Computational Biology and Bioinformatics

Summary

Our work is focussed on the following fields:

·  Evolution and emergence of signaling pathways

·  Transcription regulation

·  Integrative Biology to disease

·  Systems Biology

Our Research

Our Expertise:

1. Evolutionary analyses: Systematic computational analyses of large protein families to i) identify ancestral components (Rojas & Doolittle, 2002, JME), ii) to accurately classify protein members (Proell et al., 2008, PlosONE) and iii) to decipher “sub/neo-functionalization” codes (Rojas et al., 2012, JCB).

2. Structural Bioinformatics: i) by identifying structural/functional modules in relevant cell signaling pathways (Tong, et al., 2003, Prot. Sci.; Sánchez-Pulido, et al., 2004, BMC Bioinf.; Rojas et al., 2005, FEBS J; Sánchez-Pulido et al., 2007, TiBS), ii) by finding particular regions suitable for crystallization experiments (Magnusson et al., 2004, PNAS; Sonnenberg et al., 2006, JMB), and iii) systematic analyses of protein-protein interactions for drug targeting (Fuentes et al., Curr. Op. Drug Discov., 2009).

3. Comparative Genomics: i) comparative large-scale analyses of apoptotic proteins (Reed et al., 2003, Gen. Res.) and ii) helped to identify key regulators of cardiac development (Grego-Bessa et al., 2007, Dev. Cell). Iii) extensive experience in regulatory mechanisms of bacterial transcription (Velazquez et al., 2007, J. Bacteriol; Trigo et al., 2009, FEMS Microbiol Rev; de Lorenzo et al., 2010).

4. Tools and methods: since the development of COGENT++ one of the first genome database framework using integration paradigms (Goldovsky et al., 2005, Bioinformatics) the group has been active in this subject. Examples are “CARGO” (Cases et al., 2007, NAR) a proof of concept selected as the visualization platform by the excellence networks Biosapiens and Embrace, “Bionemo” (Carbajosa, et al., 2009, NAR), and “SIRES” (Campillos et al., 2010, NAR) and methods developed in the context of integration for systems Biology (“CO-CITE”, Rojas et al., 2012, PlosONE).

5. Collaborations with experimental groups. Producing working hypothesis to help experimental procedures that have produced relevant outcomes like i) GAS1 is a novel Ret kinase signaling member (Cabrera et al., 2006, JBC), ii) Filamin-A is a crucial target for actin rearrangement in HIV infection (Jiménez-Baranda et al., 2007, Nat. Cell. Biol.) iii) sequence/structure determinants in leukocytes mobility (Mañes et al., 2011, FASEB J).