Thomas E. Gorochowski

A genome-integrated Cas12m in E. coli shows no measurable growth cost, reverses repression faster than dCas9, and supports NOT gates, a two-layer buffer and a two-pathway pigment circuit.

The paper develops a workflow combining robotics, nanopore sequencing, and computational tools to characterize recombinase-based genetic circuits efficiently and at high resolution.

This study investigates untemplated DNA synthesis by polymerases, showing that environmental conditions influence sequence composition and providing data for guided DNA synthesis.

The paper develops a sequencing-based framework and a neural network model to predict plasmid propagation from sequence, revealing sequence-encoded interactions that influence plasmid stability and host compatibility.

The paper develops a platform to infer digital twins of light-responsive microorganisms using imaging data, enabling accurate simulation of their movement behaviors.

The paper introduces SHARK, a series of Pir E. coli strains designed for efficient cloning of R6K plasmids, showing they are >100-fold more efficient than a commercial strain for complex cloning.

This paper introduces SIMPLIFE, a computational workflow for designing optimal insertion sites for conjugation tags in proteins, demonstrating its use in augmenting T7 RNA polymerase function.

This paper introduces a Cas9-based method for targeted long-read metabarcoding, enabling multiplexed enrichment of marker genes without PCR, and demonstrates its effectiveness in characterizing complex microbial and nematode communities.

The paper introduces POLAR-seq, a low-cost method to analyze combinatorial genetic libraries by sequencing long amplicons to identify genotype-phenotype relationships in yeast.

This paper uses transfer learning to adapt a deep learning model for predicting protein expression from 5'UTR sequences across different experimental contexts in E. coli.

This paper develops a probabilistic coarse-grained model to design repeat protein structural dynamics efficiently, demonstrating its application to modular repeat proteins.

This paper engineers fluorescent orthogonal ribosomes to monitor synthetic protein production in bacteria, identifying an insertion site that enhances ribosome activity and enables dynamic tracking.

This paper develops FORE-CAST, a Python package for simulating and analyzing MPRAs to improve experimental design and inference of genetic function.

The paper introduces an open-source platform for controlling microscopic collectives using light-based microenvironments.

This study shows that endogenous proteolysis systems in E. coli are more efficient than foreign ones for improving cellular robustness under nutrient stress.

The paper uses direct RNA sequencing to characterize engineered transcript isoforms and demonstrates how transcriptional terminators can be tuned to control read-through.

Cheetah is a computational toolkit that integrates real-time microscopy analysis with cellular control algorithms, demonstrating improved segmentation accuracy over thresholding methods in bacterial and mammalian cells.

This paper develops stringent gene expression systems by regulating both transcription and translation, achieving high induction ratios and reduced leakiness in both in vivo and cell-free systems.

This paper introduces genetic devices that can be dynamically tuned after construction to adjust their response functions and logic gate transitions.

The paper introduces the SBOL Visual 2 Ontology to standardize the mapping of genetic elements to visual glyphs, facilitating tool development and integration with biological standards.

The paper combines Ribo-seq and RNA-seq to quantify translation initiation rates, termination efficiencies, and frameshifting in E. coli, revealing insights into translational regulation and stress responses.

The paper identifies heat-shock promoters that activate rapidly in response to synthetic gene expression in E. coli and uses them to build a CRISPR/dCas9-based feedback system that improves protein yield by adjusting synthetic construct expression based on cellular burden.

The paper analyzes how feed-forward loop motifs are organized in networks, revealing architectural principles and their functional implications in Escherichia coli metabolic networks.