 | Since May of 2009, I work in the Computational Cell Biology Group [CCBG] at the Institute for Predictive and Personalised Medicine of Cancer, [IMPPC] in Badalona (Barcelona, Spain). |
+ Scientific background
I am Biologist by training and became a bioinformatitian by chance trying to understand evolutionary patterns.
My point: Biology is the key, and I use bioinformatics as a tool to address biological questions (others use pipets), both approaches are necessary.
Main interests: genome evolution, protein function and regulation, and hypothesis generation.
Summary of my research experience:
03/06-05/09: Staff Scientist at the National Center for Spanish Cancer Research (Centro Nacional de Investigaciones Oncológicas) [CNIO] in the Structural Computational Biology Group [SBBP], Madrid, Spain. Protein function, sequence and structural analyses, hypothesis generation, data integration, visualisation tools.
11/03-03/06: Posdoctoral associate at Spanish Centre for Biotechnology [CNB]. In (former)[PDG] and in the DIO, Madrid-Spain. Sequence and structural analyses, protein function, hypothesis generation.
11/01-10/03: Posdoctoral associate at Dr. Godzik's lab at The Burnham Institute, La Jolla, CA, USA. Modeling, structural analyses, phylogenetic analyses, protein function.
12/00-11/01: NASA-NSCORT fellow in Dr.Doolittle's lab at The University of California in San Diego [UCSD], San Diego, CA, USA. Evolutionary analyses, experimental work.
1998-12/00: Predoc and Posdoc at The Sidney Kimmel Cancer Center (Now merged with the Burnham Institute) with Prof. Michael McClelland. San Diego, CA, USA. There I completed my Ph.D studies in bacterial phylogeny and learnt some molecular biology techiques.
+ 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. PMID: 19396737 [PUBMED]
- 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. PMID: 19348628 [PUBMED]
- Cacas, J, Marmey, P., Montillet, JL., Sayegh-Alhamdia,M.,Jalloul, A., Rojas-Mendoza, AM.,Cleviret, A., Michel,N.A novel patatin-like protein from cotton plant, GhPat1, is co-expresed with GhLox1 during Xanthomonas campestris-mediated hypersensitive cell death.In Press: Plant Cell Reports.2008.
- 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.PMID: 18446235 [PUBMED]
- 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. PMID: 18573101 [PUBMED]
- Mathieu-Daude F, Lafay B, Touzet O, Lelivre J, Parrado F, Bosseno MF, Rojas AM, Fatha S, Ouaissi A, Brenire SF. Exploring the FL-160-CRP gene family through sequence variability of the complement regulatory protein (CRP) expressed by the trypomastigote stage of Trypanosoma cruzi Infect Genet Evol 2008. Jan 16. PMID: 18296127 [PUBMED]
- Sanchez-Pulido, L, Valencia, A, Rojas, AM. Are Promyelocytic Leukaemia Protein Nuclear Bodies a scaffold for caspase-2 programmed cell death? TiBS Online August 10, 2007. [PUBMED]
- 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. Nat. Cell. Biol. Published online: 17 June 2007 [PUBMED]
- López, G., Rojas, A., Tress, M., Valencia, A. Assessment of Predictions Submitted for the CASP7 Function Prediction Category. Proteins 2007. [PUBMED]
- 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. Nuc. Acids. Res. 2007. [PUBMED]
- Sonnenberg, A., Rojas, A., de Pereda, J. The structure of a tandem pair of spectrin repeats of plectin reveals a modular organization of the plakin domain. J. Mol. Biol. 2007 Mar 7; [Epub ahead of print] PMID: 17397861. [PUBMED]
- 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. Dev. Cell 2007 Mar;12(3):415-29. PMID: 17336907[PUBMED]
- 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. NAR.Jul 2006:34 W110-115.[PUBMED]
- Cabrera, JR., Sanchez-Pulido,L., Rojas,AM., Valencia,A., Mañes,S., Naranjo,JR., Mellström, B.GAS1 is related to the GDNF family receptors alpha and regulates ret signalingJBC published March 20, 2006 as doi:10.1074/jbc.M509572200 [PUBMED]
- Rojas AM, Sanchez-Pulido L, Futterer A, van Wely KH, Martinez-A C, Valencia A. Death inducer obliterator protein 1 in the context of DNA regulation. Sequence analyses of distant homologues point to a novel functional role.FEBS J. 2005 Jul;272(14):3505-11. PMID: 16008551 [PubMed]
- de Juan D, Mellado M, Rodriguez-Frade JM, Hernanz-Falcon P, Serrano A, Del Sol A, Valencia A, Martinez-A C, Rojas AM. A framework for computational and experimental methods: Identifying dimerization residues in CCR chemokine receptors.Bioinformatics. 2005 Sep 1;21 Suppl 2:ii13-ii18. PMID: 16204091 [PubMed]
- 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. Proc Natl Acad Sci U S A. 2004 May 25;101(21):7913-8. Epub 2004 May 17. PMID: 15148379 [PubMed]
- Sanchez-Pulido L, Rojas AM, Valencia A, Martinez-A C, Andrade MA. ACRATA: a novel electron transfer domain associated to apoptosis and cancer.BMC Cancer. 2004 Dec 29;4(1):98. PMID: 15623366 [PubMed]
- Sanchez-Pulido L, Rojas AM, van Wely KH, Martinez-A C, Valencia A. SPOC: a widely distributed domain associated with cancer, apoptosis andtranscription.BMC Bioinformatics. 2004 Jul 7;5:91. PMID: 15239844 [PubMed]
- Liu T*, Rojas A*, Ye Y, Godzik A. Homology modeling provides insights into the binding mode of thePAAD/DAPIN/pyrin domain, a fourth member of the CARD/DD/DED domain family.Protein Sci. 2003 Sep;12(9):1872-81. * indicates equal contribution PMID: 12930987 [PubMed]
- 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, GodzikA; RIKEN GER Group; GSL Members. Comparative analysis of apoptosis and inflammation genes of mice and humans.Genome Res. 2003 Jun;13(6B):1376-88. PMID: 12819136 [PubMed]
- Ana Rojas, Russell F. Doolittle.The Occurrence of Type S1A Serine Proteases in Sponge and Jellyfish.J. Mol. Evol. 2002:55(6):790-794 PMID: 17476731. [PubMed]
- Marmey P, Rojas-Mendoza A, de Kochko A, Beachy RN, Fauquet CM. Characterization of the protease domain of Rice tungro bacilliform virus responsible for the processing of the capsid protein from the polyprotein.Virol J. 2005 Apr 14;2(1):33. PMID: 15831103 [PubMed]
- Rojas AM, de Los Ríos JE, Fischer-Le Saux M, Jiménez P, Reche P, Bonneau S, Sutra L, Mathieu-Daude F, McClelland M. Erwinia toletana sp. nov., associated with Pseudomonas savastanoi-induced treeknots.Int J Syst Evol Microbiol. 2004 Nov;54(Pt 6):2217-22. PMID: 15545461 [PubMed]
- Reche MP, Jiménez PA, Alvarez F, García de los Ríos JE, Rojas AM, de PedroP. Incidence of salmonellae in captive and wild free-living raptorial birds incentral Spain.J Vet Med B Infect Dis Vet Public Health. 2003 Feb;50(1):42-4. PMID: 12710500 [PubMed]
- Reche MP, Echeita MA, de los Ríos JE, Usera MA, Jiménez PA, Rojas AM, Colás J, Rodriguez I. Comparison of phenotypic and genotypic markers for characterization of anoutbreak of Salmonella serotype Havana in captive raptors.J Appl Microbiol. 2003;94(1):65-72. PMID: 12492925 [PubMed]
- Reche MP, García de los Ríos JE, Jiménez PA, Rojas AM, Rotger R. gyrA Mutations associated with nalidixic acid-resistant salmonellae from wildbirds.Antimicrob Agents Chemother. 2002 Sep;46(9):3108-9. No abstract available. PMID: 12183286 [PubMed]
- Jiménez Gomez PA, García de los Ríos JE, Rojas Mendoza A, de Pedro Ramonet P, García Albiach R, Reche Sainz MP. Molecular basis of quinolone resistance in Escherichia coli from wild birds.Can J Vet Res. 2004 Jul;68(3):229-31. PMID: 15352551 [PubMed]
- Alvarez Dávila F,García de los Ríos JE,Jiménez P,Rojas A, Reche P., Troya, M. Phenotypicvariability in different strains of Pseudomonas syringae subsp. savastanoi isolated from different hosts.Eur. J. Plant Pathol . 1998. 104:603-609 SpringerLink
- Ana Rojas, David de Juan and Alfonso Valencia (2006).Molecular interactions: Learning from protein complexes. In Silico Technologies in Drug Target Indetification and Validation. Leon/Markel eds. CRC Taylor and Francis Group. Drug Discovery Series/6. Boca Raton, FL.
- Alonso, A., Rojas, A., Godzik, A. and Mustelin, T. (2003). Title: Protein Phosphatases: the dual-specific protein tyrosine phosphatase family. In Topics in Current Genetics. Vol.5, SpringerLink.
- García de los Ríos J.E., Jiménez P., Reche P., Rojas A., Colás J., Gallego M. y Corroto M. Incidencia de microorganismos Gram-positivos en el programa de cría de cernícalo primilla en el Hospital de Fauna Salvaje de GREFA. En: Biología y Situación del Cernícalo Primilla Ed. GREFA- Comunidad de Madrid. 2001. Pp:101-106 (Spanish).
- Jiménez P., Rojas A., Reche P., García de los Ríos J.E., Colás J., Gallego M. y Corroto M. Casos clínicos en cernícalos primilla atendidos en GREFA durante el año 1999. En: Biología y Situación del Cernícalo Primilla Ed. GREFA- Comunidad de Madrid. 2001. Pp: 113-117 (Spanish).
- Jiménez P., Reche P., Rojas A., Colás J., Gallego M., Corroto M. y García de los Ríos J.E. Microbiota Gram-negativa normal en cloaca de cernícalo primilla: incidencia en huevos abortados en el programa de cria. En: Biología y Situación del Cernicalo Primilla. Ed. GREFA- Comunidad de Madrid. 2000. Pp.107-112 (Spanish).
+ Teaching
+ I helped to organise
- ENFIN-DREAM meeting 2008, Madrid
- ESF-Genomes to Systems-Poster
- Madrid-ECCB05