CBBiO Computational Biology and Bioinformatics

Curriculum Vitae

Ana M. Rojas Mendoza

I investigate how proteins evolve and acquire function, combining evolutionary biology, structural bioinformatics, and AI.

I am a Research Scientist at CSIC and Director of the Department of Evolutionary Dynamics at CABD. My group develops computational methods and tools to understand protein diversity and extend functional annotation, including the FANTASIA suite.

Career and roles Publications Research funding Outreach and service Leadership Teaching Training Internationalisation
Ana M. Rojas Mendoza

Overview

Scientific trajectory

I trained in Biological Sciences in Madrid and developed my research in the United States and Spain, including periods at UC San Diego and Sanford Burnham. I established my independent group in 2009. My work connects molecular biology, protein evolution, structural bioinformatics, and computational methods.

Highlights

Research, leadership, and training

  • Scientific contributions. With my group and collaborators, I develop FANTASIA and study how protein language models can inform functional annotation and molecular evolution. Selected contributions.
  • Independent leadership. I have led an independent group since 2009 and have directed the Department of Evolutionary Dynamics at CABD since 2026. Career and roles.
  • Competitive funding. My project leadership includes CONVERGE and MULTIMORPH, and I co-lead the FAIRFUN4Biodiversity consortium. Research projects.
  • International scientific service. I serve as Associate Editor of NAR Genomics and Bioinformatics and as Track Chair and Executive Committee member of Function COSI, alongside scientific advisory and research evaluation roles. Leadership and service.
  • Training researchers. I supervise doctoral, master’s, and undergraduate research and teach in master’s and doctoral programs. Mentoring and teaching.

Career

Positions and training

Academic training

  • PhD in Biology, Universidad San Pablo, 1999
  • Biology degree with thesis, Universidad Complutense de Madrid, 1998
  • Biology degree, Universidad Complutense de Madrid, 1994

Research positions

  • 2023-present. Research Scientist, CSIC; Director of Evolutionary Dynamics at CABD since 2026.
  • 2017-2023. CSIC Tenured Scientist, first at IBiS and later at CABD, Seville.
  • 2013-2017. Senior Principal Investigator, IBiS, Seville.
  • 2009-2013. Junior Group Leader, IMPPC, Badalona.
  • 2006-2009. Staff scientist, CNIO, Madrid.
  • 2003-2006. Marie Curie postdoctoral fellow, CNB-CSIC, Madrid. Supervisor: Alfonso Valencia.
  • 2001-2003. Postdoctoral researcher, Sanford Burnham Medical Research Institute, USA. Supervisor: Adam Godzik.
  • 2000-2001. NASA-NSCORT postdoctoral fellow, UC San Diego, USA. Supervisor: R. F. Doolittle.
  • 1998-2000. Predoctoral researcher, Sidney Kimmel Cancer Center, USA. Supervisor: Michael McClelland.

I established my independent group in 2009 in Barcelona and later moved to Seville, first at IBiS and then at CABD, where I lead the group today. My research spans protein family evolution, protein signaling, omics integration, and computational method development. In recent years, I have extended this work to AI and protein language models.

I study how sequence, structure, and evolution shape protein function, and develop methods to make functional annotation more scalable and biologically meaningful. Alongside research, I mentor scientists, evaluate research, contribute to scientific communities, and communicate computational biology and AI in biomedicine to wider audiences.

Research

Topics and methods to address

  • Protein evolution, structure, and biological function
  • Protein language models and AI-based functional annotation
  • Computational biology resources, pipelines, and comparative analysis
  • Systems biology and biomedical collaborations

Contributions

Selected scientific contributions

  • Functional annotation. With my group and collaborators, I develop FANTASIA to extend protein functional annotation using language models, building on our work in model organisms and across the animal tree of life.
  • FANTASIA suite publication. With my co-authors, I present a reproducible and configurable framework for protein functional annotation in FANTASIA suite: a reproducible and configurable framework for embedding-based functional annotation of proteins (NAR Genomics and Bioinformatics, 2026).
  • Molecular evolution. I investigate how protein embeddings inform evolutionary analysis, including our work on evolutionary and functional organization across the Ras superfamily.
  • Protein structure and function. I study multifunctional proteins and metamorphic conformations, including computational approaches to identifying proteins that can adopt different structures.
  • Earlier foundations. My research also includes DNA damage response evolution, mismatch repair, nuclear receptor signaling, and omics integration.

Browse the complete publication archive

Publications

Complete publication list

2026-2024
  1. Bastolla, U., Aurell, E., Cocco, S., Liberles, D., Micheletti, C., Orellana, L., Rojas, A., Talavera, D., Valencia, A. 2026. Evolutionary Intelligence: How coevolution opened the way to the AlphaFold revolution. Journal of Molecular Evolution. In press.
  2. Cases, I., Valencia, A., Rojas, AM. 2026. Protein Language Model Embeddings Recover Evolutionary and Functional Organization Across the Ras Superfamily. Journal of Molecular Evolution. Publication
  3. Pérez-Canales, FM., Domínguez-Rodríguez, À., Carbonetto, B., Fernández, R., Cases, I., Rojas, AM. 2026. FANTASIA suite: a reproducible and configurable framework for embedding-based functional annotation of proteins. NAR Genomics and Bioinformatics. 8(3):lqag106. Publication
  4. Fernandez, R.*., Valverde, S., Bombarely, A., Cases, I., Handley, S., Rojas, AM.*. 2026. Rethinking molecular evolution through protein language model embeddings. Trends in Genetics. DOI
  5. Rodríguez-Rodríguez, M., Alanís-Domínguez, E., Casimiro-Soriguer, C.S., l Ortiz de la Rosa JM., , Soto-Gallego, C., Dorado Pardo, J., Rojas, AM., Lepe, JA., Rodríguez-Villodres,A. 2026. Essential role of the leucine-293 for the AmpC β-lactamase in the resistance to cefepime, cefiderocol, and new β-lactams/β-lactamase inhibitor combinations in Enterobacter hormaechei. International Journal of Antimicrobial Agents. DOI
  6. Pérez-Canales FM, Alanís-Domínguez E, Rojas AM*. Computational Identification of Potential Shape-Shifting Proteins from Structures. Methods Mol Biol. 2025;2979:157-164. doi: 10.1007/978-1-0716-4828-5_10. PMID: 41174312. PID2021-127503OB-I00, EOSC-OSCARS No. 101129751, CEX2020-001088 DOI
  7. Martínez-Redondo* GI, Perez-Canales FM, Carbonetto B, Fernández JM, Barrios-Núñez I, Vázquez-Valls M, Cases I, Rojas AM*, Fernández R*. FANTASIA leverages language models to decode the functional dark proteome across the animal tree of life. Commun Biol. 2025 Aug 14;8(1):1227. doi: 10.1038/s42003-025-08651-2. PMID: 40813894; PMCID: PMC12354702. PID2021-127503OB-I00, EOSC-OSCARS No. 101129751, MDM-2016-0687. DOI
  8. Valverde, S., Vidiella, B., Martínez-Redondo, G., Duran-Nebreda, S., Fernández, R., Bombarely, A., Rojas AM., and Bentley, R.A., 2025. Structural Changes in Gene Ontology Reveal Modular and Complex Representations of Biological Function. Mol Biol Evol. doi: 10.1093/molbev/msaf148. PID2021-127503OB-I00. DOI
  9. Cases I, Martínez-Redondo G, Fernández R, Rojas AM*. Functional Annotation of Proteomes Using Protein Language Models: A High-Throughput Implementation of the ProtTrans Model. Methods Mol Biol. 2025; 2941:127-137. doi: 10.1007/978-1-0716-4623-6_8. PMID: 40601255. PID2021-127503OB-I00, LifeHUB/CSIC research network (PIE-202120E047) DOI
  10. Verdugo-Sivianes EM, Espinosa-Sánchez A, Cases I, Rojas AM, Otero-Albiol D, Romero L, Blanco JR, Carnero A. MEG8 as an antagonistic pleiotropic mechanism in breast cancer. Cell Death Discov. 2024 Dec 20;10(1):509. doi: 10.1038/s41420-024-02272-0. PMID: 39706842; PMCID: PMC11662018. DOI
  11. Barrios-Núñez I, Martínez-Redondo GI, Medina-Burgos P, Cases I, Fernández R*, Rojas AM*. Decoding functional proteome information in model organisms using protein language models. NAR Genom Bioinform. 2024 Jul 2;6(3):lqae078. doi: 10.1093/nargab/lqae078. PMID: 38962255; PMCID: PMC11217674. PID2021-127503OB-I00, MDM-2016-0687, LifeHUB/CSIC Research Network [PIE-202120E047] DOI
2023-2020
  1. Alegre-Martí A, Jiménez-Panizo A, Martínez-Tébar A, Poulard C, Peralta-Moreno MN, Abella M, Antón R, Chiñas M, Eckhard U, Piulats JM, Rojas AM, Fernández-Recio J, Rubio-Martínez J, Le Romancer M, Aytes Á, Fuentes-Prior P, Estébanez-Perpiñá E. A hotspot for posttranslational modifications on the androgen receptor dimer interface drives pathology and anti-androgen resistance. Sci Adv. 2023 Mar 17;9(11):eade2175. doi: 10.1126/sciadv.ade2175. Epub 2023 Mar 15. PMID: 36921044; PMCID: PMC10017050. RTI2018-096735-B-100. DOI
  2. Mencucci, M.V, Rojas-Mendoza, A.M., .., Maiztegui, B. 2022. Identification of novel microRNAs associated with type 2 diabetes by an integrative bioinformatic analysis. Human Gene. 10.1016/j.humgen.2022.20112.
  3. Jiménez-Panizo A, Alegre-Martí A, Tettey TT, Fettweis G, Abella M, Antón R, Johnson TA, Kim S, Schiltz RL, Núñez-Barrios I, Font-Díaz J, Caelles C, Valledor AF, Pérez P, Rojas AM, Fernández-Recio J, Presman DM, Hager GL, Fuentes-Prior P, Estébanez-Perpiñá E. The multivalency of the glucocorticoid receptor ligand-binding domain explains its manifold physiological activities. Nucleic Acids Res. 2022 Dec 9;50(22):13063-13082. doi: 10.1093/nar/gkac1119. PMID: 36464162; PMCID: PMC9825158. RTI2018-096735-B-100. DOI
  4. Libros Blancos Desafíos Científicos 2030. 2022. CSIC: Vol. 3 Genome and Epigenetics (coordinadora del capítulo 2) y Vol. 5 Brain, Mind and behaviour (participante del reto 2).
  5. Verdugo-Sivianes EM, Rojas AM, Muñoz-Galván S, Otero-Albiol D, Carnero A. Mutation of SPINOPHILIN (PPP1R9B) found in human tumors promotes the tumorigenic and stemness properties of cells. Theranostics. 2021 Jan 19;11(7):3452-3471. doi: 10.7150/thno.53572. PMID: 33537097; PMCID: PMC7847670. RTI2018-096735-B-I00. DOI
  6. Santana-Molina C*, Rivas-Marin E, Rojas AM*, Devos DP*. Origin and Evolution of Polycyclic Triterpene Synthesis. Mol Biol Evol. 2020 Jul 1;37(7):1925-1941. doi: 10.1093/molbev/msaa054. PMID: 32125435; PMCID: PMC7306690. RTI2018-096735-B-100 DOI
2019-2014
  1. Martín-Doncel E, Rojas AM, Cantarero L, Lazo PA. VRK1 functional insufficiency due to alterations in protein stability or kinase activity of human VRK1 pathogenic variants implicated in neuromotor syndromes. Sci Rep. 2019 Sep 16;9(1):13381. doi: 10.1038/s41598-019-49821-7. PMID: 31527692; PMCID: PMC6746721. RTI2018-096735-B-I00. DOI
  2. Andrés-León E, Rojas AM*. miARma-Seq, a comprehensive pipeline for the simultaneous study and integration of miRNA and mRNA expression data. Methods. 2019 Jan 1;152:31-40. doi: 10.1016/j.ymeth.2018.09.002. Epub 2018 Sep 22. PMID: 30253202. DOI
  3. Jiménez-Panizo A, Pérez P, Rojas AM, Fuentes-Prior P, Estébanez-Perpiñá E. Non-canonical dimerization of the androgen receptor and other nuclear receptors: implications for human disease. Endocr Relat Cancer. 2019 Aug;26(8):R479-R497. doi: 10.1530/ERC-19-0132. PMID: 31252411. RTI2018-096735-B-I00. DOI
  4. Fuentes-Prior P, Rojas A, Hagler AT, Estébanez-Perpiñá E. Diversity of Quaternary Structures Regulates Nuclear Receptor Activities. Trends Biochem Sci. 2019 Jan;44(1):2-6. doi: 10.1016/j.tibs.2018.09.005. Epub 2018 Oct 4. PMID: 30293659. DOI
  5. López-Jiménez E, Rojas AM, Andrés-León E. RNA sequencing and Prediction Tools for Circular RNAs Analysis. Adv Exp Med Biol. 2018; 1087:17-33. doi: 10.1007/978-981-13-1426-1_2. PMID: 30259354. DOI
  6. Silva J, Aivio S, Knobel PA, Bailey LJ, Casali A, Vinaixa M, Garcia-Cao I, Coyaud É, Jourdain AA, Pérez-Ferreros P, Rojas AM, Antolin-Fontes A, Samino-Gené S, Raught B, González-Reyes A, Ribas de Pouplana L, Doherty AJ, Yanes O, Stracker TH. EXD2 governs germ stem cell homeostasis and lifespan by promoting mitoribosome integrity and translation. Nat Cell Biol. 2018 Feb;20(2):162-174. doi: 10.1038/s41556-017-0016-9. Epub 2018 Jan 15. PMID: 29335528. DOI
  7. Andrés-León E*, Cases I, Alonso S*, Rojas AM*. Novel miRNA-mRNA interactions conserved in essential cancer pathways. Sci Rep. 2017 Apr 7;7:46101. doi: 10.1038/srep46101. PMID: 28387377; PMCID: PMC5384238. FP7-REGPOT-2012-2013-1 DOI
  8. Castañeda-García A, Prieto AI, Rodríguez-Beltrán J, Alonso N, Cantillon D, Costas C, Pérez-Lago L, Zegeye ED, Herranz M, Plociński P, Tonjum T, García de Viedma D, Paget M, Waddell SJ, Rojas AM*, Doherty AJ*, Blázquez J*. A non-canonical mismatch repair pathway in prokaryotes. Nat Commun. 2017 Jan 27;8:14246. doi: 10.1038/ncomms14246. PMID: 28128207; PMCID: PMC5290159. DOI
  9. Andrés-León E, Cases I, Arcas A, Rojas AM*. DDRprot: a database of DNA damage response-related proteins. Database (Oxford). 2016 Aug 29;2016:baw123. doi: 10.1093/database/baw123. PMID: 27577567; PMCID: PMC5004197. FP7-REGPOT-2012-2013-1, PS09/02111. DOI
  10. Andrés-León E, Núñez-Torres R, Rojas AM*. miARma-Seq: a comprehensive tool for miRNA, mRNA and circRNA analysis. Sci Rep. 2016 May 11;6:25749. doi: 10.1038/srep25749. Erratum (url correction) in: Sci Rep. 2018 Jan 08;8:46928. doi: 10.1038/srep46928. PMID: 27167008; PMCID: PMC4863143. FP7-REGPOT-2012-2013-1 DOI
  11. Tristán-Clavijo E, Scholl FG, Macaya A, Iglesias G, Rojas AM, Lucas M, Castellano A, Martinez-Mir A. Dominant-negative mutation p.Arg324Thr in KCNA1 impairs Kv1.1 channel function in episodic ataxia. Mov Disord. 2016 Nov;31(11):1743-1748. doi: 10.1002/mds.26737. Epub 2016 Aug 1. PMID: 27477325. DOI
  12. Terré B, Piergiovanni G, Segura-Bayona S, Gil-Gómez G, Youssef SA, Attolini CS, Wilsch-Bräuninger M, Jung C, Rojas AM, Marjanović M, Knobel PA, Palenzuela L, López-Rovira T, Forrow S, Huttner WB, Valverde MA, de Bruin A, Costanzo V, Stracker TH. GEMC1 is a critical regulator of multiciliated cell differentiation. EMBO J. 2016 May 2;35(9):942-60. doi: 10.15252/embj.201592821. Epub 2016 Mar 1. PMID: 26933123; PMCID: PMC5207319. DOI
  13. Lacalle RA, de Karam JC, Martínez-Muñoz L, Artetxe I, Peregil RM, Sot J, Rojas AM, Goñi FM, Mellado M, Mañes S. Type I phosphatidylinositol 4-phosphate 5-kinase homo- and heterodimerization determines its membrane localization and activity. FASEB J. 2015 Jun;29(6):2371-85. doi: 10.1096/fj.14-264606. Epub 2015 Feb 24. PMID: 25713054. DOI
  14. Pons T, Paramonov I, Boullosa C, Ibáñez K, Rojas AM, Valencia A. A common structural scaffold in CTD phosphatases that supports distinct catalytic mechanisms. Proteins. 2014 Jan;82(1):103-18. doi: 10.1002/prot.24376. Epub 2013 Sep 10. PMID: 23900790. DOI
  15. Arcas A, Fernández-Capetillo O, Cases I, Rojas AM*. Emergence and evolutionary analysis of the human DDR network: implications in comparative genomics and downstream analyses. Mol Biol Evol. 2014 Apr;31(4):940-61. doi: 10.1093/molbev/msu046. Epub 2014 Jan 16. PMID: 24441036; PMCID: PMC3969565. PS09/02111 DOI
  16. Rojas, A.M., Valencia, A. (2014). Evolution of the Ras Superfamily of GTPases. In: Wittinghofer, A. (eds) Ras Superfamily Small G Proteins: Biology and Mechanisms 1. Springer, Vienna. DOI
  17. Tzou WS, Chu Y, Lin TY, Hu CH, Pai TW, Liu HF, Lin HJ, Cases I, Rojas A, Sanchez M, You ZY, Hsu MW. Molecular evolution of multiple-level control of heme biosynthesis pathway in animal kingdom. PLoS One. 2014 Jan 28;9(1):e86718. doi: 10.1371/journal.pone.0086718. PMID: 24489775; PMCID: PMC3904948. DOI
  18. Basilico F, Maffini S, Weir JR, Prumbaum D, Rojas AM, Zimniak T, De Antoni A, Jeganathan S, Voss B, van Gerwen S, Krenn V, Massimiliano L, Valencia A, Vetter IR, Herzog F, Raunser S, Pasqualato S, Musacchio A. The pseudo GTPase CENP-M drives human kinetochore assembly. Elife. 2014 Jul 8;3:e02978. doi: 10.7554/eLife.02978. PMID: 25006165; PMCID: PMC4080450. DOI
2013-2006
  1. Lopez-Contreras AJ, Ruppen I, Nieto-Soler M, Murga M, Rodriguez-Acebes S, Remeseiro S, Rodrigo-Perez S, Rojas AM, Mendez J, Muñoz J, Fernandez-Capetillo O. A proteomic characterization of factors enriched at nascent DNA molecules. Cell Rep. 2013 Apr 25;3(4):1105-16. doi: 10.1016/j.celrep.2013.03.009. Epub 2013 Mar 28. PMID: 23545495; PMCID: PMC3714744. DOI
  2. Arcas A, Cases I, Rojas AM*. Serine/threonine kinases and E2-ubiquitin conjugating enzymes in Planctomycetes: unexpected findings. Antonie Van Leeuwenhoek. 2013 Oct;104(4):509-20. doi: 10.1007/s10482-013-9993-2. Epub 2013 Aug 6. PMID: 23918348. DOI
  3. Athiyarath R, Arora N, Fuster F, Schwarzenbacher R, Ahmed R, George B, Chandy M, Srivastava A, Rojas AM, Sanchez M, Edison ES. Two novel missense mutations in iron transport protein transferrin causing hypochromic microcytic anaemia and haemosiderosis: molecular characterization and structural implications. Br J Haematol. 2013 Nov;163(3):404-7. doi: 10.1111/bjh.12487. Epub 2013 Jul 24. PMID: 23888904. DOI
  4. Rojas AM*, Fuentes G, Rausell A, Valencia A*. The Ras protein superfamily: evolutionary tree and role of conserved amino acids. J Cell Biol. 2012 Jan 23;196(2):189-201. doi: 10.1083/jcb.201103008. Erratum (incorrect reference) in: J Cell Biol. 2012 Feb 20;196(4):545. PMID: 22270915; PMCID: PMC3265948. PS09/02111. DOI
  5. Rojas AM*, Santamaria A*, Malik R*, Jensen TS, Körner R, Morilla I, de Juan D, Krallinger M, Hansen DA, Hoffmann R, Lees J, Reid A, Yeats C, Wehner A, Elowe S, Clegg AB, Brunak S, Nigg EA, Orengo C, Valencia A, Ranea JA. Uncovering the molecular machinery of the human spindle--an integration of wet and dry systems biology. PLoS One. 2012; 7(3):e31813. doi: 10.1371/journal.pone.0031813. Epub 2012 Mar 9. PMID: 22427808; PMCID: PMC3302876. DOI
  6. Vallespinós M, Fernández D, Rodríguez L, Alvaro-Blanco J, Baena E, Ortiz M, Dukovska D, Martínez D, Rojas A, Campanero MR, Moreno de Alborán I. B Lymphocyte commitment program is driven by the proto-oncogene c-Myc. J Immunol. 2011 Jun 15;186(12):6726-36. doi: 10.4049/jimmunol.1002753. Epub 2011 May 13. PMID: 21572027. DOI
  7. Palczewska M, Casafont I, Ghimire K, Rojas AM, Valencia A, Lafarga M, Mellström B, Naranjo JR. Sumoylation regulates nuclear localization of repressor DREAM. Biochim Biophys Acta. 2011 May;1813(5):1050-8. doi: 10.1016/j.bbamcr.2010.11.001. Epub 2010 Nov 9. PMID: 21070824. DOI
  8. Mañes S, Fuentes G, Peregil RM, Rojas AM, Lacalle RA. An isoform-specific PDZ-binding motif targets type I PIP5 kinase beta to the uropod and controls polarization of neutrophil-like HL60 cells. FASEB J. 2010 Sep;24(9):3381-92. doi: 10.1096/fj.09-153106. Epub 2010 May 4. PMID: 20442317. DOI
  9. Cacas JL, Marmey P, Montillet JL, Sayegh-Alhamdia M, Jalloul A, Rojas-Mendoza A, Clérivet A, Nicole M. A novel patatin-like protein from cotton plant, GhPat1, is co-expressed with GhLox1 during Xanthomonas campestris-mediated hypersensitive cell death. Plant Cell Rep. 2009 Jan;28(1):155-64. doi: 10.1007/s00299-008-0622-x. Epub 2008 Oct 11. PMID: 18850102. DOI
  10. Krallinger M, Rojas AM, Valencia A. Creating reference datasets for systems biology applications using text mining. Ann N Y Acad Sci. 2009 Mar;1158:14-28. doi: 10.1111/j.1749-6632.2008.03750.x. PMID: 19348628. DOI
  11. Fuentes G, Oyarzabal J, Rojas AM*. Databases of protein-protein interactions and their use in drug discovery. Curr Opin Drug Discov Devel. 2009 May;12(3):358-66. PMID: 19396737.
  12. Mathieu-Daudé F, Lafay B, Touzet O, Lelièvre J, Parrado F, Bosseno MF, Rojas AM, Fatha S, Ouaissi A, Brenière SF. Exploring the FL-160-CRP gene family through sequence variability of the complement regulatory protein (CRP) expressed by the trypomastigote stage of Trypanosoma cruzi. Infect Genet Evol. 2008 May;8(3):258-66. doi: 10.1016/j.meegid.2007.12.010. Epub 2008 Jan 16. PMID: 18296127. DOI
  13. Bayón Y, Trinidad AG, de la Puerta ML, Del Carmen Rodríguez M, Bogetz J, Rojas A, De Pereda JM, Rahmouni S, Williams S, Matsuzawa S, Reed JC, Crespo MS, Mustelin T, Alonso A. KCTD5, a putative substrate adaptor for cullin3 ubiquitin ligases. FEBS J. 2008 Aug;275(15):3900-10. doi: 10.1111/j.1742-4658.2008.06537.x. Epub 2008 Jun 28. PMID: 18573101. DOI
  14. Proell M, Riedl SJ, Fritz JH, Rojas AM, Schwarzenbacher R. The Nod-like receptor (NLR) family: a tale of similarities and differences. PLoS One. 2008 Apr 30;3(4):e2119. doi: 10.1371/journal.pone.0002119. PMID: 18446235; PMCID: PMC2323615. DOI
  15. Sanchez-Pulido L, Valencia A, Rojas AM*. Are promyelocytic leukaemia protein nuclear bodies a scaffold for caspase-2 programmed cell death? Trends Biochem Sci. 2007 Sep;32(9):400-6. doi: 10.1016/j.tibs.2007.08.001. Epub 2007 Aug 10. PMID: 17693089. MIRG-CT-2005-016499, LSGH-CT-2005-518254 DOI
  16. López G, Rojas A, Tress M, Valencia A. Assessment of predictions submitted for the CASP7 function prediction category. Proteins. 2007; 69 Suppl 8:165-74. doi: 10.1002/prot.21651. PMID: 17654548. DOI
  17. Cases I, Pisano DG, Andres E, Carro A, Fernández JM, Gómez-López G, Rodriguez JM, Vera JF, Valencia A, Rojas AM*. CARGO: a web portal to integrate customized biological information. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W16-20. doi: 10.1093/nar/gkm280. Epub 2007 May 5. PMID: 17483515; PMCID: PMC1933121. MIRG-CT-2005-016499 DOI
  18. Jiménez-Baranda S, Gómez-Moutón C, Rojas A, Martínez-Prats L, Mira E, Ana Lacalle R, Valencia A, Dimitrov DS, Viola A, Delgado R, Martínez-A C, Mañes S. Filamin-A regulates actin-dependent clustering of HIV receptors. Nat Cell Biol. 2007 Jul;9(7):838-46. doi: 10.1038/ncb1610. Epub 2007 Jun 17. PMID: 17572668. MIRG-CT-2005-016499. DOI
  19. Grego-Bessa J, Luna-Zurita L, del Monte G, Bolós V, Melgar P, Arandilla A, Garratt AN, Zang H, Mukouyama YS, Chen H, Shou W, Ballestar E, Esteller M, Rojas A, Pérez-Pomares JM, de la Pompa JL. Notch signaling is essential for ventricular chamber development. Dev Cell. 2007 Mar;12(3):415-29. doi: 10.1016/j.devcel.2006.12.011. PMID: 17336907; PMCID: PMC2746361. DOI
  20. Sonnenberg A, Rojas AM, de Pereda JM. The structure of a tandem pair of spectrin repeats of plectin reveals a modular organization of the plakin domain. J Mol Biol. 2007 May 18;368(5):1379-91. doi: 10.1016/j.jmb.2007.02.090. Epub 2007 Mar 7. PMID: 17397861. MIRG-CT-2005-016499. DOI
  21. Cabrera JR, Sanchez-Pulido L, Rojas AM, Valencia A, Mañes S, Naranjo JR, Mellström B. Gas1 is related to the glial cell-derived neurotrophic factor family receptors alpha and regulates Ret signaling. J Biol Chem. 2006 May 19;281(20):14330-9. doi: 10.1074/jbc.M509572200. Epub 2006 Mar 20. PMID: 16551639. DOI
  22. Carro A, Tress M, de Juan D, Pazos F, Lopez-Romero P, del Sol A, Valencia A, Rojas AM*. TreeDet: a web server to explore sequence space. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W110-5. doi: 10.1093/nar/gkl203. PMID: 16844971; PMCID: PMC1538789. DOI
  23. Ana Rojas, David de Juan and Alfonso Valencia (2006). Molecular interactions: Learning from protein complexes. In Silico Technologies in Drug Target Identification and Validation, edited by Darryl León and Scott Markel, Volume 6 of Drug Discovery Series. Boca Raton, FL: CRC Press, Taylor & Francis Group, 2006. ISBN: 1-57444-478-6, 489 pages.
2005-1998
  1. de Juan D, Mellado M, Rodríguez-Frade JM, Hernanz-Falcón P, Serrano A, del Sol A, Valencia A, Martínez-A C, Rojas AM. A framework for computational and experimental methods: identifying dimerization residues in CCR chemokine receptors. Bioinformatics. 2005 Sep 1;21 Suppl 2:ii13-8. doi: 10.1093/bioinformatics/bti1101. PMID: 16204091. DOI
  2. Marmey P, Rojas-Mendoza A, de Kochko A, Beachy RN, Fauquet CM. Characterization of the protease domain of Rice tungro bacilliform virus responsible for the processing of the capsid protein from the polyprotein. Virol J. 2005 Apr 14;2:33. doi: 10.1186/1743-422X-2-33. PMID: 15831103; PMCID: PMC1087892. DOI
  3. Rojas AM, Sanchez-Pulido L, Fütterer A, van Wely KH, Martinez-A C, Valencia A. Death inducer obliterator protein 1 in the context of DNA regulation. Sequence analyses of distant homologues point to a novel functional role. FEBS J. 2005 Jul;272(14):3505-11. doi: 10.1111/j.1742-4658.2005.04759.x. PMID: 16008551. LSHG-CT-2004-503567 DOI
  4. Sánchez-Pulido L, Rojas AM, Valencia A, Martínez-A C, Andrade MA. ACRATA: a novel electron transfer domain associated to apoptosis and cancer. BMC Cancer. 2004 Dec 29;4:98. doi: 10.1186/1471-2407-4-98. PMID: 15623366; PMCID: PMC546010. DOI
  5. Rojas AM, Rios JEGL, Saux MF, Jimenez P, Reche P, Bonneau S, Sutra L, Mathieu-Daudé F, McClelland M. Erwinia toletana sp. nov., associated with Pseudomonas savastanoi-induced tree knots. Int J Syst Evol Microbiol. 2004 Nov;54(Pt 6):2217-2222. doi: 10.1099/ijs.0.02924-0. PMID: 15545461. DOI
  6. Jiménez Gómez PA, García de los Rios JE, Rojas Mendoza A, de Pedro Ramonet P, García Albiach R, Reche Sainz MP. Molecular basis of quinolone resistance in Escherichia coli from wild birds. Can J Vet Res. 2004 Jul;68(3):229-31. PMID: 15352551; PMCID: PMC1142146.
  7. Magnusson OT, Toyama H, Saeki M, Rojas A, Reed JC, Liddington RC, Klinman JP, Schwarzenbacher R. Quinone biogenesis: Structure and mechanism of PqqC, the final catalyst in the production of pyrroloquinoline quinone. Proc Natl Acad Sci U S A. 2004 May 25;101(21):7913-8. doi: 10.1073/pnas.0402640101. Epub 2004 May 17. PMID: 15148379; PMCID: PMC419531. DOI
  8. Sánchez-Pulido, L., Rojas AM, van Wely KH, Martínez-A.C, Valencia A. 2004. SPOC: a widely distributed domain associated with cancer, apoptosis and transcription. BMC Bioinformatics. 5:91. PMID: 15239844 | DOI: 10.1186/1471-2407-4-98 DOI
  9. Reed JC, Doctor K, Rojas A, Zapata JM, Stehlik C, Fiorentino L, Damiano J, Roth W, Matsuzawa S, Newman R, Takayama S, Marusawa H, Xu F, Salvesen G, Godzik A; RIKEN GER Group; GSL Members. Comparative analysis of apoptosis and inflammation genes of mice and humans. Genome Res. 2003 Jun;13(6B):1376-88. doi: 10.1101/gr.1053803. PMID: 12819136; PMCID: PMC403667. DOI
  10. Reche MP, Echeita MA, de los Rios JE, Usera MA, Jiménez PA, Rojas AM, Colás J, Rodriguez I. Comparison of phenotypic and genotypic markers for characterization of an outbreak of Salmonella serotype Havana in captive raptors. J Appl Microbiol. 2003; 94(1):65-72. doi: 10.1046/j.1365-2672.2003.01791.x. PMID: 12492925. DOI
  11. Liu T*, Rojas A*, Ye Y, Godzik A. 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 Sci. 2003 Sep;12(9):1872-81. doi: 10.1110/ps.0359603. PMID: 12930987; PMCID: PMC2323985. DOI
  12. Alonso, A., Rojas, A., Godzik, A., Mustelin, T. (2004). The dual-specific protein tyrosine phosphatase family. In: Ariño, J.n., Alexander, D.R. (eds) Protein Phosphatases. Topics in Current Genetics, vol 5. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-40035-6_16 DOI
  13. Reche MP, Jiménez PA, Alvarez F, García de los Rios JE, Rojas AM, de Pedro P. Incidence of salmonellae in captive and wild free-living raptorial birds in central Spain. J Vet Med B Infect Dis Vet Public Health. 2003 Feb;50(1):42-4. doi: 10.1046/j.1439-0450.2003.00623.x. PMID: 12710500. DOI
  14. Reche MP, García de los Ríos JE, Jiménez PA, Rojas AM, Rotger R. gyrA Mutations associated with nalidixic acid-resistant salmonellae from wild birds. Antimicrob Agents Chemother. 2002 Sep;46(9):3108-9. doi: 10.1128/AAC.46.9.3108-3109.2002. PMID: 12183286; PMCID: PMC127419. DOI
  15. Rojas A, Doolittle RF. The occurrence of type S1A serine proteases in sponge and jellyfish. J Mol Evol. 2002 Dec;55(6):790-4. doi: 10.1007/s00239-002-2361-x. PMID: 17476731. Wrongly indexed by PubMed in 2006 DOI
  16. Alvarez Dávila F, García de los Ríos JE, Jiménez P, Rojas A, Reche P., Troya, M.. Phenotypic variability in different strains of Pseudomonas syringae subsp. savastanoi isolated from different hosts. Eur. J. Plant Pathol. 1998, 104:603-609 DOI: 10.1023/A:1008604011154 DOI
  17. García de los Ríos J.E., Jiménez P., Reche P., Rojas A., Colás J., Gallego M. y Corroto M. (2001) Incidencia de microorganismos Gram-positivos en el programa de cría de cernícalo primilla en el Hospital de Fauna Salvaje de GREFA. En: En: Biologí¬a y Situación del Cerní¬calo Primilla. Ed. GREFA- Comunidad de Madrid. 2001. Pp:101-106 (Spanish).
  18. Jiménez P., Rojas A., Reche P., García de los Ríos J.E., Colás J., Gallego M. y Corroto M. (2001) Casos clí¬nicos en cerní¬calos primilla atendidos en GREFA durante el año 1999. En: Biologí¬a y Situación del Cerní-calo Primilla. Ed. GREFA- Comunidad de Madrid. 2001. Pp: 113-117 (Spanish).
  19. Jiménez P., Reche P., Rojas A., Colás J., Gallego M., Corroto M. y García de los Ríos J.E. (2000) Microbiota Gram-negativa normal en cloaca de cerní¬calo primilla: incidencia en huevos abortados en el programa de cria. . En: En: Biologí¬a y Situación del Cerní¬calo Primilla. Ed. GREFA- Comunidad de Madrid. 2000. Pp.107-112 (Spanish).

Funding

Competitive projects and innovation

Current and recent funding

  • CONVERGE (PID2024-162736OB-I00), 2025-2028. Principal Investigator on molecular convergence in evolution at planetary scale.
  • 2025AEP078, 2025. CSIC support project at CABD. Principal Investigator.
  • AndaluciaConCiencia (FCT-24-20159), 2025. Research team member.
  • FAIRFUN4Biodiversity, OSCARS-EOSC, 2025-2027. CABD PI and consortium co-lead for AI-based functional annotation of biodiversity genomics resources.
  • MULTIMORPH (PID2021-127503OB-I00), from 2022. Principal Investigator on the metamorphic capabilities of multifunctional proteins.
  • 2021AEP065, 2021. CSIC support project at CABD. Principal Investigator.
  • María de Maeztu / CABD (CEX2020-001088-M). Unit guarantor within the CABD excellence framework.
  • María de Maeztu / CABD (MDM-2016-0687), 2017-2021. Member of the unit from 2018.
  • DescriptEvol (RTI2018-096735-B-I00), 2019-2022. Principal Investigator on protein evolution through computational descriptors.
  • Advanced diagnostic tools for CoQ deficiency syndrome (P18-RT-4572), 2020-2022. Research team member.
  • PS09/02111, 2009-2013. Principal Investigator on inflammatory disease and colon cancer links through in silico analysis.

Earlier European and international projects

  • Marie Curie IRG (MIRG-CT-2005-016499), 2006-2009. Principal Investigator on CAPFM, a knowledge network portal for cancer and apoptotic functional modules.
  • ITRIBIS (FP7-REGPOT-2012-2013-1), 2013-2016. Research team member in the European program to strengthen translational research capacity at IBiS.
  • ENFIN (LSGH-CT-2005-518254), 2005-2011. Investigator in the European Experimental Network for Functional Integration.
  • COMBIO (LSGH-CT-2004-503568), 2004-2007. Investigator in the European project bringing computational biology to the bench.
  • GENEFUN (LSGH-CT-2004-503567), 2004-2008. Investigator in a European project on in silico prediction of gene function.
  • NIH-1P01-63201, 2001-2003. Investigator in Adam Godzik’s group on data mining approaches to apoptosis regulation.
  • NASA-NSCORT Fellowship, 2000-2001. Competitive postdoctoral fellowship at UC San Diego focused on evolutionary and structural bioinformatics.

Transfer and innovation

  • Cátedra ENIA Google Spain - University of Seville in Artificial Intelligence, 2024-2026. Member of the research team.
  • Service contracts with REPSOL under confidentiality agreement, 2015.
  • Patent: Cepas de Mycobacterium hipermutables (P201531949), Spain and UK, 2015.
  • Open computational resources and pipelines developed across multiple projects.

Leadership

Scientific service, networks, and representation

Scientific leadership

  • Director of the Department of Evolutionary Dynamics, CABD, since 2026.
  • Track Chair and Executive Committee member of Function COSI since 2023.
  • Executive Committee member of the CSIC network BCB.HUB since 2023.
  • Coordinator of the PAIDI excellence group CBIOEVOL since 2023.
  • Member of the CSIC network Life.Hub since 2022.
  • Founding member and elected Research Officer of SEBiBC, 2022-2024.

Evaluation and advisory roles

  • Scientific Advisory Board member, Institut de Génétique & Développement de Rennes, since 2025.
  • President and External Scientific Committee member, IMIB-Arrixaca, since 2019.
  • I serve as Associate Editor of NAR Genomics and Bioinformatics (NARGAB).
  • Evaluator for AEI, ANR, BBSRC, La Caixa, Ikerbasque, European Commission panels, and other international programs.
  • Regular member of academic and research evaluation committees at CSIC, ISCIII, and universities.

Visibility

Invited talks, international activity, and conference organization

Recent invited and selected talks

  • ISMB/ECCB 2026, Washington DC. Selected talk on protein embeddings and functional specificity.
  • Journal of Molecular Evolution Symposium 2025, Madrid. Invited plenary on transformers, protein function, and similarity.
  • ISMB/ECCB 2025, Liverpool. Selected talk on protein language models in functional annotation.
  • Barcelona Supercomputing Center seminar 2025. Talk on decoupling function from evolutionary conservation using protein language models.
  • Invited seminars in Murcia, Bordeaux, Malaga, and Seville on dark proteomes, function annotation, and AI-based approaches.

International profile

  • About six years of postdoctoral and early-career research in the United States.
  • Long-term collaborations across Europe and the United States through Marie Curie, ENFIN, Epigenesys, and EOSC-linked initiatives.
  • Teaching, seminars, and conference participation in Spain, the UK, France, Italy, Poland, Morocco, Singapore, Mexico, and the USA.

Conference organization

  • Organizer for Function COSI activities at ISMB 2024, 2025, and 2026.
  • Scientific committee member for SEBiBC congresses and JBI/ELIXIR meetings.
  • Local organizer or steering contributor for ECCB 2022 and multiple earlier Spanish and European bioinformatics meetings.
  • Lead organizer of the 2014 Bioinformatics Meeting in Seville with competitive event funding and student travel support.

Outreach

Public engagement and communication

Structured programs

  • Ciencia en el Barrio, CSIC, since 2023, with the workshop La llave de tu ADN.
  • Repeated participation in 11F activities for schools across Seville province since 2018.
  • European Researchers’ Night 2026: El ChatGPT de las proteínas.

Schools and public events

  • Visits and talks at IES Letanias, Ramón Carande, Santa Aurelia, Félix Rodríguez de la Fuente, Rodrigo Caro, Los Álamos, Albero, Fernando de Herrera, San Francisco de Paula International School, and other schools.
  • Pint of Science 2019: Secuencias de ADN, el asesino vivía en Sacramento.
  • Semana de la Ciencia y la Tecnología CSIC 2019: Enróllate con un científico.

Training

Supervision, teaching, and academic formation

Doctoral supervision

  • I currently supervise PhD research by Antonio Velasco, Enrique Alanís Domínguez, Patricia Medina Burgos, and Alex Domínguez.
  • I have supervised completed doctoral research by Eduardo Andrés León, Aida Arcas Mantas, and Eduard Porta-Pardo.
  • I also supervise visiting researchers and project-linked trainees in protein language models, structural bioinformatics, and multifunction prediction.

Master’s and undergraduate mentoring

  • My master’s supervision includes Alberto del Cueto, Nazaret Navarro Cruz, Patricia Medina Burgos, Rocío Núñez Torres, Álvaro Ponce Cabrera, Joel López, Aida Arcas Mantas, Clara Muñoz, Javier García Flores, and Marta Sotelo Montoro.
  • My undergraduate supervision includes Gabriel Jiménez, Francisco José Ruiz Mota, Javier Tubio, and earlier project students.

Teaching

  • I coordinate and teach Aplicaciones y Discusiones en Medicina Clínica in the Máster Universitario en Análisis de Datos Ómicos y Biología de Sistemas (MADOBIS), jointly offered by UNIA and the University of Seville.
  • I teach in the Máster Universitario en Investigación Biomédica, University of Seville, through the Department of Genetics.
  • I teach in the Data Science y Big Data master’s program, University of Seville.
  • I am an external lecturer in the doctoral program Ingeniería, Ciencia de Datos y Bioinformática.
  • I have been an external lecturer in the UPO doctoral program in Biotechnology, Engineering and Chemical Technology since 2018.
  • I have also taught in master’s and doctoral programs in Barcelona and Madrid, and in international courses including EMBO and COST activities.