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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.
Dopazo J. Formulating and testing hypotheses in functional genomics. Artif Intell Med. 2009;45:97-107. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18789659.
Dopazo J. Formulating and testing hypotheses in functional genomics. Artif Intell Med. 2009;45(2-3):97-107. doi:10.1016/j.artmed.2008.08.003.
Moreno-Manzano V, Rodríguez-Jiménez FJ, Aceña-Bonilla JL, et al. FM19G11, a new hypoxia-inducible factor (HIF) modulator, affects stem cell differentiation status. The Journal of biological chemistry. 2010;285:1333-42.
Hernáez JRodríguez, Cucchi MEsperanza, Cravero S, et al. The first complete genomic structure of Butyrivibrio fibrisolvens and its chromid. Microb Genom. 2018;4(10). doi:10.1099/mgen.0.000216.
Peña A, Teeling H, Huerta-Cepas J, et al. Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains. The ISME journal. 2010.
Punt PJ, van Biezen N, Conesa A, Albers A, Mangnus J, van den Hondel C. Filamentous fungi as cell factories for heterologous protein production. Trends Biotechnol. 2002;20:200-6. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11943375.
Chacón-Solano E, León C, Díaz F, et al. Fibroblast activation and abnormal extracellular matrix remodelling as common hallmarks in three cancer-prone genodermatoses. Br J Dermatol. 2019;181(3):512-522. doi:10.1111/bjd.17698.
Al-Shahrour F, Diaz-Uriarte R, Dopazo J. FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics. 2004;20:578-80. Available at: http://bioinformatics.oxfordjournals.org/content/20/4/578.abstract.
Al-Shahrour F, Minguez P, Tarraga J, et al. FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. Nucleic Acids Res. 2007;35:W91-6. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17478504.
Al-Shahrour F, Minguez P, Tárraga J, et al. FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. Nucleic Acids Res. 2007;35(Web Server issue):W91-6. doi:10.1093/nar/gkm260.
Salavert J, Tomás A, Tárraga J, Medina I, Dopazo J, Blanquer I. Fast inexact mapping using advanced tree exploration on backward search methods. BMC Bioinformatics. 2015;16:18. doi:10.1186/s12859-014-0438-3.
Fonseca RF, de Carvalho FM, Poletta FA, et al. Family-based genome-wide association study in Patagonia confirms the association of the DMD locus and cleft lip and palate. Eur J Oral Sci. 2015;123(5):381-384. doi:10.1111/eos.12212.
Robledo M, González-Neira A, Dopazo J. f single nucleotide polymorphism arrays: Design, tools and applications. In: Microarray Technology Through Applications. Microarray Technology Through Applications. New York, USA: Taylor & Francis, F. Falciani; 2007.
E
Ventoso I, Kochetov A, Montaner D, Dopazo J, Santoyo J. Extensive translatome remodeling during ER stress response in mammalian cells. PLoS One. 2012;7(5):e35915. doi:10.1371/journal.pone.0035915.
Lagarde J, Uszczynska-Ratajczak B, Santoyo-López J, et al. Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq). Nature communications. 2016;7:12339. doi:10.1038/ncomms12339.
Lagarde J, Uszczynska-Ratajczak B, Santoyo-López J, et al. Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq). Nature Communications. 2016;7(1). doi:10.1038/ncomms12339.
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.
Martinez-Delgado B, Meléndez B, Cuadros M, et al. Expression profiling of T-cell lymphomas differentiates peripheral and lymphoblastic lymphomas and defines survival related genes. Clinical cancer research : an official journal of the American Association for Cancer Research. 2004;10:4971-82. Available at: http://clincancerres.aacrjournals.org/content/10/15/4971.long.
Conesa A, van De Velde F, van Rantwijk F, Sheldon RA, van den Hondel CA, Punt PJ. Expression of the Caldariomyces fumago chloroperoxidase in Aspergillus niger and characterization of the recombinant enzyme. J Biol Chem. 2001;276:17635-40. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11278701.
Dopazo J, Al-Shahrour F. Expression and microarrays. Methods Mol Biol. 2008;453:245-55. doi:10.1007/978-1-60327-429-6_12.
Goni JR, Vaquerizas JM, Dopazo J, Orozco M. Exploring the reasons for the large density of triplex-forming oligonucleotide target sequences in the human regulatory regions. BMC Genomics. 2006;7:63. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16566817.
Bonifaci N, Górski B, Masojć B, et al. Exploring the link between germline and somatic genetic alterations in breast carcinogenesis. PLoS One. 2010;5(11):e14078. doi:10.1371/journal.pone.0014078.
Esteban-Medina M, Peña-Chilet M, Loucera C, Dopazo J. Exploring the druggable space around the Fanconi anemia pathway using machine learning and mechanistic models. BMC Bioinformatics. 2019;20(1):370. doi:10.1186/s12859-019-2969-0.
Nobre LS, Al-Shahrour F, Dopazo J, Saraiva LM. Exploring the antimicrobial action of a carbon monoxide-releasing compound through whole-genome transcription profiling of Escherichia coli. Microbiology. 2009;155:813-24. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19246752.