Jacob B. Roberts
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View article: RB-TnSeq elucidates dicarboxylic-acid-specific catabolism in β-proteobacteria for improved plastic monomer upcycling
RB-TnSeq elucidates dicarboxylic-acid-specific catabolism in β-proteobacteria for improved plastic monomer upcycling Open
Dicarboxylic acids are key components of many polymers and plastics, making them a target for both engineered microbial degradation and sustainable bioproduction. In this study, we generated a comprehensive data set of functional evidence …
View article: Carbon-Efficient Conversion through Hydrogen and Formate-Driven Metabolism in <i>Escherichia coli</i>
Carbon-Efficient Conversion through Hydrogen and Formate-Driven Metabolism in <i>Escherichia coli</i> Open
Product yields for biomanufacturing processes are often constrained by the tight coupling of cellular energy generation and carbon metabolism in sugar-based fermentation systems. To overcome this limitation, we engineered Escherichia coli …
View article: RB-TnSeq elucidates dicarboxylic acid specific catabolism in β-proteobacteria for improved plastic monomer upcycling
RB-TnSeq elucidates dicarboxylic acid specific catabolism in β-proteobacteria for improved plastic monomer upcycling Open
Dicarboxylic acids are key components of many polymers and plastics, making them a target for both engineered microbial degradation and sustainable bioproduction. In this study, we generated a comprehensive dataset of functional evidence f…
View article: Foldy: An open-source web application for interactive protein structure analysis
Foldy: An open-source web application for interactive protein structure analysis Open
Foldy is a cloud-based application that allows non-computational biologists to easily utilize advanced AI-based structural biology tools, including AlphaFold and DiffDock. With many deployment options, it can be employed by individuals, la…
View article: Characterization and Diversification of AraC/XylS Family Regulators Guided by Transposon Sequencing
Characterization and Diversification of AraC/XylS Family Regulators Guided by Transposon Sequencing Open
In this study, we explored the development of engineered inducible systems. Publicly available data from previous transposon sequencing assays were used to identify regulators of metabolism in Pseudomonas putida KT2440. For AraC fam…
View article: Automated Platform for the Plasmid Construction Process
Automated Platform for the Plasmid Construction Process Open
There is a growing need for applications capable of handling large synthesis biology experiments. At the core of synthetic biology is the process of cloning and manipulating DNA as plasmids. Here, we report the development of an applicatio…
View article: Module-Based Polyketide Synthase Engineering for <i>de Novo</i> Polyketide Biosynthesis
Module-Based Polyketide Synthase Engineering for <i>de Novo</i> Polyketide Biosynthesis Open
Polyketide retrobiosynthesis, where the biosynthetic pathway of a given polyketide can be reversibly engineered due to the colinearity of the polyketide synthase (PKS) structure and function, has the potential to produce millions of organi…
View article: Maximizing Heterologous Expression of Engineered Type I Polyketide Synthases: Investigating Codon Optimization Strategies
Maximizing Heterologous Expression of Engineered Type I Polyketide Synthases: Investigating Codon Optimization Strategies Open
Type I polyketide synthases (T1PKSs) hold enormous potential as a rational production platform for the biosynthesis of specialty chemicals. However, despite great progress in this field, the heterologous expression of PKSs remains a major …
View article: Characterization and diversification of AraC/XylS family regulators guided by transposon sequencing
Characterization and diversification of AraC/XylS family regulators guided by transposon sequencing Open
In this study, we explored the development of engineered inducible systems. Publicly available data from previous transposon sequencing assays were used to identify regulators of metabolism in Pseudomonas putida KT2440. For the AraC-family…
View article: Maximizing Heterologous Expression of Engineered Type I Polyketide Synthases: Investigating Codon Optimization Strategies
Maximizing Heterologous Expression of Engineered Type I Polyketide Synthases: Investigating Codon Optimization Strategies Open
Type I polyketide synthases (T1PKSs) hold an enormous potential as a rational production platform for the biosynthesis of specialty chemicals. However, despite the great progress in this field, the heterologous expression of PKSs remains a…
View article: Foldy: a web application for interactive protein structure analysis
Foldy: a web application for interactive protein structure analysis Open
Foldy is a cloud-based application that allows non-expert scientists to easily access and utilize advanced AI-based structural biology tools, including AlphaFold and DiffDock. Built on Kubernetes, it can be deployed by universities, depart…
View article: Expanding Extender Substrate Selection for Unnatural Polyketide Biosynthesis by Acyltransferase Domain Exchange within a Modular Polyketide Synthase
Expanding Extender Substrate Selection for Unnatural Polyketide Biosynthesis by Acyltransferase Domain Exchange within a Modular Polyketide Synthase Open
Modular polyketide synthases (PKSs) are polymerases that employ α-carboxyacyl-CoAs as extender substrates. This enzyme family contains several catalytic modules, where each module is responsible for a single round of polyketide chain exten…
View article: BaseBuddy v1
BaseBuddy v1 Open
The software "BaseBuddy" (basebuddy.lbl.gov) is a user-friendly web app designed for codon optimization of heterologous genes. Codon optimization is a widely used technique to enhance the expression levels of non-native genes. Our app is b…
View article: SSGUI v1.0
SSGUI v1.0 Open
SSGUI is a web-based application that integrates the integrative genomics browser (IGV) with upstream alignment pipelines enabling rapid analysis of a batch of next-generation sequencing (NGS) samples. The input to SSGUI is an NGS file sys…
View article: Engineering Pseudomonas putida KT2440 for chain length tailored free fatty acid and oleochemical production
Engineering Pseudomonas putida KT2440 for chain length tailored free fatty acid and oleochemical production Open
View article: Engineering <i>Pseudomonas putida</i> KT2440 for chain length tailored free fatty acid and oleochemical production
Engineering <i>Pseudomonas putida</i> KT2440 for chain length tailored free fatty acid and oleochemical production Open
Despite advances in understanding the metabolism of Pseudomonas putida KT2440, a promising bacterial host for producing valuable chemicals from plant-derived feedstocks, a strain capable of producing free fatty acid-derived chemicals has n…