals dampened and phase-advanced rhythms in sun-exposed human skin

This study compares circadian rhythms in photoprotected and photoexposed human skin, finding reduced rhythmic genes and advanced peak times in sun-exposed skin.

The transcription factor ATML1 maintains giant cell identity by inducing synthesis of its own (very) long-chain fatty acid-containing ligands

The paper shows that high ATML1 concentrations induce VLCFA synthesis, which maintains giant cell identity by promoting auto-activation through lipid ligand binding.

Disrupting cellular memory to overcome drug resistance

The paper develops a method to quantify gene expression memory and identify regulators of cell state transitions, showing that modulating PI3K and TGF-β pathways can reduce drug resistance in melanoma.

Benchmarking Gene Regulatory Network Inference Methods on Simulated and Experimental Data

This study benchmarks gene regulatory network inference methods on simulated and experimental single-cell E. coli data, finding moderate accuracy and highlighting method-specific performance differences.

Limits on Inferring Gene Regulatory Networks Subjected to Different Noise Mechanisms

This study investigates the feasibility of inferring gene regulatory networks under different noise mechanisms and shows that extrinsic noise improves inference accuracy compared to intrinsic noise.

Relative stability of mRNA and protein severely limits inference of gene networks from single-cell mRNA measurements

The paper shows that the relative stability of mRNA and protein limits gene network inference from single-cell RNA data, using synthetic and real yeast data.

A Scalable, Open-Source Implementation of a Large-Scale Mechanistic Model for Single Cell Proliferation and Death Signaling

The paper develops an open-source, scalable mechanistic model for single-cell proliferation and death signaling, demonstrating its application to understand IFNγ's anti-proliferative effects.

A fluctuation-based approach to infer kinetics and topology of cell-state switching

This paper introduces a fluctuation-based method to infer cell-state switching kinetics and topology from a single time point measurement, applicable when repeated measurements are not feasible.

Optimal Chemotherapy Scheduling for Non-Genetic Drug Resistance

This paper models transient drug resistance in tumors and finds continuous therapy is optimal under estimated parameters, but alternating schedules can be optimal under different conditions.

Gene networks with transcriptional bursting recapitulate rare transient coordinated expression states in cancer

The paper shows that transcriptional bursting in gene networks can produce rare coordinated high expression states in cancer cells, which are linked to drug resistance.