Matthew D. Shoulders

This study uses machine learning to guide directed evolution of plant Rubisco, identifying variants with improved catalytic efficiency and carboxylation rates.

This paper develops a looped-translation system in bacteria to synthesize ultra-large fibrous proteins, achieving molecular weights exceeding titin and enabling secretion.

RubiSpec-MS measures Rubisco's SC/O using LC-MS/MS, offering a faster, more accessible alternative to radiolabeled methods with comparable accuracy.

This paper develops CRISPR-MACE, a platform for continuous directed evolution of CRISPR-Cas9 in human cells, generating variants with enhanced DNA binding and resistance to AcrIIA4.

The paper shows that HSF1 activation supports the emergence of cancer-associated p53 mutations by enhancing their fitness under nutlin-3 pressure.

This study uses iPSC-derived cartilage to show that the Arg719Cys COL2A1 mutation causes defective proteostasis, leading to abnormal matrix deposition and disease.

This paper uses in vivo directed evolution to improve the oxygen resistance of a fast Rubisco variant from Gallionellaceae, identifying mutations that enhance carboxylation efficiency under ambient oxygen.

The paper develops an iPSC-derived cartilage model to study COL2A1 mutations, revealing that Arg719Cys substitution causes defective collagen-II folding and secretion, leading to matrix dysfunction and osteoarthritis.

The paper introduces two metrics to quantify drug-target interactions across genetic variants and drug panels, and analyzes their interactions in a beta-lactamase and beta-lactam drug system.

The paper analyzes how mutations affect biophysical subspaces of DHFR enzymes, revealing epistatic and pleiotropic interactions across different phenotypic dimensions.