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I'm head of the Sequence Analysis and Structure Prediction Service at the CNB-CSIC and senior researcher in the Computational Systems Biology Group
Centro Nacional de Biotecnologia (CNB-CSIC)
Darwin 3
28049 Madrid, Spain
Tel: +34 915854676


Biotechnology uses cellular and biomolecular processes to develop technologies and products that improve the quality of our life. However, in contrast to other technological areas, we are still very far for understanding how biological organisms work.

Working in a biotechnology research ceter, my goal is to study the functional organization of cells at the molecular level using computational approaches. I study the functions and interactions of proteins and chemical compounds in the cell from a systems biology persepective. I'm specially interested in the study of cellular dysfunctions that lead to human disease.

My current research focuses on the functional study of molecular networks, with two applications:
  • Systems biomedicine
  • Chemical biology and metabolomics
I've also developed computational methods and tools in the area of:
  • Functional bioinformatics
  • Integrated data analysis
  • Biological data management



Practical Protein Bioinformatics Pazos F and Chagoyen M
Practical Protein Bioinformatics
2015, Springer

ISBN 978-3-319-12726-2 (Hardcover)
ISBN 978-3-319-12727-9 (eBook)

[More info]

Articles in international journals

Hervas M, Navajas R, Chagoyen M, Garcia JA, Martinez-Turiño S
Phosphorylation-related cross-talk between distant regions of the core region of the coat protein contributes to virion assembly of Plum Pox virus
Mol Plant Microbe Interact. 2019 (Epub) [PubMed] [Full article]

Brown P, RELISH Consortium, Y Zhou
Large expert-curated database for benchmarking document similarity detection in biomedical literature search
Database. 2019 baz085 [Full article]

Chagoyen M, Ranea JA, Pazos F
Applications of molecular networks in biomedicine
Biology Methods and Protocols. 2019 4(1):bpz012 [Full article]

Pazos F, Chagoyen M
Characteristics and evolution of the ecosystem of software tools supporting research in molecular biology
Briefings in Bioinformatics. 2019 20(4):1329[PubMed] [Full article]

Chagoyen M, Poyatos JF
Complex genetic and epigenetic regulation deviates gene expression from a unifying global transcriptional program
PLoS Computational Biology. 2019 15(9):e1007353 [PubMed] [Full article]

Vallejo-Diaz J, Chagoyen M, Olazabal-Moran M, Gonzalez-Garcia A, Carrera AC
The Opposing Roles of PIK3R1/p85α and PIK3R2/p85β in Cancer
Trends in Cancer. 2019 5:233-244 [PubMed] [Full article]

Lopez-Ibañez J, Martin LT, Chagoyen M, Pazos F
Bacterial Feature Finder (BaFF)-a system for extracting features overrepresented in sets of prokaryotic organisms
Bioinformatics. 2019 35:3482 [PubMed] [Full article] [Web Server]

Gonzalez-Perez S, Pazos F, Chagoyen M
Factors affecting interactome-based prediction of human genes associated with clinical signs
BMC Bioinformatics. 2017 18:340 [PubMed] [Full article]

Lopez-Ibañez J, Pazos F, Chagoyen M
MBROLE 2.0 - functional enrichment of chemical compounds
Nucleic Acids Res. 2016 44(W1):W201-W204 [PubMed] [Full article] [Web server]

Fernandez-Novo S, Pazos F, Chagoyen M
Rare disease relations through common genes and protein interactions
Mol Cell Probes. 2016 30:178-181 [PubMed] [Full article] [Web server]

Chagoyen M, Pazos F
Characterization of clinical signs in the human interactome
Bioinformatics. 2016 32:1761-1765 [PubMed] [Full article]

Chagoyen M, Garcia-Martin JA, Pazos F
Practical analysis of specificity-determining residues in protein families
Brief Bioinform. 2016 17(2):255-61.[PubMed] [Full article]

Carvajal N, Martinez-Garcia M, Chagoyen M, Morcillo N, Pino A, Lorda I, Trujillo-Tiebas MJ
Clinical, genetics and bioinformatics characterization of a campomelic dysplasia case report
Gene. 2016 577(2):289-92. [PubMed] [Full article]

Buey RM, Ledesma-Amaro R, Velázquez-Campoy A, Balsera M, Chagoyen M, de Pereda JM, Revuelta JL
Guanine nucleotide binding to the Bateman domain mediates the allosteric inhibition of eukaryotic IMP dehydrogenases
Nat Commun. 2015 6:8923 [PubMed] [Full article]

Chevalier F, Nieminen K, Sanchez-Ferrero JC, Rodriguez ML, Chagoyen M, Hardtke CS, Cubas P
Strigolactone promotes degradation of DWARF14, an α/β hydrolase essential for strigolactone signaling in Arabidopsis
Plant Cell. 2014 26(3):1134-50 [PubMed] [Full article]

de Lucas S, Oliveros JC, Chagoyen M, Ortin J
Functional signature for the recognition of specific target mRNAs by human Staufen1 protein
Nucleic Acids Res. 2014 42(7):4516-26 [PubMed] [Full article]

Chagoyen M, Carrascosa JL, Pazos F, Valpuesta JM
Molecular determinants of the ATP hydrolysis asymmetry of the CCT chaperonin complex
Proteins. 2014 82:703-707 [PubMed] [Full article]

Cuervo A, Chagoyen M, Pulido-Cid M, Camacho A, Carrascosa JL
Structural characterization of T7 tail machinery reveals a conserved tubular structure among other Podoviridae family members and suggests a common mechanism for DNA delivery
Bacteriophage. 2013 3:e27011 [Full article]

Chagoyen M, Pazos F
Tools for the functional interpretation of metabolomic experiments
Briefings in Bioinformatics. 2013 14: 737-744 [PubMed] [Full article]

Cuervo A, Pulido-Cid M, Chagoyen M, Arranz R, Gonzalez-Garcia VA, Garcia-Doval C, Caston JR, Valpuesta JM, van Raaij MJ, Martin-Benito J, Carrascosa JL
Structural Characterization Of The Bacteriophage T7 Tail Machinery
J Biol Chem. 2013 288:26290-9 [PubMed] [Full article] [JBC Cover] [JBC paper of the week]

Zurita E, Chagoyen M, Cantero M, Alonso R, Gonzalez-Neira A, Lopez-Jimenez A, Lopez-Moreno JA, Landel CP, Benitez J, Pazos F, Montoliu L
Genetic polymorphisms among C57BL/6 mouse inbred strains
Transgenic Research. 2011 20:481-9 [PubMed] [Full article]

Chagoyen M, Pazos F
MBRole: enrichment analysis of metabolomic data
Bioinformatics. 2011 27:730-731 [PubMed] [Full article] [Web server]

Kumar A, Redondo-Muñoz J, Perez-Garcia V, Cortes I, Chagoyen M, Carrera AC
Nuclear but not cytosolic phosphoinositide 3-kinase Beta has an essential function in cell survival
Mol Cell Biol. 2011 31:2122-33 [PubMed] [Full article]

Chagoyen M, Pazos F
Quantifying the Biological Significance of Gene Ontology Biological Processes - Implications for the Analysis of Systems-wide data
Bioinformatics. 2010 26:378-384 [PubMed] [Full article]

Vazquez M, Carmona-Saez P, Nogales-Cadenas R, Chagoyen M, Tirado F, Carazo JM,  Pascual-Montano A
SENT: semantic features in text
Nucleic Acids Research. 2009 37:W153-9. [PubMed] [Full article]

Chagoyen M, Carazo JM,  Pascual-Montano A
Assessment of protein set coherence using functional annotations
BMC Bioinformatics. 2008 9:444. [PubMed] [Full article] [Project Web]

Carmona-Saez P, Chagoyen M, Tirado F, Carazo JM,  Pascual-Montano A
GENECODIS: A web-based tool for finding significant concurrent annotations in gene lists
Genome Biology. 2007 8:R3. [PubMed] [Full article] [Software]

Pascual-Montano A, Carmona-Saez P, Chagoyen M, Tirado F, Carazo JM,  Pascual-Marqui RD.
bioNMF: A versatile tool for non-negative matrix factorization in biology
BMC Bioinformatics. 2006 7(1):366. [PubMed] [Full article]

Chagoyen M, Carmona-Saez P, Gil C, Carazo JM, Pascual-Montano A.
A literature-based similarity metric for biological processes
BMC Bioinformatics. 2006 7(1):363. [PubMed] [Full article] [Project Web]

Carmona-Saez P, Chagoyen M, Rodriguez A, Trelles O, Carazo JM, Pascual-Montano A.
Integrated analysis of gene expression by association rules discovery
BMC Bioinformatics. 2006 7(1):54. [PubMed] [Full article] [Project Web]

Chagoyen M, Carmona-Saez P, Shatkay H, Carazo JM, Pascual-Montano A.
Discovering semantic features in the literature: a foundation for building functional associations
BMC Bioinformatics. 2006 7(1):41. [PubMed] [Full article] [Project Web]

Heymann JB, Chagoyen M, Belnap DM.
Common conventions for interchange and archiving of three-dimensional electron microscopy information in structural biology
J Struct Biol. 2005 151(2):196-207. [PubMed]

Chagoyen M, Kurul ME, De-Alarcon PA, Carazo JM, Gupta A.
Designing and executing scientific workflows with a programmable integrator
Bioinformatics. 2004 20(13):2092-100. [PubMed] [Full article]

Henrick K, Newman R, Tagari M, Chagoyen M.
EMDep: a web-based system for the deposition and validation of high-resolution electron microscopy macromolecular structural information
J Struct Biol. 2003 144(1-2):228-37. [PubMed]

Jimenez-Lozano N, Chagoyen M, Cuenca-Alba J, Carazo JM.
FEMME database: topologic and geometric information of macromolecules
J Struct Biol. 2003 144(1-2):104-13. [PubMed]

Tagari M, Newman R, Chagoyen M, Carazo JM, Henrick K.
New electron microscopy database and deposition system
Trends Biochem Sci. 2002 27(11):589. [PubMed]

Kalko SG, Chagoyen M, Jimenez-Lozano N, Verdaguer N, Fita I, Carazo JM.
The need for a shared database infrastructure: combining X-ray crystallography and electron microscopy
Eur Biophys J. 2000 29(6):457-62. [PubMed]

Lindek S, Fritsch R, Machtynger J, de Alarcon PA, Chagoyen M.
Design and realization of an on-line database for multidimensional microscopic images of biological specimens
J Struct Biol. 1999 125(2-3):103-11. [PubMed]

Carazo JM, Stelzer EH, Engel A, Fita I, Henn C, Machtynger J, McNeil P, Shotton DM, Chagoyen M, de Alarcon PA, Fritsch R, Heymann JB, Kalko S, Pittet JJ, Rodriguez-Tome P, Boudier T.
Organising multi-dimensional biological image information: the BioImage Database
Nucleic Acids Res. 1999 27(1):280-3. [PubMed] [Full article]

Marco S, Chagoyen M, de la Fraga LG, Carazo JM, Carrascosa JL.
A variant to the ‘Random Approximation’ of the reference-free algorithm
. 1996 66(1-2):5-10. [Full article]

Conference proceedings and book chapters

Chagoyen M, Lopez-Ibañez J, Pazos F.
Functional Analysis of Metabolomics Data.
Data Mining Techniques for the Life Sciences. 2016; 1415:399-406.
Springer-Verlag doi: 10.1007/978-1-4939-3572-7_20 [Springer Link]

Vazquez M, Chagoyen M, Pascual-Montano A.
Named entity recognition and normalization: A domain-specific language approach
Advances in Soft Computing. 2009; 147-155
Springer-Verlag. ISBN 978-354085860-7 [Springer Link]

Neves M, Chagoyen M, Carazo JM, Pascual-Montano A.
CBR-Tagger: a case-based reasoning approach to the gene/protein mention problem
BioNLP '08 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing. 2008; 108-109
ISBN 978-1-932432-11-4 [ACM DL] [Full document]

Chagoyen M, Fernandes H, Carazo JM, Pascual-Montano A.
Functional classification of genes using non-negative independent component analysis
Bonilla LL, Moscoso M, Platero G, et al. (Eds)
Springer-Verlag. ISBN 978-3-540-71991-5 [Springer Link]

Sanchez-Alberca A, Garcia-Garcia R, Sorzano COS, Gutierrez-Cossio C, Chagoyen M, Lopez, MF.
AMON: A software system for automatic generation of ontology mappings
2005 Portuguese Conference on Artificial Intelligence, Proceedings. 2005; 120-127
IEEE. ISBN 978-0-7803-9365-3 [IEEE Xplore]

Jimenez-Lozano N, Chagoyen M, de-Alarcon PA, Carazo JM.
Extracting and searching for structural information: a multiresolution approach
Methods in Protein and Proteome Analysis. 2004; 341-358
Kamp RM, Calvete JJ, Choli-Papadopoulou T (Eds).
Springer-Verlag. ISBN 3-540-20222-6 [Springer Link]

Chagoyen M, Kurul, ME, de-Alarcon PA, Santini, S, Ludascher, B, Carazo JM, Gupta A.
A semantic mediation approach for problems in computational molecular biology
IEEE Computer Soc. ISBN 0-7695-2000-6 [IEEE Xplore]

Carazo JM, de Alarcon PA, Chagoyen M
Image databases: What are they and what do they bring to microscopy
Microscopy and Microanalysis. 2003; 9(S02): 1570-1571 [Cambridge Journals]

Cristobal G, Chagoyen M, Escalante-Ramirez B, Lopez JR
Wavelet-based denoising methods. A comparative study with applications in microscopy
ISBN 0-8194-2213-4 [SPIE DL]

Other scientific documents

Chagoyen M.
Integration of biological data: systems, infrastructures and programmable tools. PhD. Thesis
Escuela Politecnica Superior. Universidad Autonoma Madrid, Spain. May, 2005
[Full document]

Chagoyen M.
Mejora y evaluacion de la calidad de imagenes mediantes metodos de representacion multiescala.
Proyecto Fin de Carrera (Master Thesis)
E.T.S. Ingenieros de Telecomunicacion. Universidad Politecnica de Madrid, Spain. May, 1996

Selected projects

BIOIMAGE A european database of biological volume images (1996-1999) - EU Research Project
IIMS Integration of information about macromolecular structure (2000-2003) - EU Researh Project
TEMBLOR The European Molecular Biology linked resources (2002-2005) - EU Research Project
EMBRACE A european model for bioinformatics research and community education (2005-2010) - EU Research Project