Julio is the leader of the Computational Biology Lab at MBG-CSIC (Pontevedra, Spain), an institute of CSIC (Spanish National Research Council). More info at https://www.bangalab.org
Our research is focused in computational systems and synthetic biology.
We use mathematical modelling, simulation and optimization to understand complex biological systems and processes.
Current research topics include:
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Reverse engineering: systems identification (dynamic modelling) of biological networks
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Projects: Working Group Nicole Radde, SteaPKMod
Institutions: University of Stuttgart
https://orcid.org/0000-0002-5300-0915Currently I focuse on the integration of data into multi-scale models with statistical methods and uncertainty tracking in the research unit QuaLiPerF.
Projects: SysMO-LAB, MOSES, PSYSMO, SulfoSys, SulfoSys - Biotec, EraCoBiotech 2 nd call proposal preparation, Make Me My Model, Mechanism based modeling viral disease ( COVID-19 ) dynamics in human population, Modelling COVID-19 epidemics, SNAPPER: Synergistic Neurotoxicology APP for Environmental Regulation, Xenophiles Systems Biology, Thermodynamics, Non equilibrium thermodynamics, Book on Thermodynamics, and kinetics, Teaching Alien Biology, Outdated material, Fusion-fission-mitophagy, Stochastics and bursting
Institutions: Manchester Centre for Integrative Systems Biology, University of Manchester, VU University Amsterdam, University of Amsterdam, Systems Biology Amsterdam
https://orcid.org/0000-0002-0443-6114Systems Biologist at University of Amsterdam, Free University Amsterdam, University of Manchester, Infrastructure Systems Biology.NL (ISBE.NL), Systems Biology Amsterdam.
Projects: COVID-19 Disease Map
Institutions: University of Tübingen
https://orcid.org/0000-0002-1240-5553Expertise: Systems Biology, Computational Systems Biology, Databases, Dynamic modelling, Java, Mathematical modelling, Metabolic Engineering, Disease Maps, Curation, Modeling, Data Integration, Constraint-based Modelling, Parameter estimation
Tools: SBML, SBGN, SBGNML, JSBML, Jupyter, Python, cobrapy toolbox, SBSCL, InSilico, Kinetic Modeling
Andreas Dräger is the assistant professor for Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens at the University of Tübingen in Germany. His group aims to combat the spreading antibiotics resistances by using mathematical modeling and computer simulation of bacterial systems up to entire microbiomes and host-pathogen interactions. In doing so, his group actively contributes to the advancement of various COMBINE standards.
Projects: COVID-19 Disease Map
Institutions: Barcelona Supercomputing Center
https://orcid.org/0000-0002-7696-1241I completed my BSc in Biology and MSc in Cell Biology by the University of Valencia. During my last undergrad year I participated in synthetic biology’s iGEM competition where I dove in the use of models in Biology, which pushed me to pursue a PhD in the Department of Applied Mathematics in the Technical University of Valencia.
My research on Metabolic Engineering of hydrogen in cyanobacteria led me to be visiting researcher at Uppsala University, Denmark Technical University and EMBL Heidelberg. ...
I'm currently a Postdoc at the Institute of Technical Biochemistry in Stuttgart University. My project involves the experimental validation of the Indirect Enzymatic Dehydration Via Phosphorylation and Dephosphorylation of Isobutanol for Isobutene production.
Projects: EmPowerPutida, COVID-19 Disease Map
Institutions: Wageningen University & Research, University Maastricht
https://orcid.org/0000-0003-3091-3962Expertise: Systems Biology, Mathematical modelling, Biotechnology, Synthetic Biology, Metabolic Engineering, metabolism, Metabolic Networks, SARS-CoV 2, COVID-19, Pathway Curation, Pathway Analysis, Network Analysis
Tools: Matlab, Computational Systems Biology, Flux balance analysis, omics analysis, Python, R, Constraint-based analysis
My research interest is in studying cellular and molecular pathways of COVID-19 disease.
Projects: EmPowerPutida
Institutions: Wageningen University & Research
Projects: BioZEment 2.0, BESTER, Auromega, C1Pro, AquaHealth (ERA-BlueBio)
Institutions: SINTEF
Projects: INBioPharm
Institutions: Norwegian University of Science and Technology
Projects: WURSynBio
Institutions: Wageningen University & Research
Projects: WURSynBio, INDIE - Biotechnological production of sustainable indole
Institutions: Wageningen University & Research
Projects: EmPowerPutida
Institutions: University of Stuttgart
Expertise: Molecular Biology, Metabolic Engineering
PhD student, Institute of Biochemical Engineering at the University of Stuttgart
Projects: SYSTERACT
Institutions: University of Tübingen
Expertise: Microbiology, Molecular Biology, Genetics, Transcriptomics, Metabolic Engineering, nitrogen metabolism, Streptomyces coelicolor, Actinobacteria, antibiotic production
Tools: Fermentation, Genetic modification, Molecular biology techniques (RNA/DNA/Protein), Proteomics, Transcriptomics, Biochemistry and protein analysis
Expertise: Genetics, Microbiology, Metabolic Engineering
Tools: antiSMASH, CloneManager, artemis
Team leader "Quantitative Microbial Phenotyping" Institute of Bio- and Geosciences, IBG-1: Biotechnology Forschungszentrum Jülich GmbH 52425 Jülich, Germany
Expertise: Microbiology, genetic engineering, Fermentation, Cell biology, Metabolic Engineering
Research Scientist in the Biotechnology and Nanomedicine department at the non-profit research institution, SINTEF, in Norway.
Projects: SilicoTryp, SYSTERACT, SynBio4Flav
Institutions: University of Glasgow, Chalmers University of Technology
https://orcid.org/0000-0002-3593-5792Projects: MetApp, LEANPROT, C1Pro
Institutions: SINTEF, Norwegian University of Science and Technology
Since 1st of January 2015 I am Professor in synthetic biology at the Norwegian University of Science and Technology (NTNU) institute of biotechnology. Before that I was research director in the non-profit research institution SINTEF. My major research activities are within microbial molecular biology, mainly combining metabolic engineering, synthetic biology and systems biology to develop microbial cell factories, and focusing both on the products and on the raw materials. The research includes ...
Projects: SysMO DB, Whole body modelling of glucose metabolism in malaria patients, Manchester Institute for Biotechnology, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, GenoSysFat, DigiSal, FAIRDOM user meeting
Institutions: University of Manchester - Department of Computer Science, Manchester Centre for Integrative Systems Biology, University of Manchester
https://orcid.org/0000-0003-4958-0184Interested in systems + synthetic biology, biotechnology, mountaineering, swimming, running, and the occasional cup of tea. Once diagnosed as an ENFP.
Projects: COSMIC
Institutions: University of Nottingham
A molecular microbiologist with a passion for Clostridia! Interested in the development of more effective countermeasures (diagnosis, prevention & treatment) against pathogens, specifically Clostridium difficile and Clostridium botulinum as well as the exploitation of the medical and industrial properties of beneficial strains, specifically in cancer therapy and biofuel production
Projects: COSMIC
Institutions: Wageningen University & Research
Expertise: Microbiology, Genetics, Molecular Biology, Systems Biology, Anaerobic Microbiology, Clostridial Genetics, Metabolic Engineering, Synthetic Biology, bacterial metabolism, carbon metabolism, Clostridium
Tools: Microbiology, Molecular Biology, Chromatography, Molecular biology techniques (RNA/DNA/Protein)
I'm an experimentalist 'Pre-doc' (I still have to finish my PhD thesis) and my work on the COSMIC project will focus on setting up a metabolomic analysis method for Clostridium acetobutylicum. In the past I have worked on metabolic engineering of the same organism by disrupting genes to asses their impact on acid and solvent formation. I'm looking forward to joining the COSMIC web-community. It hopefully will all us to stay in touch and update each other on advances in the (computer)lab.
Projects: BaCell-SysMO
Institutions: University of Greifswald
Projects: PSYSMO, DigiSal, GenoSysFat, HUMET Startup, EmPowerPutida, MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum animal vaccine, SAFE-Aqua, INDIE - Biotechnological production of sustainable indole
Institutions: Helmholtz Centre for Infection Research Braunschweig, Wageningen University & Research
Expertise: Microbiology, Mathematical modelling of biosystems and bioprocesses, Optimal experimental design, Systems Biology, Biotechnology
Tools: Bioinformatics, Genetic modification, Proteomics, Fermentation, Microarray analysis, Computational Systems Biology, Metabolic Engineering, microbiology techniques, reverse engineering, computational platform development, metabolic netwlrk visualization
My research activities has been to use mathematical models and Computational Biology to answer biological questions, intertwining in silico and experimental methods at all stages. I have a strong interest in exploring the interfaces between Fundamental Biology and bona fide Engineering, specifically in the realm of environmental and industrial problems. The research goals of my group are to contribute to the elucidation of mechanisms underlying basic cellular processes, evolution and ecological ...
Projects: BaCell-SysMO
Institutions: University of Braunschweig
University Education: 1987-1993, Biotechnology (Diploma), Technische Universität Braunschweig, Germany.
Dissertation: 1993-1996, Disseration German Research Centre for Biotechnology, Biochemical Engineering Division, Braunschweig, Germany.
Habiliation: 2006, Saarland University, Saarbrücken, Germany.
Positions 1993-1996: Research Assistant, German Research Centre for Biotechnology, Biochemical Engineering Division, Braunschweig, Germany. 1997-1998: Post-doc at Department of Applied Chemistry & ...
Engineering next level photosynthesis-PhotoBoost is a 4-year research and innovation action that aims to significantly improve the efficiency of photosynthesis in plants. The optimisation of photosynthesis will be achieved by capitalising on multidisciplinary approaches including computational biology, metabolic modelling, systems biology, enzyme and pathway engineering, synthetic biology, and the multigene transformation of two major C3 crops: potato and rice. The PhotoBoost project will deliver ...
Programme: Independent Projects
Public web page: http://www.photoboost.org
Organisms: Solanum tuberosum, Oryza sativa
RobOKoD algorithm was, designed then implemented as part of a study in RobOKoD: microbial strain design for (over)production of target compounds. (http://fairdomhub.org/publications/236). It was used to generate a strain of e.coli for producing butanol, that was then compared to an experimental strain. It was shown to perform better than similar methods (OptKnock, and RobustKnock).
Submitter: Natalie Stanford
Biological problem addressed: Model Analysis Type
Investigation: Designing a new way to predict engineering stra...
Organisms: No organisms
Models: iNS142 RobOKoD Redesigned Butanol Producing.
SOPs: RobOKoD SOP for Redesigning Butanol Producing S...
Data files: FBA result of RobOKoD designed e.coli strain.
Snapshots: No snapshots
First version of Genome-scale metabolic model (GEM) for reconstraction of flavonoids biosynthetic pathways. This model includes as a chassis , the Pseudomonas Putida GEM (iJN1411) . It includes the metabolic reconstruction of more than 500 flavonoids and more than 500 reactions related to the flavonoid biosynthesis.
Creators: David San León Granado, Juan Nogales, Álvaro Gargantilla Becerra
Submitter: David San León Granado
Model type: Metabolic network
Model format: SBML
Environment: Matlab
Organism: Pseudomonas putida
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
The model presents a multi-compartmental (mesophyll, phloem and root) metabolic model of growing Arabidopsis thaliana. The flux balance analysis (FBA) of the model quantifies: sugar metabolism, central carbon and nitrogen metabolism, energy and redox metabolism, proton turnover, sucrose translocation from mesophyll to root and biomass growth under both dark- and light-growth conditions with corresponding growth either on starch (in darkness) or on CO2 (under light). The FBA predicts that ...
Creators: Maksim Zakhartsev, Olga Krebs, Irina Medvedeva, Ilya Akberdin, Yuriy Orlov
Submitter: Maksim Zakhartsev
Model type: Metabolic network
Model format: SBML
Environment: Not specified
Organism: Arabidopsis thaliana
Investigations: Metabolic analysis of effects of sucrose transl... and 1 hidden item
Studies: Analysis of central carbon and energy metabolis... and 1 hidden item
Assays: Flux Balance Analysis of multi-compartment meta... and 1 hidden item
Abstract (Expand)
Authors: J. Amaral, A. K. M. Lobo, E. Carmo-Silva
Date Published: 11th Dec 2023
Publication Type: Journal
PubMed ID: 38058283
Citation: New Phytol. 2024 Jan;241(1):35-51. doi: 10.1111/nph.19369.
Abstract (Expand)
Authors: S. Vijayakumar, Y. Wang, G. Lehretz, S. Taylor, E. Carmo-Silva, S. Long
Date Published: 30th Jan 2024
Publication Type: Journal
PubMed ID: 37921015
Citation: Plant J. 2024 Jan;117(2):561-572. doi: 10.1111/tpj.16512. Epub 2023 Nov 3.