Lou, A., Chagoyen, M., & Poyatos, J. F. (2025). Cell atlases and the Developmental Foundations of the Phenotype. https://doi.org/10.1101/2025.01.20.633901

Alías-Segura, S., Pazos, F., & Chagoyen, M. (2024). Differential expression and co-expression reveal cell types relevant to genetic disorder phenotypes. Bioinformatics, 40(11). https://doi.org/10.1093/bioinformatics/btae646

Moreno, F. J., Pazos, F., Garrido‐Romero, M., Payen, C., Borrego‐Yaniz, G., Chagoyen, M., Corzo, N., Denis, M., Fablet, C., Fernández, M., Granja, A., Guinebretière, M., Guyard, M., Jiménez‐Saiz, R., Keita, A., Kerouanton, A., Márquez, A., Martín, J., Montilla, A., et al. (2024). Roadmap for the integration of gastro‐intestinal (GI) tract microbiomes (human and domestic animal) in risk assessments under EFSA’s remit [JB]. EFSA Supporting Publications, 21(2). https://doi.org/10.2903/sp.efsa.2024.EN-8597

Novoa, J., López-Ibáñez, J., Chagoyen, M., Ranea, J. A. G., & Pazos, F. (2024). CoMentG: comprehensive retrieval of generic relationships between biomedical concepts from the scientific literature. Database, 2024. https://doi.org/10.1093/database/baae025

Chagoyen, M., & Poyatos, J. F. (2024). Disentangling protein metabolic costs in human cells and tissues. PNAS Nexus, 4(1). https://doi.org/10.1093/pnasnexus/pgaf008

Garrido-Romero, M., Pazos, F., Sánchez-Martínez, E., Benito, C., Gómez-Ruiz, J. Á., Borrego-Yaniz, G., Bowes, C., Broll, H., Caminero, A., Caro, E., Chagoyen, M., Chemaly, M., Fernández-Dumont, A., Gisavi, H., Gkrintzali, G., Khare, S., Margolles, A., Márquez, A., Martín, J., … Moreno, F. J. (2024). Relevance of gut microbiome research in food safety assessment. Gut Microbes, 16(1). https://doi.org/10.1080/19490976.2024.2410476

Novoa, J., Chagoyen, M., Benito, C., Moreno, F. J., & Pazos, F. (2023). PMIDigest: Interactive Review of Large Collections of PubMed Entries to Distill Relevant Information. Genes, 14(4), 942. https://doi.org/10.3390/genes14040942

Neves, R. P. das, Chagoyen, M., Martinez-Lorente, A., Iñiguez, C., Calatrava, A., Calabuig, J., & Iborra, F. J. (2023). Each Cellular Compartment Has a Characteristic Protein Reactive Cysteine Ratio Determining Its Sensitivity to Oxidation. Antioxidants, 12(6), 1274. https://doi.org/10.3390/antiox12061274

Lopez-Ibañez, J., Pazos, F., & Chagoyen, M. (2023). MBROLE3: improved functional enrichment of chemical compounds for metabolomics data analysis. Nucleic Acids Research, 51(W1), W305–W309. https://doi.org/10.1093/nar/gkad405

Pazos, F., Chagoyen, M., Seoane, P., & Ranea, J. A. G. (2022). CoMent: Relationships Between Biomedical Concepts Inferred From the Scientific Literature. Journal of Molecular Biology, 434(11), 167568. https://doi.org/10.1016/j.jmb.2022.167568

Ranea, J. A. G., Perkins, J., Chagoyen, M., Díaz-Santiago, E., & Pazos, F. (2022). Network-Based Methods for Approaching Human Pathologies from a Phenotypic Point of View. Genes, 13(6), 1081. https://doi.org/10.3390/genes13061081

Fernández-Millán, E., Ramos, S., Álvarez-Cilleros, D., Samino, S., Amigó, N., Correig, X., Chagoyen, M., Álvarez, C., & Martín, M. Á. (2022). Urinary Metabolomics Study on the Protective Role of Cocoa in Zucker Diabetic Rats via 1H-NMR-Based Approach. Nutrients, 14(19), 4127. https://doi.org/10.3390/nu14194127

Lopez-Ibañez, J., Pazos, F., & Chagoyen, M. (2021). Predicting biological pathways of chemical compounds with a profile-inspired approach. BMC Bioinformatics, 22(1). https://doi.org/10.1186/s12859-021-04252-y

Hervás, M., Navajas, R., Chagoyen, M., García, J. A., & Martínez-Turiño, S. (2020). Phosphorylation-Related Crosstalk Between Distant Regions of the Core Region of the Coat Protein Contributes to Virion Assembly of Plum Pox Virus. Molecular Plant-Microbe Interactions®, 33(4), 653–667. https://doi.org/10.1094/mpmi-10-19-0305-r

Jabato, F. M., Seoane, P., Perkins, J. R., Rojano, E., García Moreno, A., Chagoyen, M., Pazos, F., & Ranea, J. A. G. (2020). Systematic identification of genetic systems associated with phenotypes in patients with rare genomic copy number variations. Human Genetics, 140(3), 457–475. https://doi.org/10.1007/s00439-020-02214-7

Brown, P., Tan, A.-C., El-Esawi, M. A., Liehr, T., Blanck, O., Gladue, D. P., Almeida, G. M. F., Cernava, T., Sorzano, C. O., Yeung, A. W. K., Engel, M. S., Chandrasekaran, A. R., Muth, T., Staege, M. S., Daulatabad, S. V., Widera, D., Zhang, J., Meule, A., … Zhou, Y. (2019). Large expert-curated database for benchmarking document similarity detection in biomedical literature search. Database, 2019. https://doi.org/10.1093/database/baz085

Chagoyen, M., Ranea, J. A. G., & Pazos, F. (2019). Applications of molecular networks in biomedicine. Biology Methods and Protocols, 4(1). https://doi.org/10.1093/biomethods/bpz012

Chagoyen, M., & Poyatos, J. F. (2019). Complex genetic and epigenetic regulation deviates gene expression from a unifying global transcriptional program. PLOS Computational Biology, 15(9), e1007353. https://doi.org/10.1371/journal.pcbi.1007353

González-Pérez, S., Pazos, F., & Chagoyen, M. (2017). Factors affecting interactome-based prediction of human genes associated with clinical signs. BMC Bioinformatics, 18(1). https://doi.org/10.1186/s12859-017-1754-1

Chagoyen, M., López-Ibáñez, J., & Pazos, F. (2016). Functional Analysis of Metabolomics Data. Data Mining Techniques for the Life Sciences, 399–406. https://doi.org/10.1007/978-1-4939-3572-7_20

Carvajal, N., Martínez-García, M., Chagoyen, M., Morcillo, N., Pino, A., Lorda, I., & Trujillo-Tiebas, M. J. (2016). Clinical, genetics and bioinformatics characterization of a campomelic dysplasia case report. Gene, 577(2), 289–292. https://doi.org/10.1016/j.gene.2015.11.039

Chagoyen, M., & Pazos, F. (2016). Characterization of clinical signs in the human interactome. Bioinformatics, 32(12), 1761–1765. https://doi.org/10.1093/bioinformatics/btw054

Fernandez-Novo, S., Pazos, F., & Chagoyen, M. (2016). Rare disease relations through common genes and protein interactions. Molecular and Cellular Probes, 30(3), 178–181. https://doi.org/10.1016/j.mcp.2016.03.004

Pazos, F., & Chagoyen, M. (2015). Practical Protein Bioinformatics. Springer International Publishing. https://doi.org/10.1007/978-3-319-12727-9

Buey, R. M., Ledesma-Amaro, R., Velázquez-Campoy, A., Balsera, M., Chagoyen, M., de Pereda, J. M., & Revuelta, J. L. (2015). Guanine nucleotide binding to the Bateman domain mediates the allosteric inhibition of eukaryotic IMP dehydrogenases. Nature Communications, 6(1). https://doi.org/10.1038/ncomms9923

Chagoyen, M., García-Martín, J. A., & Pazos, F. (2015). Practical analysis of specificity-determining residues in protein families. Briefings in Bioinformatics, 17(2), 255–261. https://doi.org/10.1093/bib/bbv045

Chagoyen, M., Carrascosa, J. L., Pazos, F., & Valpuesta, J. M. (2014). Molecular determinants of the ATP hydrolysis asymmetry of the CCT chaperonin complex. Proteins: Structure, Function, and Bioinformatics, 82(5), 703–707. Portico. https://doi.org/10.1002/prot.24510

de Lucas, S., Oliveros, J. C., Chagoyen, M., & Ortín, J. (2014). Functional signature for the recognition of specific target mRNAs by human Staufen1 protein. Nucleic Acids Research, 42(7), 4516–4526. https://doi.org/10.1093/nar/gku073

Cuervo, A., Pulido-Cid, M., Chagoyen, M., Arranz, R., González-García, V. A., Garcia-Doval, C., Castón, J. R., Valpuesta, J. M., van Raaij, M. J., Martín-Benito, J., & Carrascosa, J. L. (2013). Structural Characterization of the Bacteriophage T7 Tail Machinery. Journal of Biological Chemistry, 288(36), 26290–26299. https://doi.org/10.1074/jbc.m113.491209

Cuervo, A., Chagoyen, M., Pulido-Cid, M., Camacho, A., & Carrascosa, J. L. (2013). Structural characterization of T7 tail machinery reveals a conserved tubular structure among otherPodoviridaefamily members and suggests a common mechanism for DNA delivery. Bacteriophage, 3(4), e27011. https://doi.org/10.4161/bact.27011

Chagoyen, M., & Pazos, F. (2012). Tools for the functional interpretation of metabolomic experiments. Briefings in Bioinformatics, 14(6), 737–744. https://doi.org/10.1093/bib/bbs055

Kumar, A., Redondo-Muñoz, J., Perez-García, V., Cortes, I., Chagoyen, M., & Carrera, A. C. (2011). Nuclear but Not Cytosolic Phosphoinositide 3-Kinase Beta Has an Essential Function in Cell Survival. Molecular and Cellular Biology, 31(10), 2122–2133. https://doi.org/10.1128/mcb.01313-10

Chagoyen, M., & Pazos, F. (2011). MBRole: enrichment analysis of metabolomic data. Bioinformatics, 27(5), 730–731. https://doi.org/10.1093/bioinformatics/btr001

Zurita, E., Chagoyen, M., Cantero, M., Alonso, R., González-Neira, A., López-Jiménez, A., López-Moreno, J. A., Landel, C. P., Benítez, J., Pazos, F., & Montoliu, L. (2010). Genetic polymorphisms among C57BL/6 mouse inbred strains. Transgenic Research, 20(3), 481–489. https://doi.org/10.1007/s11248-010-9403-8

Chagoyen, M., & Pazos, F. (2009). Quantifying the biological significance of gene ontology biological processes—implications for the analysis of systems-wide data. Bioinformatics, 26(3), 378–384. https://doi.org/10.1093/bioinformatics/btp663

Vazquez, M., Carmona-Saez, P., Nogales-Cadenas, R., Chagoyen, M., Tirado, F., Carazo, J. M., & Pascual-Montano, A. (2009). SENT: semantic features in text. Nucleic Acids Research, 37(Web Server), W153–W159. https://doi.org/10.1093/nar/gkp392

Chagoyen, M., Fernandes, H., Carazo, J. M., & Pascual-Montano, A. (2008). Functional Classification of Genes Using Non-Negative Independent Component Analysis. Progress in Industrial Mathematics at ECMI 2006, 571–575. https://doi.org/10.1007/978-3-540-71992-2_93

Neves, M., Chagoyen, M., Carazo, J. M., & Pascual-Montano, A. (2008). CBR-Tagger. Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing - BioNLP ’08, 108. https://doi.org/10.3115/1572306.1572333

Chagoyen, M., Carazo, J. M., & Pascual-Montano, A. (2008). Assessment of protein set coherence using functional annotations. BMC Bioinformatics, 9(1). https://doi.org/10.1186/1471-2105-9-444

Carmona-Saez, P., Chagoyen, M., Tirado, F., Carazo, J. M., & Pascual-Montano, A. (2007). GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists. Genome Biology, 8(1). https://doi.org/10.1186/gb-2007-8-1-r3

Carmona-Saez, P., Chagoyen, M., Rodriguez, A., Trelles, O., Carazo, J. M., & Pascual-Montano, A. (2006). Integrated analysis of gene expression by association rules discovery. BMC Bioinformatics, 7(1). https://doi.org/10.1186/1471-2105-7-54

Chagoyen, M., Carmona-Saez, P., Shatkay, H., Carazo, J. M., & Pascual-Montano, A. (2006). Discovering semantic features in the literature: a foundation for building functional associations. BMC Bioinformatics, 7(1). https://doi.org/10.1186/1471-2105-7-41

Pascual-Montano, A., Carmona-Saez, P., Chagoyen, M., Tirado, F., Carazo, J. M., & Pascual-Marqui, R. D. (2006). bioNMF: a versatile tool for non-negative matrix factorization in biology. BMC Bioinformatics, 7(1). https://doi.org/10.1186/1471-2105-7-366

Chagoyen, M., Carmona-Saez, P., Gil, C., Carazo, J. M., & Pascual-Montano, A. (2006). A literature-based similarity metric for biological processes. BMC Bioinformatics, 7(1). https://doi.org/10.1186/1471-2105-7-363

Heymann, J. B., Chagoyen, M., & Belnap, D. M. (2005). Common conventions for interchange and archiving of three-dimensional electron microscopy information in structural biology. Journal of Structural Biology, 151(2), 196–207. https://doi.org/10.1016/j.jsb.2005.06.001

Chagoyen, M., Kurul, M. E., De-Alarcón, P. A., Carazo, J. M., & Gupta, A. (2004). Designing and executing scientific workflows with a programmable integrator. Bioinformatics, 20(13), 2092–2100. https://doi.org/10.1093/bioinformatics/bth209

Jiménez-Lozano, N., Chagoyen, M., Cuenca-Alba, J., & Carazo, J. M. (2003). FEMME database: topologic and geometric information of macromolecules. Journal of Structural Biology, 144(1–2), 104–113. https://doi.org/10.1016/j.jsb.2003.09.014

Henrick, K., Newman, R., Tagari, M., & Chagoyen, M. (2003). EMDep: a web-based system for the deposition and validation of high-resolution electron microscopy macromolecular structural information. Journal of Structural Biology, 144(1–2), 228–237. https://doi.org/10.1016/j.jsb.2003.09.009

Tagari, M., Newman, R., Chagoyen, M., Carazo, J.-M., & Henrick, K. (2002). New electron microscopy database and deposition system. Trends in Biochemical Sciences, 27(11), 589. https://doi.org/10.1016/s0968-0004(02)02176-x

Carazo, J. M., Stelzer, E. H. K., Engel, A., Fita, I., Henn, C., Machtynger, J., McNeil, P., Shotton, D. M., Chagoyen, M., de Alarcon, P. A., Fritsch, R., Heymann, J. B., Kalko, S., Pittet, J. J., Rodriguez-Tome, P., & Boudier, T. (1999). Organising multi-dimensional biological image information: The BioImage Database. Nucleic Acids Research, 27(1), 280–283. https://doi.org/10.1093/nar/27.1.280

Lindek, S., Fritsch, R., Machtynger, J., de Alarcón, P. A., & Chagoyen, M. (1999). Design and Realization of an On-line Database for Multidimensional Microscopic Images of Biological Specimens. Journal of Structural Biology, 125(2–3), 103–111. https://doi.org/10.1006/jsbi.1999.4092

Cristobal, G., Chagoyen, M., Escalante-Ramirez, B., & Lopez, J. R. (1996). <title>Wavelet-based denoising methods: a comparative study with applications in microscopy</title> Wavelet Applications in Signal and Image Processing IV, 2825, 660–671. https://doi.org/10.1117/12.255299

Marco, S., Chagoyen, M., de la Fraga, L. G., Carazo, J. M., & Carrascosa, J. L. (1996). A variant to the “random approximation” of the reference-free alignment algorithm. Ultramicroscopy, 66(1–2), 5–10. https://doi.org/10.1016/s0304-3991(96)00083-6

Vazquez, M., Chagoyen, M., & Pascual-Montano, A. (n.d.). Named Entity Recognition and Normalization: A Domain-Specific Language Approach. 2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2008), 147–155. https://doi.org/10.1007/978-3-540-85861-4_18

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