Our research work
Browse through our publication’s repository
Our research work
Browse through our publication’s repository
Lastest publications
From 2017 onward
- Tsampika M.; Gargantilla-Becerra, A.; Cerro Sánchez, C.; Rivero-Buceta, V.; Prieto, MA. and Nogales, J. A model-driven approach to upcycling recalcitrant feedstocks in Pseudomonas putida by de-coupling PHA production from nutrient limitation. Cell Reports, 2024, Mar 21; 43 (4):113979.
- Castillo, M.; Guevara, G.; Baldanta, S.; Rodríguez, P. S.; Agudo, L.; Nogales, J.; Carrasco, A. D.; Arribas-Aguilar, F.; Pérez-Pérez, J.; García, J. L. Characterization of Limnospira platensis PCC 9108 RM and CRISPR-Cas systems. Microbiological Research 2024, 279, 127572.
- Santos-Merino, M.; Gargantilla Becerra, Á.; de la Cruz, F.; Nogales, J. Highlighting the potential of Synechococcus elongatus PCC 7942 as platform to produce omega-3 fatty acids through an updated genome-scale metabolic modelling. Frontiers in Microbiology 2023, 14, 681.
- Martínez-García, E.; Fraile, S.; Algar, E.; Aparicio, T.; Velázquez, E.; Calles, B.; Tas, H.; Blázquez, B.; Martín, B.; Prieto, C. SEVA 4.0: an update of the Standard European Vector Architecture database for advanced analysis and programming of bacterial phenotypes. Nucleic Acids Research 2023, 51 (D1), D1558-D1567.
- Magadán-Corpas, P.; Ye, S.; Pérez-Valero, Á.; McAlpine, P. L.; Valdés-Chiara, P.; Torres-Bacete, J.; Nogales, J.; Villar, C. J.; Lombó, F. Optimized de novo eriodictyol biosynthesis in Streptomyces albidoflavus using an expansion of the Golden Standard toolkit for its use in Actinomycetes. International Journal of Molecular Sciences 2023, 24 (10), 8879.
- Hogle, M.; Imhof, B.; Hoheneder, W.; Armstrong, R.; Ieropoulos, I.; Wallis, L.; You, J.; Nogales, J. Living architecture: metabolic applications for next-generation, selectively programmable bioreactors. In Urban and Regional Agriculture, Academic Press, 2023; pp 595-614.
- Herencias, C.; Rivero-Buceta, M. V.; Salgado, S.; Baquero, F.; del Campo, R.; Nogales, J.; Prieto, M. A. Bdellovibrio’s Prey-Independent Growth is Fuelled by Amino Acids as a Carbon Source. bioRxiv 2023, 2023.2011. 2024.568592.
- Dräger, A.; Mihail, A.; Almaas, E.; Benfeitas, R.; Benito-Vaquerizo, S.; Blank, L. M.; Hancock, J. M.; Kittikunapong, C.; König, M.; Li, F. standard-GEM: standardization of open-source genome-scale metabolic models. 2023.
- del Olmo Lianes, I.; Yubero, P.; Gómez-Luengo, Á.; Nogales, J.; Espeso, D. R. Technical upgrade of an open-source liquid handler to support bacterial colony screening. Frontiers in Bioengineering and Biotechnology 2023, 11, 1202836.
- Carranza-Saavedra, D.; Torres-Bacete, J.; Blázquez, B.; Sanchez, C. P.; Zapata Montoya, J.; Nogales, J. System metabolic engineering of Escherichia coli W for the production of 2-ketoisovalerate using unconventional feedstock. Frontiers in Bioengineering and Biotechnology 2023, 11, 567.
- Blázquez, B.; San León, D.; Rojas, A.; Tortajada, M.; Nogales, J. New insights on metabolic features of Bacillus subtilis based on multistrain genome-scale metabolic modeling. International Journal of Molecular Sciences 2023, 24 (8), 7091.
- Blázquez, B.; León, D. S.; Torres-Bacete, J.; Gómez-Luengo, Á.; Kniewel, R.; Martínez, I.; Sordon, S.; Wilczak, A.; Salgado, S.; Huszcza, E. Golden Standard: a complete standard, portable, and interoperative MoClo tool for model and non-model proteobacteria. Nucleic Acids Research 2023, 51 (19), e98-e98.
- Anton, M.; Almaas, E.; Benfeitas, R.; Benito-Vaquerizo, S.; Blank, L. M.; Dräger, A.; Hancock, J. M.; Kittikunapong, C.; König, M.; Li, F. standard-GEM: standardization of open-source genome-scale metabolic models. bioRxiv 2023, 2023.2003. 2021.512712.
- Altamira-Algarra, B.; Rueda, E.; Lage, A.; San Leon, D.; Martinez-Blanch, J. F.; Nogales, J.; Garcia, J.; Gonzalez-Flo, E. New strategy for bioplastic and exopolysaccharides production: Enrichment of field microbiomes with cyanobacteria. New Biotechnology 2023, 78, 141-149.
- Tiso, T.; Winter, B.; Wei, R.; Hee, J.; de Witt, J.; Wierckx, N.; Quicker, P.; Bornscheuer, U. T.; Bardow, A.; Nogales, J. The metabolic potential of plastics as biotechnological carbon sources–review and targets for the future. Metabolic engineering 2022, 71, 77-98.
- Santos-Merino, M.; Gutiérrez-Lanza, R.; Nogales, J.; García, J. L.; de la Cruz, F. Synechococcus elongatus PCC 7942 as a platform for bioproduction of omega-3 fatty acids. Life 2022, 12 (6), 810.
- San León D, and Nogales J. Towards merging Bottom-up and Top-down model-based designing of synthetic microbial communities. Current Opin in Microbiol 2022, 69, 102169.
- Nogales, J.; Garmendia, J. Bacterial metabolism and pathogenesis intimate intertwining: time for metabolic modelling to come into action. Microbial Biotechnology 2022, 15 (1), 95.
- Manoli MT, Nogales J, and Prieto A. Synthetic control of metabolic states in Pseudomonas putida by tuning polyhydroxyalkanoate cycle. Mbio 2022, 13 (1), e01794-21.
- López-López, N.; León, D. S.; de Castro, S.; Díez-Martínez, R.; Iglesias-Bexiga, M.; Camarasa, M. J.; Menéndez, M.; Nogales, J.; Garmendia, J. Interrogation of Essentiality in the Reconstructed Haemophilus influenzae Metabolic Network Identifies Lipid Metabolism Antimicrobial Targets: Preclinical Evaluation of a FabH β-Ketoacyl-ACP Synthase Inhibitor. Msystems 2022, 7 (2), e01459-01421.
- Gómez-Álvarez, H.; Iturbe, P.; Rivero-Buceta, V.; Mines, P.; Bugg, T. D.; Nogales, J.; Díaz, E. Bioconversion of lignin-derived aromatics into the building block pyridine 2, 4-dicarboxylic acid by engineering recombinant Pseudomonas putida strains. Bioresource Technology 2022, 346, 126638.
- Torres-Bacete, J.; García, J. L.; Nogales, J. A portable library of phosphate-depletion based synthetic promoters for customable and automata control of gene expression in bacteria. Microbial biotechnology 2021.
- Rouches, E.; Gómez-Álvarez, H.; Majira, A.; Martín-Moldes, Z.; Nogales, J.; Díaz, E.; Bugg, T.; Baumberger, S. Assessment strategy for bacterial lignin depolymerization: Kraft lignin and synthetic lignin bioconversion with Pseudomonas putida. Bioresource Technology Reports 2021, 15, 100742.
- Gudmundsson, S.; Nogales, J. Recent advances in model-assisted metabolic engineering. Current Opinion in Systems Biology 2021, 28, 100392.
- García-Jiménez, B.; Torres-Bacete, J.; Nogales, J. Metabolic modelling approaches for describing and engineering microbial communities. Computational and Structural Biotechnology Journal 2021, 19, 226-246.
- Ballerstedt, H.; Tiso, T.; Wierckx, N.; Wei, R.; Averous, L.; Bornscheuer, U.; O’Connor, K.; Floehr, T.; Jupke, A.; Klankermayer, J. MIXed plastics biodegradation and UPcycling using microbial communities: EU Horizon 2020 project MIX-UP started January 2020. Environmental Sciences Europe 2021, 33 (1), 99.
- Sánchez-Clemente, R.; Guijo, M. I.; Nogales, J.; Blasco, R. Carbon source influence on extracellular pH changes along bacterial cell-growth. Genes 2020, 11 (11), 1292.
- Nogales, J.; Mueller, J.; Gudmundsson, S.; Canalejo, F. J.; Duque, E.; Monk, J.; Feist, A. M.; Ramos, J. L.; Niu, W.; Palsson, B. O. High‐quality genome‐scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities. Environmental microbiology 2020, 22 (1), 255-269.
- Moreno-Avitia, F.; Utrilla, J.; Bolívar, F.; Nogales, J.; Escalante, A. Metabolic reconstruction of Pseudomonas chlororaphis ATCC 9446 to understand its metabolic potential as a phenazine-1-carboxamide-producing strain. Applied Microbiology and Biotechnology 2020, 1-14.
- Manoli, M.-T.; Tarazona, N.; Mato, A.; Maestro, B.; Sanz, J. M.; Nogales, J.; Prieto, M. A. Molecular Basis of Medium-Chain Lenght-PHA Metabolism of Pseudomonas putida. The Handbook of Polyhydroxyalkanoates: Microbial Biosynthesis and Feedstocks 2020, 89.
- Lieven, C.; Beber, M. E.; Olivier, B. G.; Bergmann, F. T.; Ataman, M.; Babaei, P.; Bartell, J. A.; Blank, L. M.; Chauhan, S.; Correia, K. MEMOTE for standardized genome-scale metabolic model testing. Nature biotechnology 2020, 38 (3), 272-276.
- Herencias, C.; Salgado-Briegas, S.; Prieto, M. A.; Nogales, J. Providing new insights on the biphasic lifestyle of the predatory bacterium Bdellovibrio bacteriovorus through genome-scale metabolic modeling. Plos Computational Biology 2020, 16 (9), e1007646.
- Goris, T.; Pérez-Valero, Á.; Martínez, I.; Yi, D.; Fernández-Calleja, L.; San León, D.; Bornscheuer, U. T.; Magadán-Corpas, P.; Lombó, F.; Nogales, J. Repositioning microbial biotechnology against COVID-19: the case of microbial production of flavonoids. Microbial biotechnology 2020.
- García-Romero, I.; Nogales, J.; Díaz, E.; Santero, E.; Floriano, B. Understanding the metabolism of the tetralin degrader Sphingopyxis granuli strain TFA through genome-scale metabolic modelling. Scientific Reports 2020, 10 (1), 8651.
- Galán, B.; Santos-Merino, M.; Nogales, J.; De la Cruz, F.; García, J. L. Microbial oils as nutraceuticals and animal feeds. Health consequences of microbial interactions with hydrocarbons, oils, and lipids 2020, 401-445.
- Uluşeker, C.; Torres-Bacete, J.; García, J. L.; Hanczyc, M. M.; Nogales, J.; Kahramanoğulları, O. Quantifying dynamic mechanisms of auto-regulation in Escherichia coli with synthetic promoter in response to varying external phosphate levels. Scientific reports 2019, 9 (1), 2076.
- Molina, L.; Rosa, R. L.; Nogales, J.; Rojo, F. Pseudomonas putida KT2440 metabolism undergoes sequential modifications during exponential growth in a complete medium as compounds are gradually consumed. Environmental microbiology 2019, 21 (7), 2375-2390.
- Molina, L.; La Rosa, R.; Nogales, J.; Rojo, F. Influence of the Crc global regulator on substrate uptake rates and the distribution of metabolic fluxes in Pseudomonas putida KT2440 growing in a complete medium. Environmental microbiology 2019, 21 (11), 4446-4459.
- Campaña, A. R.; Bacete, J. T.; Enrique, J. N. Engineering self-regulated synthetic gene expression systems and its application on controlled protein expression. Biosaia: Revista de los másteres de Biotecnología Sanitaria y Biotecnología Ambiental, Industrial y Alimentaria 2019,(8).
- MARTIN-MOLDES, Z.; SANZ, D.; NOGALES, J.; CARMONA, M.; DIAZ, E. Anaerobic Pathways for the Catabolism of Aromatic Compounds. Lignin Valorization: Emerging Approaches 2018, 19, 333.
- García-Jiménez, B.; García, J. L.; Nogales, J.FLYCOP: metabolic modeling-based analysis and engineering microbial communities. Bioinformatics 2018, 34 (17), i954-i963.
- Durante-Rodríguez, G.; Gómez-Álvarez, H.; Nogales, J.; Carmona, M.; Díaz, E. One-component systems that regulate the expression of degradation pathways for aromatic compounds. Cellular Ecophysiology of Microbe: Hydrocarbon and Lipid Interactions 2018, 137-175.
- Armstrong, R.; Ieropoulos, I.; Wallis, L.; You, J.; Nogales, J. Living Architecture: Metabolic applications for next-generation, selectively-programmable bioreactors. 2018.
- Uluşeker, C.; Torres, J.; García, J. L.; Hanczyc, M. M.; Nogales, J.; Kahramanoğulları, O. A dynamic model of the phosphate response system with synthetic promoters in Escherichia coli. In Artificial Life Conference Proceedings, 2017; MIT Press One Rogers Street, Cambridge, MA 02142-1209, USA journals-info …: pp 412-419.
- Pérez-Regidor, L.; Guzmán-Caldentey, J.; Rodríguez, C. F.; Billod, J.-M.; Nogales, J.; Martín-Santamaría, S. Current Challenges in the Computational Modelling of Molecular Recognition Processes. 2017.
- Nogales, J.; Gudmundsson, S.; Duque, E.; Ramos, J. L.; Palsson, B. O. Expanding the computable reactome in Pseudomonas putida reveals metabolic cycles providing robustness. BioRxiv 2017, 139121.
- Nogales, J.; García, J. L.; Díaz, E. Degradation of aromatic compounds in Pseudomonas: a systems biology view. Aerobic utilization of hydrocarbons, oils and lipids 2017, 1-49.
- Nogales, J. A practical protocol for genome-scale metabolic reconstructions. Hydrocarbon and Lipid Microbiology Protocols: Genetic, Genomic and System Analyses of Pure Cultures 2017, 197-221.
- Morillas, C. M.; Enrique, J. N.; Delgado, J. G. H. Genome-Scale in silico Reconstruction of the Reactive Oxygen Species (ROS) Generating Metabolism in Pseudomonas putida KT2440 and Study of the role of ROS in Different Metabolic Processes. Biosaia: Revista de los másteres de Biotecnología Sanitaria y Biotecnología Ambiental, Industrial y Alimentaria 2017, (6).
- Molina-García, L.; Moreno-del Álamo, M.; Botias, P.; Martín-Moldes, Z.; Fernández, M.; Sánchez-Gorostiaga, A.; Alonso-del Valle, A.; Nogales, J.; García-Cantalejo, J.; Giraldo, R. Outlining core pathways of amyloid toxicity in bacteria with the RepA-WH1 prionoid. Frontiers in microbiology 2017, 8, 255718.
- Gudmundsson, S.; Agudo, L.; Nogales, J. Applications of genome-scale metabolic models of microalgae and cyanobacteria in biotechnology. In Microalgae-based biofuels and bioproducts, Woodhead Publishing, 2017; pp 93-111.
- Armstrong, R.; Ferracina, S.; Caldwell, G.; Ieropoulos, I.; Rimbu, G.; Adamatzky, A.; Phillips, N.; De Lucrezia, D.; Imhof, B.; Hanczyc, M. M. Living architecture (LIAR): metabolically engineered building units. Cultivated building materials 2017, 168-175.
- Armstrong, R.; Caldwell, G. S.; Ferracina, S.; Adamatzky, A.; Ieropoulos, I. A.; Nogales, J.; Garcia, J. L.; Imhof, B.; Hoheneder, W.; De Lucrezia, D. Living architecture: A modular and programmable synthetic ecosystem for the built environment. In Proceedings of the British Phycological Society annual meeting 2017, 2017.