About

FOCUS on protein function and evolution.

We are a team of computational biologists, biotechnologists, and engineers using computational methods aiming to make sense about protein function using AI-based methodologies.

The Computational Biology and Bioinformatics Group:

Was founded on 2009 in Barcelona (IMPPC, now IGTP), and moved to Seville at IBIS in 2013, and later in 2018 at CABD.
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
Past members are currently PI's, technical supervisors of Bioinformatics facilities, or work in Industry.
CBBIO is a garantor of the renewed accreditation of Excellence "María de Maeztu" Unit, from the Spanish Excellence Centers Network (SOMMA).

Our Research

How do proteins evolve?
How do proteins (multi)-function?
How to better define "protein function" to address automatic annotation?

Highlighted contributions (all times)

Testing protein language models for functional annotation: Decoding proteome functional information in model organisms using protein language 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).

CBBIO github

People

Ana M. Rojas Mendoza	CBBIO's Principal Investigator Research CSIC scientist (Inv. científica)	Find About me
Ildefonso Cases Díaz	Tenured CSIC scientist (Científico Titular) CBBIO's Associate Investigator CABD Bioinformatics Unit Head	icasdia@upo.es
Patricia Medina Burgos	Biotechnologist PhD student, will defend in 2025	CBBiO
Francisco M. Pérez Canales	Engineer, Information systems in Biology PhD student in Comp. Science	fmpercan@upo.es
Enrique Alanís Domínguez	Biologist PhD student	ealadom@upo.es

Name	Past position	Current Position
Eduardo Andrés León (2014-2016)	PhD student (defended in 2017)	Tenured scientist (CT) CSIC at IPBLN-CSIC. Granada. Spain.
Juan A. Cordero Varela (2016-2018)	Technician (at IBIS)	Technical supervisor of the Bioinformtics Unit, IBIS, Seville. Spain.
Rocío Nuñez Torres (2016)	UOC, Master's student	Researcher at CNIO, Madrid. Spain.
Eduard Porta Pardo (2012-2013)	PhD student (defended in 2013).	Junior Group Leader, Inst. Josep Carreras, Barcelona. Spain.
Aida Arcas Manta (2010-2013)	PhD student (defended in 2013).	Senior Bioinformatician at Clarivate inc.
Israel Barrios Núñez (2019-2023)	Technician, engineer.	Cuerpo Nacional de Policía (CNP)
Ida Paramonov (IMPPC, 2011-2013)	Programmer and data analyst.	Now Data analyst at CNAG, Barcelona. Spain.

Alex Domínguez Rodríguez (at CABD)	TFM student	UAB, Barcelona.
Francisco José Ruiz Mota (at CABD)	Graduate student	University of Seville.
Alberto del Cueto (at CABD)	Master´s	UOC.
Gabriel Jiménez Reyes (at CABD)	TFM (2024).	VIU, Valencia.
Nazaret Navarro Cruz (at CABD, 2022)	Master's	MADOBIS, Sevilla.
Antonio Parra Sevilla (at CABD, 2019)	TFM	Univ. Vigo.
Alba Gutiérrez (at IMPPC, 2010)	TFM.	Lecturer at Harvard Univ, USA.
Joel López Bercianos(at IMPPC, 2010)	TFM	CTO at BTC assessors, Andorra.

Name	Reference lab
Cayetano Navas Enamorado	PhD researcher, Marta González-Freire's lab, ES. (2024)
Jake Fowler	PhD researcher, PhD researcher, Paul Taylor's lab, UK (2024)
Sandra Moreu	PhD researcher, Marián Ros lab, ES. (2024)
Gemma Martínez Redondo	PhD researcher, Rosa Fernández lab. (2022)
M Victoria Mencucci	Posdoctoral researcher, Univ de la Plata, ARG. (2019)

Dr. Rosa Fernández	(CSIC Tenured Researcher, IBE, Barcelona, Spain).
Prof. Katharina Hoff	(Univ of Greifswald. Germany.
Prof. Aureliano Bombarely	(CSIC Research Professor, IBMPC, Valencia, Spain).
Prof. 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. Silvia Salas	Profesor. CABD-UPO, Sevilla, Spain).
Prof. Paul Taylor	(Professor, University of Leeds, UK)
Prof. Fernando Casares	(Research Prof. CABD-CSIC, Sevilla, Spain)
PDr. Amancio Carnero	(Research Prof. IBIS, Sevilla)
Prof. Alfonso Valencia	(Life Sciences Dept. Director, BSC, Barcelona)

PI's (Short) Biosketch

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.

Publications (since 2009)

Barrios-Núñez, I.; Martínez-Redondo, G.; Medina-Burgos, P.; Cases, I.; Fernández, R; Rojas, A.M. 2024. Decoding proteome functional information in model organisms using protein language models (ref).
Martínez-Redondo, G;Barrios-Núñez, I; Vázquez-Valls,M, Rojas AM, Fernández, R; 2024. Illuminating the functional landscape of the dark proteome across the Animal Tree of Life through natural language processing models.
Special dossier about AI (in Spanish), outreach. "La inteligencia artificial en biociencias", by the Spanish Society for Molecular Biology and Biochemistry (ref).
Verdugo-Sivianes EM, Espinosa-Sánchez A, Cases I, Rojas AM, Otero-Albiol D, Romero L, Blanco JR, Carnero A. 2024 MEG8 as an antagonistic pleiotropic mechanism in breast cancer (ref).
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. (ref).
Jimenez-Panizo, A. et al., 2022. The multivalency of the glucocorticoid receptor ligand-binding domain explains its manifold physiological activities. Nucleic Acids Research (ref).
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 (ref).
Santana-Molina, C; Rivas-Marin, E; Rojas, AM*; & Devos, D.P.* 2020. Origin and evolution of polycyclic triterpene synthesis. Molecular Biology and Evolution (ref).
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 (ref).
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. (ref).
Andrés-León, E; Rojas, AM. 2019. miARma-Seq, a comprehensive pipeline for the simultaneous study and integration of miRNA and mRNA expression data. METHODS.(ref).
Fuentes-Prior, P; Rojas, A; Hagler, AT; Estébanez-Perpiña, E. 2018. Diversity of Quaternary Structures Regulates Nuclear Receptor Activities. Trends in Biochemical Sciences. (ref).
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 (ref).
López-Jiménez, E; Rojas, AM; Andrés-León, E. 2018. RNA sequencing and Prediction Tools for Circular RNAs Analysis. Adv. Exp Med Biol. <(ref).
Andrés-León, E.; Cases, I.; Alonso, S.*; and Rojas, A.M.* 2017. Novel miRNA-mRNA interactions conserved in essential cancer pathways. Scientific Reports (ref).
Castañeda-García, A; et. al., - Rojas, A.M.*; Doherty, A.J.*; & Blazquez, J.* 2017. A non-canonical mismatch repair pathway in prokaryotes. Nature Communications (ref).
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 (ref).
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. (ref).
Andrés-León E, Núñez-Torres R, & Ana M Rojas. 2016. miARma-Seq: a comprehensive tool for miRNA, mRNA, and circRNA analysis. Scientific Reports. (ref).
Terré B, et. al., 2016. GEMC1 is a critical regulator of multiciliated cell differentiation. EMBO Journal. (ref).
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. (ref).
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. (ref).
Basilico F, et al.2014. The pseudo GTPase CENP-M drives human kinetochore assembly. Elife. (ref).
Tzou W-S, et al. 2014. Molecular evolution of multiple-level control of heme biosynthesis pathway in the animal kingdom. PLOS One. (ref).
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. (ref).
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. (ref).
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. (ref).
López-Contreras, AJ., et al. 2013. A proteomic characterization of factors enriched on nascent DNA molecules. Cell Reports. (ref).
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. (ref).
Rojas, A.M.*, et al. 2012. The Ras protein superfamily: Evolutionary tree and role of conserved amino acids. The Journal of Cell Biology. (ref).
Vallespinós, M., et. al., 2011. B Lymphocyte Commitment Program Is Driven by the Proto-oncogene c-myc. The Journal of Immunology. (ref).
Palczewska, M., et al. 2011. Sumoylation regulates nuclear localization of repressor DREAM. Biochimica et Biophysica Acta. (ref).
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. (ref).
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. (ref).
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. (ref).
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. (ref).

Contact

We are always open to informal requests to join the lab. Contact Ana (+(34) 954 977 373,) or Alonso directly, or any member of the group listed above.

Location

CBBIO is currently located at the Andalusian Center for Developmental Biology (CABD-CSIC), in beautiful Seville (Spain).

Map location to Universidad Pablo de Olavide. Carretera de Utrera km1, 41013 Sevilla,Spain

CABD Phone: +34 954977911 - To call from a UPO phone: 67911, Security: +34 954349200; Fax: +34 954349376

About

FOCUS on protein function and evolution.

Our Research

People

Current People

Former People

TFM and grad students

Visitors

Collaborators

PI's (Short) Biosketch

Publications (since 2009)

Contact

Location