Systems biomedicine 

Research

Our group is interested in computational data analysis in systems biomedicine, focusing primarily on the study of rare diseases. Most of these diseases present significant alterations in the nervous system, highlighting the need to study them with a deep understanding of neurobiology. We approach the systemic study of these diseases through the integrated analysis of multi-omics data (such as molecular networks and transcriptional data, with a special focus on single-cell data) and clinical data.

We address the following fundamental in-silico questions: What can data from healthy tissues (from adults, developmental animal models, and organoids) tell us about the alterations that occur in pathological situations? Can we computationally characterize these known pathological processes? Which cell types and subtypes are affected? Given the central role of the nervous system in organismal homeostasis, which manifestations are primary and which are secondary to the etiology of the disease? Can these analyses aid in the discovery of new genes and molecular mechanisms in undiagnosed patients?

Team 

Mónica Chagoyen

Principal Investigator

Alicia Lou Gracia

Predoctoral researcher

Jorge Novoa Rodríguez

Predoctoral researcher

Alejandro Rodríguez Sancho

TFM Student

Pablo Miguel López

TFG Student

Publications of the last 10 years

• Alias-Segura S, Pazos F, Chagoyen M. Differential expression and co-expression reveal cell types relevant to genetic disorder phenotypes Bioinformatics 2024 40(11):btae646 DOI: 10.1093/bioinformatics/btae646
• Garrido-Romero M, Pazos F, Sánchez-Martínez E, Benito C, Gómez-Ruiz JÁ, 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, Merten C, Montilla A, Muñoz-Labrador A, Novoa J, Paraskevopoulos K, Payen C, Withers H, Ruas-Madiedo P, Ruiz L, Sanz Y, Jiménez-Saiz R, Moreno FJ. Relevance of gut microbiome research in food safety assessment. Gut Microbes 2024 16(1):2410476 DOI: 10.1080/19490976.2024.2410476
• Novoa J, López-Ibáñez J, Chagoyen M, Ranea JAG, Pazos F. CoMentG: comprehensive retrieval of generic relationships between biomedical concepts from the scientific literature Database (Oxford) 2024 2:2024:baae025 DOI: 10.1093/database/baae025
• Lopez-Ibañez J, Pazos F, Chagoyen M. MBROLE3: improved functional enrichment of chemical compounds for metabolomics data analysis. Nucleic Acids Research 2023 DOI: 10.1093/nar/gkad405
• 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 DOI: 10.3390/antiox12061274
• 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 DOI: 10.3390/genes14040942
• 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 DOI: 10.3390/nu14194127
• 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 2022 Jun 17;13(6):1081. DOI: 10.3390/genes13061081
• Pazos F, Chagoyen M, Seoane P, Ranea JAG. CoMent: Relationships Between Biomedical Concepts Inferred From the Scientific Literature. J Mol Biol. 2022 Jun 15;434(11):167568. DOI: 10.1016/j.jmb.2022.167568
• Lopez-Ibañez J, Pazos F, Chagoyen M. Predicting biological pathways of chemical compounds with a profile-inspired approach BMC Bioinformatics 2021 22:320 DOI: 10.1186/s12859-021-04252-y
• 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 DOI: 10.1007/s00439-020-02214-7
• 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):653-667 DOI: 10.1094/mpmi-10-19-0305-r
• Brown P, RELISH Consortium, Y Zhou. Large expert-curated database for benchmarking document similarity detection in biomedical literature search. Database. 2019 baz085 DOI: 10.1093/database/baz085
• Chagoyen M, Ranea JA, Pazos F. Applications of molecular networks in biomedicine. Biology Methods and Protocols. 2019 4(1):bpz012 DOI: 10.1093/biomethods/bpz012
• 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 DOI: 10.1093/bib/bby001
• 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 DOI: 10.1371/journal.pcbi.1007353
• 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 DOI: 10.1093/bioinformatics/btz099
• 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 DOI: 10.1016/j.trecan.2019.02.009
• Gonzalez-Perez S, Pazos F, Chagoyen M. Factors affecting interactome-based prediction of human genes associated with clinical signs. BMC Bioinformatics. 2017 18:340 DOI: 10.1186/s12859-017-1754-1
• Lopez-Ibañez J, Pazos F, Chagoyen M. MBROLE 2.0 – Functional enrichment of chemical compounds. Nucleic Acids Res 2016 44(W1):W201-W204 DOI: 10.1093/nar/gkw253
• Chagoyen M and Pazos F. Characterization of clinical signs in the human interactome. Bioinformatics 2016 32:1761-1765 DOI: 10.1093/bioinformatics/btw054
• Fernandez-Novo S, Pazos F, Chagoyen M. Rare disease relations through common genes and protein interactions. Mol Cell Probes. 2016 30:178-181 DOI: 10.1016/j.mcp.2016.03.004
• Chagoyen M, García-Martín JA, Pazos F. Practical analysis of specificity-determining residues in protein families. Brief Bioinform. 2016 17(2):255-61 DOI: 10.1093/bib/bbv045
• Chagoyen M, López-Ibáñez J, Pazos F. Functional analysis of metabolomics data. Methods in Mol Biol 2016 1415:399-406 DOI: 10.1007/978-1-4939-3572-7_20
• Carvajal N, Martínez-García 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 DOI: 10.1016/j.gene.2015.11.039

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