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AI-Guided Promoter Engineering: Beyond Natural Expression Levels
AI-Driven Precision for High-Yield Engineering The Challenge: Even with advanced genetic tools, protein expression often remains suboptimal due to weak or slow-acting regulatory elements. The Innovation: The team demonstrated a breakthrough Design-Build-Test workflow. By combining biophysical modeling with synthetic biology libraries, they engineered biosensors with vastly improved sensitivity and speed. Rational Design over Trial-and-Error: Instead of random mutations, we us
Jan 10


Overcoming the challenges of genetic instability in multicopy gene design
Abstract In modern bioengineering, multicopy gene constructs are essential for reaching high protein yields and metabolic flux. However, these systems often suffer from severe genetic instability due to recombination and evolutionary pressure. Our team’s latest research, published in NAR Genomics and Bioinformatics, introduces ChimeraUGEM: a sophisticated tool that leverages biophysical modeling to design genetically stable multicopy sequences. By optimizing the "coding-regul
Dec 29, 2025


AI-directed gene fusing prolongs the evolutionary half-life of synthetic gene circuits
Abstract Evolutionary instability is a persistent challenge in synthetic biology, often leading to the loss of heterologous gene expression over time. Here, we present STABLES, a gene fusion strategy that links a gene of interest (GOI) to an essential endogenous gene (EG), with a “leaky” stop codon in between. This ensures both selective pressure against deleterious mutations and the high expression of the GOI. By leveraging a machine learning framework, we predict optimal GO
Dec 15, 2025


Deciphering plasmid replication dynamics: a computational approach to predict ColE1-like plasmid copy number
Abstract Plasmids constitute a key tool in synthetic biology, providing a versatile framework for various research and industrial ventures. An essential determinant of plasmid functionality is its copy number, impacting both protein production rates and host cell metabolic burden. However, currently there is no model that can computationally predict the plasmid copy number from the sequence of its origin of replication (ORI). We present a novel software solution tailored to s
Jul 17, 2025


Genome scale analysis of Escherichia coli with a comprehensive prokaryotic sequence-based biophysical model of translation initiation and elongation
Abstract Translation initiation in prokaryotes is affected by the mRNA folding and interaction of the ribosome binding site with the...
Jul 15, 2025


Whole cell biophysical modeling of codontRNA competition reveals novel insightsrelated to translation dynamics
Abstract The importance of mRNA translation models has been demonstrated across many fields of science and biotechnology. However, a...
Jul 15, 2025


Breakthrough in CRISPR Gene Silencing: EXPosition Tool Predicts Expression & Knockout Success
A tool for CRISPR-Cas9 sgRNA evaluation based on computational models of gene expression Background CRISPR is widely used to silence...
Dec 24, 2024


Decoding Chloroplast Translation: Novel Models and Insights for Gene Expression Engineering
Modeling the effect of rRNA-mRNA interactions and mRNA folding on mRNA translation in chloroplasts The process of translation initiation...
Dec 22, 2024


Beyond Initiation: The Role of rRNA-mRNA Interactions in Shaping Bacterial Translation Efficiency
Prokaryotic rRNA-mRNA interactions are involved in all translation steps and shape bacterial transcripts The well-established...
Dec 22, 2024


Engineering Microbiomes: Computational Frameworks for Targeted Genetic Modifications and Enhanced Biosafety
Modulating Gene Expression within a Microbiome Based on Computational Models Recent research in the field of bioinformatics and molecular...
Dec 22, 2024


Unveiling the Role of 3D Chromosomal Structure in CRISPR Efficiency and sgRNA Design
Strong association between genomic 3D structure and CRISPR cleavage efficiency CRISPR is a gene editing technology which enables precise...
Dec 22, 2024


Improved miRNA-mRNA Interaction Prediction with miBSIM: Enhanced Accuracy and Cell-Specific Insights
Advanced computational predictive models of miRNA - mRNA interaction efficiency The modeling of miRNA-mRNA interactions holds...
Dec 22, 2024


Beyond Codon Optimization: Key Determinants of Recombinant Protein Yields in Tobacco Expression Systems
Modeling coding sequence design for virus-based expression in tobacco Transient expression in Tobacco is a popular way to produce...
Dec 22, 2024


Webinar - unlocking the potential of recombinant proteins
Recap of our webinar with Dr. Guy Bushkin, director of product and synthetic biology We had an incredible session with Guy Bushkin, as...
Nov 30, 2024


Predictive Design for Stable Gene Constructs
Evolutionary Stability Optimizer (ESO) A Novel Approach to Identify and Avoid Mutational Hotspots in DNA Sequences While Maintaining High...
Jul 8, 2024


Adapting Gene Expression to any Organism with ChimeraUGEM
ChimeraUGEM: unsupervised gene expression modeling in any given organism Motivation Regulation of the amount of protein that is...
Jul 8, 2024


Algorithms for ribosome traffic engineering and their potential in improving host cells’ titer and growth rate | nature.com
mRNA translation is a fundamental cellular process consuming most of the intracellular energy; thus, it is under extensive evolutionary...
Jul 8, 2024


Quantitative Modeling of Ribosomal Small Subunit Dynamics Using TCP-seq data
Modeling the ribosomal small subunit dynamic in s. cerevisiae based on TCP-seq data Translation Complex Profile Sequencing (TCP-seq), a...
Jul 8, 2024


Unsupervised Learning for Heterologous Gene Expression Optimization Based on Host Genomic Context
Motivation: Dozens of studies in recent years have demonstrated that codon usage encodes various aspects related to all stages of gene...
Jul 8, 2024


High-resolution modeling of the selection on local mRNA folding strength in coding sequences across the tree of life
mRNA can form local secondary structure within the protein-coding sequence, and the strength of this structure is thought to influence...
Jul 8, 2024
Research Powering Our Solutions
Read about our peer-reviewed publications, science and magic.
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