• Del Rio-Lavín A, Díaz-Arce N, Larraín MA, Araneda C, Rodríguez-Ezpeleta N, Jiménez E, Pardo MA (2022). Population structure and geographic origin assignment of Mytilus galloprovincialis mussels using SNPs. Aquaculture 550: 737836


  • Canals O, Mendibil I, Santos M, Irigoien X, Rodriguez-Ezpeleta N (2021). Vertical stratification of environmental DNA in the open ocean captures ecological patterns and behavior of deep-sea fishes. Limnology & Oceanography Letters 6: 339-347
  • Aguirre-Sarabia I, Diaz-Arce N, Pereda-Agirre I, Mendibil I, Urtizberea A, Gerritsen HD, Burns F, Holmes I, Landa J, Coscia I, Quincoces I, Santurtun M, Zanzi A, Martinsohn JT, Rodríguez-Ezpeleta N (2021). Evidence of stock connectivity, hybridization and misidentification in white anglerfish support the need for adopting a genetics-informed fisheries management approach. Evolutionary Applications 9: 2221-2230
  • Rodríguez-Ezpeleta N, Zinger L, Kinziger A, Bik HM, Bonin A, Coissac E, Emerson BC, Lopes CM, Pelletier TA, Taberlet P and Narum S (2021). Biodiversity monitoring using environmental DNA Mol Ecol Resour 5: 1405-1409
  • Rodriguez-Ezpeleta N, Morissette O, Bean CW, Manu S, Banerjee P, Lacoursière-Roussel A, Beng KC, Alter SE, Roger F, Holman LE, Stewart KA, Monaghan MT, Mauvisseau Q, Mirimin L, Wangensteen OS, Antognazza CM, Helyar SJ, de Boer H, Monchamp M-E, Nijland R, Abbott CL, Doi H, Barnes MA, Leray M, Hablützel PI and Deiner K (2021). Trade-offs between reducing complex terminology and producing accurate interpretations from environmental DNA: Comment on “Environmental DNA: What’s behind the term?” by Pawlowski et al., (2020). Mol. Ecol. 19: 4601-4605
  • Jansen T, Nielsen EE, Rodriguez-Ezpeleta N, Arrizabalaga H, Post S, MacKenzie BR (2021). Atlantic bluefin tuna (Thunnus thynnus) in Greenland – mixed-stock origin, diet, hydrographic conditions and repeated catches in this new fringe area. Canadian Journal of Fisheries and Aquatic Sciences: 78(4): 400-408
  • Artetxe-Arrate I, Fraile I, Marsac F, Farley JH, Rodriguez-Ezpeleta N, Davies CR, Clear N, Grewe P, Murua H (2021). A review of the fisheries, life history and stock structure of tropical tuna (Skipjack Katsuwonus pelamis, yellowfin Thunnus albacares and bigeye Thunnus obesus) in the Indian Ocean. Advances in Marine Biology 88: 39-89
  • Artetxe-Arrate I, Fraile I, Farley J, Darnaude AM, Clear N, Rodriguez-Ezpeleta N, […], Davies CR, Marsac F, Murua H (2021) Otolith chemical fingerprints of skipjack tuna (Katsuwonus pelamis) in the Indian Ocean: First insights into stock structure delineation. PLOS ONE 16(3): e0249327
  • Gilbey J, Carvalho G, Castillo R, Coscia I, […], Rodriguez-Ezpeleta N, Silva G, Strammer I, Vasemagi A, Volckaert FAM (2021). Life in a drop: sampling environmental DNA for fishery management and ecosystem monitoring. Marine Policy 124: 104331
  • Marden E, Abbot RJ, Austerlitz F, […], Rodriguez-Ezpeleta N, […], Narum S, Rieseberg L (2020). Sharing and reporting benefits from Biodiversity Research. Molecular Ecology 30: 1103–1107


  • Pearman JK, Chust G, Aylagas E, Villarino E, Watson JR, […], Rodriguez-Ezpeleta N, Uyarra MC, Carvalho S (2020). Pan-regional marine benthic cryptobiome Diversity patterns revealed by metabarcoding Autonomous Reef Monitoring Structures. Molecular Ecology 29: 4882-4897
  • Brophy D, Rodriguez-Ezpeleta N, Fraile I, Arrizabalaga H (2020). Combining genetic markers with stable isotopes in otoliths reveals complexity in the stock structure of Atlantic bluefin tuna (Thunnus thynnus). Scientific Reports 10:14675
  • Fraija-Fernandez N, Bouquieaux MC, Rey A, Mendibil I, Cotano U, Irigoien X, Santos M, Rodriguez-Ezpeleta N (2020). Marine water environmental DNA provides a comprehensive fish diversity assessment and reveals spatial patterns in a large oceanic area. Ecology and Evolution 10: 7560-7584
  • Hernandez I, Alfaro B, Rodriguez-Ezpeleta N (2020) Enhancing high throughput sequencing unveils changes in bacterial communities during ready-to-eat lettuce spoilage. Journal of Horticulture and Postharvest Research 3: 297-310
  • Rey A, Basurko OC, Rodriguez-Ezpeleta, N (2020). Considerations for metabarcoding-based port biological baseline surveys aimed at marine non-indigenous species monitoring and risk-assessments. Ecology and Evolution 10: 2452-2465


  • Leone A, Álvarez P, García D, Saborido-Rey F, Rodriguez-Ezpeleta N (2019). Genome-wide SNP based population structure in European hake reveals the need for harmonizing biological and management units. ICES J Mar. Sci. 76: 2260-2266
  • Rey A, Carney KJ, Quinones LE, Pagenkopp Lohan K, Ruiz GM, Basurko OC, Rodriguez-Ezpeleta N (2019). Environmental DNA metabarcoding: a promising tool for ballast water monitoring. Environmental Science and Technology 53: 11849- 11859
  • Rodríguez-Ezpeleta N, Díaz-Arce N, Walter III, JF, Richardson DER, Rooker JR, […], Fromentin JM, Arrizabalaga H (2019). Improved Atlantic bluefin tuna management through genetic assignment of natal origin. Frontiers in Ecology and the Environment 17: 439-444
  • Díaz -Arce N, Rodríguez -Ezpeleta N (2019). Selecting RAD-seq data analysis parameters for population genetics: the more the better? Frontiers in Genetics 10:533
  • Azpeitia K, Rodriguez-Ezpeleta N, Mendiola D (2019). Settlement and recruitment pattern variability of the mussel Mytilus galloprovincialis Lmk. from the Bay of Biscay (Basque Country). Regional Studies in Marine Science 27: 100523


  • Aylagas E, Borja A, Muxika I, Rodríguez-Ezpeleta N (2018). Adapting metabarcoding-based benthic biomonitoring into routine marine ecological status assessment networks. Ecological Indicators 95: 194-202
  • Puncher GN, Cariani A, Maes GE, van Houdt J, Herten K, Cannas R, Rodriguez-ezpeleta N, […], Arrizabalaga H, Tinti F (2018). Spatial dynamics and mixing of bluefin tuna in the Atlantic Ocean and Mediterranean Sea revealed using next generation sequencing. Molecular Ecology Resources 18: 620-638
  • Van Wyngaarden M, Snelgrove PVR, DiBacco C, Hamilton LC, Rodríguez-Ezpeleta N, Zhan L, Beiko RG, Bradbury IR (2018). Oceanographic variation influences spatial genomic structure in the sea scallop, Placopecten magellanicus. Ecology and Evolution 8: 2824-2841
  • Villarino E, Watson JR, Jönson B, Gasol JM, […], Corell J, Rodríguez-Ezpeleta N, […], Duarte C, Irigoien X, Chust G (2018). Large-scale ocean connectivity and planktonic body size. Nature Communications 9:142.
  • Rey A, Basurco OC, Rodriguez-Ezpeleta N (2018).The challenges and promises of genetic approaches for ballast water monitoring. Journal of Sea Research 133:134-145


  • Rodríguez-Ezpeleta N, Álvarez P, Irigoien X. (2017). Genetic diversity and connectivity in Maurolicus muelleri in the Bay of Biscay inferred from thousands of SNP markers. Frontiers in Genetics 8:195.
  • Tricarico E, Borrell YJ, Garcia-Vazquez E, Rico JM, Rech S, Scapini S, Johovic I, Rodriguez-Ezpeleta N, Basurko OC, Rey A, Gough P, Aquiloni L, Sposimo P, Inghilesi AF, Haubrock P, Delgado JF, Skukan R, Hall D, Marsh-Smith S, Kilbey D,  Monteoliva AP, Muha TP, Rodriguez-Rey M, Rolla M, Rehwald HK, Garcia de Leaniz C, Consuegra S (2017). Developing innovative methods to face aquatic invasions in Europe: the Aquainvad-ED project. Management of Biological Invasions. 8: 403:408
  • Cuende E, Mendibil I, Bachiller E, Álvarez P, Cotano U, Rodriguez-Ezpeleta N (2017). A Real-time PCR approach to detect predation on anchovy and sardine early life stages. Journal of Sea Research 130: 204-209
  • Van Wyngaarden M, Snelgrove PVR, DiBacco C, Hamilton LC, Rodríguez-Ezpeleta N, Stanley RRE, Bradbury IR (2017). Identifying patterns of dispersal, connectivity, and selection in the sea scallop, Placopecten magellanicus, using RAD-seq derived SNPs. Evolutionary Applications 10: 102–117
  • Aylagas E, Borja A, Tangherlini M, Dell´Anno A, Corinaldesi C, Michell CT, Irigoien X, Danovaro R, Rodríguez-Ezpeleta N (2017). A bacterial community-based index to assess the ecological status of estuarine and coastal environments. Marine Pollution Bulletin. 114: 679-688


  • Danovaro R, Carugati L, Berzano M, Cahill AE, […], Rodriguez-Ezpeleta N, […], Cochrane SKJ, Mangoni O, Borja A (2016). Implementing and innovating marine monitoring approaches for assessing marine environmental status. Frontiers in Marine Science. 3: 213
  • Aylagas E, Mendibil I, Borja A, Rodriguez-Ezpeleta N (2016). Laboratory guidelines for metabarcoding marine benthic macroinvertebrates: sample processing for biomonitoring and assessment purposes. Frontiers in Marine Science. 3: 203
  • Díaz-Arce N, Arrizabalaga H, Murua H, Irigoien X, Rodríguez-Ezpeleta N (2016). RAD-seq derived genome-wide nuclear markers resolve the phylogeny of tunas. Molecular Phylogenetics and Evolution. 102:202-207
  • Aylagas E, Borja A, Irigoien X, Rodríguez-Ezpeleta N (2016). Benchmarking DNA metabarcoding for biodiversity-based monitoring and assessment. Frontiers in Marine Science. 3: 96
  • Bucklin A, Lindeque P, Rodriguez-Ezpeleta N, Albaina A, Lehtiniemi M (2016). Metabarcoding of Marine Zooplankton: Prospects, Progress, and Pitfalls. Journal of Plankton Research. 38: 393–400
  • Rodriguez-Ezpeleta N, Bradbury I, Mendibil I, Álvarez P, Cotano U, Irigoien X (2016). Population structure of Atlantic Mackerel inferred from RAD-seq derived SNP markers: effects of sequence clustering parameters and hierarchical SNP selection. Molecular Ecology Resources. 16: 991–1001
  • Borja A, Elliot M, Andersen JH, Berg T, Carstensen J, Halpern BS, Heiskanen AS, Korpinen S, Lowndes JSS, Martin G, Rodriguez-Ezpeleta N (2016). Overview of integrative assessment of marine systems: the Ecosystem Approach in practice. Frontiers in Marine Science: 3:20


  • Kopf A, Bicak M, Kottman R, Schnetzer J, […], Rodriguez-Ezpeleta N, […], Amaral-Zettler L, Gilbert JA, Davies N, Field D, Glöckner FO (2015). The Ocean Sampling Day Consortium. Gigascience 4:27
  • Bradbury IR, Bowman S, Borza T, Snelgrove PVR, Hutchings JA, Berg PR, Rodríguez-Ezpeleta N, Lighten J, Ruzzante DE, Taggart C, Bentzen P (2014). Long Distance Linkage Disequilibrium and Limited Hybridization Suggest Cryptic Speciation in Atlantic Cod. PloS One 9: e106380
  • Aylagas E, Borja A, Rodríguez-Ezpeleta N (2014). Environmental Status Assessment Using DNA Metabarcoding: Towards a Genetics Based Marine Biotic Index (gAMBI). PloS One 9: e90529
  • Davies N, Field D, Amaral-Zettler L, Clark MS, […], Rodriguez-Ezpeleta N, […], Wichels A, Wooley JC, Yahara T, Zingone A; GOs-COS (2014). The founding charter of the Genomic Observatories Network. Gigascience 3:2
  • Rumbo-Feal S, Gómez MJ, Gayoso C, Alvarez-Fraga L, Cabral MP, Aransay AM, Rodríguez-Ezpeleta N, Fullaondo A, Valle J, Tomás M, Bou G, Poza M (2013). Whole Transcriptome Analysis of Acinetobacter baumannii Assessed by RNA-Sequencing Reveals Different mRNA Expression Profiles in Biofilm Compared to Planktonic Cells. PLoS One 8: e72968
  • Bourlat SJ, Borja A, Gilbert J, Taylor MI, Davies N, Weisberg SB, Griffith JF, Lettieri T, Field D, Benzie J, Glöckner FO, Rodríguez-Ezpeleta N, Faith DP, Bean TP, Obst M (2013). Genomics in marine monitoring: New opportunities for assessing marine health status. Mar Pollut Bull; 74(1):19-31
  • Vazquez-Chantada M, Gonzalez-Lahera A, Martinez-Arranz I, Garcia-Monzon C, Regueiro MM, Garcia-Rodriguez JL, Schlangen K, Mendibil I, Rodriguez-Ezpeleta N, Lozano JJ, Pedersen O, Banasik K, Justesen JM, Joergensen T, Witte DR, Laurintzen T, Hansen T, Veyrie N, Clement K, Tordjman J, Tran A, Le Marchand-Brustel Y, Buque X, Aspichueta P, Echevarria-Uraga JJ, Martin-Duce A, Caballería J, Gual P, Castro A, Mato JM, Martinez-Chantar ML and Aransay AM (2013). Solute carrier family 2 member 1 is involved in the development of nonalcoholic fatty liver disease. Hepatology, 57(2):505-14
  • Ferreiro MJ, Rodríguez-Ezpeleta N, Pérez C, Hackenberg M, Aransay AM, Barrio R, Cantera R (2012). Whole transcriptome analysis of a reversible neurodegenerative process in Drosophila reveals the regulation of potential neuroprotective genes. BMC Genomics: 13:483
  • Mosén-Ansorena D, Aransay AM and Rodríguez-Ezpeleta N (2012). Comparison of methods to detect copy number alterations in cancer using simulated and real genotyping data. BMC Bioinformatics, 13(1):192
  • Iruarrizaga-Lejarreta M, Varela-Rey M, Lozano JJ, Fernández-Ramos D, Rodríguez-Ezpeleta N, Embade N, Lu SC, van der Kraan PM, Blaney Davidson EM, Gorospe M, Mirsky R, Jessen KR, Aransay AM, Mato JM, Martínez-Chantar ML, Woodhoo A (2012). The RNA-binding protein HuR controls global changes in gene expression during Schwann cell development. The Journal of Neuroscience. 32(14):4944-58
  • Díaz-Peña R, Aransay AM, Suárez-Álvarez B, Bruges-Armas J, Rodríguez-Ezpeleta N, Regueiro M, Pimentel-Santos FM, Mulero J, Sánchez A, Collantes E, Queiro R, Ballina J, Alves H, López-Larrea C (2012). A high-density SNP genotyping approach within 19q13 chromosomic region identifies an association of a CNOT3 polymorphism with ankilosing spondylitis. Annals of the Rheumatic Diseases 71(5):714-7
  • Rodríguez-Ezpeleta N and Embley TM (2012). The SAR11 group of alpha-proteobacteria is not related to the origin of mitochondria. PLoS One. 7: e30520
  • Vandenbroeck K, Alvarez J, Swaminathan B, Alloza I, Matesanz F, Urcelay E, Comabella M, Alcina A, Fedetz M, Ortiz MA, Izquierdo G, Fernandez O, Rodriguez-Ezpeleta N, Matute C, Caillier S, Arroyo R, Montalban X, Oksenberg JR, Antigüedad and Aransay A. (2012). A cytokine gene screen uncovers SOCS1 as genetic risk factor for multiple sclerosis. Genes and Immunity 1: 21-28
  • Diaz-Peña R, Aransay AM, Bruges-Armas J, Lopez-Vazquez A, Rodríguez-Ezpeleta N, Mendibil I, Sánchez A, Torre-Alonso JC, Bettencourt BF, Alves H and Lopez-Larrea C (2011). Fine mapping of major histocompatibility complex in ankylosing spondylitis: association of HLA-DPA1 and HLA-DPB1 region. Arthritis & Rheumatism 63(11):3305-12
  • Hackenberg M, Rodriguez-Ezpeleta N and Aransay AM (2011). miRanalyzer: an update on the detection and analysis of microRNAs in high throughput sequencing experiments. Nucleic Acids Res Suppl 2:W132-8


  • Rodríguez-Ezpeleta N, Álvarez-Busto J, Imaz L, Regueiro M, Azcárate MN, Bilbao R, Iriondo M, Gil A, Estonba A and Aransay AM (2010). High-density SNP genotyping detects homogeneity of Spanish and French Basques, and confirms their genomic distinctiveness from other European populations. Hum. Genet. 128:113-117
  • Baurain D, Brinkmann H, Petersen J, Rodríguez-Ezpeleta N, Stechmann A, Demoulin V, Burger G, Lang BF and Philippe H (2010). Phylogenomic evidence for separate acquisition of plastids in cryptophytes, haptophytes and stramenopiles. Mol. Biol. Evol. 27:1698-709
  • Liu Y, Leigh J, Brinkmann H, Cushion MT, Rodriguez-Ezpeleta N, Philippe H and Lang BF (2009). Phylogenomic analyses support the monophyly of Taphrinomycotina, including Schizosaccharomyces fission yeasts. Mol. Biol. Evol. 26:27-34
  • Rodríguez-Ezpeleta N, Brinkmann H, Burger G, Roger AJ, Gray MW, Philippe H and Lang BF (2007). Toward the resolution of the eukaryotic tree: the phylogenetic positions of jakobids and cercozoans. Curr. Biol. 17:1420-1425
  • Rodríguez-Ezpeleta N, Brinkmann H, Roure B, Lartillot N, Lang BF and Philippe H (2007). Detecting and overcoming systematic errors in genome-scale phylogenies. Syst. Biol. 56:1-11
  • Roure B, Rodríguez-Ezpeleta N and Philippe H (2007). SCaFoS: a tool for Selection, concatenation and fusion of Sequences for phylogenomics. BMC Evol. Biol. 7 Supp.1: S2
  • Rodríguez-Ezpeleta N, Philippe H, Brinkmann H, Becker B and Melkonian M (2007). Phylogenetic analyses of nuclear, mitochondrial and plastid multi-gene datasets support the placement of Mesostigma in the Streptophyta. Mol Bio. Evo. 24: 723-731
  • Rodríguez-Ezpeleta N and Philippe H (2006). Plastid origin: replaying the tape. Curr. Biol. 16:R53-R56
  • Rodríguez-Ezpeleta N, Brinkmann H, Burey S, Roure B, Burger G, Loffelhardt W, Bohnert HJ, Philippe H and Lang BF (2005). Monophyly of primary photosynthetic eukaryotes: green plants, red algae, and glaucophytes. Curr. Biol. 15:1325-1330

Book chapters

  • Rey A, Corell J, Rodriguez-Ezpeleta N (2020). Metabarcoding to study zooplankton diversity. In Zooplankton Ecology (Barbosa and Teodosio, eds). CRC Press (Taylor & Francis Group) ISBN 978-1-1384-9645-3
  • Arrizabalaga H, Arregi I, Medina A, Rodriguez-Ezpeleta N, Fromentin JM, Fraile I (2019). Life history and migrations of Mediterranean bluefin populations. In The Future of Bluefin Tunas (B. Block, ed). John Hopkins University Press. ISBN 978-1-4214-2963-2
  • Aylagas E, Rodríguez-Ezpeleta N (2016). Analysis of Illumina MiSeq amplicon reads: application to benthic indices for environmental monitoring. In Methods in Molecular Biology: Marine Genomics – Methods and Protocols. Vol. 1452 (S. Bourlat, ed.) pp. 237-249. Springer, New York, USA. ISBN 978-1-4939-3774-5
  • Rodríguez-Ezpeleta N, Moreira D, Ruíz-Trillo I (2014). The Former “Protists”: Amoebozoa, Rhizaria, Excavata, Haptophyta, Cryptophyta, Heterokonta, and Alveolata. In The Tree of Life (P Vargas and R Zardoya eds.). Sinauer Associates Inc. ISBN: 978-1-60535-229-9
  • Rodríguez-Ezpeleta N, Moreira D, Ruíz-Trillo I (2012). Protistas: Amoebozoa, Rhizaria, Excavata y Chromalveolata. In El árbol de la vida (P Vargas and R Zardoya eds.) pp. 42-55. Madrid, Spain. ISBN 978-84-615-9740-6
  • Rodríguez-Ezpeleta N and Aransay AM (2011). Introduction. In Bioinformatics for High Throughput Sequencing (Rodríguez-Ezpeleta N, Hackenberg M and Aransay AM eds.). pp. 1-10. Springer, New York, NY, USA. ISBN 978-1-4614-0781-2
  • Rodríguez-Ezpeleta N and Philippe H (2009). Phylogenomics. In Encyclopaedia of Microbiology, 3rd ed. (M Schaechter ed.) pp. 633-643. Elsevier Ltd. Oxford, UK. ISBN 978-0123739391
  • Rodríguez-Ezpeleta N, Teijeiro S, Forget L, Burger G and Lang BF (2009). Construction of cDNA Libraries: Focus on Protists and Fungi. In Methods in Molecular Biology: Expressed sequence tags – generation and analysis Vol. 533 (J Parkinson, ed.) pp.1-15. Humana press Inc. Totowa, NJ, USA. ISBN 978-1588297594
  • Leigh J, Seif E, Rodríguez-Ezpeleta N, Jacob Y, Lang BF (2003). Fungal evolution meets fungal genomics. In Handbook of Fungal Biotechnology, 2nd ed. (D Arora, ed.) pp. 145-161. Marcel Dekker Inc. New York, NY, USA. ISBN 978-0-8247-4018-4

Books edited

  • Rodríguez-Ezpeleta N, Hackenberg M and Aransay AM (2011). Bioinformatics for High Throughput Sequencing. Springer, New York, NY, USA. ISBN 978-1-4614-0781-2