[affiliation
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projects ]
AffiliationTenured scientist in the Computational Systems Biology Group at the CNB-CSIC |
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Contact: Centro Nacional de Biotecnologia (CNB-CSIC) Darwin 3 28049 Madrid, Spain |
Tel: +34 915854676 monica.chagoyen[x]cnb.csic.es |
Research | |
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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:
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Publications |
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Articles in international journals |
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Lopez-Ibañez J, Pazos F, Chagoyen M MBROLE3: improved functional enrichment of chemical compounds for metabolomics data analysis. Nucleic Acids Research 2023 [PubMed] [Full article] Neves RPD, Chagoyen M, Martinez-Lorente A, Iñiguez C, Calatrava A, Calabuig J, Iborra FJ Each Cellular Compartment Has a Characteristic Protein Reactive Cysteine Ratio Determining Its Sensitivity to Oxidation Antioxidants 2023 12(6):1274 [PubMed] [Full article] Novoa J, Chagoyen M, Benito C, Moreno FJ, Pazos F. PMIDigest: Interactive Review of Large Collections of PubMed Entries to Distill Relevant Information Genes 2023 14(4):942 [PubMed] [Full article] Fernandez-Millan E, Ramos S, Alvarez-Cilleros D, Samino S, Amigo N, Correig X, Chagoyen M, Alvarez C, Martín MA. Urinary Metabolomics Study on the Protective Role of Cocoa in Zucker Diabetic Rats via 1H-NMR-Based Approach Nutrients 2022 14(9):4127 [PubMed] [Full article] Ranea JAG, Perkins J, Chagoyen M, Díaz-Santiago E, Pazos F Network-Based Methods for Approaching Human Pathologies from a Phenotypic Point of View Genes(Basel) 2022 13(6):1081 [PubMed] [Full article] Pazos F, Chagoyen M, Seoane P, Ranea JAG CoMent: Relationships Between Biomedical Concepts Inferred From the Scientific Literature J Mol Biol. 2022 434(11):167568 [PubMed] [Full article] [CoMent Web Server] Lopez-Ibañez J, Pazos F, Chagoyen M Predicting biological pathways of chemical compounds with a profile-inspired approach BMC Bioinformatics 2021 22:320 [PubMed] [Full article] [iFragMent Web Server] Jabato FM, Seoane P, Perkins JR, Rojano E, García Moreno A, Chagoyen M, Pazos F, Ranea JAG Systematic identification of genetic systems associated with phenotypes in patients with rare genomic copy number variations Hum Genet. 2021 140(3):457 [PubMed] [Full article] 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. 2020 33(4):653 [PubMed] [Full article] Chagoyen M, Ranea JA, Pazos F Applications of molecular networks in biomedicine Biology Methods and Protocols. 2019 4(1):bpz012 [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 [PubMed] [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] [BaFF 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] [MBROLE 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] [ODCs 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] [GeneCodis Web Werver] 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] [Full Article] 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] [Full Article] 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] [Full Article] 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] [Full Article] 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] [Full Article] 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] [Full Article] 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 Ultramicroscopy. 1996 66(1-2):5-10. [Full article] |
Books |
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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] |
Book chapters and conference proceedingsPazos F, Chagoyen M.Network Analysis in Systems Biology. In: Cifientes, A (Ed). Comprehensive Foodomics. 2020; 2:434-445 Elsevier ISBN: 9780128163955 [Elsevier Link] 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 PROGRESS IN INDUSTRIAL MATHEMATICS AT ECMI 2006. 2008; 12:571-575 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 PROCEEDINGS OF THE 2003 IEEE BIOINFORMATICS CONFERENCE. 2003; 386-387 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 WAVELET APPLICATIONS IN SIGNAL AND IMAGE PROCESSING IV, PTS 1 AND 2. 1996; 2825:660-671 SPIE - INT SOC OPTICAL ENGINEERING. ISBN 0-8194-2213-4 [SPIE DL] |
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Other scientific documents |
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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 |
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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 |
