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1

A bacterial community-based index to assess the ecological status of estuarine and coastal environments

Aylagas, Eva, Borja, Ángel, Tangherlini, Michael, Dell'Anno, Antonio, Corinaldesi, Cinzia, Michell, Craig T., Irigoien, Xabier, Danovaro, Roberto, Rodríguez-Ezpeleta, Naiara

Journal:

Marine Pollution Bulletin

Year:

2016

Language:

english

File:

PDF, 2.22 MB

english, 2016

2

Phylogenomic Evidence for Separate Acquisition of Plastids in Cryptophytes, Haptophytes, and Stramenopiles

Baurain, D., Brinkmann, H., Petersen, J., Rodriguez-Ezpeleta, N., Stechmann, A., Demoulin, V., Roger, A. J., Burger, G., Lang, B. F., Philippe, H.

Journal:

Molecular Biology and Evolution

Year:

2010

Language:

english

File:

PDF, 500 KB

english, 2010

3

Phylogenomic Analyses Support the Monophyly of Taphrinomycotina, including Schizosaccharomyces Fission Yeasts

Liu, Y., Leigh, J. W., Brinkmann, H., Cushion, M. T., Rodriguez-Ezpeleta, N., Philippe, H., Lang, B. F.

Journal:

Molecular Biology and Evolution

Year:

2008

Language:

english

File:

PDF, 180 KB

english, 2008

4

Environmental DNA Metabarcoding: A Promising Tool for Ballast Water Monitoring

Rey, Anaïs, Carney, Katharine J., Quinones, Luz E., Pagenkopp Lohan, Katrina M., Ruiz, Gregory M., Basurko, Oihane C., Rodríguez-Ezpeleta, Naiara

Journal:

Environmental Science & Technology

Year:

2019

Language:

english

File:

PDF, 706 KB

english, 2019

5

Detecting and Overcoming Systematic Errors in Genome-Scale Phylogenies

Rodríguez-Ezpeleta, Naiara, Brinkmann, Henner, Roure, Béatrice, Lartillot, Nicolas, Lang, B. Franz, Philippe, Hervé

Journal:

Systematic Biology

Year:

2007

Language:

english

File:

PDF, 1.69 MB

english, 2007

6

Adapting metabarcoding-based benthic biomonitoring into routine marine ecological status assessment networks

Aylagas, Eva, Borja, Ángel, Muxika, Iñigo, Rodríguez-Ezpeleta, Naiara

Journal:

Ecological Indicators

Year:

2018

Language:

english

File:

PDF, 1.60 MB

english, 2018

7

Plastid Origin: Replaying the Tape

Naiara Rodríguez-Ezpeleta, Hervé Philippe

Journal:

Current Biology

Year:

2006

Language:

english

File:

PDF, 136 KB

english, 2006

8

Monophyly of Primary Photosynthetic Eukaryotes: Green Plants, Red Algae, and Glaucophytes

Naiara Rodríguez-Ezpeleta, Henner Brinkmann, Suzanne C. Burey, Béatrice Roure, Gertraud Burger, Wolfgang Löffelhardt, Hans J. Bohnert, Hervé Philippe, B. Franz Lang

Journal:

Current Biology

Year:

2005

Language:

english

File:

PDF, 290 KB

english, 2005

9

Bioinformatics for High Throughput Sequencing Volume 35D1 || MicroRNA Expression Profiling and Discovery

Rodríguez-Ezpeleta, Naiara, Hackenberg, Michael, Aransay, Ana M.

Year:

2012

Language:

english

File:

PDF, 226 KB

english, 2012

10

Encyclopedia of Microbiology || Phylogenomics

Rodríguez-Ezpeleta, N.

Year:

2009

Language:

english

File:

PDF, 352 KB

english, 2009

11

Fine mapping of a major histocompatibility complex in ankylosing spondylitis: Association of the HLA–DPA1 and HLA–DPB1 regions

Roberto Díaz-Peña, Ana M. Aransay, Jacome Bruges-Armas, Antonio López-Vázquez, Naiara Rodríguez-Ezpeleta, Iñaki Mendibil, Alejandra Sánchez, Juan Carlos Torre-Alonso, Bruno F. Bettencourt, Juan Mulero

Journal:

Arthritis & Rheumatism

Year:

2011

Language:

english

File:

PDF, 307 KB

english, 2011

12

Bioinformatics for High Throughput Sequencing Volume 47 || Overview of Sequencing Technology Platforms

Rodríguez-Ezpeleta, Naiara, Hackenberg, Michael, Aransay, Ana M.

Year:

2012

Language:

english

File:

PDF, 352 KB

english, 2012

13

Bioinformatics for High Throughput Sequencing Volume 35D1 || Short-Read Mapping

Rodríguez-Ezpeleta, Naiara, Hackenberg, Michael, Aransay, Ana M.

Year:

2012

Language:

english

File:

PDF, 239 KB

english, 2012

14

A cytokine gene screen uncovers SOCS1 as genetic risk factor for multiple sclerosis

Vandenbroeck, K, Alvarez, J, Swaminathan, B, Alloza, I, Matesanz, F, Urcelay, E, Comabella, M, Alcina, A, Fedetz, M, Ortiz, M A, Izquierdo, G, Fernandez, O, Rodriguez-Ezpeleta, N, Matute, C, Caillier,

Journal:

Genes and Immunity

Year:

2012

Language:

english

File:

PDF, 311 KB

english, 2012

15

Environmental Status Assessment Using DNA Metabarcoding: Towards a Genetics Based Marine Biotic Index (gAMBI)

Aylagas, Eva, Borja, Ángel, Rodríguez-Ezpeleta, Naiara, Consuegra, Sofia

Journal:

Year:

2014

Language:

english

File:

PDF, 1.78 MB

english, 2014

16

Benchmarking DNA Metabarcoding for Biodiversity-Based Monitoring and Assessment

Aylagas, Eva, Borja, Ángel, Irigoien, Xabier, Rodríguez-Ezpeleta, Naiara

Journal:

Frontiers in Marine Science

Year:

2016

Language:

english

File:

PDF, 3.13 MB

english, 2016

17

Bioinformatics for High Throughput Sequencing Volume 50 || Applications of High-Throughput Sequencing

Rodríguez-Ezpeleta, Naiara, Hackenberg, Michael, Aransay, Ana M.

Year:

2012

Language:

english

File:

PDF, 302 KB

english, 2012

18

RAD-seq derived genome-wide nuclear markers resolve the phylogeny of tunas

Díaz-Arce, Natalia, Arrizabalaga, Haritz, Murua, Hilario, Irigoien, Xabier, Rodríguez-Ezpeleta, Naiara

Journal:

Molecular Phylogenetics and Evolution

Year:

2016

Language:

english

File:

PDF, 2.43 MB

english, 2016

19

Whole transcriptome analysis of a reversible neurodegenerative process inDrosophilareveals potential neuroprotective genes

Ferreiro, María, Rodríguez-Ezpeleta, Naiara, Pérez, Coralia, Hackenberg, Michael, Aransay, Ana, Barrio, Rosa, Cantera, Rafael

Journal:

Year:

2012

Language:

english

File:

PDF, 1.01 MB

english, 2012

20

Metabarcoding of marine zooplankton: prospects, progress and pitfalls

Bucklin, Ann, Lindeque, Penelope K., Rodriguez-Ezpeleta, Naiara, Albaina, Aitor, Lehtiniemi, Maiju

Journal:

Journal of Plankton Research

Year:

2016

Language:

english

File:

PDF, 272 KB

english, 2016

21

Marine Sediment Sample Pre-processing for Macroinvertebrates Metabarcoding: Mechanical Enrichment and Homogenization

Aylagas, Eva, Mendibil, Iñaki, Borja, Ángel, Rodríguez-Ezpeleta, Naiara

Journal:

Frontiers in Marine Science

Year:

2016

Language:

english

File:

PDF, 1.43 MB

english, 2016

22

Bioinformatics for High Throughput Sequencing Volume 50 || High-Throughput Sequencing Data Analysis Software: Current State and Future Developments

Rodríguez-Ezpeleta, Naiara, Hackenberg, Michael, Aransay, Ana M.

Year:

2012

Language:

english

File:

PDF, 197 KB

english, 2012

23

Bioinformatics for High Throughput Sequencing Volume 35D1 || DNA–Protein Interaction Analysis (ChIP-Seq)

Rodríguez-Ezpeleta, Naiara, Hackenberg, Michael, Aransay, Ana M.

Year:

2012

Language:

english

File:

PDF, 487 KB

english, 2012

24

Bioinformatics for High Throughput Sequencing || Dissecting Splicing Regulatory Network by Integrative Analysis of CLIP-Seq Data

Rodríguez-Ezpeleta, Naiara, Hackenberg, Michael, Aransay, Ana M.

Year:

2012

Language:

english

File:

PDF, 271 KB

english, 2012

25

Environmental DNA Metabarcoding: A Promising Tool for Ballast Water Monitoring

Rey, Anaïs, Carney, Katharine J., Quinones, Luz E., Pagenkopp Lohan, Katrina M., Ruiz, Gregory M., Basurko, Oihane C., Rodríguez-Ezpeleta, Naiara

Journal:

Environmental Science & Technology

Year:

2019

File:

PDF, 706 KB

2019

26

Settlement and recruitment pattern variability of the mussel Mytilus galloprovincialis Lmk. from SE Bay of Biscay (Basque Country)

Azpeitia, K., Rodríguez-Ezpeleta, N., Mendiola, D.

Journal:

Regional Studies in Marine Science

Year:

2019

File:

PDF, 2.38 MB

2019

27

Bioinformatics for High Throughput Sequencing Volume 1071 || Computational Infrastructure and Basic Data Analysis for High-Throughput Sequencing

Rodríguez-Ezpeleta, Naiara, Hackenberg, Michael, Aransay, Ana M.

Year:

2012

Language:

english

File:

PDF, 304 KB

english, 2012

28

SCaFoS: a tool for Selection, Concatenation and Fusion of Sequences for phylogenomics

Béatrice Roure, Naiara Rodriguez-Ezpeleta, Hervé Philippe

Journal:

BMC Evolutionary Biology

Year:

2007

Language:

english

File:

PDF, 334 KB

english, 2007

29

Bioinformatics for High Throughput Sequencing Volume 50 || Introduction

Rodríguez-Ezpeleta, Naiara, Hackenberg, Michael, Aransay, Ana M.

Year:

2012

Language:

english

File:

PDF, 156 KB

english, 2012

30

Genetic Diversity and Connectivity in Maurolicus muelleri in the Bay of Biscay Inferred from Thousands of SNP Markers

Rodriguez-Ezpeleta, Naiara, Álvarez, Paula, Irigoien, Xabier

Journal:

Frontiers in Genetics

Year:

2017

Language:

english

File:

PDF, 3.01 MB

english, 2017

31

Toward Resolving the Eukaryotic Tree: The Phylogenetic Positions of Jakobids and Cercozoans

Naiara Rodríguez-Ezpeleta, Henner Brinkmann, Gertraud Burger, Andrew J. Roger, Michael W. Gray, Hervé Philippe, B. Franz Lang

Journal:

Current Biology

Year:

2007

Language:

english

File:

PDF, 1.10 MB

english, 2007

32

A real-time PCR approach to detect predation on anchovy and sardine early life stages

Cuende, Elsa, Mendibil, Iñaki, Bachiller, Eneko, Álvarez, Paula, Cotano, Unai, Rodriguez-Ezpeleta, Naiara

Journal:

Journal of Sea Research

Year:

2017

Language:

english

File:

PDF, 416 KB

english, 2017

33

Oceanographic variation influences spatial genomic structure in the sea scallop, Placopecten magellanicus

Van Wyngaarden, Mallory, Snelgrove, Paul V. R., DiBacco, Claudio, Hamilton, Lorraine C., Rodríguez-Ezpeleta, Naiara, Zhan, Luyao, Beiko, Robert G., Bradbury, Ian R.

Journal:

Ecology and Evolution

Year:

2018

Language:

english

File:

PDF, 1.23 MB

english, 2018

34

Selecting RAD-Seq Data Analysis Parameters for Population Genetics: The More the Better?

Díaz-Arce, Natalia, Rodríguez-Ezpeleta, Naiara

Journal:

Frontiers in Genetics

Year:

2019

Language:

english

File:

PDF, 2.88 MB

english, 2019

35

Bioinformatics for High Throughput Sequencing Volume 35D1 || Generation and Analysis of Genome-Wide DNA Methylation Maps

Rodríguez-Ezpeleta, Naiara, Hackenberg, Michael, Aransay, Ana M.

Year:

2012

Language:

english

File:

PDF, 215 KB

english, 2012

36

Identifying patterns of dispersal, connectivity, and selection in the sea scallop, Placopecten magellanicus, using RAD-seq derived SNPs

Van Wyngaarden, Mallory, Snelgrove, Paul V. R., DiBacco, Claudio, Hamilton, Lorraine C., Rodríguez-Ezpeleta, Naiara, Jeffery, Nicholas W., Stanley, Ryan R.E., Bradbury, Ian R.

Journal:

Evolutionary Applications

Year:

2016

Language:

english

File:

PDF, 1.40 MB

english, 2016

37

The challenges and promises of genetic approaches for ballast water management

Rey, Anaïs, Basurko, Oihane C., Rodríguez-Ezpeleta, Naiara

Journal:

Journal of Sea Research

Year:

2017

Language:

english

File:

PDF, 893 KB

english, 2017

38

Bioinformatics for High Throughput Sequencing Volume 35D1 || Base-Calling for Bioinformaticians

Rodríguez-Ezpeleta, Naiara, Hackenberg, Michael, Aransay, Ana M.

Year:

2012

Language:

english

File:

PDF, 562 KB

english, 2012

39

Bioinformatics for High Throughput Sequencing Volume 14 || Analysis of Metagenomics Data

Rodríguez-Ezpeleta, Naiara, Hackenberg, Michael, Aransay, Ana M.

Year:

2012

Language:

english

File:

PDF, 313 KB

english, 2012

40

Bioinformatics for High Throughput Sequencing Volume 50 || || Front_matter

Rodríguez-Ezpeleta, Naiara, Hackenberg, Michael, Aransay, Ana M.

Year:

2012

Language:

english

File:

PDF, 78 KB

english, 2012

41

miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments

Hackenberg, M., Rodriguez-Ezpeleta, N., Aransay, A. M.

Journal:

Nucleic Acids Research

Year:

2011

Language:

english

File:

PDF, 149 KB

english, 2011

42

The RNA-Binding Protein Human Antigen R Controls Global Changes in Gene Expression during Schwann Cell Development

Iruarrizaga-Lejarreta, M., Varela-Rey, M., Lozano, J. J., Fernandez-Ramos, D., Rodriguez-Ezpeleta, N., Embade, N., Lu, S. C., van der Kraan, P. M., Blaney Davidson, E. N., Gorospe, M., Mirsky, R., Jes

Journal:

Journal of Neuroscience

Year:

2012

Language:

english

File:

PDF, 4.25 MB

english, 2012

43

Genome-wide SNP based population structure in European hake reveals the need for harmonizing biological and management units

Leone, Agostino, Álvarez, Paula, García, Dorleta, Saborido-Rey, Fran, Rodriguez-Ezpeleta, Naiara, Hauser, Lorenz

Journal:

ICES Journal of Marine Science

Year:

2019

Language:

english

File:

PDF, 457 KB

english, 2019

44

High-density SNP genotyping detects homogeneity of Spanish and French Basques, and confirms their genomic distinctiveness from other European populations

Naiara Rodríguez-Ezpeleta, Jon Álvarez-Busto, Liher Imaz, María Regueiro, María Nerea Azcárate, Roberto Bilbao, Mikel Iriondo, Ana Gil, Andone Estonba, Ana María Aransay

Journal:

Year:

2010

Language:

english

File:

PDF, 320 KB

english, 2010

45

Phylogenetic Analyses of Nuclear, Mitochondrial, and Plastid Multigene Data Sets Support the Placement of Mesostigma in the Streptophyta

Rodriguez-Ezpeleta, N., Philippe, H., Brinkmann, H., Becker, B., Melkonian, M.

Journal:

Molecular Biology and Evolution

Year:

2006

Language:

english

File:

PDF, 715 KB

english, 2006

46

A high density SNP genotyping approach within the 19q13 chromosome region identifies an association of a CNOT3 polymorphism with ankylosing spondylitis

Diaz-Pena, R., Aransay, A. M., Suarez-Alvarez, B., Bruges-Armas, J., Rodriguez-Ezpeleta, N., Regueiro, M., Pimentel-Santos, F. M., Mulero, J., Sanchez, A., Collantes, E., Queiro, R., Ballina, J., Alve

Journal:

Annals of the Rheumatic Diseases

Year:

2012

Language:

english

File:

PDF, 106 KB

english, 2012

47

Bioinformatics for High Throughput Sequencing Volume 35D1 || Differential Expression for RNA Sequencing (RNA-Seq) Data: Mapping, Summarization, Statistical Analysis, and Experimental Design

Rodríguez-Ezpeleta, Naiara, Hackenberg, Michael, Aransay, Ana M.

Year:

2012

Language:

english

File:

PDF, 552 KB

english, 2012

48

Comparison of methods to detect copy number alterations in cancer using simulated and real genotyping data

David Mosén-Ansorena, Ana María Aransay, Naiara Rodríguez-Ezpeleta

Journal:

BMC Bioinformatics

Year:

2012

Language:

english

File:

PDF, 1.86 MB

english, 2012

49

Bioinformatics for High Throughput Sequencing ||

Rodríguez-Ezpeleta, Naiara, Hackenberg, Michael, Aransay, Ana M.

Year:

2012

Language:

english

File:

PDF, 78 KB

english, 2012

50

Spatial dynamics and mixing of bluefin tuna in the Atlantic Ocean and Mediterranean Sea revealed using next generation sequencing

Puncher, Gregory N., Cariani, Alessia, Maes, Gregory E., Van Houdt, Jeroen, Herten, Koen, Cannas, Rita, Rodriguez-Ezpeleta, Naiara, Albaina, Aitor, Estonba, M. Andone, Lutcavage, Molly, Hanke, Alex, R

Journal:

Molecular Ecology Resources

Year:

2018

Language:

english

File:

PDF, 1.51 MB

english, 2018

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