Our Questions
- How do proteins evolve?
- How do proteins (multi)-function?
- How to better define "protein function" to address automatic annotation?
Understanding protein function and evolution
At CBBiO we approach protein function and evolution combining computational biology and protein language models.
We are a team of computational biologists, biotechnologists, and engineers using computational methods aiming to make sense about protein function using AI-based methodologies.
- 2009Group founded
- 60+Peer-reviewed outputs
- CABDCurrent home in Seville
Research
Our questions, methods, and resources
Our Methods
- Protein language models
- Sequence/structure/function computational biology
- Data analyses
Selected Work
Highlighted contributions (all times)
Embeddings to the rescue
Rethinking molecular evolution through protein language model embeddings.
PublicationFANTASIA suite: protein language models for functional discovery
FANTASIA leverages language models to decode the functional dark proteome across the animal tree of life.
CBBIO/FANTASIA, CBBIO/FANTASIA-Lite
PublicationTesting protein language models for functional annotation
Decoding proteome functional information in model organisms using protein language models.
PublicationIdentifying allosteric pathways
The multivalency of the glucocorticoid receptor ligand-binding domain explains its manifold physiological activities.
PublicationBacterial origins of sterol
Origin and Evolution of Polycyclic Triterpene Synthesis.
PublicationIntegration of -omics data using linear models
Novel miRNA-mRNA interactions conserved in essential cancer pathways.
PublicationDiscovery of a novel MMR pathway in prokaryots
A non-canonical mismatch repair pathway in prokaryotes.
PublicationEmergence of DDR pathways
Emergence and evolutionary analysis of the human DDR network: implications in comparative genomics and downstream analyses.
PublicationIdentifying novel RAS superfamily of proteins
The Ras protein superfamily: Evolutionary tree and role of conserved amino acids.
PublicationPeople
Current group
Ana M. Rojas Mendoza
Principal Investigator
Research Scientist, CSIC · Director, Evolutionary Dynamics, CABD
Ildefonso Cases Díaz
Associate Investigator
Tenured CSIC Scientist · CABD Bioinformatics Unit Head
Antonio Pérez Velasco
PhD Student
Biology · computational methods
Enrique Alanís Domínguez
PhD Student
Biology · computational methods
Alex Domínguez Rodríguez
PhD Student
xAI for multifunction prediction
Sergio Valdivia Moral
Programmer Technician
Technical support, programming, and Machine LearningMS
Marta Sotelo Montoro
TFM Student
JAE-ICURecent supervised students include Javier Tubio (TFG).
Former Members
Alumni and recent lab trajectory
- Patricia Medina Burgos. Biotechnologist. Former PhD student in computational biology.
- Francisco M. Pérez Canales. Engineer in information systems in biology. Former PhD student in computational science.
- Eduardo Andrés León. PhD student, 2014-2016. Defended in 2017. Now CSIC Tenured Scientist at IPBLN-CSIC, Granada.
- Juan A. Cordero Varela. Technician at IBiS, 2016-2018. Now Technical Supervisor of the Bioinformatics Unit at IBiS, Seville.
- Rocío Núñez Torres. UOC master’s student, 2016. Later joined CNIO, Madrid.
- Eduard Porta-Pardo. PhD student, 2012-2013. Now Junior Group Leader at the Josep Carreras Institute, Barcelona.
- Aida Arcas Mantas. PhD student, 2010-2013. Now Senior Bioinformatician at Clarivate.
- Israel Barrios Núñez. Technician and engineer, 2019-2023. Current position listed on the former site: Cuerpo Nacional de Policía.
- Ida Paramonov. Programmer and data analyst at IMPPC, 2011-2013. Later data analyst at CNAG, Barcelona.
Students
TFG, TFM, and graduate training
- Marta Sotelo Montoro. TFM student and JAE-ICU trainee at CABD.
- Javier Tubio. Recent TFG student at the University of Seville.
- Clara Muñoz. Practicals Master on the MADOBIS master, University of Seville.
- Javier García Flores. Practicals Master on the MADOBIS master, University of Seville.
- Francisco José Ruiz Mota. Graduate student at CABD. University of Seville.
- Alberto del Cueto. Master’s student at CABD. UOC.
- Gabriel Jiménez Reyes. TFM student, 2024. VIU, Valencia.
- Nazaret Navarro Cruz. Master’s student at CABD, 2022. MADOBIS, Seville.
- Antonio Parra Sevilla. TFM student at CABD, 2019. University of Vigo.
- Alba Gutiérrez. TFM student at IMPPC, 2010. Later lecturer at Harvard University, USA.
- Joel López Bercianos. TFM student at IMPPC, 2010. Later CTO at BTC assessors, Andorra.
Visitors
Visiting researchers
- Cayetano Navas Enamorado. PhD researcher from Marta González-Freire’s lab, Spain, 2024.
- Jake Fowler. PhD researcher from Paul Taylor’s lab, University of Leeds, UK, 2024.
- Sandra Moreu. PhD researcher from Marián Ros lab, Spain, 2024.
- Gemma Martínez Redondo. PhD researcher from Rosa Fernández lab, 2022.
- M. Victoria Mencucci. Postdoctoral researcher from Universidad de la Plata, Argentina, 2019.
Collaborators
Selected collaborators
- Rosa Fernández. CSIC Tenured Researcher, Institute of Evolutionary Biology, Barcelona, Spain.
- Katharina Hoff. University of Greifswald, Germany.
- Aureliano Bombarely. CSIC Research Professor, IBMCP, Valencia, Spain.
- Eva Estébanez-Perpiñá. Professor, IBUB, Barcelona, Spain.
- Harald Wodrich. Director of Research, MFP-CNRS, Bordeaux, France.
- Paul Taylor. Professor, University of Leeds, UK.
- Silvia Salas. Professor, CABD-UPO, Seville, Spain.
- Fernando Casares. Research Professor, CABD-CSIC, Seville, Spain.
- Amancio Carnero. Research Professor, IBiS, Seville, Spain.
- Alfonso Valencia. Life Sciences Department Director, BSC, Barcelona, Spain.
PI
Ana M. Rojas Mendoza
Ana M. Rojas Mendoza is a CSIC Research Scientist and, since 2026, Director of the Department of Evolutionary Dynamics at CABD.
Trained in Biological Sciences in Madrid (Spain) and later specialized through predoctoral and postdoctoral research periods in the United States and Spain, she has built a career connecting molecular biology, evolution, structural bioinformatics, and computational methods. She established her independent group in 2009 in Barcelona, and later moved to Seville first at IBiS and later CABD, where she is currently leading the group.
Her scientific trajectory spans protein family evolution, protein signaling, omics integration, and methodological development, with a clear transition in recent years toward artificial intelligence and protein language models. Current work focuses on how sequence, structure, and evolution shape protein function, and on making functional annotation more scalable and more biologically meaningful.
She combines research leadership with teaching, mentoring, scientific evaluation, and international community work, including active roles in Function COSI, SEBiBC, and CSIC research networks.
Career summary
Since 2026Director, Department of Evolutionary Dynamics
Research profileComputational biology, AI, protein language models
RecognitionFour CNEAI research periods
LeadershipFunction COSI, SEBiBC, BCB.HUB, and Life.Hub
MentoringPhD, MSc, TFG, and visiting researchers
Training
Mentoring pipeline
Ongoing doctoral supervision, master’s projects, and visiting researchers span computational biology, structural bioinformatics, and AI-based annotation.
Location
CABD-CSIC
Andalusian Center for Developmental Biology (CABD/CSIC-UPO-JA)
Avda. Rectora Rosario Valpuesta 1
41089 Dos Hermanas, Sevilla
Contact
Open to collaborations and informal enquiries
For research collaborations, student enquiries, or speaking invitations, contact the lab directly.
a.rojas.m@csic.es
CABD Phone: +34 954977911
UPO internal: 67911
Security: +34 954349200
Fax: +34 954349376
PI profile