Judith G. Berman

J-AST: a web-based analysis platform for antimicrobial susceptibility testing

J-AST is a web-based platform for analyzing antimicrobial susceptibility tests, providing automated annotation and MIC detection with high agreement with manual methods.

Quiescence improves Candida albicans survival of fungicidal drug exposure

This study shows that quiescence in Candida albicans enhances survival during antifungal drug exposure by altering cellular properties and gene expression.

Tolerance to the antifungal drug fluconazole is mediated by tuning cytoplasmic fluidity

This study shows that fluconazole tolerance in fungi is linked to decreased cytoplasmic fluidity and increased heterogeneity, mediated by changes in ribosome dynamics and P-body formation.

Sphingolipid Homeostasis, Mitochondrial Activity, and PKA Signaling Drive an Azole-Tolerant State

This study identifies Mnl1 as a repressor of azole tolerance in Candida albicans by linking it to sphingolipid metabolism, mitochondrial activity, and PKA signaling.

Drugs Commonly Used in Fungal Infection Risk Conditions Promote Drug Tolerance or Resistance in Candida albicans

This study identifies 34 drugs that affect antifungal efficacy in Candida albicans, with some promoting resistance when combined with fluconazole.

The Role of Metabolism in Shaping Enzyme Structures Over 400 Million Years of Evolution

This study uses AlphaFold2 to analyze how metabolism influenced enzyme structural evolution across 400 million years by examining 11,269 enzyme structures and their metabolic reactions.

Stress-driven emergence of heritable non-genetic drug resistance

The paper identifies a non-genetic, heritable mechanism of drug resistance in Candida albicans triggered by subtherapeutic fluconazole exposure, which can be reversed and involves prion-like epigenetic processes.

The natural diversity of the yeast proteome reveals chromosome-wide dosage compensation in aneuploids

The paper quantifies proteomic effects of aneuploidy in natural yeast isolates, finding chromosome-wide dosage compensation in the proteome but not transcriptome.

The fitness costs and benefits of trisomy of each Candida albicanschromosome

This study evaluates the fitness costs and benefits of trisomy in Candida albicans across various stress conditions, finding that specific aneuploids confer growth advantages under host-relevant stresses.

Identification of essential genes and fluconazole resistance genes in Candida glabrata by profiling of Hermes transposon insertions.

The paper identifies essential genes and fluconazole resistance genes in Candida glabrata using Hermes transposon insertion profiling and machine learning.

Comparing the utility of in vivo transposon mutagenesis approaches in yeast species to infer gene essentiality

The paper compares transposon mutagenesis methods in yeast to infer gene essentiality, finding biases in insertion sites and recommending transposon choices for accurate essentiality prediction.

Chromatin profiling of the repetitive and non-repetitive genome of the human fungal pathogen Candida albicans

The paper presents the first genome-wide chromatin profiling of histone modifications in Candida albicans, linking chromatin structure to gene expression and identifying roles of chromatin modifiers.

Selection of Candida albicans Trisomy during Oropharyngeal Infection Results in a Commensal-Like Phenotype

The paper shows that trisomy of chromosomes 5 or 6 in Candida albicans during oropharyngeal infection leads to a commensal-like phenotype with reduced virulence.

Autonomously replicating linear plasmids facilitate the analysis of replication origin function in Candida albicans

This paper identifies autonomously replicating linear plasmids in Candida albicans and shows that chromosomal origin sequences can drive plasmid replication.

Exposure to the oral host niche yields rapid phenotypic and genotypic diversification in Candida albicans

This study shows that Candida albicans rapidly generates genotypic and phenotypic diversity in the mouse oral cavity, with higher mutation rates compared to in vitro conditions.

Predicting microbial relative growth in a mixed culture from growth curve data

The paper predicts microbial relative growth in mixed cultures using growth curve data and validates it with E. coli experiments.