Patrick M. Shih

The paper designs functional transcriptional activation domains using machine learning and experimental validation, finding that over 90% of predicted sequences work in yeast.

The paper maps transcription factor effector domains in plants and compares their function across eukaryotes, revealing conserved and lineage-specific regulatory principles.

This paper introduces a membrane-free spot-plating protocol for Agrobacterium-mediated transformation of diverse yeasts, improving efficiency and reducing costs.

This paper designs novel Rubisco variants using protein language models, identifying active candidates with improved CO2/O2 specificity and structural validity.

This paper measures temperature-dependent kinetic isotope effects (KIEs) in two rubisco forms, showing their KIEs decrease linearly with temperature, impacting interpretations of carbon isotope variations in Earth and biological sciences.

This study shows that the CO2 concentrating mechanism in cyanobacteria enhances the speed of the nitrogen deprivation response by increasing Rubisco carboxylation rates.

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.

The paper models variability in Nicotiana benthamiana transient expression and provides guidelines for minimizing it through experimental design and power analysis.

The paper develops a toolkit of chromatin regulators with cross-kingdom functionality for programmable transcriptional repression and activation in eukaryotic cells.

This study introduces ENTRAP-seq, a method to measure transcriptional regulator activity in plants, and identifies novel regulatory domains in viral proteins.

This study shows that binary vector origin of replication family, not copy number, determines Agrobacterium-mediated transformation outcomes across plants and fungi.

The paper characterizes the structural and functional diversity of rubisco by synthesizing and analyzing diverse sequences, revealing a dimeric origin and a novel large rubisco structure.

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 study engineers cytokinin regulators in Arabidopsis to modulate root development by tuning gene expression through synthetic biology.

The paper maps the sequence-to-function relationship of rubisco by assaying single amino acid mutants in E. coli, identifying conserved positions and mutations that improve CO2 affinity.

The paper identifies a Prochlorococcus lineage in oxygen deficient zones that expresses both form I and form II rubiscos, suggesting an adaptation to low oxygen environments.

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

This study produces diverse human milk oligosaccharides (HMOs) in transgenic plants, demonstrating their potential for cost-effective and sustainable large-scale production compared to microbial methods.

The paper identifies and validates activation domains in non-transcription factor proteins across Arabidopsis and yeast, discovering novel coactivators and universal genetic parts for synthetic biology.

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.

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

The paper characterizes two glutarate-sensing transcription factors in Pseudomonas putida and develops biosensors to detect glutarate flux for metabolic engineering.