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. pmc 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. pmc 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. doi 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
  6. pmc 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
  7. doi 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. pmc 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
  9. doi 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
  10. pmc 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

Publications22

  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
    ..This tool offers a suitable platform for functional genomics research in non-model species. B2G is an intuitive and interactive desktop application that allows monitoring and comprehension of the whole annotation and analysis process...
  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 large amount of data, multiplicity of experimental conditions and the dynamic nature of the experiments poses great challenges to data analysis...
  3. pmc 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. pmc 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. doi 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...
  6. pmc 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...
  7. doi 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. pmc 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...
  9. doi 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...
  10. pmc 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. doi 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. pmc Defining the genomic signature of totipotency and pluripotency during early human development
    Amparo Galan
    Valencia Node of The National Stem Cell Bank, Centro de Investigacion Principe Felipe, Valencia, Spain
    PLoS ONE 8:e62135. 2013
    ....
  14. pmc 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...
  15. pmc 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...
  16. pmc 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...
  17. 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...
  18. pmc 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...
  19. pmc 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...
  20. doi 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...
  21. 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...
  22. pmc 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)...