Genomic Resources

Here our relevant publications

POPULATION GENOMICS

  • I. Montes, I. Zarraonaindia, M. Iriondo, W.S. Grant, C. Manzano, U. Cotano, D. Conklin, X. Irigoien, A. Estonba. 2016. Transcriptome analysis deciphers evolutionary mechanisms underlying genetic differentiation between coastal and offshore anchovy populations in the Bay of Biscay. Marine Biology, 163(10):205.
  • I. Montes, M. Iriondo, C. Manzano, M. Santos, D. Conklin, G.R. Carvalho, X. Irigoien, A. Estonba. 2016. No loss of genetic diversity in the exploited and recently collapsed population of Bay of Biscay anchovy (Engraulis encrasicolus, L.). Marine Biology, 163(5):98.
  • M. Muñoz-Colmenero, G-J. Jeunen, Y. J. Borrell, J. L. Martinez, P. Turrero, E. Garcia-Vazquez. 2015. Response of top Shell assemblages to cyclogenesis disturbances. A case study in the Bay of Biscay. Marine Environmental Research, 112: 2-10.
  • I. Miguel, L. Garnery, M. Iriondo, M. Baylac, C. Manzano, S. Sheppard, A. Estonba. 2015. Origin, evolution and conservation of the honey bees from La Palma Island (Canary Islands): molecular and morphological data. Journal of Apicultural Research 54(5):427-440.
  • P. Turrero, M. Muñoz-Colmenero, A. Prado, E. Garcia-Vazquez. 2014. Long-term impacts of human harvesting on shellfish: North Iberian top shells and limpets from the Upper Palaeolithic to the present. Journal of Marine Systems, 139: 51-57.
  • M. J. Sanz-Martin, A. Estonba, C. Manzano, M. Iriondo, G. Pérez-Suárez, A. Fernández, F. Palacios. 2014.  Genetic Structure of Brown and Iberian Hare Populations in Northern Iberia: Implications for Conservation of Genetic Diversity. Journal of Wildlife Management, 78(4):632-644.
  • U. Laconcha, M. Iriondo, H. Arrizabalaga, C. Manzano, P. Markaide, I. Montes, I. Zarraonaindia, I. Velado, E. Bilbao, N. Goñi, J. Santiago, A. Domingo, S. Karakulak, I.K. Oray, A. Estonba. 2014. New nuclear SNP markers unravel the genetic structure and effective population size of albacore tuna (Thunnus alalunga). PLoS ONE, 10(6):e0128247.
  • G. Chust, A. Albaina, A. Aranburu, A. Borja, O. E. Diekmann, A. Estonba, J. Franco, J. M. Garmendia, M. Iriondo, I. Muxika, F. Rendo, J. G. Rodríguez, O. Ruiz-Larrañaga, E. A. Serrão, M. Valle. 2013. Connectivity, neutral theories, and the assessment of species vulnerability to global change in temperate estuaries. Estuarine Coastal and Shelf Science (ECSS), 131:52-63.A.
  • Albaina, M. Iriondo, I. Velado, U. Laconcha, I. Zarraonaindia, H. Arrizabalaga, N. Goñi, M. Lutcavage, W. S. Grant, A. Estonba. 2013. Single nucleotide polymorphism discovery in albacore and Atlantic bluefin tuna provide insights into world-wide population structure. Animal Genetics, 44(6):678-92.
  • M. Muñoz-Colmenero, P. Turrero, J. L. Horreo, E. Garcia-Vazquez. 2012. Evolution of limpet assemblages driven by environmental changes and harvesting in North Iberia. Marine Ecology Progress Series, 466: 121-131.
  • I. Montes, M. Iriondo, C. Manzano, H. Arrizabalaga, E. Jiménez, M. A. Pardo, N. Goñi, C. A. Davies, A. Estonba. 2012. Worldwide genetic structure of albacore (Thunnus alalunga) revealed by microsatellite DNA markers. Marine Ecology Progress Series, 471:183-191.
  • I. Zarraonaindia, M. Iriondo, A. Albaina, M. A. Pardo, C. Manzano, W. S. Grant, X. Irigoien, A. Estonba. 2012. Multiple SNP markers reveal fine-scale population and deep phylogeographic structure in European anchovy (Engraulis encrasicolus L.). PLoS ONE, 7(7):e42201.
  • I. Miguel, M. Baylac, M. Iriondo C. Manzano, L. Garnery, A. Estonba. 2011. Both geometric morphometric and microsatellite data consistently support the differentiation of the Apis mellifera M evolutionary branch. Apidologie, 42:150-161.
  • I. Zarraonaindia, M.A. Pardo, M. Iriondo, C. Manzano, A. Estonba. 2009. Microsatellite variability in European anchovy (Engraulis encrasicolus) calls for further investigation of its genetic structure and biogeography. ICES Journal of Marine Science, 56:2176-2182.
  • I. Miguel, M. Iriondo, L. Garnery, S. Sheppard, A. Estonba. 2007. Gene flow within the M evolutionary lineage of Apis mellifera: role of the Pyrenees, isolation by distance and post-glacial re-colonization routes in the western Europe. Apidologie, 38:141-155.

GENETIC FINGERPRINTING

  • M. Muñoz-Colmenero, J. L. Martinez, A. Roca, E. Garcia-Vazquez. 2017. NGS tools for traceability in candies as high processed food products: Ion Torrent PGM versus conventional PCR-cloning. Food Chemistry, 214: 631-636.
  • M. Muñoz-Colmenero, J. L. Martinez, A. Roca, E. Garcia-Vazquez. 2016. Authentication of commercial Candy ingredients using DNA PCR-cloning methodology. Journal of the Science of Food and Agriculture,96: 859-867.
  • M. Muñoz-Colmenero, O. Blanco, V. Arias, J. L. Martinez, E. Garcia-Vazquez. 2016. DNA authentication of fish products reveals mislabeling associated to seafood processing. Fisheries, 41: 130-140.
  • M. Muñoz-Colmenero, J. L. Martinez, A. Roca, E. Garcia-Vazquez. 2016. Detection of Different DNA Animal Species in Commercial Candy Products. Journal of Food Science, 81: T801-T809.
  • Muñoz-Colmenero, M. Klett-Mingo, O. Blanco, J. L. Martinez, E. Garcia-Vazquez. 2015. Evolution of hake mislabeling niches in commercial markets. Food Control, 54: 267-274.
  • M. Muñoz-Colmenero, J. L. Martinez, A. Roca, E. Garcia-Vazquez. 2014. Obtención de ADN a partir de golosinas para detección de alérgenos. Tecnifood, Enero/Febrero: 120-123.

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. Biased complement deposition and CR3 polymorphism-associated enhanced class switching characterizes anti-nucleic acid response in lupus erythematosus. 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.

GENOMICS OF NON-MODEL SPECIES

  • A.* Albaina, A.* Cariani, G.* Maes, J.V. * Houdt, P. Addis, R. Cannas, G. Heinisch, U. Laconcha, M. Lutcavage, P. Markaide, E. Pintus, A. Estonba, F. Tinti, H. Arrizabalaga (* equal contribution). High-throughput SNP development in Atlantic bluefin tuna using a combine gDNA and cDNA sequencing strategy. PLoS ONE (submitted).
  • 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. Estonba. 18S V9 Metabarcoding Correctly Depicts Plankton Estuarine Community Drivers. Mar Ecol Prog Ser (submitted).
  • Aguirre, D. Abad, A. Albaina, M.S. Goñi-Urriza, A. Estonba, I. Zarraonaindia. Unraveling the environmental and anthropogenic drivers of bacterial community changes in the estuary of Bilbao and its tributaries. PLoS One (submitted).
  • I. Belda, I. Zarraonaindia, M. Perisin, A. Palacios, A. Acedo. From vineyard soil to wine microbiome: scientific-industrial context, technological advances and future perspectives. Frontiers Microbiology (submitted).
  • 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.
  • A. Albaina, X. Irigoien, U. Aldalur, U. Cotano, M. Santos, G. Boyra, A. Estonba. 2015. A real-time PCR assay to estimate invertebrate and fish predation on anchovy eggs in the Bay of Biscay. Progress in Oceanography, 131: 82–99.
  • M. Pawluczyk, J. Weiss, M.G. Links, M.E. Aranguren, M.D. Wilkinson, M. Egea-Cortines. 2015. Quantitative evaluation of bias in PCR amplification and Next Generation Sequencing derived from metabarcoding samples. Analytical and Bioanalytical Chemistry 2015: 1-8.Max E.
  • J.L. Horreo, D. Abad, E. Dopico, M. Oberlin, E. Garcia-Vazquez. 2015. Expansion of Non-Native Brown Trout in South Europe May Be Inadvertently Driven by Stocking: Molecular and Social Survey in the North Iberian Narcea River. Int J Mol Sci, 16(7): 15546–15559.
  • A. Albaina, X. Irigoien, U. Aldalur, G. Boyra, M. Santos, A. Estonba. in press first published online: November 23, 2014. Macrozooplankton predation impact on anchovy (Engraulis encrasicolus) eggs mortality at the Bay of Biscay shelf break spawning centre. Ices Journal of Marine Science, 72(5):1370-1379.
  • 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
  • C.J. Fox, M.I. Taylor, J. van der Kooij, N. Taylor, S.M. Milligan, A. Albaina, S. Pascoal, D. Lallias, M. Maillard, E. Hunter. 2012. Identification of marine fish egg predators using molecular probes. Marine Ecology Progress Series, 462: 205–218
  • A. Albaina, M. Taylor, C. Fox. 2012. Molecular detection of plaice remains in the stomachs of potential predators on a flatfish nursery ground. Marine Ecology Progress Series, 444:223-238.

BIOINFORMATICS

  • M. Aranguren, M. Wilkinson. 2015. Enhanced reproducibility of SADI web service workflows with Galaxy and Docker. GigaScience, 4:59.
  • A. Rodríguez González, A. Callahan, J. Cruz-Toledo, A. Garcia, M.E. Aranguren, M. Dumontier, M.D. Wilkinson. 2014. Automatically exposing OpenLifeData via SADI semantic Web Services. Journal of Biomedical Semantics 2014, 5(1):42+
  • M.E. Aranguren, A.R. Gonzalez, M.D. Wilkinson. 2014. Executing SADI services in galaxy. Journal of Biomedical Semantics, 5(1):46+