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:

Publications

Selected Highlights
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)