IMPPC Fundación Institut de Medicina Predictiva i Personalitzada del Càncer

The Computational Cell Biology Group (CCBG)'s main scientific interests are:
• Genome Evolution
• Transcription regulation
• Integrative Biology to disease
• Systems Biology

The group members have strong expertise in:

1) Hypothesis generation using exclusively computational approaches (Sanchez-Pulido et al, 2007, TiBS; Rojas et al, 2005, FEBS J; Sanchez-Pulido et al, 2004, BMC Bioinformatics).

2) Computational contribution to experimental design (Jiménez-Baranda et al, 2007, Nat. Cell. Biol.; Grego-Bessa, et al, Dev. Cell. 2007; Cabrera, JR et al, JBC, 2006; Sonnenberg et al, 2006, JMB; Magnusson et al, 2004, PNAS)

3) Evolution and sequence analyses. (Rojas & Doolittle, JME, 2002; Liu et al, Prot. Sci, 2004; Reed et al, Genome Res, 2003; Proell et al, 2008, Plos One; Bayon et al, 2005, FEBS J).

4) Bioinformatics tools. I. Cases developed one of the first software designed for experimental scientists, BioLayout Java (Goldovsky et al., 2005, App. Bioinformatics). The group also has experstise on dayabase development, suite COGENT++ (Goldovsky et al., 2005, Bioinformatics), web servers (TreeDet: http://treedetv2.bioinfo.cnio.es/treedet/index.html Carro et al, 2006, Nuc Acids Res), visualisation tools for genomic information: CARGO (http://cargo2.bioinfo.cnio.es Cases et al, 2007, Nuc Acids Res, 2007), Bionemo (http://bionemo.bioinfo.cnio.es Nuc Acids Res, 2009).

Selected publications

• Fuentes, G., Oyarzabal,J., Rojas, AM*. Databases of protein-protein interactions and their uses in drug discovery. Current Opinion in Drug Discovery and Development. (2009). 12:358-66
• Krallinger, M., Rojas AM. and Valencia, A. Creating reference datasets for Systems Biology applications using text mining. Annals of the New York Academy of Sciences.Pub online: 31 March (2009). 1158(1):14
• Carbajosa, G., Trigo, A., Valencia, A. & Cases, I*. Bionemo: molecular information on biodegradation metabolism. Nucleic Acids Research. Jan (2009). 37: D598-602.
• Carbajosa, G., Trigo, A., Valencia, A. and Cases. Bionemo: molecular information on biodegradation metabolism. Nucleic Acids Research, in press (2009)
• Proell,M., Riedl, S.J., Fritz, JH., Rojas, A.M., Schwarzenbacher, R. The Nod-like Receptor (NLR) Family: a tale of similarities and differences. PLoS One. (2008). e2119
• Bayon Y, Trinidad AG, de la Puerta ML, Del Carmen Rodriguez M, Bogetz J, Rojas A, De Pereda JM, Rahmouni S, Williams S, Matsuzawa SI, Reed JC, Crespo MS, Mustelin T, Alonso A. KCTD5, a putative substrate adaptor for cullin3 ubiquitin ligases. FEBS J.(2008).
• Sanchez-Pulido, L, Valencia, A, & Rojas, AM*. Are Promyelocytic Leukaemia Protein Nuclear Bodies a scaffold for caspase-2 programmed cell death? Trends in Biochemical Sciences. Sep;32(9):400-6. Epub (2007) Aug 10.
• Jiménez-Baranda, S, Gómez-Moutón, C., Rojas, A., Martínez-Prats, L., Mira, E., Lacalle, R.A., Valencia, A., Dimitrov, D.S., Viola, A., Delgado, R., Martínez-A, C., & Mañes, S. Filamin-A regulates actin-dependent clustering of HIV receptors. Nature Cell Biology Jul;9(7):838-46. Epub (2007) Jun 17.
• Cases, I., Pisano, D., Andrés, E., Carro, A., Fernández, J.M., Vera, J., Rodríguez, J.M., Gómez- Lopez, G., Valencia, A., & Rojas, A. CARGO: a web portal to integrate customised biological information. Nucleic Acids Research. (2007) (2007) Jul;35, W16-20. Epub (2007) May 5.
• Grego-Bessa, J., Luna-Zurita, L., del Monte, G., Bolos, V., Melgar, P., Ballestar, E., Esteller, M., Rojas, A., Perez-Pomares, JM., de la Pompa, JL. Nocht regulates morphogenetic signals required for ventricular trabeculation. Developmental Cell (2007) Mar;12(3):415-29.
• Carro, A., Tress, M., de Juan, D.,Pazos,. F., Lopez-romero,P., del Sol, A.,Valencia, A., Rojas, AM*. 2006. TreeDet: a web server to explore sequence space. Nucleic Acids Research.Jul (2006). 34 W110-115
• Goldovsky, L., Cases, I., Enright, A. and Ouzounis, C.A. BioLayoutJava, versatile network visualization of structural and functional relationships. Applied Bioinformatics, 4:71-74 (2005)
• Goldovsky, L., Janssen, P., Ahrën,D., Audit, B., Cases, I., Darzentas, N., Enright, A.J., López- Bigas, N., Peregrin-Alvarez, J.M., Smith, M., Tsoka, S., Kunin, V., and Ouzounis, C.A. CoGenT++: An extensive and extensible data environment for computational genomics. Bioinformatics, 21:3806-3810. (2005).
• Cases, I., de Lorenzo, V. Promoters in the Environment: Transcription Regulation in its natural context. : Nature Microbiology Reviews, 3:105-118 (2005)
• Magnusson OT, Toyama H, Saeki M, Rojas A, Reed JC, Liddington RC, Klinman JP, Schwarzenbacher R. Quinone biogenesis: Structure and mechanism of PqqC, the final catalyst in the production of pyrroloquinoline quinone. PNAS. (2004) May 25;101(21):7913-8.
• Reed JC, Doctor K, Rojas A, Zapata JM, Stehlik C, Fiorentino L, Damiano J, Roth W, Matsuzawa S, Newman R, Takayama S, Marusawa H, Xu F, Salvesen G, Godzik A; RIKEN GER Group; GSL Members. Comparative analysis of apoptosis and inflammation genes of mice and humans. Genome Research. (2003) Jun;13(6B):1376-88.
• Ana Rojas, Russell F. Doolittle. The Occurrence of Type S1A Serine Proteases in Sponge and Jellyfish. J. Mol. Evol. (2002). 55(6):790-794