Affiliation: Instituto Valenciano de Investigaciones Agrarias
- Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics researchAna 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...
- maSigPro: a method to identify significantly differential expression profiles in time-course microarray experimentsAna 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...
- High-throughput functional annotation and data mining with the Blast2GO suiteStefan 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...
- Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profilingIgnacio 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...
- Qualimap: evaluating next-generation sequencing alignment dataFernando 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...
- B2G-FAR, a species-centered GO annotation repositoryStefan 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...
- Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics dataFernando 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...
- Membrane transporters and carbon metabolism implicated in chloride homeostasis differentiate salt stress responses in tolerant and sensitive Citrus rootstocksJavier 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....
- Direct functional assessment of the composite phenotype through multivariate projection strategiesAna 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...
- Understanding disease mechanisms with models of signaling pathway activitiesPatricia Sebastián-León
Department of Computational Genomics, Centro de Investigación Príncipe Felipe CIPF, Avda Autopista del Saler, 16, 46012, Valencia, Spain
BMC Syst Biol 8:121. 2014..Understanding the aspects of the cell functionality that account for disease or drug action mechanisms is one of the main challenges in the analysis of genomic data and is on the basis of the future implementation of precision medicine...
- GEPAS, a web-based tool for microarray data analysis and interpretationJoaquin 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...
- Defining the genomic signature of totipotency and pluripotency during early human developmentAmparo Galan
Valencia Node of The National Stem Cell Bank, Centro de Investigacion Principe Felipe, Valencia, Spain
PLoS ONE 8:e62135. 2013....
- Histone modifications and expression of DAM6 gene in peach are modulated during bud dormancy release in a cultivar-dependent mannerCarmen 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...
- Transcriptional response of Citrus aurantifolia to infection by Citrus tristeza virusMónica 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...
- Next maSigPro: updating maSigPro bioconductor package for RNA-seq time seriesMaria José Nueda
Statistics and Operational Research Department, University of Alicante, 03690, Alicante, Spain, Genomics of Gene Expression Laboratory, Prince Felipe Research Centre, 46012 Valencia, Spain and Applied Statistics, Operational Research and Quality Department, Polytechnic University of Valencia, 46020 Valencia, Spain
Bioinformatics 30:2598-602. 2014..maSigPro is an R package specifically suited for the analysis of time-course gene expression data, which was developed originally for microarrays and hence was limited in its application to count data...
- Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity toleranceJavier 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...
- Profiling the venom gland transcriptomes of Costa Rican snakes by 454 pyrosequencingJordi 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...
- Large-scale Gene Ontology analysis of plant transcriptome-derived sequences retrieved by AFLP technologyAlessandro 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...
- Discovering gene expression patterns in time course microarray experiments by ANOVA-SCAMaria 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...
- Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experimentsFatima 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...
- Spatial differentiation in the vegetative mycelium of Aspergillus nigerAna 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...
- Development of the GENIPOL European flounder (Platichthys flesus) microarray and determination of temporal transcriptional responses to cadmium at low doseTim 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...
- Time course profiling of the retinal transcriptome after optic nerve transection and optic nerve crushMarta 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)...
- 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 thiabendazoleRob 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...