Publications

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Author Title [ Type(Desc)] Year
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Journal Article
Nueda MJ, Ferrer A, Conesa A. ARSyN: a method for the identification and removal of systematic noise in multifactorial time course microarray experiments. Biostatistics (Oxford, England). 2011.
Munro SA, Lund SP, P Pine S, et al. Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures. Nature communications. 2014;5:5125. doi:10.1038/ncomms6125.
Götz S, Arnold R, Sebastián-Leon P, et al. B2G-FAR, a species centered GO annotation repository. Bioinformatics (Oxford, England). 2011;27:919-924.
Medina I, Carbonell J, Pulido L, et al. Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Nucleic Acids Research. 2010;38:W210-W213. Featured in NAR. Available at: http://nar.oxfordjournals.org/content/38/suppl_2/W210.full.
Galan A, Diaz-Gimeno P, Poo MEugenia, et al. Defining the Genomic Signature of Totipotency and Pluripotency during Early Human Development. PloS one. 2013;8:e62135. doi:10.1371/journal.pone.0062135.
Fernandez P, Soria M, Blesa D, et al. Development, Characterization and Experimental Validation of a Cultivated Sunflower (Helianthus annuus L.) Gene Expression Oligonucleotide Microarray. PloS one. 2012;7:e45899. doi:10.1371/journal.pone.0045899.
Tarazona S, García-Alcalde F, Dopazo J, Ferrer A, Conesa A. Differential expression in RNA-seq: A matter of depth. Genome Research. 2011;21:2213-23.
Conesa-Zamora P, García-Solano J, Garcia-Garcia F, et al. Expression profiling shows differential molecular pathways and provides potential new diagnostic biomarkers for colorectal serrated adenocarcinoma. International journal of cancer. Journal international du cancer. 2012. doi:10.1002/ijc.27674.
Khalaf AA, Gmitter FG, Conesa A, Dopazo J, Moore GA. Fortunella margarita Transcriptional Reprogramming Triggered by Xanthomonas citri subsp. citri. BMC plant biology. 2011;11:159.
Leida C, Conesa A, Llácer G, Badenes MLuisa, Ríos G. Histone modifications and expression of DAM6 gene in peach are modulated during bud dormancy release in a cultivar-dependent manner. The New phytologist. 2011. doi:10.1111/j.1469-8137.2011.03863.x.
Prado-Lopez S, Conesa A, Armiñán A, et al. Hypoxia Promotes Efficient Differentiation of Human Embryonic Stem Cells to Functional Endothelium. Stem cells (Dayton, Ohio). 2010.
Jaime MDLA, Lopez-Llorca LVicente, Conesa A, et al. Identification of yeast genes that confer resistance to chitosan oligosaccharide (COS) using chemogenomics. BMC genomics. 2012;13:267. doi:10.1186/1471-2164-13-267.
Németh A, Conesa A, Santoyo-López J, et al. Initial genomics of the human nucleolus. PLoS genetics. 2010;6:e1000889. doi:10.1371/journal.pgen.1000889.
Yung S, Ledran M, Moreno-Gimeno I, et al. Large-scale transcriptional profiling and functional assays reveal important roles for Rho-GTPase signalling and SCL during haematopoietic differentiation of human embryonic stem cells. Human molecular genetics. 2011;20:4932-46.
Rizza S, Conesa A, Juarez J, et al. Microarray analysis of Etrog citron (Citrus medica L.) reveals changes in chloroplast, cell wall, peroxidase and symporter activities in response to viroid infection. Molecular plant pathology. 2012. doi:10.1111/j.1364-3703.2012.00794.x.
Garrido-Gomez T, Dominguez F, Lopez JAntonio, et al. Modeling human endometrial decidualization from the interaction between proteome and secretome. The Journal of clinical endocrinology and metabolism. 2011;96:706-16.
García-Alcalde F, García-López F, Dopazo J, Conesa A. Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data. Bioinformatics (Oxford, England). 2011;27:137-9.
van Heerden JH, Conesa A, Stein DJ, Montaner D, Russell V, Illing N. Parallel changes in gene expression in peripheral blood mononuclear cells and the brain after maternal separation in the mouse. BMC Res Notes. 2009;2:195.
Ponzoni I, Nueda M, Tarazona S, et al. Pathway network inference from gene expression data. BMC systems biology. 2014;8 Suppl 2:S7. doi:10.1186/1752-0509-8-S2-S7.
Durban J, Juárez P, Angulo Y, et al. Profiling the venom gland transcriptomes of Costa Rican snakes by 454 pyrosequencing. BMC genomics. 2011;12:259.
García-Alcalde F, Okonechnikov K, Carbonell J, et al. Qualimap: evaluating next-generation sequencing alignment data. Bioinformatics (Oxford, England). 2012;28:2678-9. doi:10.1093/bioinformatics/bts503.
Larriba E, Jaime MDLA, Carbonell-Caballero J, et al. Sequencing and functional analysis of the genome of a nematode egg-parasitic fungus, Pochonia chlamydosporia. Fungal genetics and biology : FG & B. 2014;66:69–80. doi:10.1016/j.fgb.2014.02.002.
Nueda MJosé, Carbonell J, Medina I, Dopazo J, Conesa A. Serial Expression Analysis: a web tool for the analysis of serial gene expression data. Nucleic acids research. 2010;38 Suppl:W239-45. doi:10.1093/nar/gkq488.
Rattei T, Tischler P, Götz S, et al. SIMAP–a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters. Nucleic acids research. 2010;38:D223-6.
Oppert B, Dowd SE, Bouffard P, et al. Transcriptome profiling of the intoxication response of Tenebrio molitor larvae to Bacillus thuringiensis Cry3Aa protoxin. PloS one. 2012;7:e34624. doi:10.1371/journal.pone.0034624.