Tom Ellis

Strain handling exposes IS-mediated recurrent genome reduction at a dynamic accessory locus in Komagataeibacter rhaeticus

The paper shows that routine strain handling of Komagataeibacter rhaeticus exposes recurrent genome reduction at a dynamic accessory locus, leading to phenotypic variation.

Synthetic Combinatorial Minimisation of Cell Cycle Control in Yeast

This study minimizes the yeast cell cycle gene set using synthetic genomics, identifying minimal gene combinations that maintain viability and robustness across conditions.

A signal peptide-guided platform for in situ functionalization of bacterial nanocellulose in Komagataeibacter rhaeticus

This paper benchmarks signal peptide-mediated protein translocation in Komagataeibacter rhaeticus to enable in situ functionalization of bacterial nanocellulose during biosynthesis.

Quantitative profiling of millions of nucleotides reveals sequence-encoded interactions that govern plasmid propagation

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.

Convergent evolution of psilocybin biosynthesis by psychedelic mushrooms

Comparative mushroom genomics and fly-rearing experiments reveal an alternative psilocybin biosynthetic gene cluster in Inocybe corydalina, horizontal transfer of the canonical cluster, and incomplete defense against dipteran larvae.

Unlocking Bacterial Cellulose Functionalisation: Comparative Genetic and Co-Culture Strategies in Komagataeibacter

This study evaluates genetic and co-culture strategies for functionalizing bacterial cellulose across Komagataeibacter species, showing species-specific differences but overall feasibility of modification.

Generating long deletions across the genome with pooled paired prime editing screens

This paper develops a pooled paired prime editing screen to generate large-scale deletions across the genome, identifying non-coding regions with fitness effects and demonstrating the feasibility of genome-wide deletion perturbation.

Iterative SCRaMbLE for Engineering Synthetic Genome Modules and Chromosomes

The paper demonstrates iterative SCRaMbLE to optimize synthetic genome modules and chromosomes in yeast by selecting for improved growth phenotypes.

Engineered Transcription Factor Binding Arrays for DNA-based Gene Expression Control in Mammalian Cells

This paper introduces RE array plasmids and the CTRL method to control gene expression by sequestering transcription factors in mammalian cells.

Cultivating Future Materials: Artificial Symbiosis for Bulk Production of Bacterial Cellulose Composites

This paper develops an artificial symbiotic system between bacteria and algae to produce bulk bacterial cellulose in static conditions.

SubtiToolKit - a bioengineering kit for Bacillus subtilis and Gram-positive bacteria.

The paper introduces SubtiToolKit, a cloning toolkit for Bacillus subtilis and Gram-positive bacteria, enabling efficient DNA construct design for various genetic applications.

Randomizing the human genome by engineering recombination between repeat elements

This paper develops a CRISPR-based method to generate large-scale structural genomic rearrangements in human cells, revealing selection pressures and gene expression impacts of these changes.

Modulating Bacterial Nanocellulose Crystallinity through Post-Transcriptional Repression in Komagataeibacter xylinus

This paper develops sRNA-based post-transcriptional repression cassettes to modulate BC crystallinity in K. xylinus, achieving gene expression reductions and structural changes in nanocellulose.

Engineered yeast multicellularity via synthetic cell-cell adhesion and direct-contact signalling

This paper introduces synthetic tools for engineering multicellularity in yeast by enabling contact-dependent signaling and adhesion, allowing for the creation of multicellular logic circuits and protein interaction sensors.

Combinatorial Design Testing in Genomes with POLAR-seq

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.

Synthetic genome modules designed for programmable silencing of functions and chromosomes

The paper demonstrates the design of synthetic genome modules for programmable silencing in yeast using dCreSIR, a system that controls gene expression through loxPsym sites.

Design, Construction, and Functional Characterization of a tRNA Neochromosome in Yeast

A de novo yeast neochromosome carrying all 275 tRNA genes was built and characterized; it imposes a growth burden, with genome doubling and deletions in haploids possibly reflecting compensation.

Self-dyeing textiles grown from cellulose-producing bacteria with engineered tyrosinase expression

This paper engineers Komagataeibacter rhaeticus to produce self-dyeing bacterial cellulose through melanin biosynthesis, enabling sustainable textile fabrication.

Synthetic yeast chromosome XI design enables extrachromosomal circular DNA formation on demand

The paper constructs a synthetic yeast chromosome XI and demonstrates how non-coding DNA modifications affect cell fitness, enabling on-demand extrachromosomal circular DNA formation.

Komagataeibacter tool kit (KTK): a modular cloning system for multigene constructs and programmed protein secretion from cellulose producing bacteria

The paper introduces a modular cloning system for genetic engineering in Komagataeibacter bacteria to enable multigene construct assembly and programmed protein secretion.

Living materials with programmable functionalities grown from engineered microbial co-cultures

This paper develops a synthetic symbiotic co-culture system to engineer bacterial cellulose with programmable functional properties.

Engineering a model cell for rational tuning of GPCR signaling

The paper constructs a synthetic GPCR signaling system in yeast to predictably tune cellular responses to stimuli using computational and experimental methods.

Engineered cell-to-cell signalling within growing bacterial cellulose pellicles

This paper engineers cell-to-cell communication in bacterial cellulose-producing bacteria to enable differential gene expression based on proximity within growing materials.

Cell-free prediction of protein expression costs for growing cells

The paper predicts the cost of protein expression in E. coli using a cell-free assay and computational model to assess resource consumption and differentiate between gene expression and metabolic pathway burdens.

Burden-driven feedback control of gene expression

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.

Rational Design Of RNA Structures That Predictably Tune Eukaryotic Gene Expression

This paper designs RNA hairpin structures to predictably tune gene expression in yeast by modulating translation initiation efficiency, outperforming promoter mutation approaches.

Tunable Extracellular Self-Assembly of Multi-Protein Conjugates from Bacillus subtilis

This paper demonstrates a method for tunable extracellular self-assembly of multi-protein conjugates using Bacillus subtilis, enhancing enzyme resilience and enabling functional multi-protein complex formation.

Quantifying cellular capacity to identify gene expression designs with reduced burden

The paper introduces an in vivo monitor to quantify cellular capacity in E. coli and identifies gene expression designs with reduced burden that outperform less efficient designs.