Research Group

Detalle de: Computational Biology and Bioinformatics (CBBIO.CABD)

Title	Computational Biology and Bioinformatics (CBBIO.CABD)
Description	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 of protein function using AI-based methodologies. Recent work includes FANTASIA, functional annotation with protein language models, protein embedding perspectives on molecular evolution, and computational approaches linking sequence, structure, and biological function across diverse organisms.
Home Page	https://www.bioinfocb.es
Contact Email	a.rojas.m@csic.es
Collaborating Companies
Spin Off
Patents	Blázquez-Gómez, Jesús, Castañeda-García, Alfredo, Prieto-Márquez Ana I., Rojas-Mendoza, Ana M., Wadel, Simon; Cantillon, Daire; Doherty, A. P201531949. “Cepas de Mycobacterium hipermutables”. España y UK, 31/12/2015. SAS/CSIC/USE
Hpc Resources	Drago, CESGA, UPO
Institution	CABD
Ontology	Omics, Computational Methods, Resources, Transcriptomics, RNA Sequencing (RNA-seq), Data Analysis, Artificial Intelligence, Machine Learning in Biology, Bioinformatics Software and Tools, Analysis packages (R, Python, etc.), Data Visualization, Applications of Computational Biology, Model organisms, Bioinformatics enabling techniques, Standards in Computational Biology, Genomics, Large language models, Functional genomics, Functional annotation, Function prediction, Structural bioinformatics, Expression Profiling, Computational models and simulations, Gene regulatory networks, Computational Techniques, High-performance Computing, Systems Biology, Genomic Annotation, Epigenomics, DNA methylation, Integrative Analysis, Regulatory biology, Containers Computing, Statistical Methods for Biology, Frequentist analysis, Molecular evolution, FAIRfication, Sequence analysis, Sequence Alignment, Phylogenetic Analysis, Mutation Analysis and design, Chromatin accessibility, Proteomics, Experimental design, Multivariate statistics, Network Biology, Biomolecular simulation, Structure-function relationship, Drug Discovery and design, Evolutionary rates, Single-cell omics, Single-cell (scRNA-seq), Structure prediction, Molecular Interactions/Docking, Development, Bayesian statistics, Non-parametric statistics, Non-model organisms, Deep Learning in Biology, Cloud Computing, Structural genomics, Knowledge graphs
Tools	FANTASIA (Functional ANnoTAtion based on embedding space SImilArity)
Service Units	Bioinformatics Unit at the CABD
Research Lines	Protein multifunction, Protein evolution, Protein Language Models
Funded Projects	Cátedra ENIA Google Spain/Universidad de Sevilla en Inteligencia Artificial
Selected Publications	Functional Annotation of Proteomes Using Protein Language Models: A High-Throughput Implementation of the ProtTrans Model Book / chapter · 2025 MEG8 as an antagonistic pleiotropic mechanism in breast cancer Article · 20 Dec 2024 Leveraging Natural Language Processing models to decode the dark proteome across the Animal Tree of Life Preprint · 29 Feb 2024 The little skate genome and the evolutionary emergence of wing-like fins Article · 12 Apr 2023 A hotspot for posttranslational modifications on the androgen receptor dimer interface drives pathology and anti-androgen resistance Article · 17 Mar 2023 View all (62 more) The multivalency of the glucocorticoid receptor ligand-binding domain explains its manifold physiological activities Article · 5 Dec 2022 Expanded FLP toolbox for spatiotemporal protein degradation and transcriptomic profiling in Caenorhabditis elegans Article · 2 Nov 2022 Gene Regulatory Networks of Epidermal and Neural Fate Choice in a Chordate Article · 11 Mar 2022 Origin and Evolution of Polycyclic Triterpene Synthesis Article · 3 Mar 2020 VRK1 functional insufficiency due to alterations in protein stability or kinase activity of human VRK1 pathogenic variants implicated in neuromotor syndromes Article · 16 Sep 2019 Non-canonical dimerization of the androgen receptor and other nuclear receptors: implications for human disease Article · Aug 2019 Diversity of Quaternary Structures Regulates Nuclear Receptor Activities. Article · Jan 2019 EXD2 governs germ stem cell homeostasis and lifespan by promoting mitoribosome integrity and translation. Article · 15 Jan 2018 Molecular Evolution of Multiple-Level Control of Heme Biosynthesis Pathway in Animal Kingdom Article · 28 Jan 2014 Emergence and Evolutionary Analysis of the Human DDR Network: Implications in Comparative Genomics and Downstream Analyses Article · 16 Jan 2014 A common structural scaffold in CTD phosphatases that supports distinct catalytic mechanisms Article · 10 Sep 2013 Serine/threonine kinases and E2-ubiquitin conjugating enzymes in Planctomycetes: unexpected findings Article · 6 Aug 2013 Two novel missense mutations in iron transport protein transferrin causing hypochromic microcytic anaemia and haemosiderosis: molecular characterization and structural implications Article · 24 Jul 2013 A Proteomic Characterization of Factors Enriched at Nascent DNA Molecules Article · Apr 2013 Uncovering the Molecular Machinery of the Human Spindle-An Integration of Wet and Dry Systems Biology Article · 9 Mar 2012 The Ras protein superfamily: Evolutionary tree and role of conserved amino acids Article · 23 Jan 2012 Functional analysis of the integration host factor site of the σ(54) Pu promoter of Pseudomonas putida by in vivo UV imprinting. Article · 30 Sep 2011 B Lymphocyte Commitment Program Is Driven by the Proto-Oncogene c-myc Article · Jun 2011 Sumoylation regulates nuclear localization of repressor DREAM Article · May 2011 SIREs: searching for iron-responsive elements. Article · 11 May 2010 An isoform-specific PDZ-binding motif targets type I PIP5 kinase beta to the uropod and controls polarization of neutrophil-like HL60 cells Article · 4 May 2010 Transcriptional Networks that Regulate Hydrocarbon Biodegradation Book / chapter · 2010 Creating Reference Datasets for Systems Biology Applications Using Text Mining Article · Mar 2009 Bionemo: molecular information on biodegradation metabolism. Article · 1 Jan 2009 Systemic approaches to biodegradation. Article · Jan 2009 A novel patatin-like protein from cotton plant, GhPat1, is co-expressed with GhLox1 during Xanthomonas campestris-mediated hypersensitive cell death Article · 11 Oct 2008 KCTD5, a putative substrate adaptor for cullin3 ubiquitin ligases Article · 11 Jul 2008 Exploring the FL-160-CRP gene family through sequence variability of the complement regulatory protein (CRP) expressed by the trypomastigote stage of Trypanosoma cruzi Article · May 2008 The Nod-Like Receptor (NLR) Family: A Tale of Similarities and Differences Article · 30 Apr 2008 The ancestral role of the phosphoenolpyruvate-carbohydrate phosphotransferase system (PTS) as exposed by comparative genomics. Article · Oct 2007 Are promyelocytic leukaemia protein nuclear bodies a scaffold for caspase-2 programmed cell death? Article · Sep 2007 Filamin-A regulates actin-dependent clustering of HIV receptors Article · 17 Jun 2007 The phosphotransferase system formed by PtsP, PtsO, and PtsN proteins controls production of polyhydroxyalkanoates in Pseudomonas putida. Article · 15 Jun 2007 The structure of a tandem pair of spectrin repeats of plectin reveals a modular organization of the plakin domain Article · May 2007 Notch signaling is essential for ventricular chamber development Article · Mar 2007 Assessment of predictions submitted for the CASP7 function prediction category Article · 2007 TreeDet: a web server to explore sequence space Article · 1 Jul 2006 Gas1 is related to the glial cell-derived neurotrophic factor family receptors alpha and regulates Ret signaling Article · May 2006 CoGenT++: an extensive and extensible data environment for computational genomics. Article · 1 Oct 2005 A framework for computational and experimental methods: Identifying dimerization residues in CCR chemokine receptors Article · 1 Sep 2005 Death inducer obliterator protein 1 in the context of DNA regulation - Sequence analyses of distant homologues point to a novel functional role Article · Jul 2005 Characterization of the protease domain of Rice tungro bacilliform virus responsible for the processing of the capsid protein from the polyprotein Article · 14 Apr 2005 Promoters in the environment: transcriptional regulation in its natural context. Article · Feb 2005 BioLayout(Java): versatile network visualisation of structural and functional relationships. Article · 2005 ACRATA: a novel electron transfer domain associated to apoptosis and cancer Article · 29 Dec 2004 Erwinia toletana sp. nov., associated with Pseudomonas savastanoi-induced tree knots Article · 1 Nov 2004 SPOC: A widely distributed domain associated with cancer, apoptosis and transcription Article · 7 Jul 2004 Quinone biogenesis: Structure and mechanism of PqqC, the final catalyst in the production of pyrroloquinoline quinone Article · 17 May 2004 Transcription Mediated By rpoN-Dependent Promoters Book / chapter · 2004 The sigma54 regulon (sigmulon) of Pseudomonas putida. Article · 27 Nov 2003 Heavy metal tolerance and metal homeostasis in Pseudomonas putida as revealed by complete genome analysis. Article · 27 Nov 2003 Homology modeling provides insights into the binding mode of the PAAD/DAPIN/pyrin domain, a fourth member of the CARD/DD/DED domain family Article · Sep 2003 COmplete GENome Tracking (COGENT): a flexible data environment for computational genomics. Article · 22 Jul 2003 Transcription regulation and environmental adaptation in bacteria. Article · Jun 2003 Comparative analysis of apoptosis and inflammation genes of mice and humans Article · Jun 2003 Incidence of salmonellae in captive and wild free-living raptorial birds in central Spain Article · 22 Jan 2003 Myriads of protein families, and still counting. Article · 2003 Beyond 100 genomes. Article · 2003 The occurrence of type S1A serine proteases in sponge and jellyfish Article · 1 Dec 2002 The grammar of (micro)biological diversity. Article · Nov 2002 gyrA mutations associated with nalidixic acid-resistant salmonellae from wild birds Article · Sep 2002 Expression systems and physiological control of promoter activity in bacteria Article · Jun 1998
Researchers	Ana Rojas, Ildefonso Cases

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