Ana M. Rojas

×

I am a (Ronin) computational Biologist working in evolution, structural Bioinformatics and Integration

... among other things
Ana

I am a Biologist by training Ph.D. in Biology (Molecular Microbiology).

My focus in on evolution, sequence/structure analyses in signalling pathways.

I lead the Bioinformatics and Computational Biology Group [CbBIO] @ Institute of Biomedicine in Seville-[IBIS] since September 2013.

I supervise the Bioinformatics Unit at IBiS.

In 2017 I have become a CSIC researcher


Interests


  • Group site CBBiO
  • Protein families

  • Structure/Fucntion

  • Evolution:NucS
  • Signaling
  • Integration:Intregration

Tools


  • For transcriptomcis (Dockerized) miArmaSeq:miArma
  • Code Survival (Github) miRNAs-mRNAs-survival-TCGA:Correlations
  • The human DNA Damage Proteins DATABASE
  • People (All times)


    Idelfonso Cases Now at REDgene Bioinformatics

    Eduardo Andres Leon now at IPBLN-CSIC

    Aida Arcas Mantas now at Instituto de Neurociencias

    Eduard Porta Pardo now at BSC.

    Juan A. Cordero at IBIS

    Ida Paramonov

    Joel Lopez Bercianos now at Echevarne Laboratories

    Alba Gutierrez now at Harvard Medical School

    Cristina Gordon (Graduate student)

    Javier Macias (Master student, Univ Sevilla)

    Alvaro Ponce (Master student, Univ Vic)

    Sara Sanchez

    Yosu Odriozola

    Rocio Nuñez now at CNIO

    05/2009-09/2013 Junior Group Leader Insitute for Predictive and Personalized Medicine of Cancer [IMPPC], Badalona, ES
    06/2012-09/2013 Adjunt Researcher Barcelona Supercomputing Center [BSC], Barcelona, ES
    03/2006-05/2009 Staff Scientist in Alfonso Valencia's lab National Center for Spanish Cancer Research (Centro Nacional de Investigaciones Oncológicas) [CNIO], Madrid, ES
    11/2003-03/2006 Posdoctoral associate in Alfonso Valencia's lab Spanish Centre for Biotechnology [CNB], Madrid, ES
    11/2001-10/2003 Posdoctoral associate in Adam Godzik's lab (now Sandforburnham) The Burnham Institute, La Jolla, CA, US
    12/2000-11/2001 NASA-NSCORT fellow in RF Doolittle's lab The University of California in San Diego [UCSD], La Jolla, CA, US
    1998-12/2000 Pre and Posdoc in Michael McClelland's lab The Sidney Kimmel Cancer Center (Now merged with the Burnham Institute), La Jolla, CA, US

    My Google citations

    1. Andres-Leon, E., Cases, I., Alonso,S.* and Rojas, A.M.*. 2017 Novel miRNA-mRNA interactions conserved in essential cancer pathways. Scientific ReportsDOI:10.1038/srep46101 [HERE].

    2. Castaneda-Garcia, A; Prieto, A.I., Rodriguez-Beltran, J., Alonso, N., Cantillon, D., Costas. C., Perez-Lago, L., Zegeye, E.D.., Herranz, M., Plocinski, P., Tonjum, T., Garcia de Viedma, D., Paget, M, Waddell, S.J., Rojas, A.M.*, Doherty, A.J.*, & Blazquez, J* 2017 A non-canonical mismatch repair pathway in prokaryotes. Nature communications DOI:10.1038/ncomms14246 [PDF]
    3. Andres-Leon, E., Cases, I., Arcas, A., & Rojas, A.M. 2016 DDRprot: a database of DNA damage response-related proteins. DATABASE DOI: 10.1093/database/baw123 [PubMED]

    4. Tristán-Clavijo E, G.-Scholl F, Macaya, A, Iglesias G, Rojas AM, Lucas, M, Castellano A, Martinez-Mir, A. 2016 Dominant-negative mutation p.Arg324Thr in KCNA1 impairs Kv1.1 channel function in episodic ataxia. Movement disorders. PUBMED. DOI:10.1002/mds.26737
    5. Andres-Leon, E, Nuñez-Torres, R, & Ana M Rojas. 2016. miARma-Seq: a comprehensive tool for miRNA, mRNA and circRNA analysis. Scientific Reports. Article. doi:10.1038/srep25749
    6. Terré B, Piergiovanni G, Segura-Bayona S, Gil-Gómez G, Youssef SA, Otto-Attolini CS, Wilsch-Bräuninger M, Jung C, Rojas AM, Marjanović M, Knobel PA, Palenzuela L, López-Rovira T, Forrow S, Huttner WB, Valverde MA, de Bruin A, Costanzo A, and Stracker TH. 2016. GEMC1 is a critical regulator of multiciliated cell differentiation. EMBO Journal.Article.
    7. Lacalle,RA., Karam, JC., Martinez-Munoz,L., Aretxe,I., Peregil, RM., Sot.,J., Rojas, AM., Goni, FM.,Mellado, M. & Manes, S. 2015. Type I PIP5 kinase homo- and heterodimerization determines its membrane localization and activity FASEB J.. 29:2371.
    8. Basilico, F.*, Maffini, S*., Weir. J.R*., Prumbaum, D., Rojas, A.M, Zimniak, Z., De Antoni, A., Jeganathan, S., Voss, B., van Gerwen, S., Krenn, V., Massimiliano, L., Valencia, A., Vetter, I.R., Herzog, F., Raunser, S., Pasqualato, S & Musacchio, A. 2014 The pseudo GTPase CENP-M drives human kinetochore assembly. eLife. 3:e02978. PMID:25006165 | doi: http://dx.doi.org/10.7554/eLife.02978 [HERE]
    9. MBEcover Arcas, A., Fernandez-Capetillo, O., Cases, I & Rojas, A.M. 2014. Emergence and evolutionary analysis of the human DDR network: implications in comparative genomics and downstream analyses. Molecular Biology and Evolution. 31:940-61. PMID: 24441036 | doi: 10.1093/molbev/msu046 [Open access].



    10. Wen-Shyong Tzou mail, Ying Chu,Tzung-Yi Lin, Chin-Hwa Hu, Tun-Wen Pai, Hsin-Fu Liu, Han-Jia Lin, Ildefonso Cases, Rojas, A.M, Mayka Sanchez, Zong-Ye You, Ming-Wei Hsu. 2014. Molecular Evolution of Multiple-Level Control of Heme Biosynthesis Pathway in Animal Kingdom. PLOS One. 9:e86718. PMID: 24489775 | doi: 10.1371/journal.pone.0086718 [Open access].

    11. Arcas, A., Cases, I., & Rojas, A.M. 2013. Serine/Threonine Kinases and E2-ubiquitin conjugating enzymes in Planctomycetes: unexpected findings. Antonie van Leeuwenhoek Journal of Microbiology.104:509-520. PMID:23918348 | doi:10.1007/s10482-013-9993-2 [PubMED]

    12. Athiyarath R, Arora N, Fuster F, Schwarzenbacher R, Ahmed R, George B, Chandy M, Srivastava A, Rojas AM, Sánchez M, Edison ES. 2013. Two Novel Missense Mutations in Iron Transport Protein Transferrin Causing Hypochromic Microcytic Anaemia and Haemosiderosis: molecular characterisation and structural implications. J. Brit Haematol. 163:404-407. PMID:23888904 | doi: 10.1111/bjh.12487 [PubMED]

    13. Pons,T., Paramonov, I., Boullosa, C., Ibañez, K., Rojas, A.M., & Valencia, A. 2013. . A common structural scaffold in CTD phosphatases that supports distinct catalytic mechanisms. Proteins. 82:103-118. PMID:23900790 | doi: 10.1002/prot.24376. [PubMED].

    14. Lopez-Contreras, AJ., Ruppen, I.,Nieto-Soler, M., Murga, M., Rodriguez, S., Remeseiro, S., Rodrigo, S., Rojas, A., Mendez, J., Muñoz, J, Fernandez-Capetillo, O. 2013. A proteomic characterization of factors enriched on nascent DNA molecules. Cell Reports. [Open access].25:1105-16. PMID:23545495 | doi: 10.1016/j.celrep.2013.03.009

    15. Rojas, A.M.*, Santamaria, A.*,Malik, R.*, Jensen, T.S.*, Koerner, R., Morilla, I., de Juan,D., Krallinger, M., Hansen, D.A., Hoffmann,R., Lees,J., Reid, A., Yeats, C., Wehner, A., Elowe, S., Clegg. A.B., Brunak.,S., Nigg,E.A., Orengo, C., Valencia, A., Ranea., J.A.G. 2012. Uncovering the molecular machinery of the human spindle - an integration of wet and dry systems biology. PLOS One. [Open access]. 7:e31813. PMID:22427808 | doi:10.1371/journal.pone.0031813.

    16. Rojas, A.M., Fuentes, G., Rausell, A., Valencia, A. 2012. The Ras protein superfamily: Evolutionary tree and role of conserved amino acids. The Journal of Cell Biology. 196:189-201. PMID:22270915 | doi: 10.1083/jcb.201103008. [Free].

    1. Vallespinós, M., Fernandez, D., Rodríguez, L., Alvaro-Blanco, J., Baena, E., Ortiz, M., Dukovska, D., Martinez, D., Rojas, A., Campanero, M., Moreno de Alborán, I. 2011. B Lymphocyte Commitment Program Is Driven by the Proto-oncogene c-myc. The Journal of Immunology. 186:6726-36. PMID: 21572027 | doi: 10.4049/jimmunol.1002753. [Free]
    2. Palczewska, M, Casafont I, Ghimire K, Rojas AM, Valencia A, Lafarga M, Mellstrom B, Naranjo JR. 2011. Sumoylation regulates nuclear localization of repressor DREAM. Biochim Biophys Acta 1181:1050-8. PMID: 21070824 | doi: 10.1016/j.bbamcr.2010.11.001. [PubMED]
    3. Mañes, S, Fuentes, G., Peregil, RM., Rojas AM. and Lacalle, RA. 2010. An isoform-specific PDZ-binding motif targets type I PIP5 kinase beta to the uropod and controls polarization of neutrophil-like HL60 cells. FASEB Journal 24:3381-92. PMID: 20442317 | doi: 10.1096/fj.09-153106. [Free].
    4. Fuentes, G., Oyarzabal, J., Rojas, AM. Databases of protein-protein interactions and their uses in drug discovery. 2009. Current Opinion in Drug Discovery and Development12:358-66. PMID: 19396737 [PubMED]
    5. Krallinger, M., Rojas AM. and Valencia, A. 2009. 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 | DOI: 10.1111/j.1749-6632.2008.03750.x [PubMED]
    6. Cacas, J, Marmey, P., Montillet, JL., Sayegh-Alhamdia,M.,Jalloul, A., Rojas-Mendoza, AM.,Cleviret, A., Michel,N. 2009. A novel patatin-like protein from cotton plant, GhPat1, is co-expresed with GhLox1 during Xanthomonas campestris-mediated hypersensitive cell death. Plant Cell Reports. 28:155-64. PMID: 18850102 | DOI: 10.1007/s00299-008-0622-x [PubMED]
    7. Proell,M., Riedl, S.J., Fritz, JH., Rojas, A.M., Schwarzenbacher, R. 2008. The Nod-like Receptor (NLR) Family: a tale of similarities and differences. PLoS One. e2119.PMID: 18446235 | DOI: 10.1371/journal.pone.0002119 [PubMED]
    8. 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. 2008. KCTD5, a putative substrate adaptor for cullin3 ubiquitin ligases. FEBS J. PMID: 18573101 | DOI: 10.1111/j.1742-4658.2008.06537.x [PubMED]
    9. Mathieu-Daude F, Lafay B, Touzet O, Lelivre J, Parrado F, Bosseno MF, Rojas AM, Fatha S, Ouaissi A, Brenire SF. 2008. 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 PMID: 18296127 | DOI: 10.1016/j.meegid.2007.12.010[PubMED]
    10. Sanchez-Pulido, L, Valencia, A, Rojas, AM. 2007. Are Promyelocytic Leukaemia Protein Nuclear Bodies a scaffold for caspase-2 programmed cell death? Trends in Biochemical Sciences. 32:400-6. PMID:17693089 | DOI: 10.1016/j.tibs.2007.08.001 [PubMED]
    11. 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. 2007. Filamin-A regulates actin-dependent clustering of HIV receptors. Nature Cell Biology . 9:838-46. PMID: 17572668 | DOI: 10.1038/ncb1610 [PubMED]
    12. López, G., Rojas, A., Tress, M., Valencia, A. 2007. Assessment of Predictions Submitted for the CASP7 Function Prediction Category. Proteins 69 Suppl 8:165-74. PMID: 17654548 | DOI: 10.1002/prot.21651. [PubMED]
    13. Cases, I., Pisano, D., Andrés, E., Carro, A., Fernández, J.M., Vera, J., Rodríguez, J.M., Gómez- Lopez, G., Valencia, A., Rojas, A. 2007. CARGO: a web portal to integrate customised biological information. Nuc. Acids. Res. 35(Web Server issue):W16-20. PMID: 17483515 | DOI: 10.1093/nar/gkm280. [PubMED]
    14. Sonnenberg, A., Rojas, A., de Pereda, J. 2007. The structure of a tandem pair of spectrin repeats of plectin reveals a modular organization of the plakin domain. J. Mol. Biol. 368:1379-91. PMID: 17397861 | DOI: 10.1016/j.jmb.2007.02.090. [PubMED]
    15. 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. 2007. Nocht regulates morphogenetic signals required for ventricular trabeculation. Dev. Cell 12:415-29. PMID: 17336907 | DOI: 10.1016/j.devcel.2006.12.011. [PubMED]
    16. 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. 34 W110-115. PMID: 16844971| DOI: 10.1093/nar/gkl203. [PubMED]
    17. Cabrera, JR., Sanchez-Pulido,L., Rojas, AM., Valencia,A., Mañes,S., Naranjo,JR., Mellström, B. 2006. GAS1 is related to the GDNF family receptors alpha and regulates ret signaling. J. Biol. Chem. PMID:16551639 | doi:10.1074/jbc.M509572200 [Free].

    1. Rojas AM, Sanchez-Pulido L, Futterer A, van Wely KH, Martinez-A C, Valencia A. 2005. Death inducer obliterator protein 1 in the context of DNA regulation. Sequence analyses of distant homologues point to a novel functional role. FEBS J. 272:3505-11. PMID: 16008551 | DOI: 10.1111/j.1742-4658.2005.04759.x [PubMED]
    2. de Juan D, Mellado M, Rodriguez-Frade JM, Hernanz-Falcon P, Serrano A, Del Sol A, Valencia A, Martinez-A C, Rojas AM. 2005. A framework for computational and experimental methods: Identifying dimerization residues in CCR chemokine receptors.Bioinformatics. 21 Suppl 2:ii13-ii18. PMID: 16204091 | doi: 10.1093/bioinformatics/bti1101 [Free]
    3. Magnusson OT, Toyama H, Saeki M, Rojas A, Reed JC, Liddington RC, Klinman JP, Schwarzenbacher R. 2004. Quinone biogenesis: Structure and mechanism of PqqC, the final catalyst in the production of pyrroloquinoline quinone. Proc Natl Acad Sci U S A. 101:7913-8. PMID: 15148379 | doi: 10.1073/pnas.0402640101 [Free]
    4. Sanchez-Pulido L, Rojas AM, Valencia A, Martinez-A C, Andrade MA. 2004. ACRATA: a novel electron transfer domain associated to apoptosis and cancer.BMC Cancer. 4:98. PMID: 15623366 | DOI: 10.1186/1471-2407-4-98 [PubMED]
    5. Sanchez-Pulido L, Rojas AM, van Wely KH, Martinez-A C, Valencia A. 2004. SPOC: a widely distributed domain associated with cancer, apoptosis andtranscription.BMC Bioinformatics. 5:91. PMID: 15239844 | DOI: 10.1186/1471-2407-4-98 [PubMED]
    6. Liu T*, Rojas A*, Ye Y, Godzik A. 2003. 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. 12:1872-81. * indicates equal contribution PMID: 12930987 | DOI: 10.1110/ps.0359603 [PubMED]
    7. 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. 2003. Comparative analysis of apoptosis and inflammation genes of mice and humans.Genome Res. 13(6B):1376-88. PMID: 12819136 | DOI: 10.1101/gr.1053803 [PubMED]
    8. Ana Rojas, Russell F. Doolittle. 2002. The Occurrence of Type S1A Serine Proteases in Sponge and Jellyfish.J. Mol. Evol. 55:790-794 PMID: 17476731 | DOI: 10.1007/s00239-002-2361-x. Wrongly indexed by PubMed. [PubMED]
    9. Marmey P, Rojas-Mendoza A, de Kochko A, Beachy RN, Fauquet CM. 2005. Characterization of the protease domain of Rice tungro bacilliform virus responsible for the processing of the capsid protein from the polyprotein. Virol J. 2:33. PMID: 15831103 | DOI: 10.1186/1743-422X-2-33. [PubMED]
    10. Rojas AM, de Los Ríos JE, Fischer-Le Saux M, Jiménez P, Reche P, Bonneau S, Sutra L, Mathieu-Daude F, McClelland M. 2004. Erwinia toletana sp. nov., associated with Pseudomonas savastanoi-induced treeknots. Int J Syst Evol Microbiol. 54:2217-22. PMID: 15545461 | DOI: 10.1099/ijs.0.2924-0 [PubMED]
    11. Reche MP, Jiménez PA, Alvarez F, García de los Ríos JE, Rojas AM, de PedroP. 2003. Incidence of salmonellae in captive and wild free-living raptorial birds incentral Spain. J Vet Med B Infect Dis Vet Public Health.50:42-4. PMID: 12710500 | DOI: 10.1046/j.1439-0450.2003.00623.x. [PubMED]
    12. Reche MP, Echeita MA, de los Ríos JE, Usera MA, Jiménez PA, Rojas AM, Colás J, Rodriguez I. 2003. Comparison of phenotypic and genotypic markers for characterization of anoutbreak of Salmonella serotype Havana in captive raptors.J Appl Microbiol. 94:65-72. PMID: 12492925 | DOI: 10.1046/j.1365-2672.2003.01791.x [PubMED]
    13. Reche MP, García de los Ríos JE, Jiménez PA, Rojas AM, Rotger R. 2002. gyrA Mutations associated with nalidixic acid-resistant salmonellae from wildbirds. Antimicrob Agents Chemother. 46:3108-9. No abstract available. PMID: 12183286 | DOI: 10.1128/AAC.46.9.3108-3109.2002 [PubMED]
    14. Jiménez Gomez PA, García de los Ríos JE, Rojas Mendoza A, de Pedro Ramonet P, García Albiach R, Reche Sainz MP. 2004. Molecular basis of quinolone resistance in Escherichia coli from wild birds. Can J Vet Res. 68:229-31. PMID: 15352551 [PubMED]
    15. Alvarez Dávila F, García de los Ríos JE,Jiménez P, Rojas A, Reche P., Troya, M. 1998.Phenotypic variability in different strains of Pseudomonas syringae subsp. savastanoi isolated from different hosts. Eur. J. Plant Pathol . 104:603-609 DOI: 10.1023/A:1008604011154 SpringerLink

    1. Ana M. Rojas and Alfonso Valencia (2014). Evolution of the Ras Superfamily of GTPases. In: Ras Superfamily Small G Proteins: Biology and Mechanisms 1. pp, 3-23. A. Wittinghofer (ed.). Springer-Verlag, Wien. [Springer Link]

    2. 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.
    3. 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.
    4. García de los Ríos J.E., Jiménez P., Reche P., Rojas A., Colás J., Gallego M. y Corroto M. (2001) 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).
    5. Jiménez P., Rojas A., Reche P., García de los Ríos J.E., Colás J., Gallego M. y Corroto M. (2001) 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).
    6. Jiménez P., Reche P., Rojas A., Colás J., Gallego M., Corroto M. y García de los Ríos J.E. (2000) 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