Research Group

Detalle de: Dynamics Biodesign Lab

Title	Dynamics Biodesign Lab
Description	Our biodesign studio creates innovative solutions for automated biofoundries, fostering sustainable industrial biotechnology across the bioeconomy sectors. We combine synthetic biology, machine learning, and biosensor and pathway dynamic regulation design to produce next-generation bio-based chemicals.
Home Page	https://carbonelllab.org/
Contact Email	pablo.carbonell@csic.es
Collaborating Companies
Spin Off
Patents
Hpc Resources
Institution	I2SYSBIO
Ontology	Computational Methods, Computational models and simulations, Synthetic biology
Tools	Detspace, Selenzyme, Sensbio, RetroPath2.0, Galaxy-SynBioCAD
Service Units
Research Lines	Synthetic biology towards precise fermentations and biomanufacturing
Funded Projects	SMARTBIOFAB. Smart biomanufacturing processes: dynamic regulation, optimization and machine learning., BIOECODBTL. Biodesign for the bioeconomy: efficient biomanufacturing through the Design-Build-Test-Learn cycle
Selected Publications	DetSpace: a web server for engineering detectable pathways for bio-based chemical production Article · 18 Apr 2024 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 View all (60 more) 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 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 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 Retrosynthetic design of heterologous pathways Book / chapter · 2013 Fuzzy Logic Applications in Control Theory and Systems Biology Article · 2013 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
Researchers	Pablo Carbonell

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