Martínez-Nava GAngélica, Altamirano-Molina E, Vázquez-Mellado J, et al. Metatranscriptomic analysis reveals gut microbiome bacterial genes in pyruvate and amino acid metabolism associated with hyperuricemia and gout in humans. Sci Rep. 2025;15(1):9981. doi:10.1038/s41598-025-93899-1.

Greene D, De Wispelaere K, Lees J, et al. Mutations in the small nuclear RNA gene RNU2-2 cause a severe neurodevelopmental disorder with prominent epilepsy. Nature Genetics. 2025. doi:10.1038/s41588-025-02159-5.

Niarakis A, Ostaszewski M, Mazein A, et al. Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches. Front Immunol. 2024;14:1282859. doi:10.3389/fimmu.2023.1282859.

Moura DS, Mondaza-Hernandez JL, Sanchez-Bustos P, et al. HMGA1 regulates trabectedin sensitivity in advanced soft-tissue sarcoma (STS): A Spanish Group for Research on Sarcomas (GEIS) study. Cell Mol Life Sci. 2024;81(1):219. doi:10.1007/s00018-024-05250-y.

Mavillard F, Perez-Florido J, Ortuno FM, et al. The Iberian Roma Population Variant Server (IRPVS). J Genet Genomics. 2024. doi:10.1016/j.jgg.2024.03.006.

Casimiro-Soriguer CS, Perez-Florido J, Robles EA, et al. The integrated genomic surveillance system of Andalusia (SIEGA) provides a One Health regional resource connected with the clinic. Sci Rep. 2024;14(1):19200. doi:10.1038/s41598-024-70107-0.

Esteban-Medina M, Loucera C, Rian K, et al. The mechanistic functional landscape of retinitis pigmentosa: a machine learning-driven approach to therapeutic target discovery. J Transl Med. 2024;22(1):139. doi:10.1186/s12967-024-04911-7.

Casimiro-Soriguer CS, Perez-Florido J, Lara M, et al. Molecular and phylogenetic characterization of the monkeypox outbreak in the South of Spain. Health Sci Rep. 2024;7(3):e1965. doi:10.1002/hsr2.1965.

Pellegrinelli V, Figueroa-Juárez E, Samuelson I, et al. Defective extracellular matrix remodeling in brown adipose tissue is associated with fibro-inflammation and reduced diet-induced thermogenesis. Cell Rep. 2023;42(6):112640. doi:10.1016/j.celrep.2023.112640.

Perez-Florido J, Casimiro-Soriguer CS, Ortuno F, et al. Detection of High Level of Co-Infection and the Emergence of Novel SARS CoV-2 Delta-Omicron and Omicron-Omicron Recombinants in the Epidemiological Surveillance of Andalusia. Int J Mol Sci. 2023;24(3). doi:10.3390/ijms24032419.

Chaves-Blanco L, de Salazar A, Fuentes A, et al. Evaluation of a combined detection of SARS-CoV-2 and its variants using real-time allele-specific PCR strategy: an advantage for clinical practice. Epidemiol Infect. 2023;151:e201. doi:10.1017/S095026882300184X.

Loucera C, Carmona R, Bostelmann G, et al. Evidence of the association between increased use of direct oral anticoagulants and a reduction in the rate of atrial fibrillation-related stroke and major bleeding at the population level (2012-2019). Med Clin (Barc). 2023. doi:10.1016/j.medcli.2023.10.008.

Sola-García A, Cáliz-Molina MÁngeles, Espadas I, et al. Metabolic reprogramming by Acly inhibition using SB-204990 alters glucoregulation and modulates molecular mechanisms associated with aging. Commun Biol. 2023;6(1):250. doi:10.1038/s42003-023-04625-4.

Corrales P, Martin-Taboada M, Vivas-García Y, et al. microRNAs-mediated regulation of insulin signaling in white adipose tissue during aging: Role of caloric restriction. Aging Cell. 2023:e13919. doi:10.1111/acel.13919.

Loucera C, Carmona R, Esteban-Medina M, et al. Real-world evidence with a retrospective cohort of 15,968 COVID-19 hospitalized patients suggests 21 new effective treatments. Virol J. 2023;20(1):226. doi:10.1186/s12985-023-02195-9.

Loucera C, Perez-Florido J, Casimiro-Soriguer CS, et al. Assessing the Impact of SARS-CoV-2 Lineages and Mutations on Patient Survival. Viruses. 2022;14(9). doi:10.3390/v14091893.

Cruz R, de Almeida SDiz-, Heredia MLópez, et al. Novel genes and sex differences in COVID-19 severity. Hum Mol Genet. 2022. doi:10.1093/hmg/ddac132.

Olivares-González L, Velasco S, Gallego I, et al. An SPM-Enriched Marine Oil Supplement Shifted Microglia Polarization toward M2, Ameliorating Retinal Degeneration in  Mice. Antioxidants (Basel). 2022;12(1). doi:10.3390/antiox12010098.

Martorell-Marugán J, López-Domínguez R, García-Moreno A, et al. A comprehensive database for integrated analysis of omics data in autoimmune diseases. BMC Bioinformatics. 2021;22(1):343. doi:10.1186/s12859-021-04268-4.

Ostaszewski M, Niarakis A, Mazein A, et al. COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Mol Syst Biol. 2021;17(10):e10387. doi:10.15252/msb.202110387.

Moura DS, Peña-Chilet M, Varela JAntonio Co, et al. A DNA damage repair gene-associated signature predicts responses of patients with advanced soft-tissue sarcoma to treatment with trabectedin. Mol Oncol. 2021;15(12):3691-3705. doi:10.1002/1878-0261.12996.

Villalba-Benito L, López-López D, Torroglosa A, et al. Genome-wide analysis of DNA methylation in Hirschsprung enteric precursor cells: unraveling the epigenetic landscape of enteric nervous system developmentAbstractBackgroundResultsConclusionsGraphic abstract. Clinical Epigenetics. 2021;13(1). doi:10.1186/s13148-021-01040-6.

Millán-Esteban D, Peña-Chilet M, García-Casado Z, et al. Mutational Characterization of Cutaneous Melanoma Supports Divergent Pathways Model for Melanoma Development. Cancers (Basel). 2021;13(20). doi:10.3390/cancers13205219.

Vázquez-Costa JFrancisco, Payá-Montes M, Martínez-Molina M, et al. Presenilin-1 Mutations Are a Cause of Primary Lateral Sclerosis-Like Syndrome. Front Mol Neurosci. 2021;14:721047. doi:10.3389/fnmol.2021.721047.

Loucera C, Peña-Chilet M, Esteban-Medina M, et al. Real world evidence of calcifediol or vitamin D prescription and mortality rate of COVID-19 in a retrospective cohort of hospitalized Andalusian patients. Sci Rep. 2021;11(1):23380. doi:10.1038/s41598-021-02701-5.

Mirzayi C, Renson A, Zohra F, et al. Reporting guidelines for human microbiome research: the STORMS checklist. Nat Med. 2021;27(11):1885-1892. doi:10.1038/s41591-021-01552-x.

Tenorio-Castaño J, Morte B, Nevado J, et al. Schuurs?Hoeijmakers Syndrome (PACS1 Neurodevelopmental Disorder): Seven Novel Patients and a Review. Genes. 2021;12(5):738. doi:10.3390/genes12050738.

Méndez-Salazar EOrlando, Vázquez-Mellado J, Casimiro-Soriguer CS, et al. Taxonomic variations in the gut microbiome of gout patients with and without tophi might have a functional impact on urate metabolism. Mol Med. 2021;27(1):50. doi:10.1186/s10020-021-00311-5.

Ostaszewski M, Mazein A, Gillespie ME, et al. COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms. Sci Data. 2020;7(1):136. doi:10.1038/s41597-020-0477-8.

Salgado D, Armean IM, Baudis M, et al. The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research. F1000Res. 2020;9. doi:10.12688/f1000research.24887.1.

Palomero L, Galván-Femenía I, de Cid R, et al. Immune Cell Associations with Cancer Risk. iScience. 2020;23(7):101296. doi:10.1016/j.isci.2020.101296.

García-León FJavier, Villegas-Portero R, Goicoechea-Salazar JAntonio, Muñoyerro-Muñiz D, Dopazo J. [Impact assessment on data protection in research projects]. Gac Sanit. 2020;34(5):521-523. doi:10.1016/j.gaceta.2019.10.006.

Martin-Broto J, Hindi N, Grignani G, et al. Nivolumab and sunitinib combination in advanced soft tissue sarcomas: a multicenter, single-arm, phase Ib/II trial. J Immunother Cancer. 2020;8(2). doi:10.1136/jitc-2020-001561.

Bogliolo M, Pujol R, Aza-Carmona M, et al. Optimised molecular genetic diagnostics of Fanconi anaemia by whole exome sequencing and functional studies. J Med Genet. 2020;57(4):258-268. doi:10.1136/jmedgenet-2019-106249.

Galvez JM, Castillo-Secilla D, Herrera LJ, et al. Towards Improving Skin Cancer Diagnosis by Integrating Microarray and RNA-Seq Datasets. IEEE J Biomed Health Inform. 2020;24(7):2119-2130. doi:10.1109/JBHI.2019.2953978.

Menden MP, Wang D, Mason MJ, et al. Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. Nat Commun. 2019;10(1):2674. doi:10.1038/s41467-019-09799-2.

Gómez-López G, Dopazo J, Cigudosa JC, Valencia A, Al-Shahrour F. Precision medicine needs pioneering clinical bioinformaticians. Brief Bioinform. 2019;20(3):752-766. doi:10.1093/bib/bbx144.

Fourati S, Talla A, Mahmoudian M, et al. A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-06735-8.

López M, Rueda A, Florido JP, et al. Evolution of the Quorum network and the mobilome (plasmids and bacteriophages) in clinical strains of Acinetobacter baumannii during a decade. Sci Rep. 2018;8(1):2523. doi:10.1038/s41598-018-20847-7.

Puig-Butille JAnton, Gimenez-Xavier P, Visconti A, et al. Genomic expression differences between cutaneous cells from red hair color individuals and black hair color individuals based on bioinformatic analysis. Oncotarget. 2017;8(7):11589-11599. doi:10.18632/oncotarget.14140.

Matalonga L, Bravo M, Serra-Peinado C, et al. Mutations in TRAPPC11 are associated with a congenital disorder of glycosylation. Hum Mutat. 2017;38(2):148-151. doi:10.1002/humu.23145.

Gui H, Schriemer D, Cheng WW, et al. Whole exome sequencing coupled with unbiased functional analysis reveals new Hirschsprung disease genes. Genome biology. 2017;18:48. doi:10.1186/s13059-017-1174-6.

Gui H, Schriemer D, Cheng WW, et al. Whole exome sequencing coupled with unbiased functional analysis reveals new Hirschsprung disease genes. Genome Biology. 2017;18(1). doi:10.1186/s13059-017-1174-6.

Dopazo J, Amadoz A, Bleda M, et al. 267 Spanish exomes reveal population-specific differences in disease-related genetic variation. Molecular biology and evolution. 2016. doi:10.1093/molbev/msw005.

Lupo V, Garcia-Garcia F, Sancho P, et al. Assessment of Targeted Next-Generation Sequencing as a Tool for the Diagnosis of Charcot-Marie-Tooth Disease and Hereditary Motor Neuropathy. The Journal of molecular diagnostics : JMD. 2016. doi:10.1016/j.jmoldx.2015.10.005.

Sanghez V, Cubuk C, Sebastián-Leon P, et al. Chronic subordination stress selectively downregulates the insulin signaling pathway in liver and skeletal muscle but not in adipose tissue of male mice. Stress (Amsterdam, Netherlands). 2016:1-11. doi:10.3109/10253890.2016.1151491.

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.

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.

Sanchez-Mut JV, Heyn H, Vidal E, et al. Human DNA methylomes of neurodegenerative diseases show common epigenomic patterns. Transl Psychiatry. 2016;6:e718. doi:10.1038/tp.2015.214.

Ibáñez M, Carbonell-Caballero J, García-Alonso L, et al. The Mutational Landscape of Acute Promyelocytic Leukemia Reveals an Interacting Network of Co-Occurrences and Recurrent Mutations. PLoS One. 2016;11(2):e0148346. doi:10.1371/journal.pone.0148346.

Sevilla T, Lupo V, Martínez-Rubio D, et al. Mutations in the MORC2 gene cause axonal Charcot-Marie-Tooth disease. Brain. 2016;139(Pt 1):62-72. doi:10.1093/brain/awv311.

Urreizti R, Roca-Ayats N, Trepat J, et al. Screening of CD96 and ASXL1 in 11 patients with Opitz C or Bohring-Opitz syndromes. Am J Med Genet A. 2016;170A(1):24-31. doi:10.1002/ajmg.a.37418.

Razzoli M, Frontini A, Gurney A, et al. Stress-induced activation of brown adipose tissue prevents obesity in conditions of low adaptive thermogenesis. Mol Metab. 2016;5(1):19-33. doi:10.1016/j.molmet.2015.10.005.

Lucariello M, Vidal E, Vidal S, et al. Whole exome sequencing of Rett syndrome-like patients reveals the mutational diversity of the clinical phenotype. Hum Genet. 2016;135(12):1343-1354. doi:10.1007/s00439-016-1721-3.

de la Rosa LRodríguez, Sánchez-Calderón H, Contreras J, et al. Comparative gene expression study of the vestibular organ of the Igf1 deficient mouse using whole-transcript arrays. Hearing research. 2015. doi:10.1016/j.heares.2015.08.016.

Sevilla T, Sivera R, Martínez-Rubio D, et al. The EGR2 gene is involved in axonal Charcot-Marie-Tooth disease. Eur J Neurol. 2015;22(12):1548-55. doi:10.1111/ene.12782.

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.

Amadoz A, Sebastián-Leon P, Vidal E, Salavert F, Dopazo J. Using activation status of signaling pathways as mechanism-based biomarkers to predict drug sensitivity. Sci Rep. 2015;5:18494. doi:10.1038/srep18494.

F Carmona J, Davalos V, Vidal E, et al. A Comprehensive DNA Methylation Profile of Epithelial-to-Mesenchymal Transition. Cancer research. 2014;74:5608?19. doi:10.1158/0008-5472.CAN-13-3659.

del Pozo MGonzález-, Méndez-Vidal C, Santoyo-López J, et al. Deciphering intrafamilial phenotypic variability by exome sequencing in a Bardet-Biedl family. Mol Genet Genomic Med. 2014;2(2):124-33. doi:10.1002/mgg3.50.

del Pozo MGonzález-, Méndez-Vidal C, Santoyo-López J, et al. Deciphering intrafamilial phenotypic variability by exome sequencing in a Bardet?Biedl family. Molecular Genetics & Genomic Medicine. 2014;2:124-133. doi:10.1002/mgg3.50.

del Pozo MGonzález-, Méndez-Vidal C, Bravo-Gil N, et al. Exome sequencing reveals novel and recurrent mutations with clinical significance in inherited retinal dystrophies. PLoS One. 2014;9(12):e116176. doi:10.1371/journal.pone.0116176.

Tenorio J, Mansilla A, Valencia M, et al. A New Overgrowth Syndrome is Due to Mutations in RNF125. Human mutation. 2014;35:1436?1441. doi:10.1002/humu.22689.

Méndez-Vidal C, Bravo-Gil N, del Pozo MGonzález-, et al. Novel RP1 mutations and a recurrent BBS1 variant explain the co-existence of two distinct retinal phenotypes in the same pedigree. BMC Genet. 2014;15:143. doi:10.1186/s12863-014-0143-2.

García-Alonso L, Jiménez-Almazán J, Carbonell-Caballero J, et al. The role of the interactome in the maintenance of deleterious variability in human populations. Mol Syst Biol. 2014;10:752. doi:10.15252/msb.20145222.

García-Cazorla A, Oyarzabal A, Fort J, et al. Two novel mutations in the BCKDK (branched-chain keto-acid dehydrogenase kinase) gene are responsible for a neurobehavioral deficit in two pediatric unrelated patients. Hum Mutat. 2014;35(4):470-7. doi:10.1002/humu.22513.

Sebastián-Leon P, Vidal E, Minguez P, et al. Understanding disease mechanisms with models of signaling pathway activities. BMC systems biology. 2014;8:121. doi:10.1186/s12918-014-0121-3.

Sebastián-Leon P, Vidal E, Minguez P, et al. Understanding disease mechanisms with models of signaling pathway activities. BMC systems biology. 2014;8:121. doi:10.1186/s12918-014-0121-3.

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(4):e62135. doi:10.1371/journal.pone.0062135.

Tort F, García-Silva MTeresa, Ferrer-Cortès X, et al. Exome sequencing identifies a new mutation in SERAC1 in a patient with 3-methylglutaconic aciduria. Mol Genet Metab. 2013;110(1-2):73-7. doi:10.1016/j.ymgme.2013.04.021.

Sánchez-Tena S, Lizarraga D, Miranda A, et al. Grape antioxidant dietary fiber (GADF) inhibits intestinal polyposis in ApcMin/+ mice: relation to cell cycle and immune response. Carcinogenesis. 2013. doi:10.1093/carcin/bgt140.

Sánchez-Tena S, Lizarraga D, Miranda A, et al. Grape antioxidant dietary fiber inhibits intestinal polyposis in ApcMin/+ mice: relation to cell cycle and immune response. Carcinogenesis. 2013;34(8):1881-8. doi:10.1093/carcin/bgt140.

Iglesias JManuel, Beloqui I, Garcia-Garcia F, et al. Mammosphere Formation in Breast Carcinoma Cell Lines Depends upon Expression of E-cadherin. PLoS ONE. 2013;8:e77281 -. Available at: http://dx.doi.org/10.1371%2Fjournal.pone.0077281.

Iglesias JManuel, Beloqui I, Garcia-Garcia F, et al. Mammosphere formation in breast carcinoma cell lines depends upon expression of E-cadherin. PLoS One. 2013;8(10):e77281. doi:10.1371/journal.pone.0077281.

Sánchez-Tena S, Reyes-Zurita FJ, Díaz-Moralli S, et al. Maslinic Acid-Enriched Diet Decreases Intestinal Tumorigenesis in Apc(Min/+) Mice through Transcriptomic and Metabolomic Reprogramming. PloS one. 2013;8:e59392. doi:10.1371/journal.pone.0059392.

Méndez-Vidal C, del Pozo MGonzález-, Vela-Boza A, et al. Whole-exome sequencing identifies novel compound heterozygous mutations in USH2A in Spanish patients with autosomal recessive retinitis pigmentosa. Molecular vision. 2013;19:2187-95. Available at: http://www.molvis.org/molvis/v19/2187/.

García-Alonso L, Alonso R, Vidal E, et al. Discovering the hidden sub-network component in a ranked list of genes or proteins derived from genomic experiments. Nucleic Acids Res. 2012;40(20):e158. doi:10.1093/nar/gks699.

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.

Carbonell J, Alloza E, Arce P, et al. A map of human microRNA variation uncovers unexpectedly high levels of variability. Genome medicine. 2012;4:62. doi:10.1186/gm363.

Lorente-Galdos B, Medina I, Morcillo-Suarez C, et al. Select your SNPs (SYSNPs): a web tool for automatic and massive selection of SNPs. International journal of data mining and bioinformatics. 2012;6:324-34. Available at: http://inderscience.metapress.com/content/f76740x8071u513n/.

De Baets G, Van Durme J, Reumers J, et al. SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants. Nucleic Acids Res. 2012;40(Database issue):D935-9. doi:10.1093/nar/gkr996.

Heyn H, Vidal E, Sayols S, et al. Whole-genome bisulfite DNA sequencing of a DNMT3B mutant patient. Epigenetics. 2012;7(6):542-50. doi:10.4161/epi.20523.

Trevino V, Tadesse MG, Vannucci M, et al. Analysis of normal-tumour tissue interaction in tumours: prediction of prostate cancer features from the molecular profile of adjacent normal cells. PloS one. 2011;6:e16492.

Prieur X, Mok CYL, Velagapudi VR, et al. Differential Lipid Partitioning Between Adipocytes and Tissue Macrophages Modulates Macrophage Lipotoxicity and M2/M1 Polarization in Obese Mice. Diabetes. 2011;60:797-809.

Negredo A, Palacios G, Vázquez-Morón S, et al. Discovery of an ebolavirus-like filovirus in europe. PLoS pathogens. 2011;7:e1002304.

Vivas Y, Martinez-Garcia C, Izquierdo A, et al. Early peroxisome proliferator-activated receptor gamma regulated genes involved in expansion of pancreatic beta cell mass. BMC Med Genomics. 2011;4:86. doi:10.1186/1755-8794-4-86.

Lüke L, Vicens A, Serra F, et al. Sexual selection halts the relaxation of protamine 2 among rodents. PloS one. 2011;6:e29247. doi:10.1371/journal.pone.0029247.

Cuenca-Bono B, García-Molinero V, Pascual-García P, et al. SUS1 introns are required for efficient mRNA nuclear export in yeast. Nucleic acids research. 2011;39:8599-611.

Bediaga NG, Acha-Sagredo A, Guerra I, et al. DNA methylation epigenotypes in breast cancer molecular subtypes. Breast Cancer Res. 2010;12(5):R77. doi:10.1186/bcr2721.

Galan A, Montaner D, M Póo E, et al. Functional genomics of 5- to 8-cell stage human embryos by blastomere single-cell cDNA analysis. PLoS One. 2010;5(10):e13615. doi:10.1371/journal.pone.0013615.

Shi L, Campbell G, Jones WD, et al. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nature biotechnology. 2010;28:827-38. Available at: http://www.nature.com/nbt/journal/v28/n8/full/nbt.1665.html.

Aggarwal M, Sánchez-Beato M, Gómez-López G, et al. Functional signatures identified in B-cell non-Hodgkin lymphoma profiles. Leuk Lymphoma. 2009;50(10):1699-708. doi:10.1080/10428190903189035.

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.

Valls J, Grau M, Sole X, et al. CLEAR-test: combining inference for differential expression and variability in microarray data analysis. J Biomed Inform. 2008;41:33-45. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17597009.

Tarraga J, Medina I, Carbonell J, et al. GEPAS, a web-based tool for microarray data analysis and interpretation. Nucleic Acids Res. 2008;36:W308-14. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18508806.

Tárraga J, Medina I, Carbonell J, et al. GEPAS, a web-based tool for microarray data analysis and interpretation. Nucleic Acids Res. 2008;36(Web Server issue):W308-14. doi:10.1093/nar/gkn303.

Wilkinson MD, Senger M, Kawas E, et al. Interoperability with Moby 1.0--it's better than sharing your toothbrush!. Brief Bioinform. 2008;9(3):220-31. doi:10.1093/bib/bbn003.

Wilkinson MD, Senger M, Kawas E, et al. Interoperability with Moby 1.0?it?s better than sharing your toothbrush!. Brief Bioinform. 2008;9:220-31. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18238804.

Reumers J, Conde L, Medina I, et al. Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases. Nucleic Acids Res. 2008;36(Database issue):D825-9. doi:10.1093/nar/gkm979.

Reumers J, Conde L, Medina I, et al. Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases. Nucleic Acids Res. 2008;36:D825-9. Available at: http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D825.

Saar K, Beck A, Bihoreau MT, et al. SNP and haplotype mapping for genetic analysis in the rat. Nat Genet. 2008;40:560-6. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18443594.

Saar K, Beck A, Bihoreau M-T, et al. SNP and haplotype mapping for genetic analysis in the rat. Nat Genet. 2008;40(5):560-6. doi:10.1038/ng.124.

Agudo M, Perez-Marin MC, Lonngren U, et al. Time course profiling of the retinal transcriptome after optic nerve transection and optic nerve crush. Mol Vis. 2008;14:1050-63. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18552980.

Hernandez P, Huerta-Cepas J, Montaner D, et al. Evidence for systems-level molecular mechanisms of tumorigenesis. BMC Genomics. 2007;8:185. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17584915.

Hernández P, Huerta-Cepas J, Montaner D, et al. Evidence for systems-level molecular mechanisms of tumorigenesis. BMC Genomics. 2007;8:185. doi:10.1186/1471-2164-8-185.

Rico D, Vaquerizas JM, Dopazo H, Bosca L. Identification of conserved domains in the promoter regions of nitric oxide synthase 2: implications for the species-specific transcription and evolutionary differences. BMC Genomics. 2007;8:271. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17686182.

Conesa A, Forment J, Gadea J, van Dijk J. Microarray Technology in Agricultural Research. In:  Microarray Technology Through Applications. Microarray Technology Through Applications. F. Falciani. Publisher: Taylor and Francis Group; 2007:173-209.

Levin AM, de Vries RP, Conesa A, et al. Spatial differentiation in the vegetative mycelium of Aspergillus niger. Eukaryot Cell. 2007;6:2311-22. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17951513.

Al-Shahrour F, Minguez P, Tarraga J, et al. BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments. Nucleic Acids Res. 2006;34:W472-6. Available at: http://nar.oxfordjournals.org/content/34/suppl_2/W472.long.

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.

Montaner D, Tarraga J, Huerta-Cepas J, et al. Next station in microarray data analysis: GEPAS. Nucleic Acids Res. 2006;34:W486-91. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16845056.

Gabaldón T, Snel B, van Zimmeren F, Hemrika W, Tabak H, Huynen MA. Origin and evolution of the peroxisomal proteome. Biol Direct. 2006;1:8. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16556314.

Conde L, Vaquerizas JM, Dopazo H, et al. PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes. Nucleic Acids Res. 2006;34:W621-5. Available at: http://nar.oxfordjournals.org/cgi/content/full/34/suppl_2/W621.

Boxma B, de Graaf RM, van der Staay GW, et al. An anaerobic mitochondrion that produces hydrogen. Nature. 2005;434:74-9. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15744302.

Al-Shahrour F, Minguez P, Vaquerizas JM, Conde L, Dopazo J. BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments. Nucleic Acids Res. 2005;33:W460-4. Available at: http://nar.oxfordjournals.org/content/33/suppl_2/W460.long.

Forment J, Gadea J, Huerta L, et al. Development of a citrus genome-wide EST collection and cDNA microarray as resources for genomic studies. Plant Mol Biol. 2005;57:375-91. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15830128.

Vaquerizas JM, Conde L, Yankilevich P, et al. GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data. Nucleic Acids Res. 2005;33:W616-20. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15980548.

Hoffmann R, Dopazo J, Cigudosa JC, Valencia A. HCAD, closing the gap between breakpoints and genes. Nucleic Acids Res. 2005;33:D511-3. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15608250.

Santoyo J, Vaquerizas JM, Dopazo J. Highly specific and accurate selection of siRNAs for high-throughput functional assays. Bioinformatics. 2005;21:1376-82. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15591357.

Alvarez S, Diaz-Uriarte R, Osorio A, et al. A predictor based on the somatic genomic changes of the BRCA1/BRCA2 breast cancer tumors identifies the non-BRCA1/BRCA2 tumors with BRCA1 promoter hypermethylation. Clin Cancer Res. 2005;11:1146-53. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15709182.

Conde L, Vaquerizas JM, Ferrer-Costa C, de la Cruz X, Orozco M, Dopazo J. PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes. Nucleic Acids Res. 2005;33:W501-5. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15980522.

Antón J, Peña A, Valens M, et al. Salinibacter ruber: genomics and biogeography. In:  Adaptation to life in high salt concentrations in Archaea, Bacteria and Eukarya.Vol 9. Adaptation to life in high salt concentrations in Archaea, Bacteria and Eukarya. Dordrecht, Netherlands: Nina Gunde-Cimerman, Ana Plemenitas, and Aharon Oren. Kluwer Academic Publishers; 2005:257-266.

Vaquerizas JM, Dopazo J, Diaz-Uriarte R. DNMAD: web-based diagnosis and normalization for microarray data. Bioinformatics. 2004;20:3656-8. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15247094.

Herrero J, Vaquerizas JM, Al-Shahrour F, et al. New challenges in gene expression data analysis and the extended GEPAS. Nucleic Acids Res. 2004;32:W485-91. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15215434.

Vella F, Mietchen D, Gabaldón T. Perceptions about postdocs. EMBO Rep. 2004;5:1104. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15577920.

Conde L, Vaquerizas JM, Santoyo J, et al. PupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level. Nucleic Acids Res. 2004;32:W242-8. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15215388.

Koh IY, Eyrich VA, Marti-Renom MA, et al. EVA: Evaluation of protein structure prediction servers. Nucleic Acids Res. 2003;31:3311-5. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12824315.

Herrero J, Al-Shahrour F, Diaz-Uriarte R, et al. GEPAS: A web-based resource for microarray gene expression data analysis. Nucleic Acids Res. 2003;31:3461-7. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12824345.

Tamames J, Clark D, Herrero J, et al. Bioinformatics methods for the analysis of expression arrays: data clustering and information extraction. J Biotechnol. 2002;98:269-83. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12141992.

Conesa A, Jeenes D, Archer DB, van den Hondel CA, Punt PJ. Calnexin overexpression increases manganese peroxidase production in Aspergillus niger. Appl Environ Microbiol. 2002;68:846-51. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11823227.

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.

Conesa A, Punt PJ, van den Hondel CA. Fungal peroxidases: molecular aspects and applications. J Biotechnol. 2002;93:143-58. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11738721.

Tracey L, Villuendas R, Ortiz P, et al. Identification of genes involved in resistance to interferon-alpha in cutaneous T-cell lymphoma. Am J Pathol. 2002;161:1825-37. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12414529.

Iverson GM, Reddel S, Victoria EJ, et al. Use of single point mutations in domain I of beta 2-glycoprotein I to determine fine antigenic specificity of antiphospholipid autoantibodies. J Immunol. 2002;169:7097-103. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12471146.

Conesa A, Weelink G, van den Hondel CA, Punt PJ. C-terminal propeptide of the Caldariomyces fumago chloroperoxidase: an intramolecular chaperone?. FEBS Lett. 2001;503:117-20. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11513866.

Eyrich VA, Marti-Renom MA, Przybylski D, et al. EVA: continuous automatic evaluation of protein structure prediction servers. Bioinformatics. 2001;17:1242-3. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11751240.

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.

Herrero J, Valencia A, Dopazo J. A hierarchical unsupervised growing neural network for clustering gene expression patterns. Bioinformatics. 2001;17:126-36. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11238068.

Conesa A, Punt PJ, van Luijk N, van den Hondel CA. The secretion pathway in filamentous fungi: a biotechnological view. Fungal Genet Biol. 2001;33:155-71. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11495573.