Andrew D. Ellington

This study evaluates zero-shot mutation prediction models in protein engineering, finding they struggle to identify optimal mutations and predict new functions due to limitations in capturing evolutionary constraints.

This study designs and characterizes peptide-responsive biosensors that regulate gene expression using intracellular peptide effectors and transcription factors in vitro and in vivo.

This paper introduces a deep learning model that predicts biological function from chemical structure using scientific literature, identifying effective inhibitors of beta-lactamases.

This study combines machine learning and directed evolution to optimize the monooxygenase HpaBC for improved L-Dopa production activity.

This paper develops a platform for producing and engineering conductive cytochrome nanowires, achieving enhanced conductivity and enabling their use in sustainable electronic applications.

This paper introduces a computational pipeline using DNA k-mer imprints to agnostically classify and distinguish materials based on their sequence patterns.

The paper introduces a rapid, semi-quantitative LAMP-OSD test for detecting Enterococci in water, enabling visual readout and comparison with contamination standards.

The paper compares LigandMPNN and directed evolution for redesigning the effector-binding site of the RamR transcription factor, finding limited overlap between the two methods' results.

This paper develops a L-DOPA sensing system and improves biosynthesis via directed evolution, achieving high-efficiency incorporation into proteins.

This paper develops design principles for Polymerase Strand Recycling (PSR) circuits to enhance detection of microRNA inputs in cell-free biosensing systems.

This paper describes the directed evolution of a SelB variant that functions without a SECIS element and can incorporate selenocysteine and other amino acids.

This study evolves a T7 RNA polymerase variant with a capping enzyme to enable efficient gene expression in eukaryotes, showing improved performance in yeast and mammalian cells.

Ligify predicts transcription factors responsive to user-defined chemicals and generates plasmids for biosensor development, achieving 31/100 correct predictions in benchmarking.

The paper develops a biosensor-AI system to engineer E. coli for efficient production of amaryllidaceae alkaloids, achieving improved titer and reduced byproducts.

Snowprint predicts regulator:DNA interactions and designs promoters for uncharacterized regulators, enabling the discovery of new biosensors for various compounds.

This paper modifies a One Pot PURE system to enable modular incorporation of unnatural amino acids through orthogonal tRNA synthetases and stop codon suppression.

The paper describes the directed evolution of biosensors to improve detection of phloroglucinol and related single-ring aromatics.

The paper develops yeast biosensors for CB1R and CB2R to screen cannabinoids and identify structure-activity relationships.

GroovDB is a database of ligand-inducible transcription factors that provides curated data for building chemically-responsive genetic circuits.

This paper evolves highly specific and sensitive biosensors for alkaloids using a combined screening and selection approach, enabling improved microbial production of therapeutic plant metabolites.

This study engineers yeast to produce cholesterol, enabling functional expression of human opioid and other GPCRs, creating biosensors with measurable agonist responses and antagonist inhibition.

This study reviews aptamer sequence reporting in 800 papers and finds 44% report unexplained sequence alterations, with 93% of 61 reviewed publications showing altered sequences.

The paper designs synthetic promoters and CRISPR-based transcription factors to enable orthogonal gene expression control in plants, demonstrating a fully artificial Orthogonal Control System (OCS).

This paper evolves a generalist biosensor for bicyclic monoterpenes using directed evolution and a novel screening method.

This study uses 3D CNNs to predict wild-type amino acids and consensus sequences from local structural context, finding high-confidence predictions correlate with correct outcomes.

The paper identifies a prototypical DNA replication fork trap in bacteria consisting of two Ter sites, based on genome-wide analysis of Tus protein binding and comparative genomics.

The paper identifies SARS-CoV-2 neutralizing antibodies from convalescent patients and describes a novel quaternary binding mechanism using high-throughput methods.

The paper develops a RT-qPCR assay using a thermostable reverse transcriptase/DNA polymerase (RTX) and provides protocols for reagent production, aiming to improve testing scalability and reliability in resource-limited settings.

The paper demonstrates that Taq DNA polymerase can be optimized for reverse transcriptase activity, enabling its use as the sole enzyme in TaqMan RT-qPCR assays for detecting SARS-CoV-2 RNA.

This study shows that systematically introducing synonymous mutations in bacteriophage {Phi}X174 reduces viral fitness, but the effects are non-linear and gene-dependent.