Institution: CABD
Research Groups: Computational Biology and Bioinformatics (CBBIO.CABD)
Position: Científico Titular del CSIC
Contact email: i.cases@csic.es
BCB Committee: No committees assigned.
BCB Community: No communities assigned.
BCB Tools:
BCB Services: Bioinformatics Unit at the CABD
Research topics: Computational Methods, Applications of Computational Biology, Gene regulatory networks, Functional genomics, Function prediction, Functional annotation, Molecular evolution, Sequence analysis, Systems Biology, Integrative Analysis, Network Biology, Regulatory biology, Data Analysis, Artificial Intelligence, Deep Learning in Biology, Large language models, Machine Learning in Biology, Data Visualization, Omics, Epigenomics, Chromatin accessibility, DNA methylation, Genomics, Genomic Annotation, Single-cell omics, Transcriptomics, Expression Profiling, RNA Sequencing (RNA-seq), Single-cell (scRNA-seq), Resources, Bioinformatics enabling techniques, FAIRfication, Standards in Computational Biology
Publications
Martínez-Redondo, G. I., Perez-Canales, F. M., Carbonetto, B., Fernández, J. M., Barrios-Núñez, I., Vázquez-Valls, M., Cases, I., Rojas, A. M., & Fernández, R. (2025). FANTASIA leverages language models to decode the functional dark proteome across the animal tree of life. Communications Biology, 8(1). https://doi.org/10.1038/s42003-025-08651-2
Rueda, A. D., Salvador‐Martínez, I., Sospedra‐Arrufat, I., Alcaina‐Caro, A., Fernández‐Miñán, A., Burgos‐Ruiz, A. M., Cases, I., Mohedano, A., Tena, J. J., Heyn, H., Lopez‐Rios, J., & Nusspaumer, G. (2024). The cellular landscape of the endochondral bone during the transition to extrauterine life. Immunology & Cell Biology, 102(2), 131–148. Portico. https://doi.org/10.1111/imcb.12718
Marlétaz, F., de la Calle-Mustienes, E., Acemel, R. D., Paliou, C., Naranjo, S., Martínez-García, P. M., Cases, I., Sleight, V. A., Hirschberger, C., Marcet-Houben, M., Navon, D., Andrescavage, A., Skvortsova, K., Duckett, P. E., González-Rajal, Á., Bogdanovic, O., Gibcus, J. H., Yang, L., Gallardo-Fuentes, L., … Gómez-Skarmeta, J. L. (2023). The little skate genome and the evolutionary emergence of wing-like fins. Nature, 616(7957), 495–503. https://doi.org/10.1038/s41586-023-05868-1
Leon, A., Subirana, L., Magre, K., Cases, I., Tena, J. J., Irimia, M., Gomez-Skarmeta, J. L., Escriva, H., & Bertrand, S. (2022). Gene Regulatory Networks of Epidermal and Neural Fate Choice in a Chordate. Molecular Biology and Evolution, 39(4). https://doi.org/10.1093/molbev/msac055
Fragoso-Luna, A., Romero-Bueno, R., Eibl, M., Ayuso, C., Muñoz-Jiménez, C., Benes, V., Cases, I., & Askjaer, P. (2022). Expanded FLP toolbox for spatiotemporal protein degradation and transcriptomic profiling in Caenorhabditis elegans. Genetics, 223(1). https://doi.org/10.1093/genetics/iyac166
Payán-Bravo, L., Fontalva, S., Peñate, X., Cases, I., Guerrero-Martínez, J. A., Pareja-Sánchez, Y., Odriozola-Gil, Y., Lara, E., Jimeno-González, S., Suñé, C., Muñoz-Centeno, M. C., Reyes, J. C., & Chávez, S. (2021). Human prefoldin modulates co-transcriptional pre-mRNA splicing. Nucleic Acids Research, 49(11), 6267–6280. https://doi.org/10.1093/nar/gkab446
Arcas, A., Cases, I., & Rojas, A. M. (2013). Serine/threonine kinases and E2-ubiquitin conjugating enzymes in Planctomycetes: unexpected findings. Antonie van Leeuwenhoek, 104(4), 509–520. https://doi.org/10.1007/s10482-013-9993-2
Valls, M., Silva‐Rocha, R., Cases, I., Muñoz, A., & de Lorenzo, V. (2011). Functional analysis of the integration host factor site of the σ54Pu promoter of Pseudomonas putida by in vivo UV imprinting. Molecular Microbiology, 82(3), 591–601. Portico. https://doi.org/10.1111/j.1365-2958.2011.07835.x
Carbajosa, G., & Cases, I. (2010). Transcriptional Networks that Regulate Hydrocarbon Biodegradation. Handbook of Hydrocarbon and Lipid Microbiology, 1399–1410. https://doi.org/10.1007/978-3-540-77587-4_96
Campillos, M., Cases, I., Hentze, M. W., & Sanchez, M. (2010). SIREs: searching for iron-responsive elements. Nucleic Acids Research, 38(Web Server), W360–W367. https://doi.org/10.1093/nar/gkq371
Trigo, A., Valencia, A., & Cases, I. (2009). Systemic approaches to biodegradation. FEMS Microbiology Reviews, 33(1), 98–108. https://doi.org/10.1111/j.1574-6976.2008.00143.x
Carbajosa, G., Trigo, A., Valencia, A., & Cases, I. (2009). Bionemo: molecular information on biodegradation metabolism. Nucleic Acids Research, 37(Database), D598–D602. https://doi.org/10.1093/nar/gkn864
Cases, I., Velázquez, F., & de Lorenzo, V. (2007). The ancestral role of the phosphoenolpyruvate–carbohydrate phosphotransferase system (PTS) as exposed by comparative genomics. Research in Microbiology, 158(8–9), 666–670. https://doi.org/10.1016/j.resmic.2007.08.002
Velázquez, F., Pflüger, K., Cases, I., De Eugenio, L. I., & de Lorenzo, V. (2007). The Phosphotransferase System Formed by PtsP, PtsO, and PtsN Proteins Controls Production of Polyhydroxyalkanoates in Pseudomonas putida. Journal of Bacteriology, 189(12), 4529–4533. https://doi.org/10.1128/jb.00033-07
Cases, I., Pisano, D. G., Andres, E., Carro, A., Fernandez, J. M., Gomez-Lopez, G., Rodriguez, J. M., Vera, J. F., Valencia, A., & Rojas, A. M. (2007). CARGO: a web portal to integrate customized biological information. Nucleic Acids Research, 35(Web Server), W16–W20. https://doi.org/10.1093/nar/gkm280
Goldovsky, L., Cases, I., Enright, A. J., & Ouzounis, C. A. (2005). BioLayoutJava. Applied Bioinformatics, 4(1), 71–74. https://doi.org/10.2165/00822942-200504010-00009
Cases, I., & de Lorenzo, V. (2005). Promoters in the environment: transcriptional regulation in its natural context. Nature Reviews Microbiology, 3(2), 105–118. https://doi.org/10.1038/nrmicro1084
Goldovsky, L., Janssen, P., Ahren, D., Audit, B., Cases, I., Darzentas, N., Enright, A. J., Lopez-Bigas, N., Peregrin-Alvarez, J. M., Smith, M., Tsoka, S., Kunin, V., & Ouzounis, C. A. (2005). CoGenT++: an extensive and extensible data environment for computational genomics. Bioinformatics, 21(19), 3806–3810. https://doi.org/10.1093/bioinformatics/bti579
Valls, M., Cases, I., & Lorenzo, V. (2004). Transcription Mediated By rpoN-Dependent Promoters. Pseudomonas, 289–317. https://doi.org/10.1007/978-1-4419-9084-6_10
Kunin, V., Cases, I., Enright, A. J., de Lorenzo, V., & Ouzounis, C. A. (2003). Genome Biology, 4(2), 401. https://doi.org/10.1186/gb-2003-4-2-401
Janssen, P., Audit, B., Cases, I., Darzentas, N., Goldovsky, L., Kunin, V., Lopez-Bigas, N., Peregrin-Alvarez, J., Pereira-Leal, J. B., Tsoka, S., & Ouzounis, C. A. (2003). Genome Biology, 4(5), 402. https://doi.org/10.1186/gb-2003-4-5-402
Cases, I., de Lorenzo, V., & Ouzounis, C. A. (2003). Transcription regulation and environmental adaptation in bacteria. Trends in Microbiology, 11(6), 248–253. https://doi.org/10.1016/s0966-842x(03)00103-3
Janssen, P., Enright, A. J., Audit, B., Cases, I., Goldovsky, L., Harte, N., Kunin, V., & Ouzounis, C. A. (2003). COmplete GENome Tracking (COGENT): a flexible data environment for computational genomics. Bioinformatics, 19(11), 1451–1452. https://doi.org/10.1093/bioinformatics/btg161
Cases, I., Ussery, D. W., & De Lorenzo, V. (2003). The σ54 regulon (sigmulon) of Pseudomonas putida. Environmental Microbiology, 5(12), 1281–1293. Portico. https://doi.org/10.1111/j.1462-2920.2003.00528.x
Cánovas, D., Cases, I., & De Lorenzo, V. (2003). Heavy metal tolerance and metal homeostasis in Pseudomonas putida as revealed by complete genome analysis. Environmental Microbiology, 5(12), 1242–1256. Portico. https://doi.org/10.1111/j.1462-2920.2003.00463.x
Cases, I., & De Lorenzo, V. (2002). The grammar of (micro)biological diversity. Environmental Microbiology, 4(11), 623–627. Portico. https://doi.org/10.1046/j.1462-2920.2002.00346.x
Cases, I., & de Lorenzo, V. (1998). Expression systems and physiological control of promoter activity in bacteria. Current Opinion in Microbiology, 1(3), 303–310. https://doi.org/10.1016/s1369-5274(98)80034-9
Research lines:
Funding:
No funded projects.