Antonis Papachristodoulou

Quantitative Engineering and Investigation of Synthetic Sponge RNAs in E. coli

This study designs, builds, and quantitatively characterizes synthetic sponge RNAs in E. coli, revealing their ability to tune gene expression and provide a quantitative framework for spRNA-mediated regulation.

A synthetic ERFVII-dependent circuit in yeast sheds light on the regulation of early hypoxic responses of plants

The paper designs a synthetic ERFVII-dependent circuit in yeast to study hypoxia responses, finding similar fast transcriptional responses to plants but highlighting the importance of feedback loops.

Manipulating plant oxygen sensing through NCO substitution reveals trade-offs between growth and flooding tolerance

This study replaces Arabidopsis PCOs with NCOs from different species to show how enzyme activity affects hypoxia gene expression and submergence survival, but also impacts growth and biomass.

Engineering prolyl hydroxylase-dependent proteolysis enables the orthogonal control of hypoxia responses in plants

The paper engineers a synthetic system in Arabidopsis thaliana to control hypoxia responses through oxygen-dependent proteolysis, restoring responsiveness in mutants and enabling growth regulation under hypoxic conditions.

AC-BioSD : A biomolecular signal differentiator module with enhanced performance (extended version)

The paper introduces AC-BioSD, a biomolecular signal differentiator with improved performance in signal differentiation and noise attenuation.

Regulation strategies for two-output biomolecular networks

This paper develops control strategies for two-output biomolecular networks to achieve robust regulation despite coupling interactions and disturbances.

Dichotomous Feedback: A Signal Sequestration-based Feedback Mechanism for Biocontroller Design

This paper introduces a new feedback mechanism for synthetic biology, dichotomous feedback, which uses signal sequestration to improve robustness and reduce noise in biological systems.

Genome-scale metabolic modelling of lifestyle changes in Rhizobium leguminosarum

The paper reconstructs and validates a genome-scale metabolic model for Rhizobium leguminosarum, integrating it with multi-omics data to predict metabolic fluxes across different symbiotic stages.

On the Design of a PID Bio-controller with Set Point Weighting and Filtered Derivative Action

This paper designs a tunable PID bio-controller with set point weighting and filtered derivative action for biomolecular process regulation, demonstrating its effectiveness through simulations.

Biomolecular mechanisms for signal differentiation

This paper identifies biomolecular mechanisms for time derivative computation in cells and proposes synthetic differentiator designs based on natural regulatory networks.

Design of a Synthetic sRNA-based Feedback Filter Module

The paper designs and tests a synthetic sRNA-based feedback filter module that reduces noise and tunes feedback strength through mathematical modeling and experimental validation.

Characterisation and development of aspirin inducible biosensors in E. coli Nissle 1917 and SimCells

The paper develops an aspirin-inducible gene circuit in E. coli and SimCells, showing dose-dependent induction and competitive binding of SalR variants.

Synthetic negative feedback circuits using engineered small RNAs

This paper designs and builds two synthetic negative feedback circuits using engineered small RNAs, showing they can fine-tune output and reduce noise compared to traditional protein-based systems.

Visual Representation of Experimental Protocols

The paper introduces a new user interface for creating experimental protocols by manipulating diagrams to specify liquid handling operations.

Ribo-attenuators: novel elements for reliable and modular riboswitch engineering

This paper introduces Ribo-attenuators, a novel genetic element that improves the modularity and reliability of riboswitches in bacteria by reducing expression variation and contextual sensitivity.