Pablo Carbonell
Dynamics Biodesign Lab · I2SYSBIO
Biography
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Pablo Carbonell is Principal Investigator at the Institute of Integrative Systems Biology I2SysBio (UV/CSIC) former senior reader at the ai2 institute, Polytechnic University of Valencia (UPV). Pablo Carbonell leads the Dynamics BioDesign Lab (DBDL) group (https://carbonelllab.org), co-leads the Microbial Biotechnology group of ELIXIR and is member of the working group of the Global Biofoundries Alliance (GBA). Previously, he was a senior scientist at the SYNBIOCHEM Biofoundry at the University of Manchester. Pablo Carbonell's research focuses on developing innovative tools and strategies to automate and optimize biomanufacturing processes. The research employs a biofoundry approach that automates the Design-Build-Test-Learn (DBTL) cycle to accelerate the development of producer strains for bio-based compounds. We work on customized research solutions to identify novel enzymes for biocatalysis, optimize strains for fermentation processes, and develop innovative biosensors. |
Profile
| Institution | I2SYSBIO |
| Position | PTU, Científico visitante |
| Home page | http://carbonelllab.org |
| Contact email | pablo.carbonell@csic.es |
| ORCID | 0000-0002-0993-5625 |
BCB Hub
| BCB Committee | Support BCB Excellence |
| BCB Tools | Detspace, Selenzyme, Sensbio, RetroPath2.0, Galaxy-SynBioCAD |
| BCB Services |
Research
Research topics
Computational MethodsComputational models and simulationsSynthetic biology
Research lines
None
Projects, networks, transfer & teaching
Funded projects 2
Publications 77 entries
- Living buildings with living electronics: towards biologically intelligent biohybrids Article · Jun 2026
- Before LUCA: unearthing the chemical roots of metabolism Article · 2 Oct 2025
- Challenges and Opportunities in Smart Biosensing for Biomanufacturing Article · 22 Aug 2025
- Context-Aware Biosensor Design Through Biology-Guided Machine Learning and Dynamical Modeling Software · 3 Jun 2025
- DetSpace: a web server for engineering detectable pathways for bio-based chemical production Article · 18 Apr 2024
View all (72 more)
- Sensbio: an online server for biosensor design Software · 28 Feb 2023
- Transcription factor-based biosensors for screening and dynamic regulation Article · 6 Feb 2023
- SelenzymeRF: updated enzyme suggestion software for unbalanced biochemical reactions Article · Jan 2023
- Blood Glucose Estimation From Voice: First Review of Successes and Challenges Article · Sep 2022
- The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering Software · 29 Aug 2022
- Sensbio: An online server for biosensor design Preprint · 1 Aug 2022
- Fast biofoundries: coping with the challenges of biomanufacturing Article · Jul 2022
- Developing an enzyme selection tool supporting multiple hosts contexts Preprint · 10 Sep 2021
- Prototyping of microbial chassis for the biomanufacturing of high-value chemical targets Article · 8 Jun 2021
- SynBiopython: an open-source software library for Synthetic Biology Article · 1 Jan 2021
- Automated engineering of synthetic metabolic pathways for efficient biomanufacturing Article · Jan 2021
- Rapid prototyping of microbial production strains for the biomanufacture of potential materials monomers Article · Jul 2020
- Extended Metabolic Biosensor Design for Dynamic Pathway Regulation of Cell Factories Article · Jul 2020
- Galaxy-SynBioCAD: Synthetic Biology Design Automation tools in Galaxy workflows Preprint · 15 Jun 2020
- In silico design and automated learning to boost next-generation smart biomanufacturing Article · 1 Jan 2020
- Engineering Escherichia coli towards de novo production of gatekeeper (2S)-flavanones: naringenin, pinocembrin, eriodictyol and homoeriodictyol Article · 1 Jan 2020
- Pathways to cellular supremacy in biocomputing Article · 20 Nov 2019
- Identification of major malate export systems in an engineered malate-producing Escherichia coli aided by substrate similarity search Article · 22 Oct 2019
- Opportunities at the Intersection of Synthetic Biology, Machine Learning, and Automation Article · 19 Jul 2019
- SelProm: A Queryable and Predictive Expression Vector Selection Tool for Escherichia coli Article · 14 Mar 2019
- Highly multiplexed, fast and accurate nanopore sequencing for verification of synthetic DNA constructs and sequence libraries Article · 1 Jan 2019
- Efficient learning in metabolic pathway designs through optimal assembling Article · 2019
- Machine Learning of Designed Translational Control Allows Predictive Pathway Optimization in Escherichia coli Article · 18 Dec 2018
- Retrorules: A database of reaction rules for engineering biology Article · 13 Oct 2018
- An automated Design-Build-Test-Learn pipeline for enhanced microbial production of fine chemicals Article · 8 Jun 2018
- PartsGenie: an integrated tool for optimizing and sharing synthetic biology parts Article · 23 Feb 2018
- Selenzyme: enzyme selection tool for pathway design Software · 7 Feb 2018
- RetroPath2.0: A retrosynthesis workflow for metabolic engineers Software · Jan 2018
- Hepatotoxicity prediction by systems biology modeling of disturbed metabolic pathways using gene expression data Book / chapter · 2018
- Extended metabolic space modeling Book / chapter · 2018
- Enzyme Discovery: Enzyme Selection and Pathway Design Book / chapter · 2018
- Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. Article · Dec 2017
- biochem4j: Integrated and extensible biochemical knowledge through graph databases Article · 14 Jul 2017
- SYNBIOCHEM Synthetic Biology Research Centre, Manchester – A UK foundry for fine and speciality chemicals production Article · Dec 2016
- Mapping the patent landscape of synthetic biology for fine chemical production pathways Article · 3 Aug 2016
- SYNBIOCHEM–a SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals Article · 9 Jun 2016
- SensiPath: computer-aided design of sensing-enabling metabolic pathways Article · 22 Apr 2016
- Semisupervised Gaussian Process for Automated Enzyme Search Article · 30 Mar 2016
- Bioinformatics for the synthetic biology of natural products: integrating across the Design–Build–Test cycle Article · 2016
- Synthetic biology for pharmaceutical drug discovery Article · Dec 2015
- Integrated structure- and ligand-based in silico approach to predict inhibition of cytochrome P450 2D6 Article · 26 Aug 2015
- Editorial - Synthetic biology: Engineering complexity and refactoring cell capabilities Article · 21 Aug 2015
- A sense of balance: Experimental investigation and modeling of a malonyl-CoA sensor in Escherichia coli Article · 8 Apr 2015
- Exploring Brand-Name Drug Mentions on Twitter for Pharmacovigilance Book / chapter · 2015
- Computer-aided design for metabolic engineering Article · Dec 2014
- Computational protein design methods for synthetic biology Book / chapter · 13 Nov 2014
- Validation of RetroPath, a computer-aided design tool for metabolic pathway engineering Article · 15 Oct 2014
- XTMS: pathway design in an eXTended metabolic space Article · 3 May 2014
- Overcoming drug resistance through in silico prediction Article · Mar 2014
- XTMS in action: Retrosynthetic design in the extended metabolic space of heterologous pathways for high-value compounds Book / chapter · 2014
- Retropath: Automated pipeline for embedded metabolic circuits Article · 16 Oct 2013
- In Silico Mechanistic Profiling to Probe Small Molecule Binding to Sulfotransferases Article · 6 Sep 2013
- Stereo signature molecular descriptor Article · 5 Apr 2013
- Synergistic Synthetic Biology: Units in Concert Article · 2013
- Retrosynthetic design of heterologous pathways Book / chapter · 2013
- Fuzzy Logic Applications in Control Theory and Systems Biology Article · 2013
- A retrosynthetic biology approach to therapeutics: from conception to delivery Article · Dec 2012
- Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms Article · 6 Feb 2012
- Origins of specificity and promiscuity in metabolic networks Article · Dec 2011
- Compound toxicity screening and structure-activity relationship modeling in Escherichia coli Article · 9 Nov 2011
- A retrosynthetic biology approach to metabolic pathway design for therapeutic production Article · 5 Aug 2011
- Engineering antibiotic production and overcoming bacterial resistance Article · 10 Jun 2011
- Molecular signatures-based prediction of enzyme promiscuity Article · 15 Jun 2010
- Reaction network generation Book / chapter · 21 Apr 2010
- Methyl side-chain dynamics prediction based on protein structure Article · 30 Jul 2009
- Energetic determinants of protein binding specificity: Insights into protein interaction networks Article · 30 Mar 2009
- The modular organization of domain structures: Insights into protein-protein binding Article · 7 Dec 2007
- InSilicoSpectro: An open-source proteomics library Article · 7 Feb 2006
- Fuzzy TCP: A preliminary study Article · 2002
- Sensibility study of the control loops of voltage and current mode controlled DC-DC converters by means of robust parametric control theory Conference paper
- Fuzzy gain scheduling control of switch-mode DC/DC converters Conference paper
- A fuzzy backstepping controller for a pneumatic muscle actuator system Conference paper