| Year |
Citation |
Score |
| 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 |
0.35 |
|
| 2020 |
Wang H, Azuaje F, Bodenreider O, Dopazo J. Gene Expression Correlation and Gene Ontology-Based Similarity: An Assessment of Quantitative Relationships. Proceedings of the ... Ieee Symposium On Computational Intelligence in Bioinformatics and Computational Biology : Cibcb. Ieee Symposium On Computational Intelligence in Bioinformatics and Computational Biology. 2004: 25-31. PMID 25664345 DOI: 10.1109/CIBCB.2004.1393927 |
0.317 |
|
| 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 |
0.408 |
|
| 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 |
0.383 |
|
| 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 |
0.34 |
|
| 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 |
0.355 |
|
| 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 |
0.314 |
|
| 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 |
0.344 |
|
| 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 |
0.312 |
|
| 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 |
0.376 |
|
| 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 |
0.305 |
|
| 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 |
0.323 |
|
| 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 |
0.301 |
|
| 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 |
0.338 |
|
| 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 |
0.319 |
|
| 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 |
0.369 |
|
| 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 |
0.356 |
|
| 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 |
0.405 |
|
| 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 |
0.303 |
|
| 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 |
0.302 |
|
| 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 |
0.334 |
|
| 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 |
0.368 |
|
| 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 |
0.346 |
|
| 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 |
0.315 |
|
| 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 |
0.333 |
|
| 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 |
0.363 |
|
| 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 |
0.348 |
|
| 2016 |
Alic AS, Ruzafa D, Dopazo J, Blanquer I. Objective review ofde novostand-alone error correction methods for NGS data Wiley Interdisciplinary Reviews: Computational Molecular Science. 6: 111-146. DOI: 10.1002/Wcms.1239 |
0.31 |
|
| 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 |
0.307 |
|
| 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 |
0.392 |
|
| 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 |
0.342 |
|
| 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 |
0.324 |
|
| 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 |
0.36 |
|
| 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 |
0.305 |
|
| 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 |
0.349 |
|
| 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 |
0.396 |
|
| 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 |
0.421 |
|
| 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 |
0.332 |
|
| 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 |
0.358 |
|
| 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 |
0.394 |
|
| 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 |
0.302 |
|
| 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 |
0.311 |
|
| 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 |
0.364 |
|
| 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 |
0.329 |
|
| 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 |
0.432 |
|
| 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 |
0.36 |
|
| 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 |
0.353 |
|
| 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 |
0.351 |
|
| 2014 |
Puig-Butille JA, Escámez MJ, Garcia-Garcia F, Tell-Marti G, Fabra À, MartÃnez-SantamarÃa L, Badenas C, Aguilera P, Pevida M, Dopazo J, del RÃo 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 |
0.375 |
|
| 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 |
0.346 |
|
| 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 |
0.318 |
|
| 2014 |
Larriba E, Jaime MD, Carbonell-Caballero J, Conesa A, Dopazo J, Nislow C, MartÃn-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 |
0.379 |
|
| 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 |
0.355 |
|
| 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 |
0.314 |
|
| 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 |
0.325 |
|
| 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 |
0.37 |
|
| 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 |
0.369 |
|
| 2013 |
Gonzalez-Tendero A, Torre I, Garcia-Canadilla P, Crispi F, GarcÃa-GarcÃa 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 |
0.317 |
|
| 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 |
0.372 |
|
| 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 |
0.336 |
|
| 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 |
0.3 |
|
| 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 |
0.378 |
|
| 2013 |
Silbiger VN, Luchessi AD, Hirata RD, Lima-Neto LG, Cavichioli D, Carracedo A, Brión M, Dopazo J, GarcÃa-GarcÃa 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 |
0.335 |
|
| 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 |
0.387 |
|
| 2013 |
Rueda A, López FJ, Pérez J, Arce P, Cruz LM, Carbonell J, Jiménez-Almazán J, Vidal E, Antiñolo G, Dopazo J, Santoyo J. Analysis pipeline for the detection of mutations causative of rare diseases on whole exome sequencing data Embnet.Journal. 19: 79. DOI: 10.14806/Ej.19.A.647 |
0.336 |
|
| 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 |
0.336 |
|
| 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 |
0.414 |
|
| 2012 |
Fernandez P, Soria M, Blesa D, DiRienzo J, Moschen S, Rivarola M, Clavijo BJ, Gonzalez S, Peluffo L, PrÃncipi D, Dosio G, Aguirrezabal L, GarcÃa-GarcÃa 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 |
0.423 |
|
| 2012 |
GarcÃa-Alonso L, Alonso R, Vidal E, Amadoz A, de MarÃa 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 |
0.386 |
|
| 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 |
0.345 |
|
| 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 |
0.379 |
|
| 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 |
0.346 |
|
| 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 |
0.323 |
|
| 2012 |
Tarazona S, García F, Ferrer A, Dopazo J, Conesa A. NOIseq: a RNA-seq differential expression method robust for sequencing depth biases Embnet.Journal. 17: 18. DOI: 10.14806/Ej.17.B.265 |
0.391 |
|
| 2012 |
Tarazona S, Prado-López S, Dopazo J, Ferrer A, Conesa A. Variable selection for multifactorial genomic data Chemometrics and Intelligent Laboratory Systems. 110: 113-122. DOI: 10.1016/J.Chemolab.2011.10.012 |
0.388 |
|
| 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 |
0.352 |
|
| 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 |
0.42 |
|
| 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 |
0.355 |
|
| 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 |
0.32 |
|
| 2011 |
Durban J, Juárez P, Angulo Y, Lomonte B, Flores-Diaz M, Alape-Girón A, Sasa M, Sanz L, Gutiérrez JM, Dopazo J, Conesa A, Calvete JJ. Profiling the venom gland transcriptomes of Costa Rican snakes by 454 pyrosequencing. Bmc Genomics. 12: 259. PMID 21605378 DOI: 10.1186/1471-2164-12-259 |
0.318 |
|
| 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 |
0.403 |
|
| 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 |
0.33 |
|
| 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 |
0.403 |
|
| 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 |
0.375 |
|
| 2011 |
Tarazona S, Garcia-Alcalde F, Dopazo J, Ferrer A, Conesa A. Differential expression in RNA-seq: A matter of depth Genome Research. 21: 2213-2223. DOI: 10.1101/Gr.124321.111 |
0.351 |
|
| 2011 |
Cárdaba B, Aguerri M, Florido F, Montaner D, Mata M, López-Cacho J, Gallardo S, Dopazo J, Lahoz C. Gene-expression Profiling And Differential Pathways In The Sensitization And Tolerance To Allergens Journal of Allergy and Clinical Immunology. 127: AB263-AB263. DOI: 10.1016/J.Jaci.2010.12.1049 |
0.365 |
|
| 2010 |
Bonifaci N, Górski B, Masojć B, Wokołorczyk D, Jakubowska A, Dębniak T, Berenguer A, Serra Musach J, Brunet J, Dopazo J, Narod SA, Lubiński J, Lázaro C, Cybulski C, Pujana MA. Exploring the link between germline and somatic genetic alterations in breast carcinogenesis. Plos One. 5: e14078. PMID 21124932 DOI: 10.1371/Journal.Pone.0014078 |
0.323 |
|
| 2010 |
García-Alcalde F, García-López F, Dopazo J, Conesa A. Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data. Bioinformatics (Oxford, England). 27: 137-9. PMID 21098431 DOI: 10.1093/Bioinformatics/Btq594 |
0.339 |
|
| 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 |
0.317 |
|
| 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 |
0.325 |
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| 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 |
0.402 |
|
| 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 |
0.331 |
|
| 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 |
0.419 |
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| 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 |
0.413 |
|
| 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 |
0.428 |
|
| 2010 |
Montaner D, Dopazo J. Multidimensional gene set analysis of genomic data. Plos One. 5: e10348. PMID 20436964 DOI: 10.1371/journal.pone.0010348 |
0.335 |
|
| 2010 |
Németh A, Conesa A, Santoyo-Lopez J, Medina I, Montaner D, Péterfia B, Solovei I, Cremer T, Dopazo J, Längst G. Initial genomics of the human nucleolus. Plos Genetics. 6: e1000889. PMID 20361057 DOI: 10.1371/Journal.Pgen.1000889 |
0.379 |
|
| 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 |
0.366 |
|
| 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 |
0.314 |
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| 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 |
0.324 |
|
| 2010 |
Dopazo J. Functional profiling methods in cancer. Methods in Molecular Biology (Clifton, N.J.). 576: 363-74. PMID 19882272 DOI: 10.1007/978-1-59745-545-9_19 |
0.318 |
|
| 2010 |
Aggarwal M, Sánchez-Beato M, Gómez-López G, Al-Shahrour F, Martínez N, Rodríguez A, Ruiz-Ballesteros E, Camacho FI, Pérez-Rosado A, de la Cueva P, Artiga MJ, Pisano DG, Kimby E, Dopazo J, Villuendas R, et al. Functional signatures identified in B-cell non-Hodgkin lymphoma profiles. Leukemia & Lymphoma. 50: 1699-708. PMID 19863341 DOI: 10.1080/10428190903189035 |
0.351 |
|
| 2010 |
Montaner D, Dopazo J. Multidimensional Gene Set Analysis of Genomic Data Plos One. 5: e10348. DOI: 10.1371/Journal.Pone.0010348 |
0.443 |
|
| 2009 |
Nueda MJ, Sebastián P, Tarazona S, GarcÃa-GarcÃa 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 |
0.405 |
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| 2009 |
Medina I, Montaner D, Bonifaci N, Pujana MA, Carbonell J, Tarraga J, Al-Shahrour F, Dopazo J. Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies. Nucleic Acids Research. 37: W340-4. PMID 19502494 DOI: 10.1093/Nar/Gkp481 |
0.41 |
|
| 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 |
0.425 |
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| 2009 |
Nobre LS, Al-Shahrour F, Dopazo J, Saraiva LM. Exploring the antimicrobial action of a carbon monoxide-releasing compound through whole-genome transcription profiling of Escherichia coli. Microbiology (Reading, England). 155: 813-824. PMID 19246752 DOI: 10.1099/Mic.0.023911-0 |
0.339 |
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| 2009 |
Jantus Lewintre E, Reinoso Martín C, Montaner D, Marín M, José Terol M, Farrás R, Benet I, Calvete JJ, Dopazo J, García-Conde J. Analysis of chronic lymphotic leukemia transcriptomic profile: differences between molecular subgroups. Leukemia & Lymphoma. 50: 68-79. PMID 19127482 DOI: 10.1080/10428190802541807 |
0.376 |
|
| 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 |
0.415 |
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| 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 |
0.372 |
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| 2008 |
Bonifaci N, Berenguer A, Díez J, Reina O, Medina I, Dopazo J, Moreno V, Pujana MA. Biological processes, properties and molecular wiring diagrams of candidate low-penetrance breast cancer susceptibility genes. Bmc Medical Genomics. 1: 62. PMID 19094230 DOI: 10.1186/1755-8794-1-62 |
0.39 |
|
| 2008 |
Dopazo J, Al-Shahrour F. Expression and microarrays. Methods in Molecular Biology (Clifton, N.J.). 453: 245-55. PMID 18712307 DOI: 10.1007/978-1-60327-429-6_12 |
0.409 |
|
| 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 |
0.35 |
|
| 2008 |
Conesa A, Bro R, GarcÃa-GarcÃa 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 |
0.368 |
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| 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 |
0.393 |
|
| 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 |
0.394 |
|
| 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 |
0.399 |
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| 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 |
0.391 |
|
| 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 |
0.326 |
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| 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 |
0.354 |
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| 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 |
0.346 |
|
| 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 |
0.395 |
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| 2007 |
Valls J, Grau M, Solé X, Hernández P, Montaner D, Dopazo J, Peinado MA, Capellá G, Moreno V, Pujana MA. CLEAR-test: combining inference for differential expression and variability in microarray data analysis. Journal of Biomedical Informatics. 41: 33-45. PMID 17597009 DOI: 10.1016/J.Jbi.2007.05.005 |
0.351 |
|
| 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 |
0.395 |
|
| 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 |
0.407 |
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| 2007 |
Conde L, Montaner D, Burguet-Castell J, Tárraga J, Medina I, Al-Shahrour F, Dopazo J. ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling. Nucleic Acids Research. 35: W81-5. PMID 17468499 DOI: 10.1093/Nar/Gkm257 |
0.435 |
|
| 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 |
0.38 |
|
| 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 |
0.427 |
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| 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 |
0.357 |
|
| 2007 |
Milne RL, Ribas G, González-Neira A, Fagerholm R, Salas A, González E, Dopazo J, Nevanlinna H, Robledo M, Benítez J. ERCC4 associated with breast cancer risk: a two-stage case-control study using high-throughput genotyping. Cancer Research. 66: 9420-7. PMID 17018596 DOI: 10.1158/0008-5472.Can-06-1418 |
0.311 |
|
| 2007 |
Horcajadas J, Minguez P, Dopazo J, Esteban F, Pellicer A, Simon C. Gene expression analysis of the endometrium reveals that controlled ovarian stimulation induces a genomic delay with potential clinical implications Fertility and Sterility. 88: S43-S44. DOI: 10.1016/J.Fertnstert.2007.07.153 |
0.366 |
|
| 2006 |
Dopazo J. Functional interpretation of microarray experiments. Omics : a Journal of Integrative Biology. 10: 398-410. PMID 17069516 DOI: 10.1089/Omi.2006.10.398 |
0.407 |
|
| 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 |
0.633 |
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| 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 |
0.388 |
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| 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 |
0.364 |
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| 2006 |
Azuaje F, Al-Shahrour F, Dopazo J. Ontology-driven approaches to analyzing data in functional genomics. Methods in Molecular Biology (Clifton, N.J.). 316: 67-86. PMID 16671401 DOI: 10.1385/1-59259-964-8:67 |
0.421 |
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| 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 |
0.352 |
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| 2006 |
Aggarwal M, Villuendas R, Al-Shahrour F, Aguilera AS, Martinez N, Ballesteros ER, Camacho FI, Perez A, Artiga MJ, Garcia-Marco JA, Dopazo J, Piris MA. Transcriptome Classification of B-Cell Non-Hodgkins Lymphoma. Blood. 108: 819-819. DOI: 10.1182/Blood.V108.11.819.819 |
0.399 |
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| 2006 |
Lewintre EJ, Marin M, Reinoso C, Montaner D, Dopazo J, Calvete JJ, Garcia-Conde J. Analysis of B-CLL Transcriptomic and Proteomic Profiles: Differences between Molecular Subgroups. Blood. 108: 2088-2088. DOI: 10.1182/Blood.V108.11.2088.2088 |
0.399 |
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| 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 |
0.392 |
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| 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 |
0.623 |
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| 2005 |
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 Research. 33: W501-5. PMID 15980522 DOI: 10.1093/Nar/Gki476 |
0.34 |
|
| 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 |
0.418 |
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| 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 |
0.349 |
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| 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 |
0.446 |
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| 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 |
0.332 |
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| 2005 |
Hoffmann R, Dopazo J, Cigudosa JC, Valencia A. HCAD, closing the gap between breakpoints and genes. Nucleic Acids Research. 33: D511-3. PMID 15608250 DOI: 10.1093/Nar/Gki061 |
0.377 |
|
| 2005 |
Marin M, Jantus-Lewintre E, Sanz L, Garcia-Martin A, Reinoso C, Benet I, Montaner D, Vaquerizas JM, Dopazo J, Calvete JJ, Garcia-Conde J. Characterization of the Proteomic and Genomic Profiles of Chronic Lymphocytic Leukemia Patients with Distinct Clinical Prognosis According to the Mutational Status of the IgVH and BCL6 and Expression Level of CD38 and ZAP70. Blood. 106: 3272-3272. DOI: 10.1182/Blood.V106.11.3272.3272 |
0.405 |
|
| 2004 |
Santoyo J, Vaquerizas JM, Dopazo J. Highly specific and accurate selection of siRNAs for high-throughput functional assays. Bioinformatics (Oxford, England). 21: 1376-82. PMID 15591357 DOI: 10.1093/Bioinformatics/Bti196 |
0.367 |
|
| 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 |
0.409 |
|
| 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 |
0.35 |
|
| 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 |
0.643 |
|
| 2004 |
Conde L, Vaquerizas JM, Santoyo J, Al-Shahrour F, Ruiz-Llorente S, Robledo M, Dopazo J. PupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level. Nucleic Acids Research. 32: W242-8. PMID 15215388 DOI: 10.1093/Nar/Gkh438 |
0.353 |
|
| 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 |
0.406 |
|
| 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 |
0.605 |
|
| 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 |
0.624 |
|
| 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 |
0.619 |
|
| 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 |
0.58 |
|
| 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 |
0.569 |
|
| 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 |
0.539 |
|
| 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 |
0.35 |
|
| 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 |
0.562 |
|
| 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 |
0.583 |
|
| 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 |
0.51 |
|
| 2001 |
Dopazo J, Zanders E, Dragoni I, Amphlett G, Falciani F. Methods and approaches in the analysis of gene expression data. Journal of Immunological Methods. 250: 93-112. PMID 11251224 DOI: 10.1016/S0022-1759(01)00307-6 |
0.44 |
|
| 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 |
0.524 |
|
| 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 |
0.566 |
|
| 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 |
0.404 |
|
| 1998 |
Martín MJ, Núñez JI, Sobrino F, Dopazo J. A procedure for detecting selection in highly variable viral genomes: evidence of positive selection in antigenic regions of capsid protein VP1 of foot-and-mouth disease virus. Journal of Virological Methods. 74: 215-21. PMID 9779622 DOI: 10.1016/S0166-0934(98)00088-3 |
0.301 |
|
| 1994 |
Dopazo J, Sobrino F, López-Galíndez C. Estimates by computer simulation of genetic distances from comparisons of RNAse A mismatch cleavage patterns. Journal of Virological Methods. 45: 73-82. PMID 8270657 DOI: 10.1016/0166-0934(93)90141-D |
0.326 |
|
| 1991 |
Peñalva MA, Moya A, Dopazo J, Ramón D. Sequences of isopenicillin N synthetase genes suggest horizontal gene transfer from prokaryotes to eukaryotes. Proceedings. Biological Sciences. 241: 164-9. PMID 1979440 DOI: 10.1098/Rspb.1990.0081 |
0.373 |
|
| 1991 |
Villaverde A, Martínez MA, Sobrino F, Dopazo J, Moya A, Domingo E. Fixation of mutations at the VP1 gene of foot-and-mouth disease virus. Can quasispecies define a transient molecular clock? Gene. 103: 147-53. PMID 1653754 DOI: 10.1016/0378-1119(91)90267-F |
0.331 |
|
| 1988 |
Dopazo J, Sobrino F, Palma EL, Domingo E, Moya A. Gene encoding capsid protein VP1 of foot-and-mouth disease virus: a quasispecies model of molecular evolution. Proceedings of the National Academy of Sciences of the United States of America. 85: 6811-5. PMID 2842792 DOI: 10.1073/Pnas.85.18.6811 |
0.356 |
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