Jay D. Keasling

This paper uses a genomic language model to design and optimize a synthetic biosynthetic pathway for producing a non-natural molecule, achieving a 9.4-fold increase in production.

This paper introduces a carbon cofeeding strategy to overcome stoichiometric limitations in redox-balance growth coupling, enabling growth-coupled selection for biosynthetic pathways in engineered E. coli.

This paper uses synthetic biology to engineer BCG to produce HMBPP, enhancing Vγ9Vδ2 T cell expansion without feedback inhibition, offering a strategy to improve TB vaccine efficacy.

This paper refactors the Agrobacterium tumor-inducing plasmid into a minimal set of genes for plant and fungal transformation, demonstrating a bottom-up engineering approach.

This study shows the mevalonate pathway in Mycobacterium marinum is dispensable in culture but supports metabolic flexibility under stress and during hypoxia.

This paper engineers Escherichia coli to use hydrogen and formate as energy sources, improving mevalonate production by 57.6% through metabolic decoupling.

This study uses RB-TnSeq to identify genetic basis of dicarboxylic acid metabolism in β-proteobacteria, revealing distinct metabolic pathways and enabling plastic waste upcycling.

The paper develops ADhunter, a model to identify and quantify transcriptional activators in fungal genomes, expanding functional annotations across non-model species.

This paper introduces a modular polyketide synthase platform for producing diols, amino alcohols, and hydroxyacids using engineered Streptomyces albus strains.

This paper introduces a simplified, fast, and efficient method to extract amatoxins from Amanita phalloides without tissue grinding or long incubation.

BioPKS Pipeline automates the design of chimeric type I polyketide synthases and enzymatic pathways to synthesize target chemicals, achieving exact designs for 93 of 155 tested molecules and proposing routes for complex natural products.

This study uses multi-omics analysis to characterize Neurospora intermedia in oncom, revealing its role in byproduct conversion and potential for waste-to-food upcycling.

This study engineering yeast to produce kratom monoterpene indole alkaloids through synthetic pathway reconstruction and optimization, achieving a titer of ~290 µg/L.

The paper introduces a model called CSNN that uses network homophily to improve in-distribution predictions of drug-target interactions for human GPCRs.

The paper uses transposon sequencing data to characterize AraC/XylS family regulators in Pseudomonas putida, identifying inducer responses and improving inducible systems in E. coli.

This paper develops and optimizes a mevalonate-based monoterpene production platform in Corynebacterium glutamicum, achieving high titers of several monoterpenes.

This study evaluates codon optimization strategies for improving heterologous expression of engineered type I polyketide synthases in three bacterial hosts and develops an online tool for codon optimization.

The paper develops growth-coupled microbial strains for high-yield indigoidine production using iterative engineering and computational evaluation.

The paper introduces teemi, an open-source platform for bioengineering that supports simulation, data integration, and machine learning for metabolic pathway design under FAIR principles.

Foldy provides a cloud-based platform for non-expert scientists to access AI-based structural biology tools like AlphaFold and DiffDock for protein structure prediction and ligand docking.

BayFlux quantifies metabolic fluxes and their uncertainty using Bayesian inference, showing genome-scale models reduce flux uncertainty compared to core models and improve knockout predictions.

The paper introduces a family of 43 expression plasmids for precise gene expression in gram-negative bacteria, with constitutive and inducible systems tested in Escherichia coli and Pseudomonas putida.

This paper engineers Pseudomonas putida KT2440 to produce medium- and long-chain free fatty acids and oleochemicals, achieving titers up to 670 mg/L.

This paper introduces a strategy for creating configurable hydrogel compartments to enable sustained synthetic biology systems in vitro.

The paper develops a directed evolution workflow combining OrthoRep and a transcription factor-based biosensor to optimize cis,cis-muconic acid production in yeast, achieving >13-fold higher titers.

This study improves taxadiene production in Saccharomyces cerevisiae by engineering TASY solubility and optimizing bioprocess variables, achieving up to 129 mg/L at 20°C.

This paper engineers Pseudomonas taiwanensis VLB120 to produce methyl ketones with a 4-fold higher titer than previous strains, achieving 9.8 g L-1.

The paper engineers bimodular PKS systems to produce unnatural polyketides as bio-based chemicals, demonstrating both successes and challenges in product fidelity.

The paper designs synthetic control circuits in yeast to stabilize vanillin-β-glucoside production over multiple generations, achieving higher yields in fermentation.

The paper identifies an iron-dependent enzyme in plants that completes the lysine catabolism pathway, showing structural and functional conservation across species.