Pablo Minguez's web page

Researcher @ Fundacion Jimenez Diaz (Madrid, Spain), former potsdoc @ EMBL (Bork Group, Heidelberg, Germany)

Scientific interests

My research interests focus on functional genomics, network studies, post-translational regulation, protein-protein interactions as well as interactions with other molecules.


I like the idea of seeing the cell as an intricate network of molecular interactions. The elements such as proteins, metabolites and other molecules and especially their interactions are the components that constitute the engine that make the biological systems work. The spatial and temporal components filter this scaffold resulting in the wide variability of cell behaviours.

Short CV

September 2015 - present
  Researcher at the Genetics and Genomcs Unit (University Hospital Fundacion Jimenez Diaz, Madrid, Spain)


September 2009 - January 2015
  Postdoctoral fellow at Bork group (EMBL - Heidelberg).


October 2008
  PhD in Molecular Biology (Bioinformatics). Universidad Autonoma de Madrid (Madrid, Spain).
  Thesis Title: Functional profiling of genome-scale experiments. New approaches leading to a systemic analysis. [Get pdf]


September 2004 - August 2009
  PhD student & Bridging postdoc. CIPF (Valencia, Spain). From September 2004 to March 2005 at CNIO (Madrid, Spain).


January 2004 - September 2004
  Bioinformatician. European Arabidopsis Stock Centre (University of Nottingham, UK).


September 2002 - October 2003
  MSc in Bioinformatics. University of East Anglia (Norwich, UK).


September 2000 - September 2001
  Postgraduate Certificate in Education (subject Biology and Geology). Universidad Complutense (Madrid, Spain).


September 1994 - February 2000
  BSc Biological Sciences (Microbiology and environmental biology). Universidad de Alcala (Madrid, Spain).

Selected Publications               [Complete list of publications]

Yu-Wei S, Minguez P, Bork P, Auburger JJ, Guilbride DL, Kramer G and Bukau B. "Operon structure and cotranslational subunit association direct protein assembly in bacteria" Science. 2015; DOI: 10.1126/science.aac8171   [Pubmed]  [Science]


Minguez P, Ivica L, Parca L, Garcia-Alonso L, Dopazo J, Huerta-Cepas J, Bork P. "PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins" Nucl. Acids Res. 2014; 1 doi: 10.1093/nar/gku1081   [Pubmed]  [NAR]  [pdf]


Minguez P*, Ivica L*, Parca L, Bork P. "PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins." Nucl. Acids Res. 2013;41(Database issue):D306-11   [Pubmed]  [NAR]  [pdf]


Minguez P, Parca L, Diella F, Mende DR, Kumar R, Helmer-Citterich M, Gavin AC, van Noort V, Bork P. "Deciphering a global network of functionally associated post-translational modifications" Molecular Systems Biology. 2012; 8:599.   [Pubmed]  [MSB]  [pdf]  [Supplementary material]


Minguez P, Dopazo J. "Assessing the biological significance of gene expression signatures and co-expression modules by studying their network properties" PLoS One. 2011; 6(3): e17474.  [Pubmed]  [PLoSOne]  [pdf]


Al-Shahrour F, Minguez P, Marques-Bonet T, Gazave E, Navarro A and Dopazo J. "Selection upon genome architecture: conservation of functional neighborhoods with changing genes" PLoS Computational Biology. 2010;6(10):e1000953.  [PubMed]  [PLoS CB]  


Minguez P, Dopazo J. "Functional genomics and networks: new approaches in the extraction of complex gene modules." Expert Rev Proteomics. 2010;7(1):55-63.   [PubMed]  [pdf]


Minguez P, Gotz S, Montaner D, Al-Shahrour F, Dopazo J. "SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks." Nucl. Acids Res. 2009;37:W109-114.   [PubMed]  [pdf]


Minguez P, Dopazo J. "Protein Interactions for Functional Genomics." In: Li X-L, Ng S-K, eds. Biological Data Mining in Protein Interaction Networks. Hershey, USA: Idea Group Inc (IGI); 2009.   [Google Books]  [pdf]


Horcajadas JA, Minguez P, Dopazo J, et al. "Controlled ovarian stimulation induces a functional genomic delay of the endometrium with potential clinical implications." J Clin Endocrinol Metab. 2008;93:4500-10.   [PubMed]  [pdf]


Minguez P, Al-Shahrour F, Montaner D, Dopazo J. "Functional profiling of microarray experiments using text-mining derived bioentities." Bioinformatics. 2007;23:3098-9.   [PubMed]  [pdf]


Minguez P, Al-Shahrour F, Dopazo J. "A function-centric approach to the biological interpretation of microarray time-series." Genome Inform. 2006;17:57-66   [PubMed]  [pdf]  [Sup mat.]


Al-Shahrour F, Minguez P, Tarraga J, et al. "BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments." Nucleic Acids Res. 2006;34:W472-6.   [PubMed]

Bioinformatics tools, software and resources

PTMcode

Database for known and predicted functional associations between protein post-translational modifications (PTMs).
[http://ptmcode.embl.de].


Snow (Studying Networks in the Omic World)

Extracts the protein-protein interaction networks behind a list of genes/proteins (signature) and evaluates its robutness against same-size networks generated from random lists of genes/proteins.
[http://snow.bioinfo.cipf.es].


Tissues Mining Tool

Finds tissues and tissue histologies in which two lists of genes display different distributions.
[http://www.babelomics.org].


MarmiteScan

Use chemical and disease related information to detect related blocks of genes in a gene list with associated values.
[http://www.babelomics.org].


Marmite

Finds differential distributions of bioentities extracted from PubMed between two groups of genes.
[http://www.babelomics.org].


AtEnsembl

The Arabidopsis thaliana Genome browser. [http://atensembl.arabidopsis.info].