Cong T. Trinh

This study identifies DNA repair mechanisms that influence CRISPR-Cas antifungal efficacy in Candida albicans and shows how to tune Cas9 lethality through repair template availability and enzyme activity.

This paper develops a minimal phagemid packaging signal for producing high-purity CRISPR-Cas antimicrobials in Staphylococcus aureus with high titers and purity.

This study develops CRISPR-Cas antimicrobials that cotarget essential and defensive genes in Staphylococcus aureus, achieving greater potency and reduced resistance compared to single-targeting approaches.

This study identifies cellular stress tolerance as a key factor in genetic transformability of Candida species and develops a method to improve CRISPR screening efficiency.

This study uses longitudinal proteomics to analyze how Staphylococcus aureus reallocates resources during phage infection, revealing mechanisms of host defense and phage evasion.

CRISPR-GRIT enables precise multiplexed genome editing in C. albicans by integrating repair templates into guide RNAs, overcoming the need for co-transformation.

This study characterizes a novel robust Bacillus coagulans strain capable of utilizing pentose and hexose sugars, revealing proteome reallocation and metabolic strategies for biomass hydrolysate utilization.

This paper engineers a synthetic E. coli coculture to compartmentalize sugar utilization and ester biosynthesis pathways, achieving 31-fold higher isobutyl butyrate production than monocultures.

This study identifies how Yarrowia lipolytica metabolizes hydrocarbons and DP oil, revealing proteome reallocation for growth and chemical production, but also growth inhibition due to reduced protein biosynthesis.

This study demonstrates a modular design approach to selectively produce isoamyl acetate in microbes, achieving high titer, yield, and selectivity through proteome reallocation.

The paper introduces GeCCo to identify gene targets for high ionic liquid tolerance in Y. lipolytica and finds that GeCCo-selected genes, BRN1 and OYE2, enhance tolerance when overexpressed.

The paper presents a framework for engineering microbial biosynthesis of butyryl-CoA-derived esters with controllable selectivity, achieving significant production increases in target compounds.

This study introduces ModCell-HPC, a computational method for designing modular cells capable of producing large libraries of chemicals, demonstrating its effectiveness in generating E. coli strains for 161 endogenous modules.

The paper analyzes genetic and proteomic differences between undomesticated and conventional Yarrowia lipolytica strains to understand lipid metabolism and sugar utilization in biomass hydrolysates.

The paper repurposes chloramphenicol acetyltransferases to create efficient ester biosynthesis enzymes, demonstrating high titer and conversion in microbial hosts.

This study develops a genome-scale metabolic model for Clostridium thermocellum and applies it to integrate multi-omics data and design strains for biofuel and biochemical production.

This paper uses goal attainment optimization to design a modular chassis cell for efficient production of diverse products through metabolic engineering.

This study engineers a thermostable chloramphenicol acetyltransferase to enable isobutyl acetate production from cellulose by Clostridium thermocellum at elevated temperatures.

This paper demonstrates the microbial biosynthesis of lactate esters from fermentable sugars using a modular E. coli system, achieving a 4.96-fold increase in ethyl lactate production.

This study compares multi-objective evolutionary algorithms for modular cell design in biocatalysis, finding that real-world performance differs from artificial benchmarks and identifying effective parameter configurations.

The paper develops a pipeline to identify PAM sequences for CRISPR-Cas systems across bacterial genomes, finding putative PAMs for 1,049 species out of 1,493 analyzed.

This paper introduces MODCELL, a modular cell engineering framework validated experimentally to enhance strain design for biochemical production by coupling modular chassis cells with exchangeable production modules.

The paper introduces CASPER, a CRISPR tool improving on- and off-target prediction and enabling multitargeting and multispecies genome editing in non-model organisms.