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6. Micro-Variations from RNA-seq Experiments for Non-model Organisms

Author

Espinosa, Elena, Arroyo, Macarena, Larrosa, Rafael, Manchado, Manuel, Claros, M. Gonzalo, Bautista, Rocí­o, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Rojas, Ignacio, editor, Valenzuela, Olga, editor, Rojas, Fernando, editor, Herrera, Luis Javier, editor, and Ortuño, Francisco, editor

Published
2020
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8. EuroPineDB: a high-coverage web database for maritime pine transcriptome

Author

Fernández-Pozo, Noé, Canales, Javier, Guerrero-Fernández, Darío, Villalobos, David P., Díaz-Moreno, Sara M., Bautista, Rocío, Flores-Monterroso, Arantxa, Guevara, M. Ángeles, Perdiguero Jiménez, Pedro, Collada, Carmen, Cervera, M. Teresa, Soto, Álvaro, Ordás, Ricardo, Cantón, Francisco R., Ávila, Concepción, Cánovas, Francisco M., Claros, M. Gonzalo, Fernández-Pozo, Noé, Canales, Javier, Guerrero-Fernández, Darío, Villalobos, David P., Díaz-Moreno, Sara M., Bautista, Rocío, Flores-Monterroso, Arantxa, Guevara, M. Ángeles, Perdiguero Jiménez, Pedro, Collada, Carmen, Cervera, M. Teresa, Soto, Álvaro, Ordás, Ricardo, Cantón, Francisco R., Ávila, Concepción, Cánovas, Francisco M., and Claros, M. Gonzalo

Abstract

Acknowledgements The authors gratefully acknowledge the computer resources and technical support provided by the Plataforma Andaluza de Bioinformática of the University of Málaga, Spain. This study was supported by the Spanish Ministerio de Ciencia e Innovación [AGL2009-12139-C02-02, BIO2009-07490], the European Union [PLE2009-0016] and the Junta de Andalucía [CVI-6075 and BIO-114]., Pinus pinaster is an economically and ecologically important species that is becoming a woody gymnosperm model. Its enormous genome size makes whole-genome sequencing approaches are hard to apply. Therefore, the expressed portion of the genome has to be characterised and the results and annotations have to be stored in dedicated databases.Description: EuroPineDB is the largest sequence collection available for a single pine species, Pinus pinaster (maritime pine), since it comprises 951 641 raw sequence reads obtained from non-normalised cDNA libraries and high-throughput sequencing from adult (xylem, phloem, roots, stem, needles, cones, strobili) and embryonic (germinated embryos, buds, callus) maritime pine tissues. Using open-source tools, sequences were optimally pre-processed, assembled, and extensively annotated (GO, EC and KEGG terms, descriptions, SNPs, SSRs, ORFs and InterPro codes). As a result, a 10.5× P. pinaster genome was covered and assembled in 55 322 UniGenes. A total of 32 919 (59.5%) of P. pinaster UniGenes were annotated with at least one description, revealing at least 18 466 different genes. The complete database, which is designed to be scalable, maintainable, and expandable, is freely available at: http://www.scbi.uma.es/pindb/. It can be retrieved by gene libraries, pine species, annotations, UniGenes and microarrays (i.e., the sequences are distributed in two-colour microarrays; this is the only conifer database that provides this information) and will be periodically updated. Small assemblies can be viewed using a dedicated visualisation tool that connects them with SNPs. Any sequence or annotation set shown on-screen can be downloaded. Retrieval mechanisms for sequences and gene annotations are provided.Conclusions: The EuroPineDB with its integrated information can be used to reveal new knowledge, offers an easy-to-use collection of information to directly support experimental work (including microarray hybridisation), and provides deepe, Depto. de Genética, Fisiología y Microbiología, Fac. de Ciencias Biológicas, TRUE, pub

Published
2024

9. Expression Change Correlations Between Transposons and Their Adjacent Genes in Lung Cancers Reveal a Genomic Location Dependence and Highlights Cancer-Significant Genes

Author

Arroyo, Macarena, Larrosa, Rafael, Claros, M. Gonzalo, Bautista, Rocío, Hutchison, David, Editorial Board Member, Kanade, Takeo, Editorial Board Member, Kittler, Josef, Editorial Board Member, Kleinberg, Jon M., Editorial Board Member, Mattern, Friedemann, Editorial Board Member, Mitchell, John C., Editorial Board Member, Naor, Moni, Editorial Board Member, Pandu Rangan, C., Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Terzopoulos, Demetri, Editorial Board Member, Tygar, Doug, Editorial Board Member, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Rojas, Ignacio, editor, Valenzuela, Olga, editor, Rojas, Fernando, editor, and Ortuño, Francisco, editor

Published
2019
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11. NearTrans Can Identify Correlated Expression Changes Between Retrotransposons and Surrounding Genes in Human Cancer

Author

Larrosa, Rafael, Arroyo, Macarena, Bautista, Rocío, López-Rodríguez, Carmen María, Claros, M. Gonzalo, Hutchison, David, Series Editor, Kanade, Takeo, Series Editor, Kittler, Josef, Series Editor, Kleinberg, Jon M., Series Editor, Mattern, Friedemann, Series Editor, Mitchell, John C., Series Editor, Naor, Moni, Series Editor, Pandu Rangan, C., Series Editor, Steffen, Bernhard, Series Editor, Terzopoulos, Demetri, Series Editor, Tygar, Doug, Series Editor, Weikum, Gerhard, Series Editor, Rojas, Ignacio, editor, and Ortuño, Francisco, editor

Published
2018
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12. Obtaining the Most Accurate de novo Transcriptomes for Non-model Organisms: The Case of Castanea sativa

Author

Espigares, Marina, Seoane, Pedro, Bautista, Rocío, Quintana, Julia, Gómez, Luis, Claros, M. Gonzalo, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Rojas, Ignacio, editor, and Ortuño, Francisco, editor

Published
2017
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13. Combining Genetic and Transcriptomic Approaches to Identify Transporter-Coding Genes as Likely Responsible for a Repeatable Salt Tolerance QTL in Citrus

Author

Asins, Maria J., primary, Bullones, Amanda, additional, Raga, Veronica, additional, Romero-Aranda, Maria R., additional, Espinosa, Jesus, additional, Triviño, Juan C., additional, Bernet, Guillermo P., additional, Traverso, Jose A., additional, Carbonell, Emilio A., additional, Claros, M. Gonzalo, additional, and Belver, Andres, additional

Published
2023
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20. Automatic Workflow for the Identification of Constitutively-Expressed Genes Based on Mapped NGS Reads

Author

Carmona, Rosario, Seoane, Pedro, Zafra, Adoración, Jiménez-Quesada, María José, Alché, Juan de Dios, Claros, M. Gonzalo, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Ortuño, Francisco, editor, and Rojas, Ignacio, editor

Published
2016
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22. Identification of Distinctive Variants of the Olive Pollen Allergen Ole e 5 (Cu,Zn Superoxide Dismutase) throughout the Analysis of the Olive Pollen Transcriptome

Author

Zafra, Adoración, Carmona, Rosario, Jimenez-Lopez, José C., Pulido, Amada, Claros, M. Gonzalo, de Dios Alché, Juan, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, Series editor, Pevzner, Pavel, Series editor, Waterman, Michael S., Series editor, Ortuño, Francisco, editor, and Rojas, Ignacio, editor

Published
2015
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23. Identification and in silico Analysis of NADPH Oxidase Homologues Involved in Allergy from an Olive Pollen Transcriptome

Author

Jiménez-Quesada, María José, Traverso, Jose Ángel, Zafra, Adoración, Jimenez-Lopez, José C., Carmona, Rosario, Claros, M. Gonzalo, de Dios Alché, Juan, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, Series editor, Pevzner, Pavel, Series editor, Waterman, Michael S., Series editor, Ortuño, Francisco, editor, and Rojas, Ignacio, editor

Published
2015
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24. DEgenes Hunter - A Self-customised Gene Expression Analysis Workflow for Non-model Organisms

Author

González Gayte, Isabel, Bautista Moreno, Rocío, Claros, M. Gonzalo, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, Series editor, Pevzner, Pavel, Series editor, Waterman, Michael S., Series editor, Ortuño, Francisco, editor, and Rojas, Ignacio, editor

Published
2015
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25. Bioinformatics Analyses to Separate Species Specific mRNAs from Unknown Sequences in de novo Assembled Transcriptomes

Author

Velasco, David, Seoane, Pedro, Claros, M. Gonzalo, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, Series editor, Pevzner, Pavel, Series editor, Waterman, Michael S., Series editor, Ortuño, Francisco, editor, and Rojas, Ignacio, editor

Published
2015
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28. GENote v.β: A Web Tool Prototype for Annotation of Unfinished Sequences in Non-model Eukaryotes

Author

Fernández-Pozo, Noé, Guerrero-Fernández, Darío, Bautista, Rocío, Gómez-Maldonado, Josefa, Avila, Concepción, Cánovas, Francisco M., Claros, M. Gonzalo, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael S., editor, Freitas, Ana T., editor, and Navarro, Arcadi, editor

Published
2012
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31. On Selecting the Best Pre-processing Method for Affymetrix Genechips

Author

Florido, J. P., Pomares, H., Rojas, I., Calvo, J. C., Urquiza, J. M., Claros, M. Gonzalo, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Cabestany, Joan, editor, Sandoval, Francisco, editor, Prieto, Alberto, editor, and Corchado, Juan M., editor

Published
2009
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39. Insights into ROS‐dependent signalling underlying transcriptomic plant responses to the herbicide 2,4‐D

Author

Romero‐Puertas, María C., primary, Peláez‐Vico, Maria Ángeles, additional, Pazmiño, Diana M., additional, Rodríguez‐Serrano, María, additional, Terrón‐Camero, Laura, additional, Bautista, Rocío, additional, Gómez‐Cadenas, Aurelio, additional, Claros, M. Gonzalo, additional, León, José, additional, and Sandalio, Luisa M., additional

Published
2021
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50. First draft genome assembly of the Argane tree (Argania spinosa)

Author

Khayi, Slimane, primary, Azza, Nour Elhouda, additional, Gaboun, Fatima, additional, Pirro, Stacy, additional, Badad, Oussama, additional, Claros, M. Gonzalo, additional, Lightfoot, David A., additional, Unver, Turgay, additional, Chaouni, Bouchra, additional, Merrouch, Redouane, additional, Rahim, Bouchra, additional, Essayeh, Soumaya, additional, Ganoudi, Matike, additional, Abdelwahd, Rabha, additional, Diria, Ghizlane, additional, Mdarhi, Meriem Alaoui, additional, Labhilili, Mustapha, additional, Iraqi, Driss, additional, Mouhaddab, Jamila, additional, Sedrati, Hayat, additional, Memari, Majid, additional, Hamamouch, Noureddine, additional, Alché, Juan de Dios, additional, Boukhatem, Noureddine, additional, Mrabet, Rachid, additional, Dahan, Rachid, additional, Legssyer, Adelkhaleq, additional, Khalfaoui, Mohamed, additional, Badraoui, Mohamed, additional, Van de Peer, Yves, additional, Tatusova, Tatiana, additional, El Mousadik, Abdelhamid, additional, Mentag, Rachid, additional, and Ghazal, Hassan, additional

Published
2020
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