Yuichi Wakamoto

Rapid enhancement of antibiotic resistance and divergent remodeling of gene expression in single cells of bacteria

This study shows that antibiotic resistance in E. coli emerges rapidly in single cells under chloramphenicol exposure through phenotypic heterogeneity and gene expression remodeling.

Revealing global stoichiometry conservation architecture in cells from Raman spectral patterns

The paper uses Raman spectroscopy to reveal a low-dimensional stoichiometry-conserving proteome structure across bacterial and human cells, showing its role in maintaining homeostasis and enabling adaptation.

Global propagation of genetic perturbation effects through genome-wide stoichiometry conservation architecture

The paper shows that genetic perturbations affect genes maintaining stoichiometry with the perturbed gene, revealing a multi-level stoichiometry-conserving architecture across species.

Raman spectra identify vancomycin-resistant phenotypes and their transcriptomic features in Staphylococcus aureus

This study uses Raman spectroscopy to identify vancomycin-resistant phenotypes and their transcriptomic features in Staphylococcus aureus strains.

A unified framework for measuring selection on cellular lineages and traits

This paper introduces a framework to measure selection on cellular lineages and traits by expanding population growth rates using fitness cumulants, showing their relevance in regrowing processes.

History-Dependent Physiological Adaptation to Lethal Genetic Modification under Antibiotic Exposure

The paper shows that Escherichia coli can adapt to lethal genetic modifications under antibiotic exposure by restoring growth without additional mutations, but this adaptation depends on timing and environmental history.

Intrinsic growth heterogeneity of mouse leukemia cells underlies differential susceptibility to a growth-inhibiting anticancer drug

This study identifies intrinsic growth heterogeneity in mouse leukemia cells and links it to differential drug susceptibility to Mitomycin C.

Transcriptomes and Raman spectra are linked linearly through a shared low-dimensional subspace

The paper links Raman spectra and transcriptomes through a shared low-dimensional subspace, enabling reconstruction of gene expression profiles from Raman data.

Inferring Fitness Landscapes and Selection on Phenotypic States from Single-Cell Genealogical Data

The paper quantifies fitness landscapes and selection on phenotypic states using single-cell genealogical data from bacterial populations under antibiotic stress.