262 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Martorell-Marugán J, López-Domínguez R, García-Moreno A, Toro-Domínguez D, Villatoro-García JA, Barturen G, Martín-Gómez A, Troule K, Gómez-López G, Al-Shahrour F, González-Rumayor V, Peña-Chilet M, Dopazo J, Sáez-Rodríguez J, Alarcón-Riquelme ME, et al. A comprehensive database for integrated analysis of omics data in autoimmune diseases. Bmc Bioinformatics. 22: 343. PMID 34167460 DOI: 10.1186/s12859-021-04268-4  1
2021 Rian K, Hidalgo MR, Çubuk C, Falco MM, Loucera C, Esteban-Medina M, Alamo-Alvarez I, Peña-Chilet M, Dopazo J. Genome-scale mechanistic modeling of signaling pathways made easy: A bioconductor/cytoscape/web server framework for the analysis of omic data. Computational and Structural Biotechnology Journal. 19: 2968-2978. PMID 34136096 DOI: 10.1016/j.csbj.2021.05.022  0.01
2021 Dopazo J, Maya-Miles D, García F, Lorusso N, Calleja MÁ, Pareja MJ, López-Miranda J, Rodríguez-Baño J, Padillo J, Túnez I, Romero-Gómez M. Implementing Personalized Medicine in COVID-19 in Andalusia: An Opportunity to Transform the Healthcare System. Journal of Personalized Medicine. 11. PMID 34073493 DOI: 10.3390/jpm11060475  0.01
2021 Casimiro-Soriguer CS, Perez-Florido J, Fernandez-Rueda JL, Pedrosa-Corral I, Guillot-Sulay V, Lorusso N, Martinez-Gonzalez LJ, Navarro-Marí JM, Dopazo J, Sanbonmatsu-Gámez S. Phylogenetic Analysis of the 2020 West Nile Virus (WNV) Outbreak in Andalusia (Spain). Viruses. 13. PMID 34063166 DOI: 10.3390/v13050836  0.01
2021 Méndez-Salazar EO, Vázquez-Mellado J, Casimiro-Soriguer CS, Dopazo J, Çubuk C, Zamudio-Cuevas Y, Francisco-Balderas A, Martínez-Flores K, Fernández-Torres J, Lozada-Pérez C, Pineda C, Sánchez-González A, Silveira LH, Burguete-García AI, Orbe-Orihuela C, et al. Taxonomic variations in the gut microbiome of gout patients with and without tophi might have a functional impact on urate metabolism. Molecular Medicine (Cambridge, Mass.). 27: 50. PMID 34030623 DOI: 10.1186/s10020-021-00311-5  0.01
2021 Moura DS, Peña-Chilet M, Cordero Varela JA, Alvarez-Alegret R, Agra-Pujol C, Izquierdo F, Ramos R, Ortega-Medina L, Martin-Davila F, Castilla-Ramirez C, Hernandez-Leon CN, Romagosa C, Vaz Salgado MA, Lavernia J, Bagué S, ... ... Dopazo J, et al. A DNA damage repair gene-associated signature predicts responses of patients with advanced soft-tissue sarcoma to treatment with trabectedin. Molecular Oncology. PMID 33983674 DOI: 10.1002/1878-0261.12996  0.01
2021 Villalba-Benito L, López-López D, Torroglosa A, Casimiro-Soriguer CS, Luzón-Toro B, Fernández RM, Moya-Jiménez MJ, Antiñolo G, Dopazo J, Borrego S. Genome-wide analysis of DNA methylation in Hirschsprung enteric precursor cells: unraveling the epigenetic landscape of enteric nervous system development. Clinical Epigenetics. 13: 51. PMID 33750457 DOI: 10.1186/s13148-021-01040-6  1
2021 López MG, Fass M, Rivas JG, Carbonell-Caballero J, Vera P, Puebla A, Defacio R, Dopazo J, Paniego N, Hopp HE, Lia VV. Plastome genomics in South American maize landraces: chloroplast lineages parallel the geographic structuring of nuclear gene pools. Annals of Botany. PMID 33693521 DOI: 10.1093/aob/mcab038  1
2021 Rian K, Esteban-Medina M, Hidalgo MR, Çubuk C, Falco MM, Loucera C, Gunyel D, Ostaszewski M, Peña-Chilet M, Dopazo J. Mechanistic modeling of the SARS-CoV-2 disease map. Biodata Mining. 14: 5. PMID 33478554 DOI: 10.1186/s13040-021-00234-1  0.01
2020 Salgado D, Armean IM, Baudis M, Beltran S, Capella-Gutierrez S, Carvalho-Silva D, Dominguez Del Angel V, Dopazo J, Furlong LI, Gao B, Garcia L, Gerloff D, Gut I, Gyenesei A, Habermann N, et al. The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research. F1000research. 9. PMID 34367618 DOI: 10.12688/f1000research.24887.1  1
2020 Loucera C, Esteban-Medina M, Rian K, Falco MM, Dopazo J, Peña-Chilet M. Drug repurposing for COVID-19 using machine learning and mechanistic models of signal transduction circuits related to SARS-CoV-2 infection. Signal Transduction and Targeted Therapy. 5: 290. PMID 33311438 DOI: 10.1038/s41392-020-00417-y  0.01
2020 Martin-Broto J, Hindi N, Grignani G, Martinez-Trufero J, Redondo A, Valverde C, Stacchiotti S, Lopez-Pousa A, D'Ambrosio L, Gutierrez A, Perez-Vega H, Encinas-Tobajas V, de Alava E, Collini P, Peña-Chilet M, ... Dopazo J, et al. Nivolumab and sunitinib combination in advanced soft tissue sarcomas: a multicenter, single-arm, phase Ib/II trial. Journal For Immunotherapy of Cancer. 8. PMID 33203665 DOI: 10.1136/jitc-2020-001561  0.01
2020 Lopez-Lopez D, Loucera C, Carmona R, Aquino V, Salgado J, Pasalodos S, Miranda M, Alonso Á, Dopazo J. SMN1 copy-number and sequence variant analysis from next-generation sequencing data. Human Mutation. PMID 33058415 DOI: 10.1002/humu.24120  1
2020 Peña-Chilet M, Roldán G, Perez-Florido J, Ortuño FM, Carmona R, Aquino V, Lopez-Lopez D, Loucera C, Fernandez-Rueda JL, Gallego A, García-Garcia F, González-Neira A, Pita G, Núñez-Torres R, Santoyo-López J, ... ... Dopazo J, et al. CSVS, a crowdsourcing database of the Spanish population genetic variability. Nucleic Acids Research. PMID 32990755 DOI: 10.1093/nar/gkaa794  1
2020 Ostaszewski M, Mazein A, Gillespie ME, Kuperstein I, Niarakis A, Hermjakob H, Pico AR, Willighagen EL, Evelo CT, Hasenauer J, Schreiber F, Dräger A, Demir E, Wolkenhauer O, Furlong LI, ... ... Dopazo J, et al. Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms. Scientific Data. 7: 247. PMID 32678106 DOI: 10.1038/S41597-020-00589-W  1
2020 Palomero L, Galván-Femenía I, de Cid R, Espín R, Barnes DR, Cimba, Blommaert E, Gil-Gil M, Falo C, Stradella A, Ouchi D, Roso-Llorach A, Violan C, Peña-Chilet M, Dopazo J, et al. Immune Cell Associations with Cancer Risk. Iscience. 23: 101296. PMID 32622267 DOI: 10.1016/J.Isci.2020.101296  1
2020 Bojic S, Falco MM, Stojkovic P, Ljujic B, Gazdic Jankovic M, Armstrong L, Markovic N, Dopazo J, Lako M, Bauer R, Stojkovic M. Platform to study intracellular polystyrene nanoplastic pollution and clinical outcomes. Stem Cells (Dayton, Ohio). PMID 32614127 DOI: 10.1002/Stem.3244  0.01
2020 Çubuk C, Can FE, Peña-Chilet M, Dopazo J. Mechanistic Models of Signaling Pathways Reveal the Drug Action Mechanisms behind Gender-Specific Gene Expression for Cancer Treatments. Cells. 9. PMID 32610626 DOI: 10.3390/Cells9071579  0.01
2020 Ostaszewski M, Mazein A, Gillespie ME, Kuperstein I, Niarakis A, Hermjakob H, Pico AR, Willighagen EL, Evelo CT, Hasenauer J, Schreiber F, Dräger A, Demir E, Wolkenhauer O, Furlong LI, ... ... Dopazo J, et al. COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms. Scientific Data. 7: 136. PMID 32371892 DOI: 10.1038/S41597-020-0477-8  1
2020 Martin-Broto J, Cruz J, Penel N, Le Cesne A, Hindi N, Luna P, Moura DS, Bernabeu D, de Alava E, Lopez-Guerrero JA, Dopazo J, Peña-Chilet M, Gutierrez A, Collini P, Karanian M, et al. Pazopanib for treatment of typical solitary fibrous tumours: a multicentre, single-arm, phase 2 trial. The Lancet. Oncology. PMID 32066540 DOI: 10.1016/S1470-2045(19)30826-5  0.01
2020 Sundesha V, Garrayo J, Fernández JM, Codó L, Repchevsky D, Haas J, Altenhoff A, Dessimoz C, Cuesta I, Monzon S, López D, Florido JP, Dopazo J, Valencia A, Gelpi JL, et al. Scientific Communities in OpenEBench F1000research. 9. DOI: 10.7490/F1000Research.1117991.1  1
2020 Peña-Chilet M, Roldan G, Pérez-Florido J, Ortuño FM, Carmona R, Aquino-Quintans V, López-López D, Navarro A, Fernández-Rueda JL, Dopazo J. The database of Spanish population variability: a crowdsourcing resource for collecting local genomic data F1000research. 9. DOI: 10.7490/F1000Research.1117944.1  1
2020 Puerto-Camacho P, Amaral AT, Diaz-Martin J, Bolado-Carrancio A, Jordan-Perez C, Salguero-Aranda C, Esteban-Medina M, Alamo-Alvarez I, Dopazo J, Bernabeu C, Byron A, Brunton VG, Álava Ed. Abstract 6158: The relevance of endoglin and MMP14 to the metastatic potential of Ewing sarcoma cells Cancer Research. 80: 6158-6158. DOI: 10.1158/1538-7445.Am2020-6158  0.01
2019 Peña-Chilet M, Esteban-Medina M, Falco MM, Rian K, Hidalgo MR, Loucera C, Dopazo J. Using mechanistic models for the clinical interpretation of complex genomic variation. Scientific Reports. 9: 18937. PMID 31831811 DOI: 10.1038/S41598-019-55454-7  0.01
2019 Bogliolo M, Pujol R, Aza-Carmona M, Muñoz-Subirana N, Rodriguez-Santiago B, Casado JA, Rio P, Bauser C, Reina-Castillón J, Lopez-Sanchez M, Gonzalez-Quereda L, Gallano P, Catalá A, Ruiz-Llobet A, Badell I, ... ... Dopazo J, et al. Optimised molecular genetic diagnostics of Fanconi anaemia by whole exome sequencing and functional studies. Journal of Medical Genetics. PMID 31586946 DOI: 10.1136/jmedgenet-2019-106249  0.01
2019 Casimiro-Soriguer CS, Loucera C, Perez Florido J, López-López D, Dopazo J. Antibiotic resistance and metabolic profiles as functional biomarkers that accurately predict the geographic origin of city metagenomics samples. Biology Direct. 14: 15. PMID 31429791 DOI: 10.1186/S13062-019-0246-9  0.01
2019 Petkevicius K, Virtue S, Bidault G, Jenkins B, Çubuk C, Morgantini C, Aouadi M, Dopazo J, Serlie M, Koulman A, Vidal-Puig A. Accelerated phosphatidylcholine turnover in macrophages promotes adipose tissue inflammation in obesity. Elife. 8. PMID 31418690 DOI: 10.7554/Elife.47990  0.01
2019 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. 20: 370. PMID 31266445 DOI: 10.1186/S12859-019-2969-0  0.01
2019 Díez-Fuertes F, Erick de la Torre-Tarazona H, Calonge E, Pernas M, Bermejo M, García-Pérez J, Álvarez A, Capa L, García-García F, Saumoy M, Riera M, Boland-Auge A, López-Galíndez C, Lathrop M, Dopazo J, et al. Association of a single nucleotide polymorphism in ubxn6 gene with long term non progression phenotype in hiv-positive individuals. Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases. PMID 31158522 DOI: 10.1016/j.cmi.2019.05.015  1
2019 Perez-Gil D, Lopez FJ, Dopazo J, Marin-Garcia P, Rendon A, Medina I. PyCellBase, an efficient python package for easy retrieval of biological data from heterogeneous sources. Bmc Bioinformatics. 20: 159. PMID 30922213 DOI: 10.1186/S12859-019-2726-4  1
2019 Çubuk C, Hidalgo MR, Amadoz A, Rian K, Salavert F, Pujana MA, Mateo F, Herranz C, Carbonell-Caballero J, Dopazo J. Differential metabolic activity and discovery of therapeutic targets using summarized metabolic pathway models. Npj Systems Biology and Applications. 5: 7. PMID 30854222 DOI: 10.1038/s41540-019-0087-2  1
2019 Chacón-Solano E, León C, Díaz F, García-García F, García M, Escámez MJ, Guerrero-Aspizua S, Conti CJ, Mencía Á, Martínez-Santamaría L, Llames S, Pévida M, Carbonell-Caballero J, Puig-Butillé JA, Maseda R, ... ... Dopazo J, et al. Fibroblasts activation and abnormal extracellular matrix remodelling as common hallmarks in three cancer-prone genodermatoses. The British Journal of Dermatology. PMID 30693469 DOI: 10.1111/Bjd.17698  1
2019 Martin-Broto J, Stacchiotti S, Lopez-Pousa A, Redondo A, Bernabeu D, de Alava E, Casali PG, Italiano A, Gutierrez A, Moura DS, Peña-Chilet M, Diaz-Martin J, Biscuola M, Taron M, Collini P, ... ... Dopazo J, et al. Pazopanib for treatment of advanced malignant and dedifferentiated solitary fibrous tumour: a multicentre, single-arm, phase 2 trial. The Lancet. Oncology. 20: 134-144. PMID 30578023 DOI: 10.1016/S1470-2045(18)30676-4  0.01
2019 Amadoz A, Hidalgo MR, Çubuk C, Carbonell-Caballero J, Dopazo J. A comparison of mechanistic signaling pathway activity analysis methods. Briefings in Bioinformatics. 20: 1655-1668. PMID 29868818 DOI: 10.1093/Bib/Bby040  1
2019 Petkevicius K, Virtue S, Bidault G, Jenkins B, Çubuk C, Morgantini C, Aouadi M, Dopazo J, Serlie MJ, Koulman A, Vidal-Puig A. Author response: Accelerated phosphatidylcholine turnover in macrophages promotes adipose tissue inflammation in obesity Elife. DOI: 10.7554/Elife.47990.039  0.01
2019 Esteban-Medina M, Loucera C, Dopazo J, Peña-Chilet M. Mechanistic models and machine learning for drug repositioning in juvenile idiopathic arthritis F1000research. 8. DOI: 10.7490/F1000Research.1117756.1  0.01
2019 Pérez-Gutiérrez AM, Carmona R, Aquino-Quintans V, Pérez-Florido J, Peña-Chilet M, Dopazo J. Functional variant prioritization in rare diseases using a mechanistic approach F1000research. 8. DOI: 10.7490/F1000Research.1117737.1  0.01
2018 Ibáñez M, Carbonell-Caballero J, Such E, García-Alonso L, Liquori A, López-Pavía M, Llop M, Alonso C, Barragán E, Gómez-Seguí I, Neef A, Hervás D, Montesinos P, Sanz G, Sanz MA, ... Dopazo J, et al. The modular network structure of the mutational landscape of Acute Myeloid Leukemia. Plos One. 13: e0202926. PMID 30303964 DOI: 10.1371/Journal.Pone.0202926  1
2018 Rodríguez Hernáez J, Cerón Cucchi ME, Cravero S, Martinez MC, Gonzalez S, Puebla A, Dopazo J, Farber M, Paniego N, Rivarola M. The first complete genomic structure of Butyrivibrio fibrisolvens and its chromid. Microbial Genomics. PMID 30216146 DOI: 10.1099/mgen.0.000216  0.01
2018 Cubuk C, Hidalgo MR, Amadoz A, Pujana MA, Mateo F, Herranz C, Carbonell-Caballero J, Dopazo J. Gene Expression Integration into Pathway Modules Reveals a Pan-Cancer Metabolic Landscape. Cancer Research. 78: 6059-6072. PMID 30135189 DOI: 10.1158/0008-5472.Can-17-2705  1
2018 Hidalgo MR, Amadoz A, Çubuk C, Carbonell-Caballero J, Dopazo J. Models of cell signaling uncover molecular mechanisms of high-risk neuroblastoma and predict disease outcome. Biology Direct. 13: 16. PMID 30134948 DOI: 10.1186/S13062-018-0219-4  1
2018 Ferreira PG, Muñoz-Aguirre M, Reverter F, Sá Godinho CP, Sousa A, Amadoz A, Sodaei R, Hidalgo MR, Pervouchine D, Carbonell-Caballero J, Nurtdinov R, Breschi A, Amador R, Oliveira P, Çubuk C, ... ... Dopazo J, et al. The effects of death and post-mortem cold ischemia on human tissue transcriptomes. Nature Communications. 9: 490. PMID 29440659 DOI: 10.1038/S41467-017-02772-X  1
2018 Wu GA, Terol J, Ibanez V, López-García A, Pérez-Román E, Borredá C, Domingo C, Tadeo FR, Carbonell-Caballero J, Alonso R, Curk F, Du D, Ollitrault P, Roose ML, Dopazo J, et al. Genomics of the origin and evolution of Citrus. Nature. PMID 29414943 DOI: 10.1038/Nature25447  1
2018 Matalonga L, Serf A, Martinez O, Piscia D, Camacho F, Dopazo J, Capella-Gutierrez S, Valencia A, Keane T, Rambla J, Beltran S. ELIXIR Implementation Study End Report: Remote real-time visualization of human rare disease genomics data (RD-Connect) stored at the EGA F1000research. 7. DOI: 10.7490/F1000Research.1115872.1  1
2017 Dopazo J, Erten C. Graph-theoretical comparison of normal and tumor networks in identifying BRCA genes. Bmc Systems Biology. 11: 110. PMID 29166896 DOI: 10.1186/S12918-017-0495-0  0.01
2017 Gómez-López G, Dopazo J, Cigudosa JC, Valencia A, Al-Shahrour F. Precision medicine needs pioneering clinical bioinformaticians. Briefings in Bioinformatics. PMID 29077790 DOI: 10.1093/Bib/Bbx144  1
2017 Carbonell-Caballero J, Amadoz A, Alonso R, Hidalgo MR, Çubuk C, Conesa D, López-Quílez A, Dopazo J. Reference genome assessment from a population scale perspective: an accurate profile of variability and noise. Bioinformatics (Oxford, England). 33: 3511-3517. PMID 28961772 DOI: 10.1093/Bioinformatics/Btx482  1
2017 Juanes JM, Gallego A, Tárraga J, Chaves FJ, Marín-Garcia P, Medina I, Arnau V, Dopazo J. VISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapy. Bmc Bioinformatics. 18: 421. PMID 28931371 DOI: 10.1186/S12859-017-1837-Z  1
2017 Moschen S, Di Rienzo JA, Higgins J, Tohge T, Watanabe M, González S, Rivarola M, García-García F, Dopazo J, Hopp HE, Hoefgen R, Fernie AR, Paniego N, Fernández P, Heinz RA. Integration of transcriptomic and metabolic data reveals hub transcription factors involved in drought stress response in sunflower (Helianthus annuus L.). Plant Molecular Biology. PMID 28639116 DOI: 10.1007/S11103-017-0625-5  1
2017 Lopez J, Coll J, Haimel M, Kandasamy S, Tarraga J, Furio-Tari P, Bari W, Bleda M, Rueda A, Gräf S, Rendon A, Dopazo J, Medina I. HGVA: the Human Genome Variation Archive. Nucleic Acids Research. PMID 28535294 DOI: 10.1093/Nar/Gkx445  1
2017 Roca-Ayats N, Balcells S, Garcia-Giralt N, Falcó-Mascaró M, Martínez-Gil N, Abril JF, Urreizti R, Dopazo J, Quesada-Gómez JM, Nogués X, Mellibovsky L, Prieto-Alhambra D, Dunford JE, Javaid MK, Russell RG, et al. GGPS1 Mutation and Atypical Femoral Fractures with Bisphosphonates. The New England Journal of Medicine. 376: 1794-1795. PMID 28467865 DOI: 10.1056/Nejmc1612804  1
2017 Gui H, Schriemer D, Cheng WW, Chauhan RK, Antiňolo G, Berrios C, Bleda M, Brooks AS, Brouwer RW, Burns AJ, Cherny SS, Dopazo J, Eggen BJ, Griseri P, Jalloh B, et al. Whole exome sequencing coupled with unbiased functional analysis reveals new Hirschsprung disease genes. Genome Biology. 18: 48. PMID 28274275 DOI: 10.1186/S13059-017-1174-6  1
2017 Olanda R, Pérez M, Orduña JM, Tárraga J, Dopazo J. A new parallel pipeline for DNA methylation analysis of long reads datasets. Bmc Bioinformatics. 18: 161. PMID 28274198 DOI: 10.1186/s12859-017-1574-3  1
2017 Gonzalez S, Clavijo B, Rivarola M, Moreno P, Fernandez P, Dopazo J, Paniego N. ATGC transcriptomics: a web-based application to integrate, explore and analyze de novo transcriptomic data. Bmc Bioinformatics. 18: 121. PMID 28222698 DOI: 10.1186/S12859-017-1494-2  0.01
2017 Hidalgo MR, Cubuk C, Amadoz A, Salavert F, Carbonell-Caballero J, Dopazo J. High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes. Oncotarget. 8: 5160-5178. PMID 28042959 DOI: 10.18632/Oncotarget.14107  1
2017 Puig-Butille JA, Gimenez-Xavier P, Visconti A, Nsengimana J, Garcia-García F, Tell-Marti G, Escamez MJ, Newton-Bishop J, Bataille V, Del Río M, Dopazo J, Falchi M, Puig S. Genomic expression differences between cutaneous cells from red hair color individuals and black hair color individuals based on bioinformatic analysis. Oncotarget. 8: 11589-11599. PMID 28030792 DOI: 10.18632/Oncotarget.14140  0.01
2016 Falco MM, Bleda M, Carbonell-Caballero J, Dopazo J. The pan-cancer pathological regulatory landscape. Scientific Reports. 6: 39709. PMID 28000771 DOI: 10.1038/Srep39709  1
2016 Matalonga L, Bravo M, Peinado CS, García-Pelegrí E, Ugarteburu O, Vidal S, Llambrich M, Quintana E, Fuster-Jorge P, Gonzalez-Bravo MN, Beltran S, Dopazo J, Garcia-Garcia F, Foulquier F, Matthijs G, et al. Mutations in TRAPPC11 are Associated with a Congenital Disorder of Glycosylation. Human Mutation. PMID 27862579 DOI: 10.1002/Humu.23145  1
2016 Prieto J, León M, Ponsoda X, García-García F, Bort R, Serna E, Barneo-Muñoz M, Palau F, Dopazo J, López-García C, Torres J. Dysfunctional mitochondrial fission impairs cell reprogramming. Cell Cycle (Georgetown, Tex.). 0. PMID 27753531 DOI: 10.1080/15384101.2016.1241930  1
2016 Corton M, Avila-Fernández A, Campello L, Sánchez M, Benavides B, López-Molina MI, Fernández-Sánchez L, Sánchez-Alcudia R, da Silva LR, Reyes N, Martín-Garrido E, Zurita O, Fernández-San José P, Pérez-Carro R, García-García F, ... Dopazo J, et al. Identification of the Photoreceptor Transcriptional Co-Repressor SAMD11 as Novel Cause of Autosomal Recessive Retinitis Pigmentosa. Scientific Reports. 6: 35370. PMID 27734943 DOI: 10.1038/Srep35370  1
2016 Lucariello M, Vidal E, Vidal S, Saez M, Roa L, Huertas D, Pineda M, Dalfó E, Dopazo J, Jurado P, Armstrong J, Esteller M. Whole exome sequencing of Rett syndrome-like patients reveals the mutational diversity of the clinical phenotype. Human Genetics. PMID 27541642 DOI: 10.1007/S00439-016-1721-3  1
2016 Lagarde J, Uszczynska-Ratajczak B, Santoyo-Lopez J, Gonzalez JM, Tapanari E, Mudge JM, Steward CA, Wilming L, Tanzer A, Howald C, Chrast J, Vela-Boza A, Rueda A, Lopez-Domingo FJ, Dopazo J, et al. Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq). Nature Communications. 7: 12339. PMID 27531712 DOI: 10.1038/Ncomms12339  0.01
2016 Garcia-Garcia F, Panadero J, Dopazo J, Montaner D. Integrated Gene Set Analysis for microRNA Studies. Bioinformatics (Oxford, England). PMID 27324197 DOI: 10.1093/Bioinformatics/Btw334  1
2016 Salavert F, García-Alonso L, Sánchez R, Alonso R, Bleda M, Medina I, Dopazo J. Web-based network analysis and visualization using CellMaps. Bioinformatics (Oxford, England). PMID 27296979 DOI: 10.1093/Bioinformatics/Btw332  1
2016 Salavert F, Hidago MR, Amadoz A, Çubuk C, Medina I, Crespo D, Carbonell-Caballero J, Dopazo J. Actionable pathways: interactive discovery of therapeutic targets using signaling pathway models. Nucleic Acids Research. PMID 27137885 DOI: 10.1093/Nar/Gkw369  1
2016 Hillung J, García-García F, Dopazo J, Cuevas JM, Elena SF. The transcriptomics of an experimentally evolved plant-virus interaction. Scientific Reports. 6: 24901. PMID 27113435 DOI: 10.1038/Srep24901  1
2016 Bravo-Gil N, Méndez-Vidal C, Romero-Pérez L, González-del Pozo M, Rodríguez-de la Rúa E, Dopazo J, Borrego S, Antiñolo G. Improving the management of Inherited Retinal Dystrophies by targeted sequencing of a population-specific gene panel. Scientific Reports. 6: 23910. PMID 27032803 DOI: 10.1038/Srep23910  1
2016 Sanghez V, Cubuk C, Sebastián-Leon P, Carobbio S, Dopazo J, Vidal-Puig A, Bartolomucci A. 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). 1-11. PMID 26946982 DOI: 10.3109/10253890.2016.1151491  1
2016 Tarraga J, Gallego A, Arnau V, Medina I, Dopazo J. HPG pore: an efficient and scalable framework for nanopore sequencing data. Bmc Bioinformatics. 17: 107. PMID 26921234 DOI: 10.1186/s12859-016-0966-0  1
2016 Maroñas O, Latorre A, Dopazo J, Pirmohamed M, Rodríguez-Antona C, Siest G, Carracedo Á, LLerena A. Progress in pharmacogenetics: consortiums and new strategies. Drug Metabolism and Personalized Therapy. 31: 17-23. PMID 26913460 DOI: 10.1515/dmpt-2015-0039  1
2016 Ibáñez M, Carbonell-Caballero J, García-Alonso L, Such E, Jiménez-Almazán J, Vidal E, Barragán E, López-Pavía M, LLop M, Martín I, Gómez-Seguí I, Montesinos P, Sanz MA, Dopazo J, Cervera J. The Mutational Landscape of Acute Promyelocytic Leukemia Reveals an Interacting Network of Co-Occurrences and Recurrent Mutations. Plos One. 11: e0148346. PMID 26886259 DOI: 10.1371/Journal.Pone.0148346  1
2016 Puchades-Carrasco L, Jantus-Lewintre E, Pérez-Rambla C, García-García F, Lucas R, Calabuig S, Blasco A, Dopazo J, Camps C, Pineda-Lucena A. Serum metabolomic profiling facilitates the non-invasive identification of metabolic biomarkers associated with the onset and progression of non-small cell lung cancer. Oncotarget. 7: 12904-16. PMID 26883203 DOI: 10.18632/Oncotarget.7354  1
2016 Razzoli M, Frontini A, Gurney A, Mondini E, Cubuk C, Katz LS, Cero C, Bolan PJ, Dopazo J, Vidal-Puig A, Cinti S, Bartolomucci A. Stress-induced activation of brown adipose tissue prevents obesity in conditions of low adaptive thermogenesis. Molecular Metabolism. 5: 19-33. PMID 26844204 DOI: 10.1016/J.Molmet.2015.10.005  1
2016 Sanchez-Mut JV, Heyn H, Vidal E, Moran S, Sayols S, Delgado-Morales R, Schultz MD, Ansoleaga B, Garcia-Esparcia P, Pons-Espinal M, de Lagran MM, Dopazo J, Rabano A, Avila J, Dierssen M, et al. Human DNA methylomes of neurodegenerative diseases show common epigenomic patterns. Translational Psychiatry. 6: e718. PMID 26784972 DOI: 10.1038/Tp.2015.214  1
2016 Urreizti R, Roca-Ayats N, Trepat J, Garcia-Garcia F, Aleman A, Orteschi D, Marangi G, Neri G, Opitz JM, Dopazo J, Cormand B, Vilageliu L, Balcells S, Grinberg D. Screening of CD96 and ASXL1 in 11 patients with Opitz C or Bohring-Opitz syndromes. American Journal of Medical Genetics. Part A. 170: 24-31. PMID 26768331 DOI: 10.1002/Ajmg.A.37418  1
2016 Dopazo J, Amadoz A, Bleda M, Garcia-Alonso L, Alemán A, García-García F, Rodriguez JA, Daub JT, Muntané G, Rueda A, Vela-Boza A, López-Domingo FJ, Florido JP, Arce P, Ruiz-Ferrer M, et al. 267 Spanish exomes reveal population-specific differences in disease-related genetic variation. Molecular Biology and Evolution. PMID 26764160 DOI: 10.1093/Molbev/Msw005  1
2016 Carretero M, Guerrero-Aspizua S, Illera N, Galvez V, Navarro M, García-García F, Dopazo J, Jorcano JL, Larcher F, Del Rio M. Differential Features between Chronic Skin Inflammatory Diseases Revealed in Skin-Humanized Psoriasis and Atopic Dermatitis Mouse Models. The Journal of Investigative Dermatology. 136: 136-45. PMID 26763433 DOI: 10.1038/Jid.2015.362  1
2016 Lupo V, García-García F, Sancho P, Tello C, García-Romero M, Villarreal L, Alberti A, Sivera R, Dopazo J, Pascual-Pascual SI, Márquez-Infante C, Casasnovas C, Sevilla T, Espinós C. 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. 18: 225-34. PMID 26752306 DOI: 10.1016/J.Jmoldx.2015.10.005  1
2016 Sevilla T, Lupo V, Martínez-Rubio D, Sancho P, Sivera R, Chumillas MJ, García-Romero M, Pascual-Pascual SI, Muelas N, Dopazo J, Vílchez JJ, Palau F, Espinós C. Mutations in the MORC2 gene cause axonal Charcot-Marie-Tooth disease. Brain : a Journal of Neurology. 139: 62-72. PMID 26497905 DOI: 10.1093/Brain/Awv311  0.01
2016 Puchades-Carrasco L, Jantus-Lewintre E, Pérez-Rambla C, García-García F, Lucas R, Calabuig S, Blasco A, Dopazo J, Camps C, Pineda-Lucena A. Serum metabolomic profiling facilitates the non-invasive identification of metabolic biomarkers associated with the onset and progression of non-small cell lung cancer Oncotarget. 7: 12904-12916. DOI: 10.18632/oncotarget.7354  1
2016 Maroñas O, Latorre A, Dopazo J, Pirmohamed M, Rodríguez-Antona C, Siest G, Carracedo Á, Llerena A. Progress in pharmacogenetics: Consortiums and new strategies Drug Metabolism and Personalized Therapy. 31: 17-23. DOI: 10.1515/dmpt-2015-0039  1
2015 Luzón-Toro B, Bleda M, Navarro E, García-Alonso L, Ruiz-Ferrer M, Medina I, Martín-Sánchez M, Gonzalez CY, Fernández RM, Torroglosa A, Antiñolo G, Dopazo J, Borrego S. Identification of epistatic interactions through genome-wide association studies in sporadic medullary and juvenile papillary thyroid carcinomas. Bmc Medical Genomics. 8: 83. PMID 26690675 DOI: 10.1186/S12920-015-0160-7  1
2015 Amadoz A, Sebastian-Leon P, Vidal E, Salavert F, Dopazo J. Using activation status of signaling pathways as mechanism-based biomarkers to predict drug sensitivity. Scientific Reports. 5: 18494. PMID 26678097 DOI: 10.1038/Srep18494  1
2015 Luzón-Toro B, Gui H, Ruiz-Ferrer M, Sze-Man Tang C, Fernández RM, Sham PC, Torroglosa A, Kwong-Hang Tam P, Espino-Paisán L, Cherny SS, Bleda M, Enguix-Riego Mdel V, Dopazo J, Antiñolo G, García-Barceló MM, et al. Exome sequencing reveals a high genetic heterogeneity on familial Hirschsprung disease. Scientific Reports. 5: 16473. PMID 26559152 DOI: 10.1038/Srep16473  1
2015 Gil-Ibañez P, García-García F, Dopazo J, Bernal J, Morte B. Global Transcriptome Analysis of Primary Cerebrocortical Cells: Identification of Genes Regulated by Triiodothyronine in Specific Cell Types. Cerebral Cortex (New York, N.Y. : 1991). PMID 26534908 DOI: 10.1093/Cercor/Bhv273  1
2015 Porta-Pardo E, Garcia-Alonso L, Hrabe T, Dopazo J, Godzik A. A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces. Plos Computational Biology. 11: e1004518. PMID 26485003 DOI: 10.1371/Journal.Pcbi.1004518  1
2015 Martinez H, Tarraga J, Medina I, Barrachina S, Castillo M, Dopazo J, Quintana-Orti ES. Concurrent and Accurate Short Read Mapping on Multicore Processors. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 12: 995-1007. PMID 26451814 DOI: 10.1109/Tcbb.2015.2392077  1
2015 Carretero M, Guerrero-Aspizua S, Illera N, Galvez V, Navarro M, García-García F, Dopazo J, Jorcano JL, Larcher F, Del Rio M. Differential Features Between Chronic Skin Inflammatory Diseases Revealed in Skin-Humanized Psoriasis and Atopic Dermatitis Mouse Models. The Journal of Investigative Dermatology. PMID 26398345 DOI: 10.1038/jid.2015.362  1
2015 Rodríguez-de la Rosa L, Sánchez-Calderón H, Contreras J, Murillo-Cuesta S, Falagan S, Avendaño C, Dopazo J, Varela-Nieto I, Milo M. Comparative gene expression study of the vestibular organ of the Igf1 deficient mouse using whole-transcript arrays. Hearing Research. PMID 26341476 DOI: 10.1016/J.Heares.2015.08.016  0.01
2015 Fonseca RF, de Carvalho FM, Poletta FA, Montaner D, Dopazo J, Mereb JC, Moreira MA, Seuanez HN, Vieira AR, Castilla EE, Orioli IM. Family-based genome-wide association study in Patagonia confirms the association of the DMD locus and cleft lip and palate. European Journal of Oral Sciences. PMID 26331285 DOI: 10.1111/Eos.12212  1
2015 Moschen S, Bengoa Luoni S, Di Rienzo JA, Caro MD, Tohge T, Watanabe M, Hollmann J, González S, Rivarola M, García-García F, Dopazo J, Hopp HE, Hoefgen R, Fernie AR, Paniego N, et al. Integrating transcriptomic and metabolomic analysis to understand natural leaf senescence in sunflower. Plant Biotechnology Journal. PMID 26132509 DOI: 10.1111/Pbi.12422  1
2015 Alvarez-Mora MI, Rodriguez-Revenga L, Madrigal I, Garcia-Garcia F, Duran M, Dopazo J, Estivill X, Milà M. Deregulation of key signaling pathways involved in oocyte maturation in FMR1 premutation carriers with Fragile X-associated primary ovarian insufficiency. Gene. 571: 52-7. PMID 26095811 DOI: 10.1016/J.Gene.2015.06.039  1
2015 Tárraga J, Pérez M, Orduña JM, Duato J, Medina I, Dopazo J. A parallel and sensitive software tool for methylation analysis on multicore platforms. Bioinformatics (Oxford, England). PMID 26069264 DOI: 10.1093/bioinformatics/btv357  1
2015 Alonso R, Salavert F, Garcia-Garcia F, Carbonell-Caballero J, Bleda M, Garcia-Alonso L, Sanchis-Juan A, Perez-Gil D, Marin-Garcia P, Sanchez R, Cubuk C, Hidalgo MR, Amadoz A, Hernansaiz-Ballesteros RD, Alemán A, ... ... Dopazo J, et al. Babelomics 5.0: functional interpretation for new generations of genomic data. Nucleic Acids Research. 43: W117-21. PMID 25897133 DOI: 10.1093/Nar/Gkv384  1
2015 Romero A, García-García F, López-Perolio I, Ruiz de Garibay G, García-Sáenz JA, Garre P, Ayllón P, Benito E, Dopazo J, Díaz-Rubio E, Caldés T, de la Hoya M. BRCA1 Alternative splicing landscape in breast tissue samples. Bmc Cancer. 15: 219. PMID 25884417 DOI: 10.1186/S12885-015-1145-9  1
2015 Hernansaiz-Ballesteros RD, Salavert F, Sebastián-León P, Alemán A, Medina I, Dopazo J. Assessing the impact of mutations found in next generation sequencing data over human signaling pathways. Nucleic Acids Research. 43: W270-5. PMID 25883139 DOI: 10.1093/Nar/Gkv349  1
2015 Avila-Fernandez A, Perez-Carro R, Corton M, Lopez-Molina MI, Campello L, Garanto A, Fernandez-Sanchez L, Duijkers L, Lopez-Martinez MA, Riveiro-Alvarez R, Da Silva LR, Sanchez-Alcudia R, Martin-Garrido E, Reyes N, Garcia-Garcia F, ... Dopazo J, et al. Whole-exome sequencing reveals ZNF408 as a new gene associated with autosomal recessive retinitis pigmentosa with vitreal alterations. Human Molecular Genetics. 24: 4037-48. PMID 25882705 DOI: 10.1093/Hmg/Ddv140  1
2015 Carbonell-Caballero J, Alonso R, Ibañez V, Terol J, Talon M, Dopazo J. A Phylogenetic Analysis of 34 Chloroplast Genomes Elucidates the Relationships between Wild and Domestic Species within the Genus Citrus. Molecular Biology and Evolution. 32: 2015-35. PMID 25873589 DOI: 10.1093/Molbev/Msv082  1
2015 Pozo MG, Bravo-Gil N, Méndez-Vidal C, Montero-de-Espinosa I, Millán JM, Dopazo J, Borrego S, Antiñolo G. Re-evaluation casts doubt on the pathogenicity of homozygous USH2A p.C759F. American Journal of Medical Genetics. Part A. 167: 1597-600. PMID 25823529 DOI: 10.1002/Ajmg.A.37003  1
2015 Terol J, Ibañez V, Carbonell J, Alonso R, Estornell LH, Licciardello C, Gut IG, Dopazo J, Talon M. Involvement of a citrus meiotic recombination TTC-repeat motif in the formation of gross deletions generated by ionizing radiation and MULE activation. Bmc Genomics. 16: 69. PMID 25758634 DOI: 10.1186/S12864-015-1280-3  1
2015 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. 16: 18. PMID 25626517 DOI: 10.1186/s12859-014-0438-3  1
2015 Calzada D, Aguerri M, Baos S, Montaner D, Mata M, Dopazo J, Quiralte J, Florido F, Lahoz C, Cárdaba B. Therapeutic targets for olive pollen allergy defined by gene markers modulated by Ole e 1-derived peptides. Molecular Immunology. 64: 252-61. PMID 25553522 DOI: 10.1016/J.Molimm.2014.12.002  1
2015 Minguez P, Letunic I, Parca L, Garcia-Alonso L, Dopazo J, Huerta-Cepas J, Bork P. PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins. Nucleic Acids Research. 43: D494-502. PMID 25361965 DOI: 10.1093/Nar/Gku1081  1
2015 Luzón-Toro B, Bleda M, Navarro E, García-Alonso L, Ruiz-Ferrer M, Medina I, Martín-Sánchez M, Gonzalez CY, Fernández RM, Torroglosa A, Antiñolo G, Dopazo J, Borrego S. Identification of epistatic interactions through genome-wide association studies in sporadic medullary and juvenile papillary thyroid carcinomas Bmc Medical Genomics. DOI: 10.1186/s12920-015-0160-7  1
2015 Pozo MGd, Bravo-Gil N, Méndez-Vidal C, Montero-de-Espinosa I, Millán JM, Dopazo J, Borrego S, Antiñolo G. Re-evaluation casts doubt on the pathogenicity of homozygous USH2A p.C759F American Journal of Medical Genetics, Part A. 167: 1597-1600. DOI: 10.1002/ajmg.a.37003  1
2014 González-del Pozo M, Méndez-Vidal C, Bravo-Gil N, Vela-Boza A, Dopazo J, Borrego S, Antiñolo G. Exome sequencing reveals novel and recurrent mutations with clinical significance in inherited retinal dystrophies. Plos One. 9: e116176. PMID 25544989 DOI: 10.1371/Journal.Pone.0116176  1
2014 Méndez-Vidal C, Bravo-Gil N, González-Del Pozo M, Vela-Boza A, Dopazo J, Borrego S, Antiñolo G. Novel RP1 mutations and a recurrent BBS1 variant explain the co-existence of two distinct retinal phenotypes in the same pedigree. Bmc Genetics. 15: 143. PMID 25494902 DOI: 10.1186/S12863-014-0143-2  1
2014 Iglesias JM, Leis O, Pérez Ruiz E, Gumuzio Barrie J, Garcia-Garcia F, Aduriz A, Beloqui I, Hernandez-Garcia S, Lopez-Mato MP, Dopazo J, Pandiella A, Menendez JA, Martin AG. The Activation of the Sox2 RR2 Pluripotency Transcriptional Reporter in Human Breast Cancer Cell Lines is Dynamic and Labels Cells with Higher Tumorigenic Potential. Frontiers in Oncology. 4: 308. PMID 25414831 DOI: 10.3389/Fonc.2014.00308  1
2014 Torre I, González-Tendero A, García-Cañadilla P, Crispi F, García-García F, Bijnens B, Iruretagoyena I, Dopazo J, Amat-Roldán I, Gratacós E. Permanent cardiac sarcomere changes in a rabbit model of intrauterine growth restriction. Plos One. 9: e113067. PMID 25402351 DOI: 10.1371/Journal.Pone.0113067  0.01
2014 Sebastian-Leon P, Vidal E, Minguez P, Conesa A, Tarazona S, Amadoz A, Armero C, Salavert F, Vidal-Puig A, Montaner D, Dopazo J. Understanding disease mechanisms with models of signaling pathway activities. Bmc Systems Biology. 8: 121. PMID 25344409 DOI: 10.1186/S12918-014-0121-3  1
2014 Garcia-Alonso L, Jiménez-Almazán J, Carbonell-Caballero J, Vela-Boza A, Santoyo-López J, Antiñolo G, Dopazo J. The role of the interactome in the maintenance of deleterious variability in human populations. Molecular Systems Biology. 10: 752. PMID 25261458 DOI: 10.15252/Msb.20145222  1
2014 Munro SA, Lund SP, Pine PS, Binder H, Clevert DA, Conesa A, Dopazo J, Fasold M, Hochreiter S, Hong H, Jafari N, Kreil DP, ?abaj PP, Li S, Liao Y, et al. Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures. Nature Communications. 5: 5125. PMID 25254650 DOI: 10.1038/Ncomms6125  1
2014 Tenorio J, Mansilla A, Valencia M, Martínez-Glez V, Romanelli V, Arias P, Castrejón N, Poletta F, Guillén-Navarro E, Gordo G, Mansilla E, García-Santiago F, González-Casado I, Vallespín E, Palomares M, ... ... Dopazo J, et al. A new overgrowth syndrome is due to mutations in RNF125. Human Mutation. 35: 1436-41. PMID 25196541 DOI: 10.1002/humu.22689  1
2014 . A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nature Biotechnology. 32: 903-14. PMID 25150838 DOI: 10.1038/Nbt.2957  1
2014 Tárraga J, Arnau V, Martínez H, Moreno R, Cazorla D, Salavert-Torres J, Blanquer-Espert I, Dopazo J, Medina I. Acceleration of short and long DNA read mapping without loss of accuracy using suffix array. Bioinformatics (Oxford, England). 30: 3396-8. PMID 25143289 DOI: 10.1093/bioinformatics/btu553  1
2014 Carmona FJ, Davalos V, Vidal E, Gomez A, Heyn H, Hashimoto Y, Vizoso M, Martinez-Cardus A, Sayols S, Ferreira HJ, Sánchez-Mut JV, Morán S, Margelí M, Castella E, Berdasco M, ... ... Dopazo J, et al. A comprehensive DNA methylation profile of epithelial-to-mesenchymal transition. Cancer Research. 74: 5608-19. PMID 25106427 DOI: 10.1158/0008-5472.Can-13-3659  1
2014 Ponzoni I, Nueda M, Tarazona S, Götz S, Montaner D, Dussaut J, Dopazo J, Conesa A. Pathway network inference from gene expression data. Bmc Systems Biology. 8: S7. PMID 25032889 DOI: 10.1186/1752-0509-8-S2-S7  1
2014 Calpena E, Martínez-Rubio D, Arpa J, García-Peñas JJ, Montaner D, Dopazo J, Palau F, Espinós C. A novel locus for a hereditary recurrent neuropathy on chromosome 21q21. Neuromuscular Disorders. 24: 660-665. PMID 24878226 DOI: 10.1016/J.Nmd.2014.04.004  1
2014 Alemán A, Garcia-Garcia F, Medina I, Dopazo J. A web tool for the design and management of panels of genes for targeted enrichment and massive sequencing for clinical applications. Nucleic Acids Research. 42: W83-7. PMID 24861626 DOI: 10.1093/Nar/Gku472  1
2014 Alemán A, Garcia-Garcia F, Salavert F, Medina I, Dopazo J. A web-based interactive framework to assist in the prioritization of disease candidate genes in whole-exome sequencing studies. Nucleic Acids Research. 42: W88-93. PMID 24803668 DOI: 10.1093/Nar/Gku407  1
2014 Puig-Butille JA, Escámez MJ, Garcia-Garcia F, Tell-Marti G, Fabra À, Martínez-Santamaría L, Badenas C, Aguilera P, Pevida M, Dopazo J, del Río M, Puig S. Capturing the biological impact of CDKN2A and MC1R genes as an early predisposing event in melanoma and non melanoma skin cancer. Oncotarget. 5: 1439-51. PMID 24742402 DOI: 10.18632/Oncotarget.1444  1
2014 González-Del Pozo M, Méndez-Vidal C, Santoyo-Lopez J, Vela-Boza A, Bravo-Gil N, Rueda A, García-Alonso L, Vázquez-Marouschek C, Dopazo J, Borrego S, Antiñolo G. Deciphering intrafamilial phenotypic variability by exome sequencing in a Bardet-Biedl family. Molecular Genetics & Genomic Medicine. 2: 124-33. PMID 24689075 DOI: 10.1002/Mgg3.50  1
2014 López-Domingo FJ, Florido JP, Rueda A, Dopazo J, Santoyo-Lopez J. ngsCAT: a tool to assess the efficiency of targeted enrichment sequencing. Bioinformatics (Oxford, England). 30: 1767-8. PMID 24578402 DOI: 10.1093/Bioinformatics/Btu108  1
2014 Larriba E, Jaime MD, Carbonell-Caballero J, Conesa A, Dopazo J, Nislow C, Martín-Nieto J, Lopez-Llorca LV. Sequencing and functional analysis of the genome of a nematode egg-parasitic fungus, Pochonia chlamydosporia. Fungal Genetics and Biology : Fg & B. 65: 69-80. PMID 24530791 DOI: 10.1016/J.Fgb.2014.02.002  1
2014 de Castro-Miró M, Pomares E, Lorés-Motta L, Tonda R, Dopazo J, Marfany G, Gonzàlez-Duarte R. Combined genetic and high-throughput strategies for molecular diagnosis of inherited retinal dystrophies. Plos One. 9: e88410. PMID 24516651 DOI: 10.1371/Journal.Pone.0088410  0.01
2014 García-Cazorla A, Oyarzabal A, Fort J, Robles C, Castejón E, Ruiz-Sala P, Bodoy S, Merinero B, Lopez-Sala A, Dopazo J, Nunes V, Ugarte M, Artuch R, Palacín M, Rodríguez-Pombo P, 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. Human Mutation. 35: 470-7. PMID 24449431 DOI: 10.1002/Humu.22513  1
2014 Dopazo J. Genomics and transcriptomics in drug discovery. Drug Discovery Today. 19: 126-32. PMID 23773860 DOI: 10.1016/j.drudis.2013.06.003  0.01
2014 García-García F, Fernández P, Conesa A, Paniego N, Heinz R, Peluffo L, Lia V, Canal Ldl, Ribichich KF, Chan R, Rienzo JD, Dopazo J. Using high-throughput technologies to improve stress tolerance characteristics in sunflower F1000research. 5. DOI: 10.7490/F1000Research.1097168.1  1
2014 García-García F, Alemán A, Medina I, Dopazo J. TEAM: a web tool for the design, analysis and management of panels of genes for clinical applications F1000research. 5. DOI: 10.7490/F1000Research.1097156.1  1
2014 García-García F, Alemán A, Dopazo J. BIER platform: analyzing and understanding genomic and biomedical data F1000research. 5. DOI: 10.7490/F1000Research.1096997.1  1
2014 Alemán A, García-García F, Salavert F, Medina I, Dopazo J. BiERapp: a web-based interactive framework for the prioritization of disease candidate genes in whole exome sequencing studies F1000research. 5. DOI: 10.7490/F1000Research.1096994.1  1
2014 Amadoz A, Sebastián-León P, Dopazo J. Drug activity prediction using mechanism-based biomarkers F1000research. 5. DOI: 10.7490/F1000Research.1096964.1  1
2014 Amadoz A, Sebastián-León P, Salavert F, Dopazo J. PATHiPRED: prediction models using the activation status of stimulus-response signaling circuits F1000research. 5. DOI: 10.7490/F1000Research.1096796.1  1
2013 Fernández RM, Bleda M, Luzón-Toro B, García-Alonso L, Arnold S, Sribudiani Y, Besmond C, Lantieri F, Doan B, Ceccherini I, Lyonnet S, Hofstra RM, Chakravarti A, Antiñolo G, Dopazo J, et al. Pathways systematically associated to Hirschsprung's disease. Orphanet Journal of Rare Diseases. 8: 187. PMID 24289864 DOI: 10.1186/1750-1172-8-187  1
2013 Méndez-Vidal C, González-Del Pozo M, Vela-Boza A, Santoyo-López J, López-Domingo FJ, Vázquez-Marouschek C, Dopazo J, Borrego S, Antiñolo G. Whole-exome sequencing identifies novel compound heterozygous mutations in USH2A in Spanish patients with autosomal recessive retinitis pigmentosa. Molecular Vision. 19: 2187-95. PMID 24227914  1
2013 Manuel Iglesias J, Beloqui I, Garcia-Garcia F, Leis O, Vazquez-Martin A, Eguiara A, Cufi S, Pavon A, Menendez JA, Dopazo J, Martin AG. Mammosphere formation in breast carcinoma cell lines depends upon expression of E-cadherin. Plos One. 8: e77281. PMID 24124614 DOI: 10.1371/Journal.Pone.0077281  1
2013 Gonzalez-Tendero A, Torre I, Garcia-Canadilla P, Crispi F, García-García F, Dopazo J, Bijnens B, Gratacós E. Intrauterine growth restriction is associated with cardiac ultrastructural and gene expression changes related to the energetic metabolism in a rabbit model. American Journal of Physiology. Heart and Circulatory Physiology. 305: H1752-60. PMID 24097427 DOI: 10.1152/Ajpheart.00514.2013  0.01
2013 Puig-Butillé JA, Malvehy J, Potrony M, Trullas C, Garcia-García F, Dopazo J, Puig S. Role of CPI-17 in restoring skin homoeostasis in cutaneous field of cancerization: effects of topical application of a film-forming medical device containing photolyase and UV filters. Experimental Dermatology. 22: 494-6. PMID 23800065 DOI: 10.1111/Exd.12177  0.01
2013 Sebastián-León P, Carbonell J, Salavert F, Sanchez R, Medina I, Dopazo J. Inferring the functional effect of gene expression changes in signaling pathways. Nucleic Acids Research. 41: W213-7. PMID 23748960 DOI: 10.1093/Nar/Gkt451  1
2013 Medina I, Salavert F, Sanchez R, de Maria A, Alonso R, Escobar P, Bleda M, Dopazo J. Genome Maps, a new generation genome browser. Nucleic Acids Research. 41: W41-6. PMID 23748955 DOI: 10.1093/Nar/Gkt530  1
2013 Tort F, García-Silva MT, Ferrer-Cortès X, Navarro-Sastre A, Garcia-Villoria J, Coll MJ, Vidal E, Jiménez-Almazán J, Dopazo J, Briones P, Elpeleg O, Ribes A. Exome sequencing identifies a new mutation in SERAC1 in a patient with 3-methylglutaconic aciduria. Molecular Genetics and Metabolism. 110: 73-7. PMID 23707711 DOI: 10.1016/J.Ymgme.2013.04.021  1
2013 Sánchez-Tena S, Lizárraga D, Miranda A, Vinardell MP, García-García F, Dopazo J, Torres JL, Saura-Calixto F, Capellà G, Cascante M. Grape antioxidant dietary fiber inhibits intestinal polyposis in ApcMin/+ mice: relation to cell cycle and immune response. Carcinogenesis. 34: 1881-8. PMID 23615403 DOI: 10.1093/Carcin/Bgt140  1
2013 Galan A, Diaz-Gimeno P, Poo ME, Valbuena D, Sanchez E, Ruiz V, Dopazo J, Montaner D, Conesa A, Simon C. Defining the genomic signature of totipotency and pluripotency during early human development. Plos One. 8: e62135. PMID 23614026 DOI: 10.1371/Journal.Pone.0062135  1
2013 Silbiger VN, Luchessi AD, Hirata RD, Lima-Neto LG, Cavichioli D, Carracedo A, Brión M, Dopazo J, García-García F, dos Santos ES, Ramos RF, Sampaio MF, Armaganijan D, Sousa AG, Hirata MH. Novel genes detected by transcriptional profiling from whole-blood cells in patients with early onset of acute coronary syndrome. Clinica Chimica Acta; International Journal of Clinical Chemistry. 421: 184-90. PMID 23535507 DOI: 10.1016/J.Cca.2013.03.011  1
2013 Sánchez-Tena S, Reyes-Zurita FJ, Díaz-Moralli S, Vinardell MP, Reed M, García-García F, Dopazo J, Lupiáñez JA, Günther U, Cascante M. Maslinic acid-enriched diet decreases intestinal tumorigenesis in Apc(Min/+) mice through transcriptomic and metabolomic reprogramming. Plos One. 8: e59392. PMID 23527181 DOI: 10.1371/Journal.Pone.0059392  1
2013 Ariño J, Casamayor A, Pérez JP, Pedrola L, Álvarez-Tejado M, Marbà M, Santoyo J, Dopazo J. Assessing differential expression measurements by highly parallel pyrosequencing and DNA microarrays: a comparative study. Omics : a Journal of Integrative Biology. 17: 53-9. PMID 21919703 DOI: 10.1089/Omi.2011.0065  1
2013 Lopez F, Rueda A, Perez-Florido J, Arce P, Cruz L, Carbonell J, Jimenez-Almazan J, Vidal E, Antiñolo G, Dopazo J, Santoyo J. Detecting high quality variants from color-space data F1000research. 4. DOI: 10.7490/F1000Research.1094092.1  1
2012 Carcel-Trullols J, Aguilar-Gallardo C, Garcia-Alcalde F, Pardo-Cea MA, Dopazo J, Conesa A, Simón C. Transdifferentiation of MALME-3M and MCF-7 Cells toward Adipocyte-like Cells is Dependent on Clathrin-mediated Endocytosis. Springerplus. 1: 44. PMID 23961369 DOI: 10.1186/2193-1801-1-44  1
2012 Sundaram AY, Kiron V, Dopazo J, Fernandes JM. Diversification of the expanded teleost-specific toll-like receptor family in Atlantic cod, Gadus morhua Bmc Evolutionary Biology. 12. PMID 23273344 DOI: 10.1186/1471-2148-12-256  1
2012 Fernández RM, Bleda M, Núñez-Torres R, Medina I, Luzón-Toro B, García-Alonso L, Torroglosa A, Marbà M, Enguix-Riego MV, Montaner D, Antiñolo G, Dopazo J, Borrego S. Four new loci associations discovered by pathway-based and network analyses of the genome-wide variability profile of Hirschsprung's disease. Orphanet Journal of Rare Diseases. 7: 103. PMID 23270508 DOI: 10.1186/1750-1172-7-103  1
2012 Fernandez P, Soria M, Blesa D, DiRienzo J, Moschen S, Rivarola M, Clavijo BJ, Gonzalez S, Peluffo L, Príncipi D, Dosio G, Aguirrezabal L, García-García F, Conesa A, Hopp E, ... Dopazo J, et al. Development, characterization and experimental validation of a cultivated sunflower (Helianthus annuus L.) gene expression oligonucleotide microarray. Plos One. 7: e45899. PMID 23110046 DOI: 10.1371/Journal.Pone.0045899  1
2012 García-Alcalde F, Okonechnikov K, Carbonell J, Cruz LM, Götz S, Tarazona S, Dopazo J, Meyer TF, Conesa A. Qualimap: evaluating next-generation sequencing alignment data. Bioinformatics (Oxford, England). 28: 2678-9. PMID 22914218 DOI: 10.1093/Bioinformatics/Bts503  1
2012 Carbonell J, Alloza E, Arce P, Borrego S, Santoyo J, Ruiz-Ferrer M, Medina I, Jiménez-Almazán J, Méndez-Vidal C, González-Del Pozo M, Vela A, Bhattacharya SS, Antiñolo G, Dopazo J. A map of human microRNA variation uncovers unexpectedly high levels of variability. Genome Medicine. 4: 62. PMID 22906193 DOI: 10.1186/Gm363  1
2012 García-Alonso L, Alonso R, Vidal E, Amadoz A, de María A, Minguez P, Medina I, Dopazo J. Discovering the hidden sub-network component in a ranked list of genes or proteins derived from genomic experiments. Nucleic Acids Research. 40: e158. PMID 22844098 DOI: 10.1093/Nar/Gks699  1
2012 Medina I, De Maria A, Bleda M, Salavert F, Alonso R, Gonzalez CY, Dopazo J. VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing. Nucleic Acids Research. 40: W54-8. PMID 22693211 DOI: 10.1093/Nar/Gks572  1
2012 Bleda M, Medina I, Alonso R, De Maria A, Salavert F, Dopazo J. Inferring the regulatory network behind a gene expression experiment. Nucleic Acids Research. 40: W168-72. PMID 22693210 DOI: 10.1093/Nar/Gks573  1
2012 Heyn H, Vidal E, Sayols S, Sanchez-Mut JV, Moran S, Medina I, Sandoval J, Simó-Riudalbas L, Szczesna K, Huertas D, Gatto S, Matarazzo MR, Dopazo J, Esteller M. Whole-genome bisulfite DNA sequencing of a DNMT3B mutant patient. Epigenetics : Official Journal of the Dna Methylation Society. 7: 542-50. PMID 22595875 DOI: 10.4161/Epi.20523  1
2012 Ventoso I, Kochetov A, Montaner D, Dopazo J, Santoyo J. Extensive translatome remodeling during ER stress response in mammalian cells Plos One. 7. PMID 22574127 DOI: 10.1371/Journal.Pone.0035915  1
2012 Carrero R, Cerrada I, Lledó E, Dopazo J, García-García F, Rubio MP, Trigueros C, Dorronsoro A, Ruiz-Sauri A, Montero JA, Sepúlveda P. IL1β induces mesenchymal stem cells migration and leucocyte chemotaxis through NF-κB. Stem Cell Reviews. 8: 905-16. PMID 22467443 DOI: 10.1007/S12015-012-9364-9  0.01
2012 De Baets G, Van Durme J, Reumers J, Maurer-Stroh S, Vanhee P, Dopazo J, Schymkowitz J, Rousseau F. SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants. Nucleic Acids Research. 40: D935-9. PMID 22075996 DOI: 10.1093/nar/gkr996  1
2012 Rivarola M, Gonzalez S, Clavijo B, Fernandez P, Martinez M, Ceron-Cuchi M, Cravero S, Dopazo J, Farber M, Paniego N. Data Merge Annotation Pipeline (DMAP): utilizing an ontology driven database with a sequence coordinate based approach to prokaryotic annotation F1000research. 3. DOI: 10.7490/F1000Research.1090045.1  0.01
2011 Vivas Y, Martínez-García C, Izquierdo A, Garcia-Garcia F, Callejas S, Velasco I, Campbell M, Ros M, Dopazo A, Dopazo J, Vidal-Puig A, Medina-Gomez G. Early peroxisome proliferator-activated receptor gamma regulated genes involved in expansion of pancreatic beta cell mass. Bmc Medical Genomics. 4: 86. PMID 22208362 DOI: 10.1186/1755-8794-4-86  1
2011 González-del Pozo M, Borrego S, Barragán I, Pieras JI, Santoyo J, Matamala N, Naranjo B, Dopazo J, Antiñolo G. Mutation screening of multiple genes in Spanish patients with autosomal recessive retinitis pigmentosa by targeted resequencing. Plos One. 6: e27894. PMID 22164218 DOI: 10.1371/Journal.Pone.0027894  1
2011 Khalaf AA, Gmitter FG, Conesa A, Dopazo J, Moore GA. Fortunella margarita transcriptional reprogramming triggered by Xanthomonas citri subsp. citri. Bmc Plant Biology. 11: 159. PMID 22078099 DOI: 10.1186/1471-2229-11-159  1
2011 Jimenez RC, Salazar GA, Gel B, Dopazo J, Mulder N, Corpas M. myKaryoView: a light-weight client for visualization of genomic data. Plos One. 6: e26345. PMID 22046276 DOI: 10.1371/Journal.Pone.0026345  0.01
2011 De Baets G, Reumers J, Delgado Blanco J, Dopazo J, Schymkowitz J, Rousseau F. An evolutionary trade-off between protein turnover rate and protein aggregation favors a higher aggregation propensity in fast degrading proteins. Plos Computational Biology. 7: e1002090. PMID 21731483 DOI: 10.1371/Journal.Pcbi.1002090  1
2011 Sánchez R, Serra F, Tárraga J, Medina I, Carbonell J, Pulido L, de María A, Capella-Gutíerrez S, Huerta-Cepas J, Gabaldón T, Dopazo J, Dopazo H. Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. Nucleic Acids Research. 39: W470-4. PMID 21646336 DOI: 10.1093/Nar/Gkr408  1
2011 González-Pérez S, Gutiérrez J, García-García F, Osuna D, Dopazo J, Lorenzo Ó, Revuelta JL, Arellano JB. Early transcriptional defense responses in Arabidopsis cell suspension culture under high-light conditions. Plant Physiology. 156: 1439-56. PMID 21531897 DOI: 10.1104/Pp.111.177766  0.01
2011 Huerta-Cepas J, Dopazo J, Huynen MA, Gabaldón T. Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication. Briefings in Bioinformatics. 12: 442-8. PMID 21515902 DOI: 10.1093/Bib/Bbr022  1
2011 Trevino V, Tadesse MG, Vannucci M, Al-Shahrour F, Antczak P, Durant S, Bikfalvi A, Dopazo J, Campbell MJ, Falciani F. Analysis of normal-tumour tissue interaction in tumours: prediction of prostate cancer features from the molecular profile of adjacent normal cells. Plos One. 6: e16492. PMID 21479216 DOI: 10.1371/Journal.Pone.0016492  1
2011 Minguez P, Dopazo J. Assessing the biological significance of gene expression signatures and co-expression modules by studying their network properties. Plos One. 6: e17474. PMID 21408226 DOI: 10.1371/Journal.Pone.0017474  1
2011 Serra F, Arbiza L, Dopazo J, Dopazo H. Natural selection on functional modules, a genome-wide analysis. Plos Computational Biology. 7: e1001093. PMID 21390268 DOI: 10.1371/Journal.Pcbi.1001093  1
2011 Prieur X, Mok CY, Velagapudi VR, Núñez V, Fuentes L, Montaner D, Ishikawa K, Camacho A, Barbarroja N, O'Rahilly S, Sethi JK, Dopazo J, OreÅ¡ič M, Ricote M, Vidal-Puig A. Differential lipid partitioning between adipocytes and tissue macrophages modulates macrophage lipotoxicity and M2/M1 polarization in obese mice. Diabetes. 60: 797-809. PMID 21266330 DOI: 10.2337/Db10-0705  1
2010 Barragán I, Borrego S, Pieras JI, González-del Pozo M, Santoyo J, Ayuso C, Baiget M, Millan JM, Mena M, Abd El-Aziz MM, Audo I, Zeitz C, Littink KW, Dopazo J, Bhattacharya SS, et al. Mutation spectrum of EYS in Spanish patients with autosomal recessive retinitis pigmentosa. Human Mutation. 31: E1772-800. PMID 21069908 DOI: 10.1002/Humu.21334  1
2010 Galán A, Montaner D, Póo ME, Valbuena D, Ruiz V, Aguilar C, Dopazo J, Simón C. Functional genomics of 5- to 8-cell stage human embryos by blastomere single-cell cDNA analysis. Plos One. 5: e13615. PMID 21049019 DOI: 10.1371/Journal.Pone.0013615  1
2010 Al-Shahrour F, Minguez P, Marqués-Bonet T, Gazave E, Navarro A, Dopazo J. Selection upon genome architecture: conservation of functional neighborhoods with changing genes. Plos Computational Biology. 6: e1000953. PMID 20949098 DOI: 10.1371/Journal.Pcbi.1000953  1
2010 Bediaga NG, Acha-Sagredo A, Guerra I, Viguri A, Albaina C, Ruiz Diaz I, Rezola R, Alberdi MJ, Dopazo J, Montaner D, Renobales M, Fernández AF, Field JK, Fraga MF, Liloglou T, et al. DNA methylation epigenotypes in breast cancer molecular subtypes. Breast Cancer Research : Bcr. 12: R77. PMID 20920229 DOI: 10.1186/Bcr2721  1
2010 Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, Shaughnessy JD, Oberthuer A, Thomas RS, Paules RS, Fielden M, ... ... Dopazo J, et al. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nature Biotechnology. 28: 827-38. PMID 20676074 DOI: 10.1038/Nbt.1665  1
2010 Shi W, Bessarabova M, Dosymbekov D, Dezso Z, Nikolskaya T, Dudoladova M, Serebryiskaya T, Bugrim A, Guryanov A, Brennan RJ, Shah R, Dopazo J, Chen M, Deng Y, Shi T, et al. Functional analysis of multiple genomic signatures demonstrates that classification algorithms choose phenotype-related genes. The Pharmacogenomics Journal. 10: 310-23. PMID 20676069 DOI: 10.1038/Tpj.2010.35  1
2010 Nueda MJ, 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. 38: W239-45. PMID 20525784 DOI: 10.1093/Nar/Gkq488  1
2010 Medina I, Carbonell J, Pulido L, Madeira SC, Goetz S, Conesa A, Tárraga J, Pascual-Montano A, Nogales-Cadenas R, Santoyo J, García F, Marbà M, Montaner D, Dopazo J. Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Nucleic Acids Research. 38: W210-3. PMID 20478823 DOI: 10.1093/Nar/Gkq388  1
2010 Peña A, Teeling H, Huerta-Cepas J, Santos F, Yarza P, Brito-Echeverría J, Lucio M, Schmitt-Kopplin P, Meseguer I, Schenowitz C, Dossat C, Barbe V, Dopazo J, Rosselló-Mora R, Schüler M, et al. Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains. The Isme Journal. 4: 882-95. PMID 20164864 DOI: 10.1038/Ismej.2010.6  1
2010 Minguez P, Dopazo J. Functional genomics and networks: new approaches in the extraction of complex gene modules. Expert Review of Proteomics. 7: 55-63. PMID 20121476 DOI: 10.1586/Epr.09.103  1
2010 Huerta-Cepas J, Dopazo J, Gabaldón T. ETE: a python Environment for Tree Exploration. Bmc Bioinformatics. 11: 24. PMID 20070885 DOI: 10.1186/1471-2105-11-24  1
2010 Prado-Lopez S, Conesa A, Armiñán A, Martínez-Losa M, Escobedo-Lucea C, Gandia C, Tarazona S, Melguizo D, Blesa D, Montaner D, Sanz-González S, Sepúlveda P, Götz S, O'Connor JE, Moreno R, ... Dopazo J, et al. Hypoxia promotes efficient differentiation of human embryonic stem cells to functional endothelium. Stem Cells (Dayton, Ohio). 28: 407-18. PMID 20049902 DOI: 10.1002/Stem.295  1
2010 Javierre BM, Fernandez AF, Richter J, Al-Shahrour F, Martin-Subero JI, Rodriguez-Ubreva J, Berdasco M, Fraga MF, O'Hanlon TP, Rider LG, Jacinto FV, Lopez-Longo FJ, Dopazo J, Forn M, Peinado MA, et al. Changes in the pattern of DNA methylation associate with twin discordance in systemic lupus erythematosus. Genome Research. 20: 170-9. PMID 20028698 DOI: 10.1101/Gr.100289.109  1
2009 Nueda MJ, Sebastián P, Tarazona S, García-García F, Dopazo J, Ferrer A, Conesa A. Functional assessment of time course microarray data. Bmc Bioinformatics. 10: S9. PMID 19534758 DOI: 10.1186/1471-2105-10-S6-S9  1
2009 Minguez P, Götz S, Montaner D, Al-Shahrour F, Dopazo J. SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks. Nucleic Acids Research. 37: W109-14. PMID 19454602 DOI: 10.1093/Nar/Gkp402  1
2009 Montaner D, Minguez P, Al-Shahrour F, Dopazo J. Gene set internal coherence in the context of functional profiling. Bmc Genomics. 10: 197. PMID 19397819 DOI: 10.1186/1471-2164-10-197  1
2009 Dopazo J. Formulating and testing hypotheses in functional genomics Artificial Intelligence in Medicine. 45: 97-107. PMID 18789659 DOI: 10.1016/J.Artmed.2008.08.003  0.01
2009 Rocke DM, Ideker T, Troyanskaya O, Quackenbush J, Dopazo J. Papers on normalization, variable selection, classification or clustering of microarray data Bioinformatics. 25: 701-702. DOI: 10.1093/Bioinformatics/Btp038  1
2008 Horcajadas JA, Mínguez P, Dopazo J, Esteban FJ, Domínguez F, Giudice LC, Pellicer A, Simón C. Controlled ovarian stimulation induces a functional genomic delay of the endometrium with potential clinical implications. The Journal of Clinical Endocrinology and Metabolism. 93: 4500-10. PMID 18697870 DOI: 10.1210/Jc.2008-0588  0.01
2008 Conesa A, Bro R, García-García F, Prats JM, Götz S, Kjeldahl K, Montaner D, Dopazo J. Direct functional assessment of the composite phenotype through multivariate projection strategies. Genomics. 92: 373-83. PMID 18652888 DOI: 10.1016/J.Ygeno.2008.05.015  1
2008 Al-Shahrour F, Carbonell J, Minguez P, Goetz S, Conesa A, Tárraga J, Medina I, Alloza E, Montaner D, Dopazo J. Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments. Nucleic Acids Research. 36: W341-6. PMID 18515841 DOI: 10.1093/Nar/Gkn318  1
2008 Tárraga J, Medina I, Carbonell J, Huerta-Cepas J, Minguez P, Alloza E, Al-Shahrour F, Vegas-Azcárate S, Goetz S, Escobar P, Garcia-Garcia F, Conesa A, Montaner D, Dopazo J. GEPAS, a web-based tool for microarray data analysis and interpretation. Nucleic Acids Research. 36: W308-14. PMID 18508806 DOI: 10.1093/Nar/Gkn303  1
2008 Götz S, García-Gómez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, Robles M, Talón M, Dopazo J, Conesa A. High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Research. 36: 3420-35. PMID 18445632 DOI: 10.1093/Nar/Gkn176  1
2008 Saar K, Beck A, Bihoreau MT, Birney E, Brocklebank D, Chen Y, Cuppen E, Demonchy S, Dopazo J, Flicek P, Foglio M, Fujiyama A, Gut IG, Gauguier D, et al. SNP and haplotype mapping for genetic analysis in the rat. Nature Genetics. 40: 560-6. PMID 18443594 DOI: 10.1038/Ng.124  1
2008 Wilkinson MD, Senger M, Kawas E, Bruskiewich R, Gouzy J, Noirot C, Bardou P, Ng A, Haase D, Saiz Ede A, Wang D, Gibbons F, Gordon PM, Sensen CW, ... ... Dopazo J, et al. Interoperability with Moby 1.0--it's better than sharing your toothbrush! Briefings in Bioinformatics. 9: 220-31. PMID 18238804 DOI: 10.1093/Bib/Bbn003  1
2008 Reumers J, Conde L, Medina I, Maurer-Stroh S, Van Durme J, Dopazo J, Rousseau F, Schymkowitz J. Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases. Nucleic Acids Research. 36: D825-9. PMID 18086700 DOI: 10.1093/nar/gkm979  1
2008 Huerta-Cepas J, Bueno A, Dopazo J, Gabaldón T. PhylomeDB: a database for genome-wide collections of gene phylogenies. Nucleic Acids Research. 36: D491-6. PMID 17962297 DOI: 10.1093/Nar/Gkm899  1
2008 Capriotti E, Arbiza L, Casadio R, Dopazo J, Dopazo H, Marti-Renom MA. Use of estimated evolutionary strength at the codon level improves the prediction of disease-related protein mutations in humans Human Mutation. 29: 198-204. PMID 17935148 DOI: 10.1002/Humu.20628  1
2008 Montero-Conde C, Martín-Campos JM, Lerma E, Gimenez G, Martínez-Guitarte JL, Combalía N, Montaner D, Matías-Guiu X, Dopazo J, de Leiva A, Robledo M, Mauricio D. Molecular profiling related to poor prognosis in thyroid carcinoma. Combining gene expression data and biological information. Oncogene. 27: 1554-61. PMID 17873908 DOI: 10.1038/Sj.Onc.1210792  1
2007 Ruiz-Llorente S, Montero-Conde C, Milne RL, Moya CM, Cebrián A, Letón R, Cascón A, Mercadillo F, Landa I, Borrego S, Pérez de Nanclares G, Alvarez-Escolá C, Díaz-Pérez JA, Carracedo A, Urioste M, ... ... Dopazo J, et al. Association study of 69 genes in the ret pathway identifies low-penetrance loci in sporadic medullary thyroid carcinoma. Cancer Research. 67: 9561-7. PMID 17909067 DOI: 10.1158/0008-5472.Can-07-1638  1
2007 Minguez P, Al-Shahrour F, Montaner D, Dopazo J. Functional profiling of microarray experiments using text-mining derived bioentities. Bioinformatics (Oxford, England). 23: 3098-9. PMID 17855415 DOI: 10.1093/Bioinformatics/Btm445  1
2007 Hernández P, Huerta-Cepas J, Montaner D, Al-Shahrour F, Valls J, Gómez L, Capellá G, Dopazo J, Pujana MA. Evidence for systems-level molecular mechanisms of tumorigenesis. Bmc Genomics. 8: 185. PMID 17584915 DOI: 10.1186/1471-2164-8-185  1
2007 Marti-Renom MA, Rossi A, Al-Shahrour F, Davis FP, Pieper U, Dopazo J, Sali A. The AnnoLite and AnnoLyze programs for comparative annotation of protein structures. Bmc Bioinformatics. 8: S4. PMID 17570147 DOI: 10.1186/1471-2105-8-S4-S4  1
2007 Huerta-Cepas J, Dopazo H, Dopazo J, Gabaldón T. The human phylome. Genome Biology. 8: R109. PMID 17567924 DOI: 10.1186/Gb-2007-8-6-R109  1
2007 Marti-Renom MA, Pieper U, Madhusudhan MS, Rossi A, Eswar N, Davis FP, Al-Shahrour F, Dopazo J, Sali A. DBAli tools: mining the protein structure space. Nucleic Acids Research. 35: W393-7. PMID 17478513 DOI: 10.1093/Nar/Gkm236  1
2007 Al-Shahrour F, Minguez P, Tárraga J, Medina I, Alloza E, Montaner D, Dopazo J. FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. Nucleic Acids Research. 35: W91-6. PMID 17478504 DOI: 10.1093/Nar/Gkm260  1
2007 Tárraga J, Medina I, Arbiza L, Huerta-Cepas J, Gabaldón T, Dopazo J, Dopazo H. Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics. Nucleic Acids Research. 35: W38-42. PMID 17452346 DOI: 10.1093/Nar/Gkm224  1
2007 Al-Shahrour F, Arbiza L, Dopazo H, Huerta-Cepas J, Mínguez P, Montaner D, Dopazo J. From genes to functional classes in the study of biological systems. Bmc Bioinformatics. 8: 114. PMID 17407596 DOI: 10.1186/1471-2105-8-114  1
2007 Medina I, Montaner D, Tárraga J, Dopazo J. Prophet, a web-based tool for class prediction using microarray data Bioinformatics. 23: 390-391. PMID 17138587 DOI: 10.1093/Bioinformatics/Btl602  1
2006 Conde L, Vaquerizas JM, Dopazo H, Arbiza L, Reumers J, Rousseau F, Schymkowitz J, Dopazo J. PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes. Nucleic Acids Research. 34: W621-5. PMID 16845085 DOI: 10.1093/Nar/Gkl071  1
2006 Montaner D, Tárraga J, Huerta-Cepas J, Burguet J, Vaquerizas JM, Conde L, Minguez P, Vera J, Mukherjee S, Valls J, Pujana MA, Alloza E, Herrero J, Al-Shahrour F, Dopazo J. Next station in microarray data analysis: GEPAS. Nucleic Acids Research. 34: W486-91. PMID 16845056 DOI: 10.1093/Nar/Gkl197  1
2006 Al-Shahrour F, Minguez P, Tárraga J, Montaner D, Alloza E, Vaquerizas JM, Conde L, Blaschke C, Vera J, Dopazo J. BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments. Nucleic Acids Research. 34: W472-6. PMID 16845052 DOI: 10.1093/Nar/Gkl172  1
2006 Arbiza L, Dopazo J, Dopazo H. Positive selection, relaxation, and acceleration in the evolution of the human and chimp genome Plos Computational Biology. 2: 288-300. PMID 16683019 DOI: 10.1371/Journal.Pcbi.0020038  1
2006 Arbiza L, Duchi S, Montaner D, Burguet J, Pantoja-Uceda D, Pineda-Lucena A, Dopazo J, Dopazo H. Selective Pressures at a Codon-level Predict Deleterious Mutations in Human Disease Genes Journal of Molecular Biology. 358: 1390-1404. PMID 16584746 DOI: 10.1016/J.Jmb.2006.02.067  1
2006 Dopazo J, Aloy P. Discovery and hypothesis generation through bioinformatics. Genome Biology. 7: 307. PMID 16522224 DOI: 10.1186/Gb-2006-7-2-307  0.01
2006 Minguez P, Al-Shahrour F, Dopazo J. A function-centric approach to the biological interpretation of microarray time-series. Genome Informatics. 17: 57-66. DOI: 10.11234/Gi1990.17.2_57  1
2005 Vaquerizas JM, Conde L, Yankilevich P, Cabezón A, Minguez P, Díaz-Uriarte R, Al-Shahrour F, Herrero J, Dopazo J. GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data. Nucleic Acids Research. 33: W616-20. PMID 15980548 DOI: 10.1093/Nar/Gki500  1
2005 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 Research. 33: W460-4. PMID 15980512 DOI: 10.1093/Nar/Gki456  1
2005 Dopazo H, Dopazo J. Genome-scale evidence of the nematode-arthropod clade Genome Biology. 6: R41. PMID 15892869 DOI: 10.1186/Gb-2005-6-5-R41  1
2005 Al-Shahrour F, Díaz-Uriarte R, Dopazo J. Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information. Bioinformatics (Oxford, England). 21: 2988-93. PMID 15840702 DOI: 10.1093/Bioinformatics/Bti457  1
2005 Palacios J, Honrado E, Osorio A, Cazorla A, Sarrió D, Barroso A, Rodríguez S, Cigudosa JC, Diez O, Alonso C, Lerma E, Dopazo J, Rivas C, Benítez J. Phenotypic characterization of BRCA1 and BRCA2 tumors based in a tissue microarray study with 37 immunohistochemical markers. Breast Cancer Research and Treatment. 90: 5-14. PMID 15770521 DOI: 10.1007/S10549-004-1536-0  1
2005 Cascón A, Ruiz-Llorente S, Rodríguez-Perales S, Honrado E, Martínez-Ramírez A, Letón R, Montero-Conde C, Benítez J, Dopazo J, Cigudosa JC, Robledo M. A novel candidate region linked to development of both pheochromocytoma and head/neck paraganglioma. Genes, Chromosomes & Cancer. 42: 260-8. PMID 15609347 DOI: 10.1002/Gcc.20139  1
2005 Arbiza L, Dopazo J, Dopazo HJ. Differentiating Positive Selection from Acceleration and Relaxation in Human and Chimp Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.0020038.Eor  1
2004 Meléndez B, Díaz-Uriarte R, Cuadros M, Martínez-Ramírez A, Fernández-Piqueras J, Dopazo A, Cigudosa JC, Rivas C, Dopazo J, Martínez-Delgado B, Benítez J. Gene expression analysis of chromosomal regions with gain or loss of genetic material detected by comparative genomic hybridization. Genes, Chromosomes & Cancer. 41: 353-65. PMID 15382261 DOI: 10.1002/Gcc.20105  1
2004 Dopazo H, Santoyo J, Dopazo J. Phylogenomics and the number of characters required for obtaining an accurate phylogeny of eukaryote model species Bioinformatics. 20: i116-i121. PMID 15262789 DOI: 10.1093/bioinformatics/bth902  1
2004 Vaquerizas JM, Dopazo J, Díaz-Uriarte R. DNMAD: web-based diagnosis and normalization for microarray data. Bioinformatics (Oxford, England). 20: 3656-8. PMID 15247094 DOI: 10.1093/Bioinformatics/Bth401  1
2004 Herrero J, Vaquerizas JM, Al-Shahrour F, Conde L, Mateos A, Díaz-Uriarte JS, Dopazo J. New challenges in gene expression data analysis and the extended GEPAS. Nucleic Acids Research. 32: W485-91. PMID 15215434 DOI: 10.1093/Nar/Gkh421  1
2004 Al-Shahrour F, Díaz-Uriarte R, Dopazo J. FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics (Oxford, England). 20: 578-80. PMID 14990455 DOI: 10.1093/Bioinformatics/Btg455  1
2003 Herrero J, Díaz-Uriarte R, Dopazo J. An approach to inferring transcriptional regulation among genes from large-scale expression data. Comparative and Functional Genomics. 4: 148-54. PMID 18629097 DOI: 10.1002/Cfg.237  1
2003 Herrero J, Al-Shahrour F, Díaz-Uriarte R, Mateos A, Vaquerizas JM, Santoyo J, Dopazo J. GEPAS: A web-based resource for microarray gene expression data analysis. Nucleic Acids Research. 31: 3461-7. PMID 12824345 DOI: 10.1093/Nar/Gkg591  1
2003 Martin MJ, Herrero J, Mateos A, Dopazo J. Comparing bacterial genomes through conservation profiles. Genome Research. 13: 991-8. PMID 12695324 DOI: 10.1101/Gr.678303  1
2003 Herrero J, Díaz-Uriarte R, Dopazo J. Gene expression data preprocessing. Bioinformatics (Oxford, England). 19: 655-6. PMID 12651726 DOI: 10.1093/Bioinformatics/Btg040  1
2003 Karzynski M, Mateos Á, Herrero J, Dopazo J. Using a Genetic Algorithm and a Perceptron forFeature Selection and Supervised Class Learningin DNA Microarray Data Artificial Intelligence Review. 20: 39-51. DOI: 10.1023/A:1026032530166  1
2002 Herrero J, Dopazo J. Combining hierarchical clustering and self-organizing maps for exploratory analysis of gene expression patterns. Journal of Proteome Research. 1: 467-70. PMID 12645919 DOI: 10.1021/Pr025521V  1
2002 Mateos A, Dopazo J, Jansen R, Tu Y, Gerstein M, Stolovitzky G. Systematic learning of gene functional classes from DNA array expression data by using multilayer perceptrons. Genome Research. 12: 1703-15. PMID 12421757 DOI: 10.1101/Gr.192502  1
2002 Tracey L, Villuendas R, Ortiz P, Dopazo A, Spiteri I, Lombardia L, Rodríguez-Peralto JL, Fernández-Herrera J, Hernández A, Fraga J, Dominguez O, Herrero J, Alonso MA, Dopazo J, Piris MA. Identification of genes involved in resistance to interferon-alpha in cutaneous T-cell lymphoma. The American Journal of Pathology. 161: 1825-37. PMID 12414529 DOI: 10.1016/S0002-9440(10)64459-8  1
2002 Tamames J, Clark D, Herrero J, Dopazo J, Blaschke C, Fernández JM, Oliveros JC, Valencia A. Bioinformatics methods for the analysis of expression arrays: data clustering and information extraction. Journal of Biotechnology. 98: 269-83. PMID 12141992 DOI: 10.1016/S0168-1656(02)00137-2  1
2001 Elena SF, Dopazo J, Peña M, Flores R, Diener TO, Moya A. Phylogenetic analysis of viroid and viroid-like satellite RNAs from plants: A reassessment Journal of Molecular Evolution. 53: 155-159. PMID 11479686 DOI: 10.1007/S002390010203  1
2001 Dopazo J, Mendoza A, Herrero J, Caldara F, Humbert Y, Friedli L, Guerrier M, Grand-Schenk E, Gandin C, de Francesco M, Polissi A, Buell G, Feger G, García E, Peitsch M, et al. Annotated draft genomic sequence from a Streptococcus pneumoniae type 19F clinical isolate. Microbial Drug Resistance (Larchmont, N.Y.). 7: 99-125. PMID 11442348 DOI: 10.1089/10766290152044995  1
2001 Herrero J, Valencia A, Dopazo J. A hierarchical unsupervised growing neural network for clustering gene expression patterns. Bioinformatics (Oxford, England). 17: 126-36. PMID 11238068 DOI: 10.1093/Bioinformatics/17.2.126  1
2000 Oliveros JC, Blaschke C, Herrero J, Dopazo J, Valencia A. Expression profiles and biological function. Genome Informatics. Workshop On Genome Informatics. 11: 106-17. PMID 11700592  1
2000 Oliveros JC, Blaschke C, Herrero J, Dopazo J, Valencia A. Expression profiles and biological function. Genome Informatics. 11: 106-117. DOI: 10.11234/Gi1990.11.106  1
1998 Núñez JI, Blanco E, Hernández T, Dopazo J, Sobrino F. RT-PCR in foot-and-mouth. The Veterinary Quarterly. 20: 34-36. PMID 22077295 DOI: 10.1080/01652176.1998.9694963  1
1998 Blanco-Urgoiti B, Sánchez F, Pérez de San Román C, Dopazo J, Ponz F. Potato virus Y group C isolates are a homogeneous pathotype but two different genetic strains. The Journal of General Virology. 79: 2037-42. PMID 9714255 DOI: 10.1099/0022-1317-79-8-2037  0.01
1998 Núñez JI, Blanco E, Hernández T, Gómez-Tejedor C, Martín MJ, Dopazo J, Sobrino F. A RT-PCR assay for the differential diagnosis of vesicular viral diseases of swine. Journal of Virological Methods. 72: 227-35. PMID 9694330 DOI: 10.1016/S0166-0934(98)00032-9  1
1998 Sáiz J, López-Labrador F, Ampurdanés S, Dopazo J, Forns X, Sánchez-Tapias J, Rodés J. The Prognostic Relevance of the Nonstructural 5A Gene Interferon Sensitivity Determining Region Is Different in Infections with Genotype 1b and 3a Isolates of Hepatitis C Virus The Journal of Infectious Diseases. 177: 839-847. PMID 9534954 DOI: 10.1086/515243  0.01
1996 Blanco-Urgoiti B, Sánchez F, Dopazo J, Ponz F. A strain-type clustering of potato virus Y based on the genetic distance between isolates calculated by RFLP analysis of the amplified coat protein gene. Archives of Virology. 141: 2425-42. PMID 9526547 DOI: 10.1007/bf01718641  0.01
1996 Quiñones-Mateu ME, Holguín A, Dopazo J, Nájera I, Domingo E. Point mutant frequencies in the pol gene of human immunodeficiency virus type 1 are two- to threefold lower than those of env. Aids Research and Human Retroviruses. 12: 1117-28. PMID 8844016 DOI: 10.1089/Aid.1996.12.1117  1
1996 Suárez P, Zardoya R, Martín MJ, Prieto C, Dopazo J, Solana A, Castro JM. Phylogenetic relationships of european strains of porcine reproductive and respiratory syndrome virus (PRRSV) inferred from DNA sequences of putative ORF-5 and ORF-7 genes. Virus Research. 42: 159-65. PMID 8806183 DOI: 10.1016/0168-1702(95)01305-9  1
1995 Martin MJ, González-Candelas F, Sobrino F, Dopazo J. A method for determining the position and size of optimal sequence regions for phylogenetic analysis. Journal of Molecular Evolution. 41: 1128-38. PMID 8587110  1
1995 Rojas JM, Dopazo J, Santana M, López-Galíndez C, Tabarés E. Comparative study of the genetic variability in thymidine kinase and glycoprotein B genes of herpes simplex viruses by the RNase A mismatch cleavage method. Virus Research. 35: 205-14. PMID 7762293 DOI: 10.1016/0168-1702(94)00097-V  0.01
1995 Trelles-Salazar O, Zapata EL, Dopazo J, Coulson AF, Carazo JM. An image-processing approach to dotplots: an X-Window-based program for interactive analysis of dotplots derived from sequence and structural data. Computer Applications in the Biosciences : Cabios. 11: 301-8. PMID 7583699 DOI: 10.1093/bioinformatics/11.3.301  0.01
1993 Rojas JM, Dopazo J, Martín-Blanco E, López-Galíndez C, Tabarés E. Analysis of genetic variability of populations of herpes simplex viruses. Virus Research. 28: 249-61. PMID 8394041 DOI: 10.1016/0168-1702(93)90025-I  0.01
1993 Dopazo J, Dress A, Haeseler Av. Split decomposition: a technique to analyze viral evolution. Proceedings of the National Academy of Sciences of the United States of America. 90: 10320-10324. PMID 8234292 DOI: 10.1073/Pnas.90.21.10320  0.01
1993 Dopazo J, Taberner A, Moya A. Quantitative characterization of antigens using monoclonal antibody reactivities. Bioinformatics. 9: 101-107. PMID 7679608 DOI: 10.1093/Bioinformatics/9.1.101  1
1992 Sánchez CM, Gebauer F, Suñé C, Mendez A, Dopazo J, Enjuanes L. Genetic evolution and tropism of transmissible gastroenteritis coronaviruses. Virology. 190: 92-105. PMID 1326823 DOI: 10.1016/0042-6822(92)91195-Z  0.01
1991 Elena SF, Dopazo J, Flores R, Diener TO, Moya A. Phylogeny of viroids, viroidlike satellite RNAs, and the viroidlike domain of hepatitis δ virus RNA Proceedings of the National Academy of Sciences of the United States of America. 88: 5631-5634. PMID 1712103 DOI: 10.1073/Pnas.88.13.5631  1
1990 Dopazo J. Multiple sequence editing by spreadsheet. Bioinformatics. 6: 401-402. PMID 2257503 DOI: 10.1093/Bioinformatics/6.4.401  0.01
1988 Dopazo J. Reducing the effect of the data order in algorithms for constructing phylogenetic trees Bioinformatics. 4: 307-307. PMID 3167606 DOI: 10.1093/Bioinformatics/4.2.307  0.01
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