• 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. In press.
  • 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. (doi:10.1111/eva.13278)
  • 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
  • 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.
  • 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