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Institution: CABD
Research Groups: Computational Biology and Bioinformatics (CBBIO.CABD)
Position: Investigadora Cientifica
Home page: http://bioinfocb.es
Contact email: a.rojas.m@csic.es
BCB Committee: Outreach
BCB Community: Diversity genomics, Bioinformatics tools, benchmarks and data visualization, Omics data analysis and function, Structural biology and molecular simulation
BCB Tools: FANTASIA (Functional ANnoTAtion based on embedding space SImilArity)
BCB Services: No services assigned.
Research topics: Applications of Computational Biology, Development, Model organisms, Non-model organisms, Functional genomics, Function prediction, Functional annotation, Pathway analysis, Molecular evolution, Conservation Analysis, Evolutionary rates, Phylogenetic Analysis, Sequence analysis, Mapping, Sequence Alignment, Sequence error correction, Structural bioinformatics, Molecular Interactions/Docking, Mutation Analysis and design, Structure prediction, Structure-function relationship, Artificial Intelligence, Deep Learning in Biology, Knowledge graphs, Large language models, Machine Learning in Biology, Structural genomics, Resources, FAIRfication, Bioinformatics Software and Tools, Analysis packages (R, Python, etc.)
Biography: Trained as a molecular microbiologist in Madrid and the U.S. (1999), she later specialized in bioinformatics and computational biology, working in several U.S. labs from 1999 to 2003. This includes a NASA-NSCORT fellowship at UCSD in R.F. Doolittle's lab and research in Adam Godzik's lab in La Jolla, CA. Between 2003 and 2006, she continued her work in Spain, holding a Marie Curie fellowship at the CNB-CSIC in the group led by Alfonso Valencia.
In 2006, she joined CNIO as a staff scientist and established her independent group in 2009 at the former IMPPC in Badalona. In 2013, she moved her group to the Institute of Biomedicine of Seville and later to the Andalusian Center for Developmental Biology (CABD) in Seville in 2018.
She has been Track Chair of the ISCB Function COSI since 2024, is a founding member of the Spanish Society of Computational Biology (SEBIBiC) founded in 2020, and serves on the executive committee of CSIC's BCBHub network for computational biologists (2023), among different commissions.
Her current research interests focus on understanding the relationships between sequence, structure, and function, particularly focusing on the multifunctional aspects of proteins relevant to biotechnology (biosensors) and biomedicine (therapeutic drugs) through AI-based techniques. She is also involved with the ENIA Chair at USE-Google Spain for AI.
In the past, she worked as a forensic biologist, bird watcher, and field microbiologist. She has named a bacterial species, Erwinia toletana sp. nov.
Publications
Cases, I., Martínez-Redondo, G., Fernández, R., & Rojas, A. M. (2025). Functional Annotation of Proteomes Using Protein Language Models: A High-Throughput Implementation of the ProtTrans Model. Large Language Models (LLMs) in Protein Bioinformatics, 127–137. https://doi.org/10.1007/978-1-0716-4623-6_8
Martínez-Redondo, G. I., Perez-Canales, F. M., Carbonetto, B., Fernández, J. M., Barrios-Núñez, I., Vázquez-Valls, M., Cases, I., Rojas, A. M., & Fernández, R. (2025). FANTASIA leverages language models to decode the functional dark proteome across the animal tree of life. Communications Biology, 8(1). https://doi.org/10.1038/s42003-025-08651-2
Valverde, S., Vidiella, B., Martínez-Redondo, G. I., Duran-Nebreda, S., Fernández, R., Bombarely, A., Rojas, A. M., & Bentley, R. A. (2025). Structural Changes in Gene Ontology Reveal Modular and Complex Representations of Biological Function. Molecular Biology and Evolution, 42(6). https://doi.org/10.1093/molbev/msaf148
Verdugo-Sivianes, E. M., Espinosa-Sánchez, A., Cases, I., Rojas, A. M., Otero-Albiol, D., Romero, L., Blanco, J. R., & Carnero, A. (2024). MEG8 as an antagonistic pleiotropic mechanism in breast cancer. Cell Death Discovery, 10(1). https://doi.org/10.1038/s41420-024-02272-0
Martínez-Redondo, G. I., Perez-Canales, F. M., Fernández, J. M., Barrios-Núñez, I., Vázquez-Valls, M., Cases, I., Rojas, A. M., & Fernández, R. (2024). Leveraging Natural Language Processing models to decode the dark proteome across the Animal Tree of Life. https://doi.org/10.1101/2024.02.28.582465
Barrios-Núñez, I., Martínez-Redondo, G. I., Medina-Burgos, P., Cases, I., Fernández, R., & Rojas, A. M. (2024). Decoding functional proteome information in model organisms using protein language models. NAR Genomics and Bioinformatics, 6(3). https://doi.org/10.1093/nargab/lqae078
Alegre-Martí, A., Jiménez-Panizo, A., Martínez-Tébar, A., Poulard, C., Peralta-Moreno, M. N., Abella, M., Antón, R., Chiñas, M., Eckhard, U., Piulats, J. M., Rojas, A. M., Fernández-Recio, J., Rubio-Martínez, J., Le Romancer, M., Aytes, Á., Fuentes-Prior, P., & Estébanez-Perpiñá, E. (2023). A hotspot for posttranslational modifications on the androgen receptor dimer interface drives pathology and anti-androgen resistance. Science Advances, 9(11). https://doi.org/10.1126/sciadv.ade2175
Jiménez-Panizo, A., Alegre-Martí, A., Tettey, T. T., Fettweis, G., Abella, M., Antón, R., Johnson, T. A., Kim, S., Schiltz, R. L., Núñez-Barrios, I., Font-Díaz, J., Caelles, C., Valledor, A. F., Pérez, P., Rojas, A. M., Fernández-Recio, J., Presman, D. M., Hager, G. L., Fuentes-Prior, P., & Estébanez-Perpiñá, E. (2022). The multivalency of the glucocorticoid receptor ligand-binding domain explains its manifold physiological activities. Nucleic Acids Research, 50(22), 13063–13082. https://doi.org/10.1093/nar/gkac1119
Mencucci, M. V., Rojas-Mendoza, A. M., Andrés-León, E., Román, C. L., Gagliardino, J. J., Abba, M. C., & Maiztegui, B. (2022). Identification of novel microRNAs associated with type 2 diabetes by an integrative bioinformatic analysis. Human Gene, 34, 201125. https://doi.org/10.1016/j.humgen.2022.201125
Santana-Molina, C., Rivas-Marin, E., Rojas, A. M., & Devos, D. P. (2020). Origin and Evolution of Polycyclic Triterpene Synthesis. Molecular Biology and Evolution, 37(7), 1925–1941. https://doi.org/10.1093/molbev/msaa054
Fuentes-Prior, P., Rojas, A., Hagler, A. T., & Estébanez-Perpiñá, E. (2019). Diversity of Quaternary Structures Regulates Nuclear Receptor Activities. Trends in Biochemical Sciences, 44(1), 2–6. https://doi.org/10.1016/j.tibs.2018.09.005
Jiménez-Panizo, A., Pérez, P., Rojas, A. M., Fuentes-Prior, P., & Estébanez-Perpiñá, E. (2019). Non-canonical dimerization of the androgen receptor and other nuclear receptors: implications for human disease. Endocrine-Related Cancer, 26(8), R479–R497. https://doi.org/10.1530/erc-19-0132
Martín-Doncel, E., Rojas, A. M., Cantarero, L., & Lazo, P. A. (2019). VRK1 functional insufficiency due to alterations in protein stability or kinase activity of human VRK1 pathogenic variants implicated in neuromotor syndromes. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-019-49821-7
Andrés-León, E., & Rojas, A. M. (2019). miARma-Seq, a comprehensive pipeline for the simultaneous study and integration of miRNA and mRNA expression data. Methods, 152, 31–40. https://doi.org/10.1016/j.ymeth.2018.09.002
Silva, J., Aivio, S., Knobel, P. A., Bailey, L. J., Casali, A., Vinaixa, M., Garcia-Cao, I., Coyaud, É., Jourdain, A. A., Pérez-Ferreros, P., Rojas, A. M., Antolin-Fontes, A., Samino-Gené, S., Raught, B., González-Reyes, A., Ribas de Pouplana, L., Doherty, A. J., Yanes, O., & Stracker, T. H. (2018). EXD2 governs germ stem cell homeostasis and lifespan by promoting mitoribosome integrity and translation. Nature Cell Biology, 20(2), 162–174. https://doi.org/10.1038/s41556-017-0016-9
López-Jiménez, E., Rojas, A. M., & Andrés-León, E. (2018). RNA sequencing and Prediction Tools for Circular RNAs Analysis. Circular RNAs, 17–33. https://doi.org/10.1007/978-981-13-1426-1_2
Andrés-León, E., Cases, I., Arcas, A., & Rojas, A. M. (2016). DDRprot: a database of DNA damage response-related proteins. Database, 2016, baw123. https://doi.org/10.1093/database/baw123
Tzou, W.-S., Chu, Y., Lin, T.-Y., Hu, C.-H., Pai, T.-W., Liu, H.-F., Lin, H.-J., Cases, I., Rojas, A., Sanchez, M., You, Z.-Y., & Hsu, M.-W. (2014). Molecular Evolution of Multiple-Level Control of Heme Biosynthesis Pathway in Animal Kingdom. PLoS ONE, 9(1), e86718. https://doi.org/10.1371/journal.pone.0086718
Arcas, A., Fernández-Capetillo, O., Cases, I., & Rojas, A. M. (2014). Emergence and Evolutionary Analysis of the Human DDR Network: Implications in Comparative Genomics and Downstream Analyses. Molecular Biology and Evolution, 31(4), 940–961. https://doi.org/10.1093/molbev/msu046
Athiyarath, R., Arora, N., Fuster, F., Schwarzenbacher, R., Ahmed, R., George, B., Chandy, M., Srivastava, A., Rojas, A. M., Sanchez, M., & Edison, E. S. (2013). Two novel missense mutations in iron transport protein transferrin causing hypochromic microcytic anaemia and haemosiderosis: molecular characterization and structural implications. British Journal of Haematology, 163(3), 404–407. Portico. https://doi.org/10.1111/bjh.12487
Arcas, A., Cases, I., & Rojas, A. M. (2013). Serine/threonine kinases and E2-ubiquitin conjugating enzymes in Planctomycetes: unexpected findings. Antonie van Leeuwenhoek, 104(4), 509–520. https://doi.org/10.1007/s10482-013-9993-2
Lopez-Contreras, A. J., Ruppen, I., Nieto-Soler, M., Murga, M., Rodriguez-Acebes, S., Remeseiro, S., Rodrigo-Perez, S., Rojas, A. M., Mendez, J., Muñoz, J., & Fernandez-Capetillo, O. (2013). A Proteomic Characterization of Factors Enriched at Nascent DNA Molecules. Cell Reports, 3(4), 1105–1116. https://doi.org/10.1016/j.celrep.2013.03.009
Pons, T., Paramonov, I., Boullosa, C., Ibáñez, K., Rojas, A. M., & Valencia, A. (2013). A common structural scaffold in CTD phosphatases that supports distinct catalytic mechanisms. Proteins: Structure, Function, and Bioinformatics, 82(1), 103–118. Portico. https://doi.org/10.1002/prot.24376
Rojas, A. M., Santamaria, A., Malik, R., Jensen, T. S., Körner, R., Morilla, I., de Juan, D., Krallinger, M., Hansen, D. A., Hoffmann, R., Lees, J., Reid, A., Yeats, C., Wehner, A., Elowe, S., Clegg, A. B., Brunak, S., Nigg, E. A., Orengo, C., … Ranea, J. A. G. (2012). Uncovering the Molecular Machinery of the Human Spindle—An Integration of Wet and Dry Systems Biology. PLoS ONE, 7(3), e31813. https://doi.org/10.1371/journal.pone.0031813
Rojas, A. M., Fuentes, G., Rausell, A., & Valencia, A. (2012). The Ras protein superfamily: Evolutionary tree and role of conserved amino acids. Journal of Cell Biology, 196(2), 189–201. https://doi.org/10.1083/jcb.201103008
Palczewska, M., Casafont, I., Ghimire, K., Rojas, A. M., Valencia, A., Lafarga, M., Mellström, B., & Naranjo, J. R. (2011). Sumoylation regulates nuclear localization of repressor DREAM. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, 1813(5), 1050–1058. https://doi.org/10.1016/j.bbamcr.2010.11.001
Vallespinós, M., Fernández, D., Rodríguez, L., Alvaro-Blanco, J., Baena, E., Ortiz, M., Dukovska, D., Martínez, D., Rojas, A., Campanero, M. R., & Moreno de Alborán, I. (2011). B Lymphocyte Commitment Program Is Driven by the Proto-Oncogene c-myc. The Journal of Immunology, 186(12), 6726–6736. https://doi.org/10.4049/jimmunol.1002753
Mañes, S., Fuentes, G., Peregil, R. M., Rojas, A. M., & Lacalle, R. A. (2010). An isoform‐specific PDZ‐binding motif targets type I PIP5 kinase beta to the uropod and controls polarization of neutrophil‐like HL60 cells. The FASEB Journal, 24(9), 3381–3392. Portico. https://doi.org/10.1096/fj.09-153106
Krallinger, M., Rojas, A. M., & Valencia, A. (2009). Creating Reference Datasets for Systems Biology Applications Using Text Mining. Annals of the New York Academy of Sciences, 1158(1), 14–28. Portico. https://doi.org/10.1111/j.1749-6632.2008.03750.x
Proell, M., Riedl, S. J., Fritz, J. H., Rojas, A. M., & Schwarzenbacher, R. (2008). The Nod-Like Receptor (NLR) Family: A Tale of Similarities and Differences. PLoS ONE, 3(4), e2119. https://doi.org/10.1371/journal.pone.0002119
Bayón, Y., Trinidad, A. G., de la Puerta, M. L., del Carmen Rodríguez, M., Bogetz, J., Rojas, A., De Pereda, J. M., Rahmouni, S., Williams, S., Matsuzawa, S., Reed, J. C., Crespo, M. S., Mustelin, T., & Alonso, A. (2008). KCTD5, a putative substrate adaptor for cullin3 ubiquitin ligases. The FEBS Journal, 275(15), 3900–3910. Portico. https://doi.org/10.1111/j.1742-4658.2008.06537.x
Mathieu-Daudé, F., Lafay, B., Touzet, O., Lelièvre, J., Parrado, F., Bosseno, M.-F., Rojas, A. M., Fatha, S., Ouaissi, A., & Brenière, S. F. (2008). Exploring the FL-160-CRP gene family through sequence variability of the complement regulatory protein (CRP) expressed by the trypomastigote stage of Trypanosoma cruzi. Infection, Genetics and Evolution, 8(3), 258–266. https://doi.org/10.1016/j.meegid.2007.12.010
Cacas, J.-L., Marmey, P., Montillet, J.-L., Sayegh-Alhamdia, M., Jalloul, A., Rojas-Mendoza, A., Clérivet, A., & Nicole, M. (2008). A novel patatin-like protein from cotton plant, GhPat1, is co-expressed with GhLox1 during Xanthomonas campestris-mediated hypersensitive cell death. Plant Cell Reports, 28(1), 155–164. https://doi.org/10.1007/s00299-008-0622-x
Sonnenberg, A., Rojas, A. M., & de Pereda, J. M. (2007). The Structure of a Tandem Pair of Spectrin Repeats of Plectin Reveals a Modular Organization of the Plakin Domain. Journal of Molecular Biology, 368(5), 1379–1391. https://doi.org/10.1016/j.jmb.2007.02.090
Grego-Bessa, J., Luna-Zurita, L., del Monte, G., Bolós, V., Melgar, P., Arandilla, A., Garratt, A. N., Zang, H., Mukouyama, Y., Chen, H., Shou, W., Ballestar, E., Esteller, M., Rojas, A., Pérez-Pomares, J. M., & de la Pompa, J. L. (2007). Notch Signaling Is Essential for Ventricular Chamber Development. Developmental Cell, 12(3), 415–429. https://doi.org/10.1016/j.devcel.2006.12.011
Jiménez-Baranda, S., Gómez-Moutón, C., Rojas, A., Martínez-Prats, L., Mira, E., Ana Lacalle, R., Valencia, A., Dimitrov, D. S., Viola, A., Delgado, R., Martínez-A., C., & Mañes, S. (2007). Filamin-A regulates actin-dependent clustering of HIV receptors. Nature Cell Biology, 9(7), 838–846. https://doi.org/10.1038/ncb1610
López, G., Rojas, A., Tress, M., & Valencia, A. (2007). Assessment of predictions submitted for the CASP7 function prediction category. Proteins: Structure, Function, and Bioinformatics, 69(S8), 165–174. https://doi.org/10.1002/prot.21651
Sanchez-Pulido, L., Valencia, A., & Rojas, A. M. (2007). Are promyelocytic leukaemia protein nuclear bodies a scaffold for caspase-2 programmed cell death? Trends in Biochemical Sciences, 32(9), 400–406. https://doi.org/10.1016/j.tibs.2007.08.001
Cases, I., Pisano, D. G., Andres, E., Carro, A., Fernandez, J. M., Gomez-Lopez, G., Rodriguez, J. M., Vera, J. F., Valencia, A., & Rojas, A. M. (2007). CARGO: a web portal to integrate customized biological information. Nucleic Acids Research, 35(Web Server), W16–W20. https://doi.org/10.1093/nar/gkm280
Carro, A., Tress, M., de Juan, D., Pazos, F., Lopez-Romero, P., del Sol, A., Valencia, A., & Rojas, A. M. (2006). TreeDet: a web server to explore sequence space. Nucleic Acids Research, 34(Web Server), W110–W115. https://doi.org/10.1093/nar/gkl203
Cabrera, J. R., Sanchez-Pulido, L., Rojas, A. M., Valencia, A., Mañes, S., Naranjo, J. R., & Mellström, B. (2006). Gas1 Is Related to the Glial Cell-derived Neurotrophic Factor Family Receptors α and Regulates Ret Signaling. Journal of Biological Chemistry, 281(20), 14330–14339. https://doi.org/10.1074/jbc.m509572200
Rojas, A. M., Sanchez‐Pulido, L., Fütterer, A., van Wely, K. H. M., Martinez‐A, C., & Valencia, A. (2005). Death inducer obliterator protein 1 in the context of DNA regulation. The FEBS Journal, 272(14), 3505–3511. Portico. https://doi.org/10.1111/j.1742-4658.2005.04759.x
Marmey, P., Rojas-Mendoza, A., de Kochko, A., Beachy, R. N., & Fauquet, C. M. (2005). Characterization of the protease domain of Rice tungro bacilliform virus responsible for the processing of the capsid protein from the polyprotein. Virology Journal, 2(1). https://doi.org/10.1186/1743-422x-2-33
de Juan, D., Mellado, M., Rodríguez-Frade, J. M., Hernanz-Falcón, P., Serrano, A., del Sol, A., Valencia, A., Martínez-A, C., & Rojas, A. M. (2005). A framework for computational and experimental methods: Identifying dimerization residues in CCR chemokine receptors. Bioinformatics, 21(suppl_2), ii13–ii18. https://doi.org/10.1093/bioinformatics/bti1101
Sánchez-Pulido, L., Rojas, A. M., van Wely, K. H., Martinez-A, C., & Valencia, A. (2004). SPOC: A widely distributed domain associated with cancer, apoptosis and transcription. BMC Bioinformatics, 5(1). https://doi.org/10.1186/1471-2105-5-91
Magnusson, O. Th., Toyama, H., Saeki, M., Rojas, A., Reed, J. C., Liddington, R. C., Klinman, J. P., & Schwarzenbacher, R. (2004). Quinone biogenesis: Structure and mechanism of PqqC, the final catalyst in the production of pyrroloquinoline quinone. Proceedings of the National Academy of Sciences, 101(21), 7913–7918. https://doi.org/10.1073/pnas.0402640101
Sanchez-Pulido, L., Rojas, A. M., Valencia, A., Martinez-A, C., & Andrade, M. A. (2004). ACRATA: a novel electron transfer domain associated to apoptosis and cancer. BMC Cancer, 4(1). https://doi.org/10.1186/1471-2407-4-98
Rojas, A. M., Rios, J. E. G. de los, Saux, M. F.-L., Jimenez, P., Reche, P., Bonneau, S., Sutra, L., Mathieu-Daudé, F., & McClelland, M. (2004). Erwinia toletana sp. nov., associated with Pseudomonas savastanoi-induced tree knots. International Journal of Systematic and Evolutionary Microbiology, 54(6), 2217–2222. https://doi.org/10.1099/ijs.0.02924-0
Reche, M. P., Jiménez, P. A., Alvarez, F., García de los Ríos, J. E., Rojas, A. M., & De Pedro, P. (2003). Incidence of Salmonellae in Captive and Wild Free‐Living Raptorial Birds in Central Spain. Journal of Veterinary Medicine, Series B, 50(1), 42–44. Portico. https://doi.org/10.1046/j.1439-0450.2003.00623.x
Liu, T., Rojas, A., Ye, Y., & Godzik, A. (2003). Homology modeling provides insights into the binding mode of the PAAD/DAPIN/pyrin domain, a fourth member of the CARD/DD/DED domain family. Protein Science, 12(9), 1872–1881. Portico. https://doi.org/10.1110/ps.0359603
Reed, J. C., Doctor, K., Rojas, A., Zapata, J. M., Stehlik, C., Fiorentino, L., Damiano, J., Roth, W., Matsuzawa, S., Newman, R., Takayama, S., Marusawa, H., Xu, F., Salvesen, G., & Godzik, A. (2003). Comparative Analysis of Apoptosis and Inflammation Genes of Mice and Humans. Genome Research, 13(6b), 1376–1388. https://doi.org/10.1101/gr.1053803
Reche, M. P., García de los Ríos, J. E., Jiménez, P. A., Rojas, A. M., & Rotger, R. (2002). gyrA Mutations Associated with Nalidixic Acid-Resistant Salmonellae from Wild Birds. Antimicrobial Agents and Chemotherapy, 46(9), 3108–3109. https://doi.org/10.1128/aac.46.9.3108-3109.2002
Rojas, A., & Doolittle, R. F. (2002). The Occurrence of Type S1A Serine Proteases in Sponge and Jellyfish. Journal of Molecular Evolution, 55(6), 790–794. https://doi.org/10.1007/s00239-002-2361-x
Research lines:
Funding:
More info
Collaborating Companies: Miembro investigador. TSI-100930-2023-2. Contrato: Cátedra ENIA Google Spain/Universidad de Sevilla en Inteligencia Artificial. 31-08-2024/31-12-2025. IP: Carmen Barroso.
Spin-off: No
Patents: Blázquez-Gómez, Jesús, Castañeda-García, Alfredo, Prieto-Márquez Ana I., Rojas-Mendoza, Ana M., Wadel, Simon; Cantillon, Daire; Doherty, A. P201531949. “Cepas de Mycobacterium hipermutables”. España y UK, 31/12/2015. SAS/CSIC/USE
HPC Resources: Drago, CESGA, UPO
Participation in:
Master Programs: - Desde 2021. Master Universitario en análisis de datos ómicos y Biología de Sistemas. Universidad Internacional de Andalucía-Universidad de Sevilla. Asignatura: "Aplicaciones y Discusiones en Medicina Clínica”. Coordinadora de la Asignatura. - Desde 2016- Profesora externa del Máster Universitario en Investigación Biomédica, asignatura: “Genómica Funcional y Biocomputación”, Universidad de Sevilla. - Master propio en Data Science y Big Data. Facultad de Matemáticas, Universidad de Sevilla. Módulo: “Machine Learning II”.
Doctoral Programs: Desde 2018- Profesora externa de la Universidad Pablo de Olavide, en el programa de Doctorado en Biotecnología, Ingeniería y Tecnología Química, línea de Ingeniería, Ciencia de Datos y Bioinformática
National Research Networks: CSIC/BCB.Hub CSIC/Life.Hub SAB member IGDR, FR. SAB president, IMIB, ES.
International Research Networks: Desde 2024. ISCB. Track Chair of The Function Community of Interest.
Other Participation: international, csicconexion