A5026535521- Microbial Metabolic Engineering and Bioproduction
- Gene Regulatory Network Analysis
- Enzyme Catalysis and Immobilization
- Computational Drug Discovery Methods
- Viral Infectious Diseases and Gene Expression in Insects
- Biofuel production and bioconversion
- RNA and protein synthesis mechanisms
- Microbial Natural Products and Biosynthesis
- Plant biochemistry and biosynthesis
- Genetic factors in colorectal cancer
- Bioinformatics and Genomic Networks
- Colorectal Cancer Treatments and Studies
- Advanced Control Systems Optimization
- Genetics and Neurodevelopmental Disorders
- Fault Detection and Control Systems
- Colorectal Cancer Screening and Detection
- Enzyme Structure and Function
- CRISPR and Genetic Engineering
- Protein Structure and Dynamics
- Genetics, Bioinformatics, and Biomedical Research
- Epigenetics and DNA Methylation
- Autism Spectrum Disorder Research
- Fuzzy Logic and Control Systems
- Analytical Chemistry and Chromatography
- Multilevel Inverters and Converters
Universitat Politècnica de València
2001-2024
Institute for Integrative Systems Biology
2023-2024
Universitat de València
2023-2024
Consejo Superior de Investigaciones Científicas
2024
Hospital Universitario Virgen de la Arrixaca
2010-2022
University of Manchester
2015-2022
Czech Academy of Sciences, Institute of Biotechnology
2006-2019
Engineering and Physical Sciences Research Council
2016-2018
Biotechnology and Biological Sciences Research Council
2016-2018
Hospital del Mar Research Institute
2014-2016
Synthetic biology applied to industrial biotechnology is transforming the way we produce chemicals. However, despite advances in scale and scope of metabolic engineering, research development process still remains costly. In order expand chemical repertoire for production next generation compounds, a major engineering effort required novel design tools that target diversity through rapid predictable protocols. Addressing goal involves retrosynthesis approaches explore biosynthetic space....
The microbial production of fine chemicals provides a promising biosustainable manufacturing solution that has led to the successful growing catalog natural products and high-value chemicals. However, development at industrial levels been hindered by large resource investments required. Here we present an integrated Design-Build-Test-Learn (DBTL) pipeline for discovery optimization biosynthetic pathways, which is designed be compound agnostic automated throughout. We initially applied...
Our inability to predict the behavior of biological systems severely hampers progress in bioengineering and biomedical applications. We cannot effect genotype changes on phenotype, nor extrapolate large-scale from small-scale experiments. Machine learning techniques recently reached a new level maturity, are capable providing needed predictive power without detailed mechanistic understanding. However, they require large amounts data be trained. The amount quality required can only produced...
As metabolic engineering and synthetic biology progress toward reaching the goal of a more sustainable use biological resources, need increasing number value-added chemicals that can be produced in industrial organisms becomes imperative. Exploring, however, vast possibility pathways amenable to through heterologous genes expression chassis organism is complex unattainable manually. Here, we present XTMS, web-based pathway analysis platform available at http://xtms.issb.genopole.fr, which...
RetroRules is a database of reaction rules for metabolic engineering (https://retrorules.org). Reaction are generic descriptions chemical reactions that can be used in retrosynthesis workflows order to enumerate all possible biosynthetic routes connecting target molecule its precursors. The use such becoming increasingly important the context synthetic biology applied de novo pathway discovery and systems discover underground metabolism due enzyme promiscuity. Here, we provide first time...
Synthetic biology applies the principles of engineering to in order create biological functionalities not seen before nature. One most exciting applications synthetic is design new organisms with ability produce valuable chemicals including pharmaceuticals and biomaterials a greener; sustainable fashion. Selecting right enzymes catalyze each reaction step desired target compound is, however, trivial. Here, we present Selenzyme, free online enzyme selection tool for metabolic pathway design....
The field of synthetic biology aims to make the design biological systems predictable, shrinking huge space practical numbers for testing. When designing microbial cell factories, most optimization efforts have focused on enzyme and strain selection/engineering, pathway regulation, process development. In silico tools predictive bacterial ribosome binding sites (RBSs) RBS libraries now allow translational tuning biochemical pathways; however, methods predicting optimal combinations in...
Abstract Background Synthetic biology is used to develop cell factories for production of chemicals by constructively importing heterologous pathways into industrial microorganisms. In this work we present a retrosynthetic approach the therapeutics with goal developing an in situ drug delivery device host cells. Retrosynthesis, concept originally proposed synthetic chemistry, iteratively applies reversed chemical transformations (reversed enzyme-catalyzed reactions metabolic space) starting...
Metabolic circuits are a promising alternative to other conventional genetic as modular parts implementing functionalities required for synthetic biology applications. To date, metabolic design has been mainly focused on production circuits. Emergent applications such smart therapeutics, however, require that enable sensing and regulation. Here, we present RetroPath, an automated pipeline embedded explores the circuit space from given set of specifications selects best implement based...
How enzymes have evolved to their present form is linked the question of how pathways emerged and into extant metabolic networks. To investigate this mechanism, we explored chemical diversity in a largely unbiased data set catalytic reactions processed by modern across tree life. In order get quantitative estimate enzyme diversity, measure multispecificity or promiscuity using reaction molecular signatures. Our main finding that are catalyzed highly specific shared poorly divergent species,...
Genetically-encoded biosensors offer a wide range of opportunities to develop advanced synthetic biology applications. Circuits with the ability detecting and quantifying intracellular amounts compound interest are central whole-cell design for medical environmental applications, they also constitute essential parts selection regulation high-producer strains in metabolic engineering. However, number compounds that can be detected through natural mechanisms, like allosteric transcription...
Synthetic biology is today harnessing the design of novel and greener biosynthesis routes for production added-value chemicals natural products. The pathways often requires a detailed selection enzyme sequences to import into chassis at each reaction steps. To address such requirements in an automated way, we present here tool exploring space enzymatic reactions. Given provides probability estimate that catalyzes reaction. Our first considers similarity known biochemical reactions with...
Abstract Natural plant-based flavonoids have drawn significant attention as dietary supplements due to their potential health benefits, including anti-cancer, anti-oxidant and anti-asthmatic activities. Naringenin, pinocembrin, eriodictyol homoeriodictyol are classified (2S)-flavanones, an important sub-group of naturally occurring flavonoids, with wide-reaching applications in human nutrition. These four compounds occupy a central position branch point intermediates towards broad spectrum...
Bio-based production of industrial chemicals using synthetic biology can provide alternative green routes from renewable resources, allowing for cleaner processes. To efficiently produce on-demand through microbial strain engineering, biomanufacturing foundries have developed automated pipelines that are largely compound agnostic in their time to delivery. Here we benchmark the capabilities a pipeline enable rapid prototyping cell factories chemically diverse industrially relevant material...
Abstract Motivation: Enzyme promiscuity, a property with practical applications in biotechnology and synthetic biology, has been related to the evolvability of enzymes. At molecular level, several structural mechanisms have linked enzyme promiscuity families. However, it is at present unclear what extent these observations can be generalized. Here, we introduce for first time method predicting catalytic substrate using graph-based representation known as signature. Results: Our method, which...
Abstract Background We consider the possibility of engineering metabolic pathways in a chassis organism order to synthesize novel target compounds that are heterologous chassis. For this purpose, we model networks through hypergraphs where reactions represented by hyperarcs. Each hyperarc represents an enzyme-catalyzed reaction transforms set substrates into product compounds. follow retrosynthetic approach search space (hypergraphs) for (hyperpaths) linking source Results To select best...
We present an algorithm to compute molecular graph descriptors considering the stereochemistry of structure based on our previously introduced signature descriptor. The can generate two types descriptors, one which is compliant with Cahn-Ingold-Prelog priority rules, including complex structures such as fullerenes, and a computationally efficient previous definition directed acyclic that augmented chiral graph. performance in terms speed canonicalizer well modeling predicting bioactivity...