Ana Conesa

Summary

Affiliation: Instituto Valenciano de Investigaciones Agrarias
Country: Spain

Publications

  1. ncbi Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research
    Ana Conesa
    Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
    Bioinformatics 21:3674-6. 2005
  2. ncbi maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments
    Ana Conesa
    Centro de Genómica Instituto Valenciano de Investigaciones Agrarias, Apartado Oficial 46113 Moncada, Valencia, Spain
    Bioinformatics 22:1096-102. 2006
  3. ncbi High-throughput functional annotation and data mining with the Blast2GO suite
    Stefan Götz
    Bioinformatics Department, Centro de Investigacion Principe Felipe, Valencia, Spain
    Nucleic Acids Res 36:3420-35. 2008
  4. ncbi Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling
    Ignacio Medina
    Bioinformatics Department, Centro de Investigacion Principe Felipe, Autopista del Saler 16, Valencia, Spain
    Nucleic Acids Res 38:W210-3. 2010
  5. ncbi B2G-FAR, a species-centered GO annotation repository
    Stefan Götz
    Bioinformatics and Genomics Department, Centro de Investigaciones Príncipe Felipe CIPF, Valencia, Spain
    Bioinformatics 27:919-24. 2011
  6. ncbi Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data
    Fernando García-Alcalde
    Bioinformatics and Genomics Department, Centro de Investigaciones Principe Felipe, Valencia, Spain
    Bioinformatics 27:137-9. 2011
  7. ncbi Membrane transporters and carbon metabolism implicated in chloride homeostasis differentiate salt stress responses in tolerant and sensitive Citrus rootstocks
    Javier Brumos
    Instituto Valenciano de Investigaciones Agrarias, Centro de Genomica, Ctra Moncada Náquera Km 4 6, Moncada, Valencia, Spain
    Funct Integr Genomics 9:293-309. 2009
  8. ncbi Direct functional assessment of the composite phenotype through multivariate projection strategies
    Ana Conesa
    Bioinformatics Department, Centro de Investigacion Principe Felipe, Valencia, Spain
    Genomics 92:373-83. 2008
  9. ncbi Qualimap: evaluating next-generation sequencing alignment data
    Fernando García-Alcalde
    Bioinformatics and Genomics Department, Centro de Investigacion Principe Felipe, Valencia, Spain
    Bioinformatics 28:2678-9. 2012
  10. ncbi GEPAS, a web-based tool for microarray data analysis and interpretation
    Joaquin Tarraga
    Bioinformatics Department, Centro de Investigación Príncipe Felipe CIPF, Autopista del Saler 16, E46013, Valencia, Spain
    Nucleic Acids Res 36:W308-14. 2008

Collaborators

Detail Information

Publications21

  1. ncbi Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research
    Ana Conesa
    Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
    Bioinformatics 21:3674-6. 2005
    ..AVAILABILITY: Blast2GO is freely available via Java Web Start at http://www.blast2go.de. SUPPLEMENTARY MATERIAL: http://www.blast2go.de -> Evaluation...
  2. ncbi maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments
    Ana Conesa
    Centro de Genómica Instituto Valenciano de Investigaciones Agrarias, Apartado Oficial 46113 Moncada, Valencia, Spain
    Bioinformatics 22:1096-102. 2006
    ..The methodology is illustrated on both a real and a simulated microarray dataset...
  3. ncbi High-throughput functional annotation and data mining with the Blast2GO suite
    Stefan Götz
    Bioinformatics Department, Centro de Investigacion Principe Felipe, Valencia, Spain
    Nucleic Acids Res 36:3420-35. 2008
    ..Our aim is to offer biologists useful information to take into account when addressing the task of functionally characterizing their sequence data...
  4. ncbi Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling
    Ignacio Medina
    Bioinformatics Department, Centro de Investigacion Principe Felipe, Autopista del Saler 16, Valencia, Spain
    Nucleic Acids Res 38:W210-3. 2010
    ..This provides support for the functional analysis of non-model species. Mirrors of Babelomics or command line execution of their individual components are now possible. Babelomics is available at http://www.babelomics.org...
  5. ncbi B2G-FAR, a species-centered GO annotation repository
    Stefan Götz
    Bioinformatics and Genomics Department, Centro de Investigaciones Príncipe Felipe CIPF, Valencia, Spain
    Bioinformatics 27:919-24. 2011
    ..Nevertheless, many biologists, especially working with non-model organisms, still suffer from non-existing or low-coverage functional annotation, or simply struggle retrieving, summarizing and querying these data...
  6. ncbi Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data
    Fernando García-Alcalde
    Bioinformatics and Genomics Department, Centro de Investigaciones Principe Felipe, Valencia, Spain
    Bioinformatics 27:137-9. 2011
    ..An effective approach to the analysis of these complex datasets is the joined visualization of the disparate biomolecular data on the framework of known biological pathways...
  7. ncbi Membrane transporters and carbon metabolism implicated in chloride homeostasis differentiate salt stress responses in tolerant and sensitive Citrus rootstocks
    Javier Brumos
    Instituto Valenciano de Investigaciones Agrarias, Centro de Genomica, Ctra Moncada Náquera Km 4 6, Moncada, Valencia, Spain
    Funct Integr Genomics 9:293-309. 2009
    ....
  8. ncbi Direct functional assessment of the composite phenotype through multivariate projection strategies
    Ana Conesa
    Bioinformatics Department, Centro de Investigacion Principe Felipe, Valencia, Spain
    Genomics 92:373-83. 2008
    ..Two different transcriptomics studies are used to illustrate the statistical and interpretative aspects of the methodology. We demonstrate the superiority of the proposed method over equivalent approaches...
  9. ncbi Qualimap: evaluating next-generation sequencing alignment data
    Fernando García-Alcalde
    Bioinformatics and Genomics Department, Centro de Investigacion Principe Felipe, Valencia, Spain
    Bioinformatics 28:2678-9. 2012
    ..The systematic detection of such biases is a non-trivial task that is crucial to drive appropriate downstream analyses...
  10. ncbi GEPAS, a web-based tool for microarray data analysis and interpretation
    Joaquin Tarraga
    Bioinformatics Department, Centro de Investigación Príncipe Felipe CIPF, Autopista del Saler 16, E46013, Valencia, Spain
    Nucleic Acids Res 36:W308-14. 2008
    ..GEPAS is nowadays the most quoted web tool in its field and it is extensively used by researchers of many countries and its records indicate an average usage rate of 500 experiments per day. GEPAS, is available at http://www.gepas.org...
  11. ncbi Histone modifications and expression of DAM6 gene in peach are modulated during bud dormancy release in a cultivar-dependent manner
    Carmen Leida
    Instituto Valenciano de Investigaciones Agrarias IVIA, Carretera Moncada Naquera km 4 5, ES 46113 Moncada, Valencia, Spain
    New Phytol 193:67-80. 2012
    ..Analysis of chromatin modifications reinforced the role of epigenetic mechanisms in DAM6 regulation and bud dormancy release, and highlighted common features with the vernalization process in Arabidopsis thaliana and cereals...
  12. ncbi Transcriptional response of Citrus aurantifolia to infection by Citrus tristeza virus
    Mónica Gandía
    Instituto Valenciano de Investigaciones Agrarias, Ctra Moncada Naquera km 4 5, Moncada, 46113, Valencia, Spain
    Virology 367:298-306. 2007
    ..Changes detected in the transcriptome upon infecting lime with T305 may be associated either with symptom expression, with a strain-specific defense mechanism, or with a general response to stress...
  13. ncbi Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance
    Javier Terol
    Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias, Carretera Moncada, Náquera, km, 4, 5 Moncada Valencia E46113, Spain
    BMC Genomics 8:31. 2007
    ..Aside from disease resistance, major commercial traits in Citrus are improved fruit quality, higher yield and tolerance to environmental stresses, especially salinity...
  14. ncbi Profiling the venom gland transcriptomes of Costa Rican snakes by 454 pyrosequencing
    Jordi Durbán
    Consejo Superior de Investigaciones Cientificas, Jaime Roig, Valencia, Spain
    BMC Genomics 12:259. 2011
    ..In the absence of genome sequence, transcriptomes represent also valuable searchable databases for proteomic projects...
  15. ncbi Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments
    Fatima Al-Shahrour
    Department of Bioinformatics, Centro de Investigación Príncipe Felipe CIPF, Autopista del Saler 16, E46013 Valencia, Spain
    Nucleic Acids Res 36:W341-6. 2008
    ..0 technology features, a new user interface with persistent sessions and a new extended database of gene identifiers. Babelomics is available at http://www.babelomics.org...
  16. ncbi Discovering gene expression patterns in time course microarray experiments by ANOVA-SCA
    Maria José Nueda
    Departamento de Estadística e Investigación Operativa, Universidad de Alicante, Apartado 03080, Alicante, Spain
    Bioinformatics 23:1792-800. 2007
    ..Discovering experimentally relevant transcriptional changes require methodologies that take all these elements into account...
  17. ncbi Large-scale Gene Ontology analysis of plant transcriptome-derived sequences retrieved by AFLP technology
    Alessandro Botton
    Department of Environmental Agronomy and Crop Science, University of Padova, Viale dell Universita 16, Campus of Agripolis, 35020 Legnaro, Italy
    BMC Genomics 9:347. 2008
    ..In this paper, the functional annotation of about 8,000 AFLP-derived ESTs retrieved in the NCBI databases was carried out by using GO terminology...
  18. ncbi Spatial differentiation in the vegetative mycelium of Aspergillus niger
    Ana M Levin
    Microbiology, Institute of Biomembranes, Utrecht University, Padulaan 8, 3584 CH Utrecht, The Netherlands
    Eukaryot Cell 6:2311-22. 2007
    ..niger are highly differentiated. This conclusion is also indicated by the fact that distinct zones of the colony grow and secrete proteins, even after transfer to fresh medium...
  19. ncbi Development of the GENIPOL European flounder (Platichthys flesus) microarray and determination of temporal transcriptional responses to cadmium at low dose
    Tim D Williams
    School of Biosciences, The University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
    Environ Sci Technol 40:6479-88. 2006
    ..We thus describe the establishment of a useful resource for ecotoxicogenomics and the determination of the temporal molecular responses to cadmium, a prototypical heavy metal pollutant...
  20. ncbi Time course profiling of the retinal transcriptome after optic nerve transection and optic nerve crush
    Marta Agudo
    Departamento Oftalmología, Facultad de Medicina, Universidad de Murcia, Murcia Spain
    Mol Vis 14:1050-63. 2008
    ..A time-course analysis of gene regulation in the adult rat retina after intraorbital nerve crush (IONC) and intraorbital nerve transection (IONT)...
  21. ncbi Transcriptome analysis provides new insights into liver changes induced in the rat upon dietary administration of the food additives butylated hydroxytoluene, curcumin, propyl gallate and thiabendazole
    Rob Stierum
    TNO Quality of Life, Business Unit Biosciences, P O Box 360, 3700 AJ Zeist, The Netherlands
    Food Chem Toxicol 46:2616-28. 2008
    ..This study shows the value of gene expression profiling in food toxicology in terms of generating novel hypotheses on the mechanisms of action of food additives in relation to pathology...