Timothy A. Whitehead

This study introduces CHAP-SEQ to analyze how protein- and RNA-based chaperones assist in protein folding, revealing distinct mechanisms for each type.

The paper engineers a genetically encoded biosensor, PYRNSAID, to detect profen NSAIDs in wastewater with nanomolar sensitivity and demonstrates its functionality in simulated wastewater matrices.

The paper designs dynamic biosensors for detecting nitazenes and their metabolites using computational methods, achieving low nanomolar detection limits and limited cross-reactivity.

This paper computationally redesigns T7 RNA polymerase to increase its thermal stability, achieving a T50 of 54.9°C with 59% wild-type activity at 37°C.

The paper identifies small-molecule sensors using ABA receptors and demonstrates their ability to detect diverse ligands including plant natural products and synthetic chemicals.

The paper designs and engineers minimal protein-based molecular inverters and switches that respond to ligands, demonstrating tunable and modular control of post-translational signaling.

The paper improves prediction of functional protein interface sequences by integrating structural and sequence features using a graph attention model, achieving better generalization across diverse variants.

This paper shows that engineered T7 RNA polymerases can be controlled by indoles, enabling chemically inducible gene expression in synthetic biology applications.

The paper measures EC50 values for T7 RNA polymerase constructs and identifies the C-terminal T7 as a competitive inhibitor with a lower inhibition constant than the EC50 of full-length T7 RNAP.

The paper uses a PYR1 biosensor-driven CRISPR screen in Kluyveromyces marxianus to identify gene knockouts that enhance geraniol production by up to 2-fold.

This study analyzes two engineered biosensors based on PYR1 to recognize different ligands, revealing binding mechanisms and computational methods for biosensor design.

The paper introduces MAGMA-seq, a technology for quantitative analysis of antibody sequence-function relationships, demonstrating its application in mapping antibody development pathways and identifying binding determinants.

The paper identifies 5 stabilizing mutations for PYR1 variants using GMMA that increase thermal stability without affecting functionality across different ligand-binding capabilities.

The paper describes a protocol for generating saturation mutagenesis libraries of the {Phi}X174 bacteriophage using unamplified oligo pools and golden gate assembly, enabling comprehensive mutation analysis of viral proteins.