Héctor García Martín
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View article: Automation and machine learning drive rapid optimization of isoprenol production in Pseudomonas putida
Automation and machine learning drive rapid optimization of isoprenol production in Pseudomonas putida Open
Advances in genome engineering have improved our ability to perturb microbial metabolic networks, yet bioproduction campaigns often struggle with parsing complex metabolic datasets to efficiently enhance product titers. We address this cha…
View article: Predictive CRISPR-mediated gene downregulation for enhanced production of sustainable aviation fuel precursor in Pseudomonas putida
Predictive CRISPR-mediated gene downregulation for enhanced production of sustainable aviation fuel precursor in Pseudomonas putida Open
CRISPR interference (CRISPRi) has emerged as a valuable tool for redirecting metabolic flux to enhance bioproduction. However, its application is often constrained by two challenges: (i) rationally identifying effective gene targets for do…
View article: FluxRETAP: a REaction TArget Prioritization genome-scale modeling technique for selecting genetic targets
FluxRETAP: a REaction TArget Prioritization genome-scale modeling technique for selecting genetic targets Open
Motivation Metabolic engineering is rapidly evolving as a result of new advances in synthetic biology tools and automation platforms that enable high throughput strain construction, as well as the development of machine learning tools (ML)…
View article: High-Throughput Microfluidic Electroporation (HTME): A Scalable, 384-Well Platform for Multiplexed Cell Engineering
High-Throughput Microfluidic Electroporation (HTME): A Scalable, 384-Well Platform for Multiplexed Cell Engineering Open
Electroporation-mediated gene delivery is a cornerstone of synthetic biology, offering several advantages over other methods: higher efficiencies, broader applicability, and simpler sample preparation. Yet, electroporation protocols are of…
View article: Merging the computational design of chimeric type I polyketide synthases with enzymatic pathways for chemical biosynthesis
Merging the computational design of chimeric type I polyketide synthases with enzymatic pathways for chemical biosynthesis Open
Synthetic biology offers the promise of manufacturing chemicals more sustainably than petrochemistry. Yet, both the rate at which biomanufacturing can synthesize these molecules and the net chemical accessible space are limited by existing…
View article: Automation and machine learning drive rapid optimization of isoprenol production in Pseudomonas putida
Automation and machine learning drive rapid optimization of isoprenol production in Pseudomonas putida Open
Advances in genome engineering have improved our ability to perturb microbial metabolic networks, yet bioproduction campaigns often struggle with parsing complex metabolic datasets to efficiently enhance product titers. We address this cha…
View article: Prediction of metabolic dynamics through deep learning and high-throughput multiomics data
Prediction of metabolic dynamics through deep learning and high-throughput multiomics data Open
Synthetic biology’s remarkable potential to tackle important societal problems is held back by our inability to predictably engineer biological systems. Here, we collected one of the largest public multiomics synthetic biology datasets gen…
View article: Enabling malic acid production from corn-stover hydrolysate in Lipomyces starkeyi via metabolic engineering and bioprocess optimization
Enabling malic acid production from corn-stover hydrolysate in Lipomyces starkeyi via metabolic engineering and bioprocess optimization Open
Together, this work demonstrated the ability to produce organic acids in L. starkeyi with minimal byproducts. The fermentation characterization and omic analyses provide a rich dataset for understanding L. starkeyi physiology and metabolic…
View article: Predictive genome-wide CRISPR-mediated gene downregulation for enhanced bioproduction
Predictive genome-wide CRISPR-mediated gene downregulation for enhanced bioproduction Open
CRISPR interference (CRISPRi) has emerged as a valuable tool for redirecting metabolic flux to enhance bioproduction. However, conventional approaches for identifying target genes for CRISPRi-mediated downregulation have largely relied on …
View article: Machine learning-led semi-automated medium optimization reveals salt as key for flaviolin production in Pseudomonas putida
Machine learning-led semi-automated medium optimization reveals salt as key for flaviolin production in Pseudomonas putida Open
Although synthetic biology can produce valuable chemicals in a renewable manner, its progress is still hindered by a lack of predictive capabilities. Media optimization is a critical, and often overlooked, process which is essential to obt…
View article: FluxRETAP: A REaction TArget Prioritization Genome-Scale Modeling Technique for Selecting Genetic Targets
FluxRETAP: A REaction TArget Prioritization Genome-Scale Modeling Technique for Selecting Genetic Targets Open
Metabolic engineering is evolving rapidly as a result of new advances in synthetic biology and automation, as well as the irruption of machine learning (ML). ML has been shown to provide the predictive power synthetic biology lacked and ne…
View article: <i>BioPKS Pipeline</i> : An integrated platform for merging the computational design of chimeric type I polyketide synthases with enzymatic pathways for chemical biosynthesis
<i>BioPKS Pipeline</i> : An integrated platform for merging the computational design of chimeric type I polyketide synthases with enzymatic pathways for chemical biosynthesis Open
Synthetic biology offers the promise of manufacturing chemicals more sustainably than petrochemistry. Yet, both the rate at which biomanufacturing can synthesize these molecules and the net chemical accessible space are limited by existing…
View article: Machine learning-led semi-automated medium optimization reveals salt as key for flaviolin production in Pseudomonas putida
Machine learning-led semi-automated medium optimization reveals salt as key for flaviolin production in Pseudomonas putida Open
Although synthetic biology can produce valuable chemicals in a renewable manner, its progress is still hindered by a lack of predictive capabilities. Media optimization is a critical, and often overlooked, process which is essential to obt…
View article: Guide RNA structure design enables combinatorial CRISPRa programs for biosynthetic profiling
Guide RNA structure design enables combinatorial CRISPRa programs for biosynthetic profiling Open
Engineering metabolism to efficiently produce chemicals from multi-step pathways requires optimizing multi-gene expression programs to achieve enzyme balance. CRISPR-Cas transcriptional control systems are emerging as important tools for p…
View article: Genome-scale and pathway engineering for the sustainable aviation fuel precursor isoprenol production in Pseudomonas putida
Genome-scale and pathway engineering for the sustainable aviation fuel precursor isoprenol production in Pseudomonas putida Open
Sustainable aviation fuel (SAF) will significantly impact global warming in the aviation sector, and important SAF targets are emerging. Isoprenol is a precursor for a promising SAF compound DMCO (1,4-dimethylcyclooctane) and has been prod…
View article: Arrowland: an online multiscale interactive tool for -omics data visualization
Arrowland: an online multiscale interactive tool for -omics data visualization Open
Disclosed herein is Arrowland, a web-based software tool for inputting, managing and viewing multiomics data, such as transcriptomics, proteomics, metabolomics and fluxomics data in an interactive, intuitive and multiscale system.
View article: Guide RNA structure design enables combinatorial CRISPRa programs for biosynthetic profiling
Guide RNA structure design enables combinatorial CRISPRa programs for biosynthetic profiling Open
Engineering bacterial metabolism to efficiently produce chemicals and materials from multi-step pathways requires optimizing multi-gene expression programs to achieve enzyme balance. CRISPR-Cas transcriptional control systems are emerging …
View article: BayFlux: A Bayesian method to quantify metabolic Fluxes and their uncertainty at the genome scale
BayFlux: A Bayesian method to quantify metabolic Fluxes and their uncertainty at the genome scale Open
Metabolic fluxes, the number of metabolites traversing each biochemical reaction in a cell per unit time, are crucial for assessing and understanding cell function. 13 C Metabolic Flux Analysis ( 13 C MFA) is considered to be the gold stan…
View article: Accelerating engineered microbe optimization through machine learning and multi-omics datasets
Accelerating engineered microbe optimization through machine learning and multi-omics datasets Open
This project demonstrated the use of a combination of multi-omics data with deep learning and a high-throughput Design- Build-Test-Learn (DBTL) cycle to improve the production of malonic acid, a versatile product with a large market. The p…
View article: A High-Quality Genome-Scale Model for <i>Rhodococcus opacus</i> Metabolism
A High-Quality Genome-Scale Model for <i>Rhodococcus opacus</i> Metabolism Open
Rhodococcus opacus is a bacterium that has a high tolerance to aromatic compounds and can produce significant amounts of triacylglycerol (TAG). Here, we present iGR1773, the first genome-scale model (GSM) of R. opacus PD630 metabolism base…
View article: Genome-scale and pathway engineering for the sustainable aviation fuel precursor isoprenol production in<i>Pseudomonas putida</i>
Genome-scale and pathway engineering for the sustainable aviation fuel precursor isoprenol production in<i>Pseudomonas putida</i> Open
Sustainable aviation fuel (SAF) will significantly impact global warming in the aviation sector, and important SAF targets are emerging. Isoprenol is a precursor for a promising SAF compound DMCO (1,4-dimethylcyclooctane), and has been pro…
View article: BayFlux: A<i>Bay</i>esian method to quantify metabolic<i>Flux</i>es and their uncertainty at the genome scale
BayFlux: A<i>Bay</i>esian method to quantify metabolic<i>Flux</i>es and their uncertainty at the genome scale Open
Metabolic fluxes, the number of metabolites traversing each biochemical reaction in a cell per unit time, are crucial for assessing and understanding cell function. 13 C Metabolic Flux Analysis ( 13 C MFA) is considered to be the gold stan…
View article: Multilevel diffractive lens in the MWIR with extended depth-of-focus and wide field-of-view
Multilevel diffractive lens in the MWIR with extended depth-of-focus and wide field-of-view Open
Optics in the mid-wave-infra-red (MWIR) band are generally heavy, thick and expensive. Here, we demonstrate multi-level diffractive lenses; one designed using inverse design and another using the conventional propagation phase (the Fresnel…
View article: Computational Requirements in Clean Energy and Manufacturing: Summary report of the virtual workshop held on June 28-29, 2021
Computational Requirements in Clean Energy and Manufacturing: Summary report of the virtual workshop held on June 28-29, 2021 Open
On June 28–29, 2021, the US Department of Energy’s (DOE’s) Advanced Scientific Computing Research (ASCR) program in the Office of Science convened a workshop with the Energy Efficiency and Renew able Energy (EERE) program offices to assess…
View article: Biological research and self-driving labs in deep space supported by artificial intelligence
Biological research and self-driving labs in deep space supported by artificial intelligence Open
Space biology research aims to understand fundamental spaceflight effects on organisms, develop foundational knowledge to support deep space exploration and, ultimately, bioengineer spacecraft and habitats to stabilize the ecosystem of pla…
View article: Feedstocks-to-Fuels Pipeline (F2F) v1
Feedstocks-to-Fuels Pipeline (F2F) v1 Open
Sustainably grown biomass is a promising alternative to produce fuels and chemicals and reduce the dependency on fossil energy sources. However, the efficient conversion of lignocellulosic biomass into biofuels and bioproducts often requir…