Juan Nogales
Juan Nogales




Dr. Juan Nogales is currently a Junior PI (JIN) whose work is focused on deciphering the multidimensionality of microbial metabolism, its evolutionary and biotechnological implications. Juan joined to emCIB lab in 2013 where he has developed a genome-scale metabolic modeling platform and leads systems biology projects in the group. Currently he is PI and maximum responsible of RobDcode, a project focused on unravel the metabolic robustness in bacteria and LIAR, a project aimed to engineer synthetic microbial consortia as bio-sustainable building blocks for living architecture. He is cofounder of Darwin Bioprospecting Excellence, a biotech company aimed to offers bacterial solutions towards biosustainability.
















Workflow for system-level metabolic understanding and engineering at emCIBlab.



Juan received his MS in Biology and MS in Biochemistry from the University of Extremadura (1996-2002). His MS thesis was on the light-dependent regulation of the glyoxylate cycle in Chlamydomonas reinhardtii. During his PhD thesis in the CIB-CSIC (2004-2009) he explored the metabolic versatility of Pseudomonas putida towards aromatic compounds and its arising biotechnological applications, receiving his PhD in Biochemistry and Molecular Biology from the University Complutense of Madrid (Spain). Then, he delved into systems biology approaches towards system-level understanding of bacterial metabolism and its biotechnological space as postdoctoral researcher at University of Iceland (Iceland, 2010) and at University of California, San Diego (United States, 2011-2012) under the supervision of Prof Bernhard O. Palsson.



Research Articles



1. Ebrahim A, Almaas E, Bauer E, Bordbar A, Burgard AP, Chang RL, Dräger A, Famili I, Feist AM, Fleming RMT, Fong SS, Hatzimanakis V, Herrgård MJ, Holder A, Hucka, M, Hyduke D, Jamshidi N, Lee SYup, Le Novère N, Lerman JA, Lewis NE, Ma D, Mahadevan R, Maranas C, Nagarajan H, Navid A, Nielsen J, Niels LK, Nogales J, Noronha A, Pal C, Palsson BØ, Papin JA, Patil KR, Price ND, Reed JL, Saunders M, Senger RS, Sonnenschein N, Sun Y, Thiele I. Do Genome-scale Models Need Exact Solvers or Clearer Standards?. Mol Syst Biol, 2015. 11 (10), 831.

2. Martín-Moldes Z, Zamarro MT, del Cerro C, Valencia A, Gómez MJ, Arcas A, Udaondo Z, García JL, Nogales J, Carmona M, Díaz E. Whole-genome analysis of Azoarcus sp. strain CIB provides genetic insights to its different lifestyles and predicts novel metabolic features. Syst Appl Microbiol. 2015.

3. Latif H, Sahin M, Tarasova J, Tarasova Y, Portnoy V, Nogales J, Zengler K. Adaptive evolution of Thermotoga maritima reveals plasticity of the ABC transporter network. Appl. Environ Microbiol, 2015. 01365-15

4. La Rosa R, Nogales J, Rojo F. The Crc/CrcZ-CrcY global regulatory system helps the integration of gluconeogenic and glycolytic metabolism in Pseudomonas putida. Environ Microbiol, 2015 (DOI: 10.1111/1462-2920.12812)

5. El-Said Mohamed M, García JL, Martínez, I, del Cerro C, Nogales J, Díaz E. Genome Sequence of Pseudomonas azelaica Strain Aramco J. Genome Announc. 2015 Apr 30 e00037-15

6. Gudmundsson S, Nogales J. Cyanobacteria as photosynthetic biocatalysts: a systems biology perspective. Mol Biosyst. 2015 Jan 2;11(1):60-70.


1. *Monk J,*Nogales J, Palsson BO. (*Equal contribution) Optimizing genome-scale network reconstructions. Nat Biotechnol. 2014 May;32(5):447-52.

2. García JL, Rozas D, Del Cerro C, Nogales J, El-Said Mohamed M, Díaz E. Genome Sequence of Pseudomonas azelaica HBP1, Which Catabolizes 2-Hydroxybiphenyl Fungicide. Genome Announc. 2014 Feb 13;2(1).


1. Nagarajan H, Sahin M, Nogales J, Latif H, Lovley DR, Ebrahim A, Zengler K. Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii. Microb Cell Fact. 2013 Nov 25;12:118.

2. Díaz E, Jiménez JI, Nogales J. Aerobic degradation of aromatic compounds. Curr Opin Biotechnol. 2013 24 (3), 431-442.

3. Nogales J, Gudmunsson S, Thiele I. Toward systems metabolic engineering in cyanobacteria. Bioengineered. 2013 4(3):158-163.


1. Nogales J, Gudmunsson S, Thiele I. An in silico re-design of the metabolism in Thermotoga maritima for increased biohydrogen production. Int J Hydrogen Energ. 2012 Sep; 37(17):12205-18.

2. Nogales J, Gudmunsson S, Knight EM, Palsson BO, Thiele, I. Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis. PNAS. 2012 Feb 14;109(7):2678-83.


Previous work

1. Nogales J, Canales A, Jiménez-Barbero J, Serra B, Pingarrón JM, García JL, Díaz E. Unravelling the gallic acid degradation pathway in bacteria: the gal cluster from Pseudomonas putida. Mol Microbiol. 2011 Jan;79(2):359-74.

2. Nogales J, Palsson BØ, Thiele I. A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. BMC Syst Biol. 2008 Sep; 16;2:79.

3. Nogales J, Macchi R, Franchi F, Barzaghi D, Fernández C, García JL, Bertoni G, Díaz E. Characterization of the last step of the aerobic phenylacetic acid degradation pathway. Microbiology. 2007 Feb; 153(Pt 2):357-65.

4. Yuste L, Hervás AB, Canosa I, Tobes R, Jiménez JI, Nogales J, Pérez-Pérez MM, Santero E, Díaz E, Ramos JL, de Lorenzo V, Rojo F. Growth phase-dependent expression of the Pseudomonas putida KT2440 transcriptional machinery analysed with a genome-wide DNA microarray. Environ Microbiol. 2006 Jan; 8(1):165-77.

5. Nogales J, Canales A, Jiménez-Barbero J, García JL, Díaz E. Molecular characterization of the gallate dioxygenase from Pseudomonas putida KT2440: The prototype of a new subgroup of extradiol dioxygenases. J Biol Chem. 2005 Oct; 280(42):35382-90.

6. Nogales J, Guijo MI, Quesada A, Merchán F. Functional analysis and regulation of the malate synthase from Chlamydomonas reinhardtii. Planta. 2004 Jun; 219(2):325-31.


Book Chapters

1. Nogales J. and Agudo L. A practical protocol for integration of transcriptomics data into genome-scale metabolic reconstructions. Hydrocarbon and Lipids Microbiology Protocols. (Springer Protocols Handbooks) 2015.

2. Nogales J. A practical Protocol for Genome-Scale Metabolic Reconstruction. Hydrocarbon and Lipids Microbiology Protocols. (Springer Protocols Handbooks) 2014.

3. *Jiménez JI, *Nogales J, García JL, Díaz E. (*Equal contribution) A Genomic View of the Catabolism of Aromatic Compounds in Pseudomonas. Handbook of Hydrocarbon and Lipid Microbiology. 2010, Part 14, 1297-1325.



"GEnome-scale Metabolic REconstruction and analysis of Cyanobacteria: A systems biology approach towards full exploitation of their biotechnological applications". Sustainable Chemicals from Microalgae: Encompassing Biocrude through to Fine Chemicals.

The Royal Society of Chemistry. London, 19th November 2013.


PhD Dissertation (Spanish)

"Caracterización Molecular de la Ruta de Degradación de Ácido Gálico en Pseudomonas putida". University Complutense of Madrid. 2009.

Advisor: Dr. Eduardo Díaz Fernández.



Genome-scale models:

1. Pseudomonas putida.

-P. putida KT2440 (iJN746). Nogales et al 2008. mat, sbml

-P. putida F1 (iJN739). Nogales 2014. mat, sbml

2. Synechocystis sp. PCC 6803

- iJN678 version 1.1. Corrections to mass and charge balancing. Gudmundsson and Nogales 2015. mat, sbml

3. Thermotoga maritima

- iTZ479_v2. Nogales et al 2013. mat, sbml

4. Clostridium ljungdahlii

- iHN637. Nagarajan et al 2013. Heterotrophic conditions: mat, Autotrophic conditions: mat


Teaching material:

1. Master Biotecnología UCM_2016

- Power point presentations, theory1, theory2 and practices1, practices2.


- Excel templates for metabolic reconstructions, Toy model.


- Textbook E. coli model, mat.


-Supplementary resources.


PS: here, only good noise is allowed!!!

- Something for reading here

- Something for writing here

- Something for wet-lab working here

- Something for a successful cloning here

- Something for an impossible cloning here and here

- Something for everything here

- Something for students here

emCIB Lab


Juan Nogales

Junior PI Position