Erik Kubaczka

A Yeast Logic Toolkit for Fast and Efficient Assembly of Genetic Circuits

The paper introduces the Yeast Logic Toolkit (YLT), which provides pre-assembled backbones and parts for constructing genetic circuits in yeast with reduced context-dependent effects.

The Coli Toolkit (CTK): An extension of the modular Yeast Toolkit for use in E. coli

The paper introduces the Coli Toolkit (CTK), a modular cloning system for E. coli, expanding on the Yeast Toolkit to enable efficient genetic circuit assembly.

NAND Hybrid Riboswitch Design by Deep Batch Bayesian Optimization

This study designs hybrid riboswitches in yeast to emulate Boolean NAND logic using machine learning-based Bayesian optimization.

Energy Aware Technology Mapping of Genetic Logic Circuits

This paper introduces Energy Aware Technology Mapping to design genetic logic circuits with energy efficiency and functionality, showing energy efficiency improves by 37.2% over functionally optimized variants.

Context-Aware Technology Mapping in Genetic Design Automation

This work improves genetic design automation by incorporating context effects through thermodynamic models and branch-and-bound techniques, enhancing circuit prediction accuracy.

Automated Design of Robust Genetic Circuits: Structural Variants and Parameter Uncertainty

The paper introduces a method to design robust genetic circuits by adapting electronic design automation techniques to account for structural variants and parameter uncertainty in biological systems.