Genomic Resources

 

POPULATION GENOMICS

GENETIC FINGERPRINTING

GENE IDENTIFICATION FOR COMPLEX TRAITS

  • E. Ochoa, M. Iriondo, C. Manzano, A. Fullaondo, I. Villar, G. Ruiz-Irastorza, A.M. Zubiaga, A. Estonba. 2016. LDLR and PCSK9 are associated with the presence of antiphospholipid antibodies and the development of thrombosis in aPLA carriers. PLoS ONE 11(1):e0146990.
  • J. Prechl, K. Papp, Z. Hérincs, H. Peterfy, V. Lorand, Z. Szittner, J. del Amo, M. Uribarri, P. Rovero, A. Estonba, I. Paolini, P. Migliorini, O. Ruiz Larrañaga, C. Alcaro, C. Laszlo. 2016. Serological and Genetic Evidence for Altered Complement System Functionality in Systemic Lupus Erythematosus: Findings of the GAPAID Consortium. PloS ONE 11(3):e0150685.
  • O. Ruiz-Larrañaga, P. Migliorini, M. Uribarri, L. Czirják, M. C. Alcaro, J. del Amo, S. M. Iriondo, Escorza-Treviño, A. Estonba. 2016. Genetic association study of systemic lupus erythematosus and disease subphenotypes in European populations: results from GAPAID project. Clinical Rheumatology 35(5):1161-1168.
  • O. Ruiz-Larrañaga, P. Vazquez, M. Iriondo, C. Manzano, M. Agirre, J. M. Garrido, R. A. Juste, A. Estonba. Evidence for gene-gene epistatic interactions between susceptibility genes for Mycobacterium avium subsp. paratuberculosis infection in cattle. Livestock Science 195:63-66.
  • O. Ruiz-Larrañaga, M. Uribarri, M. C. Alcaro, S. Escorza-Treviño, J. del Amo, M. Iriondo, P. Migliorini, L. Czirják, A. Estonba. 2015. Genetic variants associated with RA patients and serotypes in European populations: results from GAPAID project. Clinical and Experimental Rheumatology 34(2):236-241.
  • M. Uribarri, O. Ruiz-Larrañaga, D. Arteta, L. Hernández, C. Alcaro, A. Martínez, S. Escorza-Treviño, A. Estonba, P. Migliorini, L. Czirjak, J. del Amo. 2015. Influence of MTHFR C677T polymorphism on methotrexate monotherapy discontinuation in rheumatoid arthritis patients: results from the GAPAID European Project. Clinical and Experimental Rheumatology, 33(5):0699-0705.
  • L. Valcárcel-Ocete, G. Alkorta-Aranburu, M. Iriondo, A. Fullaondo, M. García-Barcina, J.M. Fernández-García, E. Lezcano-García, J.M. Losada-Domingo, J. Ruiz-Ojeda, A. Álvarez de Arcaya, J.M. Pérez-Ramos, R.A.C. Roos, J.E. Nielsen, C. Saft, REGISTRY investigators of the European Huntington’s Disease Network, A.M. Zubiaga, A. Aguirre. 2015. Exploring genetic factors involved in Huntington disease age of onset: E2F2 as a new potential modifier gene. PLoS ONE, 10(7):e0131573.
  • P. Vazquez, O. Ruiz-Larrañaga, J.M. Garrido, I. Iriondo, C. Manzano, M. Agirre, A. Estonba, R.A. Juste. 2014. Genetic association analysis of paratuberculosis grades in Holstein-Friesian cattle. Veterinary Medicine International, 2014:321327.
  • E. Ochoa, M. Iriondo, A. Bielsa, G. Ruiz-Irastorza, A.Estonba, A. Zubiaga. 2013. Thrombotic antiphospholipid syndrome shows strong haplotypic association with SH2B3-ATXN2 locus. PLOS ONE 8(7): e67897.
  • O. Ruiz-Larrañaga, M. Iriondo, C. Manzano, M. Aguirre, J.M. Garrido, R.A. Juste, A. Estonba. 2012. Single nucleotide polymorphisms in the bovine CD209 candidate gene for susceptibility to infection by Mycobacterium avium subsp. paratuberculosis. Animal Genetics, 43(5):646-647.

GENOMIC RESOURCES OF NON-MODEL SPECIES

  • I. Montes, M. Iriondo, C. Manzano, A. Estonba. 2018. Development of gene-associated single nucleotide polymorphisms for Japanese anchovy Engraulis japonicus through cross-species amplification. Fisheries Science 84(1):1-7.
  • A. Miccoli A., Leonori I, Estonba A., De Felice A., Piccinetti C.C., Carnevali O. 2016. Clupeiformes’ Egg Envelope Proteins characterization: the case of
 Engraulis encrasicolus as a proxy for stock assessment through a novel molecular tool. Molecular Phylogenetics and Evolution 100:95-108
  • G. Catanese, I. Montes, M. Iriondo, A. Estonba, D. Iudicone, G. Procaccini. 2016. High resolution SNPs selection in Engraulis encrasicolus through Taqman OpenArray. Fisheries Research, 177:31-38.
  • Genomic Resources Development Consortium, P. Álvarez , W. Arthofer, M.M. Coelho, D. Conklin, A. Estonba, A.R. Grosso, S.J. Helyar, J. Langa, M.P. Machado, I. Montes, J. Pinho, A. Reif, M. Schartl, B.C Schlick-Steiner, J. Seeber, F.M. Steiner, C. Vilas. 2015. Genomic Resources Notes Accepted 1 June 2015 – 31 July 2015. Molecular Ecology Resources, 15(6):1510-1512.
  • I. Montes, J. Langa, C. Vilas, S.J. Helyar, P. Álvarez, D. Conklin, A. Estonba. 2015. Discovery and characterization of 80 SNPs and 1,624   SSRs in the transcriptome of Atlantic mackerel (Scomber scombrus, L) in Genomic Resources Notes Accepted 1 June 2015 to 31 July 2015. Dryad Digital Repository. http://datadryad.org/resource/doi:10.5061/dryad.3rg62
  • I. Montes, D. Conklin, A. Albaina, S. Creer, G.R. Carvalho, M. Santos, A. Estonba (* equal contribution). 2013. SNP discovery in European anchovy (Engraulis encrasicolus, L) by high-throughput transcriptome and genome sequencing. PLoS ONE 8(8): e70051.
  • I. Zarraonaindia, A. Albaina, M. Iriondo, C. Manzano, M. Pardo, X. Irigoyen, A. Estonba. 2011. Discovery and characterization of 90 SNPs in the European anchovy (Engraulis encrasicolus). Molecular Ecology Resources Primer Database (2012). http://tomato.biol.trinity.edu/manuscripts/12-2/mer-11-0256.pdf
  • Molecular Ecology Resources Primer Development Consortium, A. G. Abreu, A. Albaina, T. J. Alpermann, V. E. Apkenas, S. Bankhead-Dronnet, S. Bergek, M. L. Berumen, C. H. Cho, J. Clobert, A. Coulon, D. de Feraudy, A. Estonba, T. Hankeln, A. Hochkirch, T. W. Hsu, T. J. Huang, X. Irigoien, M. Iriondo, K. M. Kay, T. Kinitz, L. Kothera, M. le Hénanff, F. Lieutier, O. Lourdais, C. M. Macrini, C. Manzano, C. Martin, V. R. Morris, G. Nanninga, M. A. Pardo, J. Plieske, S. Pointeau, T. Prestegaard, M. Quack, M. Richard, H. M. Savage, K. D. Schwarcz, J. Shade, E. L. Simms, V. N. Solferini, V. M. Stevens, M. Veith, M. J. Wen, F. Wicker, J. M. Yost, I. Zarraonaindia. 2012. Permanent genetic resources added to Molecular Ecology Resources Database 1 October 2011-30 November 2011. Molecular Ecology Resources, 12(2):374-376.

METAGENOMICS

  • D. Abad, A. Albaina, M. Aguirre, A. Laza-Martínez, I. Uriarte, A. Iriarte, F. Villate, A. Estonba. 2016. Is metabarcoding suitable for estuarine plankton monitoring? A comparative study with microscopy. Mar Biol 163, 1–13.
  • Albaina, I. Uriarte, M. Aguirre, D. Abad, A. Iriarte, F. Villate, A. Estonba. 2016. Insights on the origin of invasive copepods colonizing Basque estuaries; a DNA barcoding approach. Mar. Biodivers Rec., 9(1).
  • L. Miralles, A. Ardura, A. Arias, Y. J. Borrell, L. Clusa, E. Dopico, A. Hernandez de Rojas, B. Lopez, M. Muñoz-Colmenero, A. Roca, A. Valiente, A. Zaiko, E. Garcia-Vazquez. 2016. Barcodes of marine invertebrates from north Iberian ports: Native diversity and resistance to biological invasions. Marine pollution Bulletin, 112: 183-188.
  • N. Sangwan, I. Zarraonaindia, J.T. Hampton-Marcell, H. Seegane, T.W. Eshoo, G. Rijal, M.C. Negri, J.A. Gilbert. 2016. Differential functional constraints cause strain-level endemism in Polynucleobacter populations. mSystems, 1(3):e00003-16.
  • A. Albaina, M. Aguirre, D. Abad, M. Santos, A. Estonba. 2016. 18S rRNA V9 metabarcoding for diet characterization: a critical evaluation with two sympatric zooplanktivorous fish species. Ecol Evol, 6: 1809–1824.
  • I. Zarraonaindia, S.M. Owens, P. Weisenhorn, K. West, J. Hampton-Marcel, S. Lax, N.A. Bokulich, D.A. Mills, G. Martin, S. Taghavi, D. van der Lelie, J.A. Gilbert. 2015. The soil microbiome influences grapevine-associated microbiota. mBio 6(2):e02527-14. doi:10.1128/mBio.02527-14.
  • I. Zarraonaindia, J. Gilbert. 2014. Probing the Microbial Mysteries of Wine. Microbe. 9 – 11, pp. 442 – 447. 2014.
  • Winston, Jarrad Hampton-Marcell, Iratxe Zarraonaindia, Sarah M. Owens, Corrie S. Moreau, Jack A. Gilbert, Josh Hartsel, Suzanne J. Kennedy, S. M. Gibbons. 2014 Understanding Cultivar-Specificity and soil determinants of the cannabis microbiome. PLoS ONE, 9(6):e99641+
  • Jack A. Gilbert, Daniel van der Lelie, Iratxe Zarraonaindia. 2014. Microbial terroir for wine grapes. Proceedings of the National Academy of Sciences, 111(1):5–6
  • Iratxe Zarraonaindia, Daniel P Smith, and Jack A Gilbert. 2013. Beyond the genome: community-level analysis of the microbial world. Biology & philosophy, 28(2):261–282

BIOINFORMATICS