Ildefonso Cases
Computational Biology and Bioinformatics (CBBIO.CABD) · CABD
Biography
|
I am a Bioinformatician with 15 years experience and a broad range of expertise. I can help you visualise, analyse, manage, integrate and distribute your biological data. This way it will be easier to extract biological meaning of it, generating more impact. We can assist you from grant writing and experimental design, to manuscript preparation. |
Profile
| Institution | CABD |
| Position | Head of Bioinformatics Unit |
| Home page | https://www.linkedin.com/in/icases/ |
| Contact email | i.cases@csic.es |
| ORCID | 0000-0002-8784-5174 |
BCB Hub
| BCB Committee | Not a member |
| BCB Tools | |
| BCB Services | Bioinformatics Unit at the CABD |
Research
Research topics
OmicsComputational MethodsResourcesTranscriptomicsRNA Sequencing (RNA-seq)Data AnalysisArtificial IntelligenceMachine Learning in BiologyBioinformatics Software and ToolsData VisualizationApplications of Computational BiologyBioinformatics enabling techniques
View all (23 more)
Standards in Computational BiologyGenomicsLarge language modelsFunctional genomicsFunctional annotationFunction predictionExpression ProfilingComputational models and simulationsGene regulatory networksSystems BiologyGenomic AnnotationEpigenomicsDNA methylationIntegrative AnalysisRegulatory biologyMolecular evolutionFAIRficationSequence analysisChromatin accessibilityNetwork BiologySingle-cell omicsSingle-cell (scRNA-seq)Deep Learning in Biology
Research lines
Publications 46 entries
- Mules in the Antiquity of Southern Iberia revealed from proteomics Article · Nov 2026
- Protein Language Model Embeddings Recover Evolutionary and Functional Organization Across the Ras Superfamily Article · 12 Sep 2026
- FANTASIA leverages language models to decode the functional dark proteome across the animal tree of life Article · 14 Aug 2025
- Regulation of transcription elongation anticipates alternative gene expression strategies across the cell cycle Preprint · 5 Jan 2025
- The cellular landscape of the endochondral bone during the transition to extrauterine life Article · 7 Jan 2024
View all (41 more)
- The little skate genome and the evolutionary emergence of wing-like fins Article · 12 Apr 2023
- 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
- Human prefoldin modulates co-transcriptional pre-mRNA splicing Article · 7 Jun 2021
- Gene expression profiling in hearts of diabetic mice uncovers a potential role of estrogen-related receptor γ in diabetic cardiomyopathy Article · Jul 2016
- Gene Expression Profiling Supports the Neural Crest Origin of Adult Rodent Carotid Body Stem Cells and Identifies CD10 as a Marker for Mesectoderm-Committed Progenitors Article · 2 Mar 2016
- Notch-regulated miR-223 targets the aryl hydrocarbon receptor pathway and increases cytokine production in macrophages from rheumatoid arthritis patients Article · 3 Feb 2016
- Deconstruction of DNA Methylation Patterns During Myogenesis Reveals Specific Epigenetic Events in the Establishment of the Skeletal Muscle Lineage Article · 21 Apr 2015
- Serine/threonine kinases and E2-ubiquitin conjugating enzymes in Planctomycetes: unexpected findings Article · 6 Aug 2013
- 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
- SIREs: searching for iron-responsive elements. Article · 11 May 2010
- Transcriptional Networks that Regulate Hydrocarbon Biodegradation Book / chapter · 2010
- Bionemo: molecular information on biodegradation metabolism. Article · 1 Jan 2009
- Systemic approaches to biodegradation. Article · Jan 2009
- Editorial Article · 9 Aug 2008
- The ancestral role of the phosphoenolpyruvate-carbohydrate phosphotransferase system (PTS) as exposed by comparative genomics. Article · Oct 2007
- The phosphotransferase system formed by PtsP, PtsO, and PtsN proteins controls production of polyhydroxyalkanoates in Pseudomonas putida. Article · 15 Jun 2007
- CARGO: a web portal to integrate customized biological information Article · 8 May 2007
- CoGenT++: an extensive and extensible data environment for computational genomics. Article · 1 Oct 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
- 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
- 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
- Myriads of protein families, and still counting. Article · 2003
- Beyond 100 genomes. Article · 2003
- The grammar of (micro)biological diversity. Article · Nov 2002
- The genomes of Pseudomonas encode a third HU protein Article · 1 May 2002
- Role of ptsO in Carbon-Mediated Inhibition of the Pu Promoter Belonging to the pWW0 Pseudomonas putida Plasmid Article · Sep 2001
- The limits to genomic predictions: role of ÏN in environmental stress survival of Pseudomonas putida Article · Apr 2001
- Evidence of Multiple Regulatory Functions for the PtsN (IIA Ntr ) Protein of Pseudomonas putida Article · Feb 2001
- The black cat/white cat principle of signal integration in bacterial promoters Article · 15 Jan 2001
- Genetic Evidence of Distinct Physiological Regulation Mechanisms in the ς 54 Pu Promoter of Pseudomonas putida Article · 15 Feb 2000
- The IIANtr (PtsN) Protein of Pseudomonas putida Mediates the C Source Inhibition of the ς54-dependent Pu Promoter of the TOL Plasmid Article · May 1999
- Expression systems and physiological control of promoter activity in bacteria Article · Jun 1998
- Design of a solubilization pathway for recombinant polypeptides in vivo through processing of a bi-protein with a viral protease Article · 1 Jun 1997
- Involvement of σ 54 in exponential silencing of the Pseudomonas putida TOL plasmid Pu promoter Article · Jan 1996
- Early and late responses of TOL promoters to pathway inducers: identification of postexponential promoters in Pseudomonas putida with lacZ-tet bicistronic reporters Article · Nov 1993
- Gene order in Prokaryotes: conservation and implications Book / chapter