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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.

Members of the group have continued their careers as Group Leaders, Heads of Bioinformatics platforms, and some became CEOs of bio-tech based companies.

The group has always corrdinated the Bioinformatics Talks seminar series in every hosting Institution.

The group is strategically located within a Maria de Maeztu Unit [DMC2], an excellence Unit from the SOMM alliance SOMMa.

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

  • how proteins evolve and acquire novel functions
  • how mutations impact a given protein function
  • how is the relationship between molecular evolution and phenotypic evolution.
  • how to better define "protein function"
  • how gene networks evolve in regeneration pathways

We are a very active, group and:

  • Organise the weekly BioinfoCABD seminars since 2018
  • Coordinate with the #Bioinformatics Platform
  • Provide training
  • We like outreach
  • We like to collaborate


Our research in selected examples

[2020] A bacterial origin for sterol synthesis? #Evolution #Phylogenetics#Structure/function #Sequence analyses #Genomic analyses:

Phylogenetic reconstructions suggest that bacteria contributed to polycyclic triterpene biosynthesis during eukaryogenesis adding another component to the eukaryotic membrane that has its origin associated with the bacterial contribution to early eukaryotic lineages..

Sterol
ML reconstruction of the triterpene cyclase family to show the evolution of the closest homologs to SHC.

[2017] A novel MMR pathway: #Evolution #Phylogenetics #Structure/function #Sequence analyses

NucS distribution was scattered around the prokaryotic genomes, and entirely absent in eukaryots. We propose the complete NucS originated as a fusion of two domains in an archeal ancestor.

Model
Origin and transference of NucS.

[2017] Novel mRNA-miRNA interactions relevant to cancer-related pathways. We analysed the 2015 TCGA data to (1) identify potential pairs of mRNA-miRNA that (2) could have predictive value in survival. #Transcriptomics #Linear Models #Integration #Methylation #CNV #MultifactorialCOX

We screened thousands of 2015 TCGA samples. 15 out of available 33 TGCA tumor types were informative. Accounting for confounding variables, gene expression is influenced by methylation and copy number variation. The most influential variable is tumor type.

mRNA/miRNA pairs specific of lung tumors.
Gene expression of single genes should NOT be used as proxy for pathway enrichment/depletion status. In cancer: gene expression should be corrected by methylation and copy number alterations. Survival analyses should be done with multifactorial Cox and taken with caution. We provide a confident statistical approach to identify novel miRNA-target relationships in different tumour types within cancer-relevant pathways. .
Survival with multifactorial Cox models

The code analyses for this paper is available .


Selected 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. 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. 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. Doi: 10.1083/jcb.201103008.

  • 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 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. DOI:10.15252/embj.201592821
  • Basilico, F.*, et al 2014 The pseudo GTPase CENP-M drives human kinetochore assembly. eLifeDoi: 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. 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. 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. 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 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 Doi: 10.1096/fj.09-153106.

  • 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. Doi:10.1371/journal.pone.0031813.
  • Pons,T., et .al., 2013. . A common structural scaffold in CTD phosphatases that supports distinct catalytic mechanisms. Proteins. Doi: 10.1002/prot.24376.
  • López-Contreras, AJ., et al 2013. A proteomic characterization of factors enriched on nascent DNA molecules. Cell Reports. Doi: 10.1016/j.celrep.2013.03.009.