Guy‐Bart Stan
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View article: Overcoming the Speed Limit of Four-Way DNA Branch Migration with Bulges in Toeholds
Overcoming the Speed Limit of Four-Way DNA Branch Migration with Bulges in Toeholds Open
Dynamic DNA nanotechnology creates programmable reaction networks and nanodevices by using DNA strands. The key reaction in dynamic DNA nanotechnology is the exchange of DNA strands between different molecular species, achieved through thr…
View article: Investigating the Potential of Division of Labor in Synthetic Bacterial Communities for the Production of Violacein
Investigating the Potential of Division of Labor in Synthetic Bacterial Communities for the Production of Violacein Open
With advancements in synthetic biology and metabolic engineering, microorganisms can now be engineered to perform increasingly complex functions, which may be limited by the resources available in individual cells. Introducing heterologous…
View article: Information propagation through enzyme-free catalytic templating of DNA dimerization with weak product inhibition
Information propagation through enzyme-free catalytic templating of DNA dimerization with weak product inhibition Open
Information propagation by sequence-specific, template-catalysed molecular assembly is a key process facilitating life’s biochemical complexity, yielding thousands of sequence-defined proteins from only 20 distinct building blocks. However…
View article: Omni-DNA: A Unified Genomic Foundation Model for Cross-Modal and Multi-Task Learning
Omni-DNA: A Unified Genomic Foundation Model for Cross-Modal and Multi-Task Learning Open
Large Language Models (LLMs) demonstrate remarkable generalizability across diverse tasks, yet genomic foundation models (GFMs) still require separate finetuning for each downstream application, creating significant overhead as model sizes…
View article: Investigating The Potential of Division of Labour in Synthetic Bacterial Communities for the Production of Violacein
Investigating The Potential of Division of Labour in Synthetic Bacterial Communities for the Production of Violacein Open
With advancements in synthetic biology and metabolic engineering, microorganisms can now be engineered to perform increasingly complex functions, which may be limited by the resources available in individual cells. Division of labour in sy…
View article: Absorb & Escape: Overcoming Single Model Limitations in Generating Genomic Sequences
Absorb & Escape: Overcoming Single Model Limitations in Generating Genomic Sequences Open
Recent advances in immunology and synthetic biology have accelerated the development of deep generative methods for DNA sequence design. Two dominant approaches in this field are AutoRegressive (AR) models and Diffusion Models (DMs). Howev…
View article: Enhancing Node Representations for Real-World Complex Networks with Topological Augmentation
Enhancing Node Representations for Real-World Complex Networks with Topological Augmentation Open
Graph augmentation methods play a crucial role in improving the performance and enhancing generalisation capabilities in Graph Neural Networks (GNNs). Existing graph augmentation methods mainly perturb the graph structures, and are usually…
View article: Design of a biomolecular adaptive controller to restore sustained periodic behavior
Design of a biomolecular adaptive controller to restore sustained periodic behavior Open
Periodic behavior is a widespread biological phenomenon occurring across various spatiotemporal scales, where upstream stimuli are encoded into dynamic intracellular signals such as oscillations, varying in duration, amplitude, and frequen…
View article: Microfluidic platform for microbial spore germination studies in multiple growth conditions
Microfluidic platform for microbial spore germination studies in multiple growth conditions Open
Spores are highly resistant dormant cells, adapted for survival and dispersal, that can withstand unfavourable environmental conditions for extended periods of time and later reactivate. Understanding the germination process of microbial s…
View article: A coarse-grained bacterial cell model for resource-aware analysis and design of synthetic gene circuits
A coarse-grained bacterial cell model for resource-aware analysis and design of synthetic gene circuits Open
Within a cell, synthetic and native genes compete for expression machinery, influencing cellular process dynamics through resource couplings. Models that simplify competitive resource binding kinetics can guide the design of strategies for…
View article: DiscDiff: Latent Diffusion Model for DNA Sequence Generation
DiscDiff: Latent Diffusion Model for DNA Sequence Generation Open
This paper introduces a novel framework for DNA sequence generation, comprising two key components: DiscDiff, a Latent Diffusion Model (LDM) tailored for generating discrete DNA sequences, and Absorb-Escape, a post-training algorithm desig…
View article: Parsley: a web app for parsing data from plate readers
Parsley: a web app for parsing data from plate readers Open
Summary As demand for the automation of biological assays has increased over recent years, the range of measurement types implemented by multiwell plate readers has broadened and the list of published software packages that caters to their…
View article: Latent Diffusion Model for DNA Sequence Generation
Latent Diffusion Model for DNA Sequence Generation Open
The harnessing of machine learning, especially deep generative models, has opened up promising avenues in the field of synthetic DNA sequence generation. Whilst Generative Adversarial Networks (GANs) have gained traction for this applicati…
View article: Information propagation through enzyme-free catalytic templating of DNA dimerization with weak product inhibition
Information propagation through enzyme-free catalytic templating of DNA dimerization with weak product inhibition Open
Information propagation by sequence-specific, template-catalyzed molecular assembly is the source of the biochemical complexity of living systems. Templating allows the production of thousands of sequence-defined proteins from only 20 dist…
View article: Information propagation through catalytic enzyme-free templating of DNA dimerisation with weak product inhibition
Information propagation through catalytic enzyme-free templating of DNA dimerisation with weak product inhibition Open
Information propagation by sequence-specific, template-catalyzed molecular assembly is the source of the biochemical complexity of living systems, allowing thousands of sequence-defined proteins to be produced from only 20 distinct buildin…
View article: Parsley: a web app for parsing data from plate readers
Parsley: a web app for parsing data from plate readers Open
As demand for the automation of biological assays has increased over recent years, the range of measurement types implemented by multiwell plate readers has broadened and the list of published software packages that caters to their analysi…
View article: Hybrid Graph: A Unified Graph Representation with Datasets and Benchmarks for Complex Graphs
Hybrid Graph: A Unified Graph Representation with Datasets and Benchmarks for Complex Graphs Open
Graphs are widely used to encapsulate a variety of data formats, but real-world networks often involve complex node relations beyond only being pairwise. While hypergraphs and hierarchical graphs have been developed and employed to account…
View article: Genomic Interpreter: A Hierarchical Genomic Deep Neural Network with 1D Shifted Window Transformer
Genomic Interpreter: A Hierarchical Genomic Deep Neural Network with 1D Shifted Window Transformer Open
Given the increasing volume and quality of genomics data, extracting new insights requires interpretable machine-learning models. This work presents Genomic Interpreter: a novel architecture for genomic assay prediction. This model outperf…
View article: Overcoming the speed limit of four‐way DNA branch migration with bulges in toeholds
Overcoming the speed limit of four‐way DNA branch migration with bulges in toeholds Open
Dynamic DNA nanotechnology involves the use of DNA strands to create programmable reaction networks and nanodevices. The key reaction in dynamic DNA nanotechnology is the exchange of DNA strands between different molecular species, which i…
View article: Host-aware RNA-based control of synthetic microbial consortia
Host-aware RNA-based control of synthetic microbial consortia Open
Microbial consortia have been utilised for centuries to produce fermented foods and have great potential in applications such as therapeutics, biomaterials, fertilisers, and biobased production. Working together, microbes become specialize…
View article: A coarse-grained bacterial cell model for resource-aware analysis and design of synthetic gene circuits
A coarse-grained bacterial cell model for resource-aware analysis and design of synthetic gene circuits Open
Synthetic genes compete among themselves and with the host cell’s genes for expression machinery, exhibiting resource couplings that affect the dynamics of cellular processes. The modeling of such couplings can be facilitated by simplifyin…
View article: Host-aware RNA-based control of microbial consortia
Host-aware RNA-based control of microbial consortia Open
Plasmid maps are provided as Genbank files.
View article: Host-aware RNA-based control of microbial consortia
Host-aware RNA-based control of microbial consortia Open
Plasmid maps are provided as Genbank files.
View article: MIRELLA: a mathematical model explains the effect of microRNA-mediated synthetic genes regulation on intracellular resource allocation
MIRELLA: a mathematical model explains the effect of microRNA-mediated synthetic genes regulation on intracellular resource allocation Open
Competition for intracellular resources, also known as gene expression burden, induces coupling between independently co-expressed genes, a detrimental effect on predictability and reliability of gene circuits in mammalian cells. We recent…
View article: When synthetic biology fails: a modular framework for predicting genetic stability in engineered cell populations
When synthetic biology fails: a modular framework for predicting genetic stability in engineered cell populations Open
Predicting the dynamics of mutation spread in engineered cell populations is a sought- after goal in synthetic biology. Until now, models that capture these processes have been lacking, either by failing to account for the diversity of mut…
View article: Robust counterselection and advanced λRed recombineering enable markerless chromosomal integration of large heterologous constructs
Robust counterselection and advanced λRed recombineering enable markerless chromosomal integration of large heterologous constructs Open
Despite advances in bacterial genome engineering, delivery of large synthetic constructs remains challenging in practice. In this study, we propose a straightforward and robust approach for the markerless integration of DNA fragments encod…