Welcome
The Computational Biology and Bioinformatics Group was founded on 2009 in Barcelona, and moved to Seville in 2013. Our research has resulted in more than 60 peer-reviewed articles, book chapters, invited reviews, and over 50 oral presentations in national and international venues. CBBIO is a garantor of the renewed accreditation of Excellence "Maria de Maeztu" Unit, from the Spanish Excellence Centers Network (SOMMA).
We are a team of computational biologists and engineers using computational methods aiming to make sense about protein function, and we are currently located at the Andalusian Center for Developmental Biology (CABD-CSIC), in beautiful Seville (Spain).
Main Focus
The main line of CBBIO's research focuses on identifying multifunctionality in proteins of biotechnological and biomedical interest using modern machine learning technologies.
Our questions:
- How do proteins evolve?
- How mutations impact function?
- How to better define "protein function" to address automatic annotation?
Publications
Selected Highlights
- EDITOR's Choice. Protein LMs benchmark for function annotation: Decoding proteome functional information in model organisms using protein language models. (2024).
- Protein LMs, developing the ProtT5-based FANTASIA tool: Illuminating the functional landscape of the dark proteome across the Animal Tree of Life through natural language processing models. (2024).
- Identifying allosteric pathways: The multivalency of the glucocorticoid receptor ligand-binding domain explains its manifold physiological activities. (2022).
- Bacterial origins of sterol: Origin and Evolution of Polycyclic Triterpene Synthesis. (2020).
- Integration of -omics data using linear models: Novel miRNA-mRNA interactions conserved in essential cancer pathways. (2017).
- Discovery of a novel MMR pathway in prokaryots: A non-canonical mismatch repair pathway in prokaryotes. (2017)
- Emergence of DDR pathways: Emergence and evolutionary analysis of the human DDR network: implications in comparative genomics and downstream analyses. (2014).
- Identifying novel RAS superfamily of proteins The Ras protein superfamily: Evolutionary tree and role of conserved amino acids. (2012).
Since 2009
- Barrios-Núñez, Israel; Martínez-Redondo, Gemma; Medina-Burgos, Patricia; Cases, Ildefonso; Fernández, Rosa; Rojas, Ana. 2023. Decoding proteome functional information in model organisms using protein language models.
- Martínez-Redondo, Gemma;Barrios-Núñez, Israel; Vázquez-Valls,Marçal, Rojas Ana M, Fernández, Rosa; 2024. Illuminating the functional landscape of the dark proteome across the Animal Tree of Life through natural language processing models.
- Alegre-Marti, A. et al., 2023. A hotspot for post-translational modifications on the androgen receptor dimer interface drives pathology and resistance to anti-androgens. Science Advances.
- Jimenez-Panizo, A. et al., 2022. The multivalency of the glucocorticoid receptor ligand-binding domain explains its manifold physiological activities. Nucleic Acids Research
- Mencucci, MV; Rojas-Mendoza, AM; Andres-León, E; Lisi-Roman, C; Gagliardino, JJ; Abba, MC; Maiztegui, B. 2022 Identification of novel microRNAs associated with type 2 diabetes by an integrative bioinformatic analysis. Human Gene In press.
- Verdugo-Sivianes, EM; Rojas, AM; Muñoz-Galván, S.; Otero-Albiol, D.; Carnero, A. 2020. Mutation of SPINOPHILIN (PPP1R9B) found in human tumors promotes the tumorigenic and stemness properties of cells. Theranostics
- Santana-Molina, C; Rivas-Marin, E; Rojas, AM*; & Devos, D.P.* 2020. Origin and evolution of polycyclic triterpene synthesis. Molecular Biology and Evolution
- Martín-Doncel, E.; Rojas, AM; Cantarero, L; & Lazo, P.A. 2019. To VRK1 functional insufficiency due to alterations in protein stability or kinase activity of human VRK1 pathogenic variants implicated in neuromotor syndromes. Scientific Reports
- Jiménez-Panizo, A.; Pérez, P.; Rojas, A.; Fuentes-Prior, P.; Estébanez-Perpiña, E. 2019. Non-canonical dimerization of the androgen receptor and other nuclear receptors: implications for human disease. Endocrine Related Cancer.
- Andrés-León, E; Rojas, AM. 2019. miARma-Seq, a comprehensive pipeline for the simultaneous study and integration of miRNA and mRNA expression data. METHODS.
- Fuentes-Prior, P; Rojas, A; Hagler, AT; Estébanez-Perpiña, E. 2018. Diversity of Quaternary Structures Regulates Nuclear Receptor Activities. Trends in Biochemical Sciences.
- Silva, J.; et. al., 2018. EXD2 governs germ stem cell homeostasis and lifespan by promoting mitoribosome integrity and translation. Nature Cell Biology DOI:10.1038/s41556-017-0016-9
- López-Jiménez, E; Rojas, AM; Andrés-León, E. 2018. RNA sequencing and Prediction Tools for Circular RNAs Analysis. Adv. Exp Med Biol.
- Andrés-León, E.; Cases, I.; Alonso, S.*; and Rojas, A.M.* 2017. Novel miRNA-mRNA interactions conserved in essential cancer pathways. Scientific Reports .
- Castañeda-García, A; et. al., - Rojas, A.M.*; Doherty, A.J.*; & Blazquez, J.* 2017. A non-canonical mismatch repair pathway in prokaryotes. Nature Communications
- Andrés-León, E.; Cases, I.; Arcas, A.; & Rojas, A.M. 2016. DDRprot: a database of DNA damage response-related proteins. DATABASE DOI: 10.1093/database/baw123
- Tristán-Clavijo E, G.-Scholl F, Macaya A, Iglesias G, Rojas AM, Lucas M, Castellano A, Martinez-Mir A. 2016. Dominant-negative mutation p.Arg324Thr in KCNA1 impairs Kv1.1 channel function in episodic ataxia. Movement Disorders.
- Andrés-León E, Núñez-Torres R, & Ana M Rojas. 2016. miARma-Seq: a comprehensive tool for miRNA, mRNA, and circRNA analysis. Scientific Reports.
- Terré B, et. al., 2016. GEMC1 is a critical regulator of multiciliated cell differentiation. EMBO Journal.
- Lacalle RA, Karam JC, Martínez-Muñoz L, Aretxe I, Peregil RM, Sot J, Rojas AM, Goi FM, Mellado M, & Mañes. 2015. Type I PIP5 kinase homo- and heterodimerization determines its membrane localization and activity. FASEB Journal.
- Arcas A, Fernández-Capetillo O, Cases I, & Rojas AM. 2014. Emergence and evolutionary analysis of the human DDR network: implications in comparative genomics and downstream analyses. Molecular Biology and Evolution.
- Basilico F, et al.2014. The pseudo GTPase CENP-M drives human kinetochore assembly. Elife.
- Tzou W-S, et al. 2014. Molecular evolution of multiple-level control of heme biosynthesis pathway in the animal kingdom. PLOS One.
- Arcas A, Cases I, & Rojas AM. 2013. Serine/Threonine Kinases and E2-ubiquitin conjugating enzymes in Planctomycetes: unexpected findings. Antonie van Leeuwenhoek Journal of Microbiology. .
- Athiyarath R, et al. 2013. Two novel missense mutations in iron transport protein transferrin causing hypochromic microcytic anaemia and haemosiderosis: molecular characterization and structural implications. Journal of British Haematology. .
- Pons T, Paramonov I, Boullosa C, Ibáñez K, Rojas AM, & Valencia A. 2013. A common structural scaffold in CTD phosphatases that supports distinct catalytic mechanisms. Proteins. .
- López-Contreras, AJ., et al. 2013. A proteomic characterization of factors enriched on nascent DNA molecules. Cell Reports. .
- Rojas, A.M.*, Santamaria, A.*, Malik, R.*, et al., 2012. Uncovering the molecular machinery of the human spindle - an integration of wet and dry systems biology. PLOS One. [.
- Rojas, A.M.*, et al. 2012. The Ras protein superfamily: Evolutionary tree and role of conserved amino acids. The Journal of Cell Biology. .
- Vallespinós, M., et. al., 2011. B Lymphocyte Commitment Program Is Driven by the Proto-oncogene c-myc. The Journal of Immunology.
- Palczewska, M., et al. 2011. Sumoylation regulates nuclear localization of repressor DREAM. Biochimica et Biophysica Acta.
- Mañes, S., Fuentes, G., Peregil, R.M., Rojas, A.M., and 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. FASEB Journal. 24:3381-3392. PMID: 20442317 | DOI: 10.1096/fj.09-153106.
- Fuentes, G., Oyarzábal, J., Rojas, A.M. 2009. Databases of protein-protein interactions and their uses in drug discovery. Current Opinion in Drug Discovery and Development.
- Krallinger, M., Rojas, A.M., and Valencia, A. 2009. Creating reference datasets for Systems Biology applications using text mining. Annals of the New York Academy of Sciences. [
- Cacas, J., Marmey, P., Montillet, J.L., Sayegh-Alhamdia, M., Jalloul, A., Rojas-Mendoza, A.M., Cleviret, A., Michel, N. 2009. A novel patatin-like protein from cotton plant, GhPat1, is co-expressed with GhLox1 during Xanthomonas campestris-mediated hypersensitive cell death. Plant Cell Reports.
People
Current Team Members
- Ildefonso Cases . Associated Investigator, CSIC tenured scientist (Científico Titular), Bioinformatics and Computational Biology.
- Francisco Miguel Pérez Canales PhD student, Engineer and programmer.
- Enrique Alanís Domínguez - PhD student, Biologist.
- Patricia Medina - PhD student, Biotechnologist.
- Francisco José Ruiz - Grad Student.
TFM students
- Gabriel Jiménez - at CABD (2024)
- Alberto del Cueto - at CABD (2024)
- Nazaret Navarro - at CABD (2022)
- Antonio Parra - at CABD (2019)
- Alba Gutiérrez - at IMPPC (2010). TFM. Now lecturer at Harvard, USA.
- Joel López - at IMPPC (2010). TFM. Now CTO at BTC assesors, Andorra.
Visitors
- Cayetano Navas - at CABD (2024). PhD researcher, Marta Glez-Freire's lab, ES.
- Gemma Martínez - at CABD (2022). PhD researcher, Rosa Fernández lab, ES.
- M Victoria Mencucci at CABD (2019). Posdoctoral researcher, ARG.
- Jake Fowler - at CABD (2024). PhD researcher, Paul Taylor's lab, UK.
- Sandra Moreu - at CABD (2024). PhD researcher, Marián Ros lab, ES.
Former
- Israel Barrios - at CABD (2019-2023). Engineer and programmer. Now national security.
- Iuan A Cordero - at IBIs (2016-2018). Technician. Now Bioinformatician at the IBIS.
- Eduardo Andrés - at CABD (2014-2016). PhD student, now Technical Head of the Bioinformatics Unit at IPBLN.
- Rocio Núñez - at IBIS (2014-2016). MS student, Now at CNIO, Madrid.
- Aida Arcas - at IMPPC (2010-2013). PhD student. Now Senior Bioinformatician at Clarivate, Madrid.
- Eduard Porta - at IMPPC(2010-2013).PhD student. Now Junior Group Leader at IJC, Barcelona.
- Ida Paramonov - at IMPPC(2011-2013). Programmer and data analyst. Now Data analyst at CNAG, Barcelona.
Main Collaborators
- Dr. Rosa Fernández (CSIC Tenured Researcher, IBE, Barcelona, Spain).
- Dr. Aureliano Bombarely (CSIC Research Professor, IBMPC, Valencia, Spain).
- Dr. Eva Estébanez-Perpiña (Professor. IBUB, Barcelona, Spain).
- Prof. Harald Wodrich (Director of Research, MPF-CNRS, Bordeaux, France).
- Prof. Paul Taylor (Professor, University of Leeds, UK).
- Dr. Travis H Stracker (now NIH, US).
- Pr. Jesús Blázquez-Gómez (CNB-CSIC, Madrid)
- Dr. Sergio Alonso (IGTP, Barcelona)
- Dr. Silvia Salas (Profesor. CABD-UPO, Sevilla, Spain).
- Dr. Fernando Casares (Research Prof. CABD-CSIC, Sevilla, Spain)
- Dr. Damien Devos (Prof. Lille,FR)
- Dr. Amancio Carnero (Research Prof. IBIS, Sevilla)
- Dr. Alfonso Valencia (Life Sciences Dept. Director, BSC, Barcelona)
The Lab head
Ana M Rojas
ORCID |
Email: a.rojas.m@csic.es |
LinkedIn |
Google Scholar |
Bluesky
Ana M. Rojas is a Research Scientist at CSIC. Her main expertise focuses on protein evolution and function. 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. Ana M. Rojas is a Research Scientist at CSIC. Her main expertise focuses on protein evolution and function. Her research has made a dual impact—advancing fundamental scientific knowledge while exploring biomedical applications. With deep expertise in protein family analysis, she was the first to analyze RIKEN sequences related to apoptosis, providing key insights into the mechanisms of NLR proteins, and identifying novel members of the RAS protein family within a comparative and evolutionary framework of small GTPases. Her collaborations with experimental groups include identifying target proteins involved in HIV infection and contributing to recent studies on the multifunctionality of nuclear receptor families, particularly the glucocorticoid receptor (GR), and the and androgen receptor (AR), as well as oncoproteins that hold great potential for with significant potential for identifying therapeutic targets. Notably, her discovery of a new DNA repair pathway in bacteria offers promising therapeutic strategies for combating antibiotic resistance. Her contribution on the bacterial origin of sterols has also shed light on one of the most debated topics in the origin of eukaryotes. On the computational side, her team has developed tools for data integration and transcriptomic analysis, and is working on methods to predict protein multifunctionality. Their recent work on benchmarking protein language
models functional annotation is among the first to further address large-scale annotation for
non-model organisms.
Short BIO
Scientific highlights