Institution: CNB

Research Groups: Systems Biotechnology Group

Position: Investigador Científico

Home page: https://systemsbiotechgroup.com/

Contact email: jnogales@cnb.csic.es

ORCID: https://orcid.org/0000-0002-4961-0833

BCB Committee: No committees assigned.

BCB Community: Mathematical modeling in computational biology, Omics data analysis and function, Bioinformatics tools, benchmarks and data visualization

BCB Tools: FLYCOP, Golden Standard

BCB Services: CNBio (CNB DNA Biofoundry)

Research topics: Microbial Communities, Model organisms, Non-model organisms, Biosystems Modeling, Metabolic modelling, Pathway analysis, Integrative Analysis, Network Biology, Pathway analysis, Deep Learning in Biology, Large language models, Machine Learning in Biology, Population genomics, Single-cell omics, Biological interpretation, Microbial communities, Amplicon Sequencing, Metagenomics, Metatranscriptomics, RNA Sequencing (RNA-seq), Single-cell (scRNA-seq), Analysis packages (R, Python, etc.)

Biography: My research focuses on multidisciplinary approaches to understanding microbial systems, ranging from the molecular characterization of key components (e.g., genes) and their interactions, to systems-level properties such as phenotype and metabolic robustness. The ultimate goal is to translate these insights into innovative applications.
I earned dual degrees in Biology and Biochemistry from the University of Extremadura (2003), where I received the Premio Extraordinario de Licenciatura. I hold a PhD in Molecular Biology from CIB-CSIC (2009) supervised by Prof. Eduardo Díaz, focused on aromatics acids degradation. From 2010 to 2013, I conducted postdoctoral research with Prof. Bernhard Palsson at the University of Iceland and UC San Diego, specializing in metabolic modelling, which led to several high-impact publications, e.g., Nature Biotechnology and PNAS. Back at CIB-CSIC (2013–2017), I developed the first genome-scale reconstruction and analysis platform in Spain. During this period, I was awarded a JIN project from the AEI and a FET-OPEN project from the EC as PI, establishing my independent research line on Systems Biotechnology. In 2016, I was offered a Ramón y Cajal fellowship (declined) and secured a tenured position at CSIC. I have led the Systems Biotechnology Group at CNB-CSIC since 2017, and in 2024, I was appointed Head of the Systems Biology Department. I have 3 sexenios (latest 2021) and 3 quinquenios (latest 2022), with 59 ISI-indexed publications: 49 research articles (43 Q1, 11 first author, 13 corresponding), 10 reviews (Q1, 4 corresponding), and 12 book chapters. My work has received over 4,300 citations, with an average of 59.7 citations/article and an H-index of 31 (Google Scholar). I have supervised 3 PhD theses (7 ongoing), 12 MSc theses, and teach in 6 Master’s programs.
As PI, I have led 18 research projects (8 international, 2 as coordinator, 10 national) and 4 private contracts (BIOPOLIS, ERCROS, MOA FOOD, REPSOL), securing €3.74M (international), €1.68M (national), and €370K (private). I serve as Scientific Lead of the CNB DNA Biofoundry (CNBIO), a CSIC core facility, and am part of the CSIC IBISBA core, contributing to European R&D&I infrastructure in industrial biotechnology. I am founding member of the SusPlast Platform (sustainable plastics and circular economy) and participate in several national and international networks, including Life-Hub, BCB, and Microbiome Connections, SynCell and Flavo-Green. Additionally, I am co-inventor of 2 PCT-extended patents and co-founder of two start-ups: Darwin Bioprospecting Excellence and Biodriven Technologies SL.

Publications
Displayed publications: 0

There are no ORCID publications associated with this user.


Funding:
  • FLAVO-GREEN: CSIC, LINCG25043. International. 01/07/2025–31/12/2027.
  • PROMISEANG: Horizon Europe, GA nº 101112378,. EU. 01/09/2023–31/08/2027.
  • DeCYPher: Horizon Europe, GA nº 101081782. EU. 01/09/2023–01/08/2027.
  • AMBIZIONE: CNB, CEX2023-001386-S. National. 01/06/2025–31/05/2029.
  • SAAMBA: MCIU/AEI/FEDER, CPP2023-010641. Industrial. 01/10/2024–01/09/2027.
  • Rob3D: MCI, PID2022-139247OB-I00. National. 01/09/2023–30/08/2026.
  • ZiRO: CSIC-REPSOL. Industrial. 01/04/2025-31/03/2026.
More info

Collaborating Companies: 1. Moa-FoodTech. https://www.moafoodtech.com/
2. Pharmamar. https://pharmamar.com/es/
3. Repsol. https://www.repsol.com/es/index.cshtml

Spin-off: 1. Biodriven Technologies. https://www.biodriventech.com/

Patents: 1. Recombinant Pseudomonas putida strains for the production of Polyhydroxyalkanoate. WO 2021/089636 A1
2. A procedure for continuous, growth-coupled and saline stress independent production of sucrose from CO2 using recombinant cyanobacteria strains. WO 2021/148693 A1.

Participation in:

Master Programs: 1. Máster Universitario en Ciudad y Arquitectura Sostenibles. Universidad de Sevilla. https://www.us.es/estudiar/que-estudiar/oferta-de-masteres/master-universitario-en-ciudad-y-arquitectura-sostenibles 2. Biotecnología Ambiental, Industrial y Alimentaria. Universidad Pablo de Olavide. https://www.upo.es/master/Master-Oficial-Biotecnologia-Ambiental-Industrial-y-Alimentaria/ 3. Máster Universitario en Biotecnología Industrial y Ambiental. Universidad Complutense de Madrid. https://www.ucm.es/biotecnologia-industrial-y-ambiental/ 4. MÁSTER UNIVERSITARIO EN BIOLOGÍA SINTÉTICA INTEGRATIVA. UIMP-CSIC. https://www.uimp.es/postgrado/estudios/fichaestudio.php?plan=P04H&any=2024-25&lan=es

National Research Networks: 1. Conexión-Vida (LifeHub-CSIC). https://lifehub.csic.es/ 2. PTI-Susplast-CSIC. Sustainable Plastics towards Circular Economy. pti-susplast.csic.es/ 3. Conexión Microbioma (Microbioma-CSIC). https://conexion-microbioma.csic.es/ 4. Industrial Biotechnology Innovation and Synthetic Biology Accelerator (IBISBA-ES) https://www.csic.es/es/investigacion/proyectos-de-investigacion/consolidacion-del-nodo-espanol-de-ibisba-infraestructura-europea-de-biotecnologia-industrial-y-biologia-sintetica

International Research Networks: 1. Industrial Biotechnology Innovation and Synthetic Biology Accelerator (IBISBA-ES) https://ibisba.eu/ 2. SynCell. European Cell Iniciative. https://syntheticcell.eu/community/juan-nogales/ 3. FlavoGreen. Red. Synthetic biology for sustainable development

Other Participation: national, international, csicconexion, csicpt