People The_PI

Welcome to CBBio

This is the computational Biology and Bioinformatics lab currently located at the Andalusian Center for Developmental Biology [CABD].

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By Aida Arcas- 2014

CBBio was founded on 2009 in Barcelona, and moved to Seville in 2013. Our research has resulted in more than 50 peer-reviewed articles, book chapters, invited reviews, and over 50 oral presentations in national and international venues. The group is a garantee for the recently renewed Maria de Maeztu award [CABD], an excellence Center/Unit from the SOMM alliance SOMMa.

We are a team of Biologists, Bioinformaticians, and Engineers using computational methods, aiming to understand:

  • how proteins evolve
  • how proteins function and how they multifunction
  • how mutations impact a given protein function
  • how to better define "protein function" to address automatic annotation
  • how gene networks evolve in regeneration pathways


Publications

  • Santana-Molina, C, Rivas-Marin, E, Rojas, AM*, & Devos, D.P.* 2020 Origin and evolution of polycyclic triterpene synthesis. Molecular Biology and Evolution Doi: 10.1093/molbev/msaa054 
  • Silva.J., et al. 2018 EXD2 governs germ stem cell homeostasis and lifespan by promoting mitoribosome integrity and translation. Nature Cell Biology DOI:10.1038/s41556-017-0016-9
  • Castañeda-García, A., et al 2017 A non-canonical mismatch repair pathway in prokaryotes. Nature communications DOI:10.1038/ncomms14246
  • Terré B, et al.,2016. GEMC1 is a critical regulator of multiciliated cell differentiation. EMBO Journal.
  • Andrés-León, E., Cases, I., Arcas, A., & Rojas, A.M. 2016 DDRprot: a database of DNA damage response-related proteins. DATABASE DOI: 10.1093/database/baw123
  • Basilico, F.*, et al., 2014 The pseudo GTPase CENP-M drives human kinetochore assembly. eLife. 3:e02978. PMID:25006165 | doi: http://dx.doi.org/10.7554/eLife.02978
  • Arcas, A., et al, 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
  • Rojas, A.M., et al., 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.

  • Jimenez-Panizo, A; Alegre-Marti,A.; Tettey, T., Fetweiss,G.; Abella-Monleon.M.; Anton, R.; Johnosn, T.; Kim, S.; Lousi, S., Nuñez-Barrios, I.; Font-Diaz, J.; Caelles, C.; Valledor, A.; Perez, P.; Rojas, A.; Fernandez-Rcio, J.; Presman, D.; Hager, D.; Fuentes-Prior, P., Estebanez-Perpiña,E.. 2022 The multivalency of the glucocorticoid receptor ligand-binding domain explains its manifold physiological activities Nucleic Acids Research In press.
  • Verdugo-Sivianes, EM, Rojas, AM, Muñoz-Galván,S., Otero-Albiol, D., Carnero, A.  2020 Mutation of SPINOPHILIN (PPP1R9B) found in human tumors promotes the tumorigenic and stemness properties of cells.   Theranostics doi:10.7150/thno.53572 
  • Martín-Doncel, E., Rojas, AM, Cantarero, L, & Lazo P.A., 2019 To VRK1 functional insufficiency due to alterations in protein stability or kinase activity of human VRK1 pathogenic variants implicated in neuromotor syndromes. Scientific Reports doi: 10.1038/s41598-019-49821-7. .
  • Jiménez-Panizo, A., et al. 2019. Non-canonical dimerization of the androgen receptor and other nuclear receptors: implications for human disease. Endocrine Related Cancer. DOI: 10.1530/ERC-19-0132. .
  • Fuentes-Prior,P., Rojas, A., Hagler, AT., Estébanez-Perpiña,E. 2018 Diversity of Quaternary Structures Regulates Nuclear Receptor Activities. Trends in Biochemical Sciences . DOI:10.1016/j.tibs.2018.09.005 .
  • Silva.J.,et al 2018 EXD2 governs germ stem cell homeostasis and lifespan by promoting mitoribosome integrity and translation. Nature Cell Biology DOI:10.1038/s41556-017-0016-9
  • Castañeda-García, A., et al 2017 A non-canonical mismatch repair pathway in prokaryotes. Nature communications DOI:10.1038/ncomms14246
  • Andrés-León, E., Cases, I., Arcas, A., & Rojas, A.M. 2016 DDRprot: a database of DNA damage response-related proteins. DATABASE DOI: 10.1093/database/baw123
  • Tristán-Clavijo E, et al 2016 Dominant-negative mutation p.Arg324Thr in KCNA1 impairs Kv1.1 channel function in episodic ataxia. Movement disorders. DOI:10.1002/mds.26737
  • Terré B, et al 2016. GEMC1 is a critical regulator of multiciliated cell differentiation. EMBO Journal.
  • Basilico, F.*, et al 2014 The pseudo GTPase CENP-M drives human kinetochore assembly. eLife. 3:e02978. PMID:25006165 | doi: http://dx.doi.org/10.7554/eLife.02978
  • Athiyarath R, et al. 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
  • 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.
  • 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.
  • 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.
  • 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.

  • Mencucci, MV, Rojas-Mendoza, AM., Andres-Leon,E., Lisi-Roman,C., Gagliardino,JJ, Abba,MC., Maiztegui,B. 2022 Identification of novel microRNAs associated with type 2 diabetes by an integrative bioinformatic analysis. Human Gene In press
  • Andrés-León, and Ana M Rojas. 2019 . miARma-Seq, a comprehensive pipeline for the simultaneous study and integration of miRNA and mRNA expression data. METHODS . DOI: 10.1016/j.ymeth.2018.09.002
  • López-Jiménez E, Rojas AM, Andres-Leon E. 2018. RNA sequencing and Prediction Tools for Circular RNAs Analysis. Adv. Exp Med Biol. doi: 10.1007/978-981-13-1426-1_2
  • Andrés-León, E., Cases, I., Alonso,S.* and Rojas, A.M.*. 2017 Novel miRNA-mRNA interactions conserved in essential cancer pathways. Scientific ReportsDOI:10.1038/srep46101
  • Andrés-León, E, Nuñez-Torres, R, & Ana M Rojas. 2016. miARma-Seq: a comprehensive tool for miRNA, mRNA and circRNA analysis. Scientific Reports. doi:10.1038/srep25749

  • Andrés-León, E., Cases, I., Alonso,S.* and Rojas, A.M.*. 2017 Novel miRNA-mRNA interactions conserved in essential cancer pathways. Scientific ReportsDOI:10.1038/srep46101
  • Andrés-León, E, Nuñez-Torres, R, & Ana M Rojas. 2016. miARma-Seq: a comprehensive tool for miRNA, mRNA and circRNA analysis. Scientific Reports. doi:10.1038/srep25749
  • Rojas, A.M.*, et al. 2012. Uncovering the molecular machinery of the human spindle - an integration of wet and dry systems biology. PLOS One. 7:e31813. PMID:22427808 | doi:10.1371/journal.pone.0031813.
  • Pons,T., et .al., 2013. . A common structural scaffold in CTD phosphatases that supports distinct catalytic mechanisms. Proteins. 82:103-118. PMID:23900790 | doi: 10.1002/prot.24376.
  • López-Contreras, AJ., et al 2013. A proteomic characterization of factors enriched on nascent DNA molecules. Cell Reports. 25:1105-16. PMID:23545495 | doi: 10.1016/j.celrep.2013.03.009.