Lucia Marucci

Harnessing Dynamic Cell Responses to Optimise Pluripotency Protocols

This study designs new pluripotency maintenance protocols by leveraging cellular response dynamics to reduce drug exposure while maintaining pluripotency in mouse embryonic stem cells.

Embedded Extremum Seeking: A Bio-synthetic Optimiser

The paper introduces an embedded extremum seeking controller that optimizes cellular behavior using synthetic genetic circuits without external sensing or actuation.

Kernel Filter-Based Adaptive Controllers For Cybergenetics Applications

This paper introduces a kernel filter for adaptive control in biological systems, showing improved performance over particle filters in parameter estimation and control accuracy.

In-vivo distributed multicellular control of gene expression in microbial consortia

This paper develops a distributed feedback control system in microbial consortia to precisely regulate gene expression across different cell populations.

In-silico and in-vitro morphometric analysis of intestinal organoids

This study develops an algorithm for counting crypt-like structures in intestinal organoids and modifies a 2D agent-based model to better simulate budding structures, showing improved agreement with experimental data.

MODEL PREDICTIVE CONTROL OF CANCER CELLULAR DYNAMICS: A NEW STRATEGY FOR THERAPY DESIGN

The paper demonstrates that adaptive model predictive control can steer cancer cell signaling dynamics to mimic wild-type cells and support combination therapy design.

Control-based continuation: a new approach to prototype synthetic gene networks

This paper introduces Control-Based Continuation (CBC) for analyzing synthetic gene networks, showing it can track bifurcation curves without relying on mathematical models and can identify bistability.

Testing theoretical minimal genomes using whole-cell models

The paper tests theoretical minimal genomes for Mycoplasma genitalium using a whole-cell model, finding that simulated minimal gene sets fail to produce dividing cells, highlighting the need for species-specific low essential gene identification.

Cheetah: a computational toolkit for cybergenetic control

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.

ChipSeg: an automatic tool to segment bacteria and mammalian cells cultured in microfluidic devices

ChipSeg segments bacterial and mammalian cells in microfluidic devices using thresholding, enabling fluorescence quantification and cell tracking in time-lapse experiments.

In vivo Feedback Control of an Antithetic Molecular-Titration Motif in Escherichia coli using Microfluidics

The paper demonstrates real-time feedback control of a molecular titration motif in E. coli using microfluidics and validates the approach with in silico simulations.

Understanding metabolic behaviour in whole-cell model output

The paper presents an analysis pipeline using machine learning and network analysis to interpret metabolic reaction fluxes from gene knockouts in a whole-cell model of Mycoplasma genitalium.

Cross-talk between Hippo and Wnt signalling pathways in intestinal crypts: insights from an agent-based model

The paper develops an agent-based model to study the interaction between Hippo and Wnt signaling pathways in intestinal crypts, showing Hippo reduces β-catenin and slows crypt turnover, and division-based Wnt spreading can form gradients.

Exploring the Dynamics of Nonlinear Biochemical Systems using Control-Based Continuation

This paper explores using control-based continuation to track dynamical features of biochemical systems, specifically bistable dynamics in gene regulation of pluripotency in embryonic stem cells.

A tunable dual-input system for ‘on-demand’ dynamic gene expression regulation

The paper develops a dual-input system to dynamically regulate gene expression and protein stability in mouse embryonic stem cells, enabling precise control of protein levels and faster response times.

The genome design suite: enabling massive in-silico experiments to design genomes.

The paper introduces PyGDS, a Python framework for in-silico genome design that enables large-scale experiments across different computational clusters.

Designing Minimal Genomes Using Whole-Cell Models

The paper presents algorithms for genome design using whole-cell models, discovering smaller minimal genomes for Mycoplasma genitalium than previously known.

Towards automated control of embryonic stem cell pluripotency

This study demonstrates automated control of pluripotency in mouse embryonic stem cells using microfluidics and feedback algorithms to regulate Rex1 expression.

A low cost, open source Turbidostat design for in-vivo control experiments in Synthetic Biology

The paper describes a low-cost, open-source turbidostat for in-vivo control experiments in synthetic biology and reports results from a 3-hour optical density control experiment.