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Alfonso Valencia - Publications

Centro Nacional de Biotecnología, Madrid, Comunidad de Madrid, Spain 

285 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 Rajewsky N, Almouzni G, Gorski SA, Aerts S, Amit I, Bertero MG, Bock C, Bredenoord AL, Cavalli G, Chiocca S, Clevers H, De Strooper B, Eggert A, Ellenberg J, Fernández XM, ... ... Valencia A, et al. Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine. Nature. PMID 33731935 DOI: 10.1038/s41586-021-03287-8  0.32
2021 Santus E, Marino N, Cirillo D, Chersoni E, Montagud A, Santuccione Chada A, Valencia A, Hughes K, Lindvall C. AI-aided Precision Medicine against COVID-19: Strategic Areas of Research and Development. Journal of Medical Internet Research. PMID 33560998 DOI: 10.2196/22453  1
2021 Cirillo D, Núñez-Carpintero I, Valencia A. Artificial Intelligence in Cancer Research: learning at different levels of data granularity. Molecular Oncology. PMID 33533192 DOI: 10.1002/1878-0261.12920  1
2021 Delso G, Cirillo D, Kaggie JD, Valencia A, Metser U, Veit-Haibach P. How to Design AI-Driven Clinical Trials in Nuclear Medicine. Seminars in Nuclear Medicine. 51: 112-119. PMID 33509367 DOI: 10.1053/j.semnuclmed.2020.09.003  1
2021 Ehrhart F, Jacobsen A, Rigau M, Bosio M, Kaliyaperumal R, Laros JFJ, Willighagen EL, Valencia A, Roos M, Capella-Gutierrez S, Curfs LMG, Evelo CT. A catalogue of 863 Rett-syndrome-causing MECP2 mutations and lessons learned from data integration. Scientific Data. 8: 10. PMID 33452270 DOI: 10.1038/s41597-020-00794-7  0.36
2021 Ferrari A, Santus E, Cirillo D, Ponce-de-Leon M, Marino N, Ferretti MT, Santuccione Chadha A, Mavridis N, Valencia A. Simulating SARS-CoV-2 epidemics by region-specific variables and modeling contact tracing app containment. Npj Digital Medicine. 4: 9. PMID 33446891 DOI: 10.1038/s41746-020-00374-4  1
2020 Cirillo D, Catuara-Solarz S, Morey C, Guney E, Subirats L, Mellino S, Gigante A, Valencia A, Rementeria MJ, Chadha AS, Mavridis N. Sex and gender differences and biases in artificial intelligence for biomedicine and healthcare. Npj Digital Medicine. 3: 81. PMID 33597695 DOI: 10.1038/s41746-020-0288-5  1
2020 Rajewsky N, Almouzni G, Gorski SA, Aerts S, Amit I, Bertero MG, Bock C, Bredenoord AL, Cavalli G, Chiocca S, Clevers H, De Strooper B, Eggert A, Ellenberg J, Fernández XM, ... ... Valencia A, et al. LifeTime and improving European healthcare through cell-based interceptive medicine. Nature. PMID 32894860 DOI: 10.1038/s41586-020-2715-9  0.32
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, ... ... Valencia A, 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  0.68
2020 Goldman MJ, Zhang J, Fonseca NA, Cortés-Ciriano I, Xiang Q, Craft B, Piñeiro-Yáñez E, O'Connor BD, Bazant W, Barrera E, Muñoz-Pomer A, Petryszak R, Füllgrabe A, Al-Shahrour F, Keays M, ... ... Valencia A, et al. A user guide for the online exploration and visualization of PCAWG data. Nature Communications. 11: 3400. PMID 32636365 DOI: 10.1038/s41467-020-16785-6  0.32
2020 Cirillo D, Catuara-Solarz S, Morey C, Guney E, Subirats L, Mellino S, Gigante A, Valencia A, Rementeria MJ, Chadha AS, Mavridis N. Sex and gender differences and biases in artificial intelligence for biomedicine and healthcare. Npj Digital Medicine. 3: 81. PMID 32529043 DOI: 10.1038/s41746-020-0288-5  1
2020 Sánchez-Valle J, Tejero H, Fernández JM, Juan D, Urda-García B, Capella-Gutiérrez S, Al-Shahrour F, Tabarés-Seisdedos R, Baudot A, Pancaldi V, Valencia A. Interpreting molecular similarity between patients as a determinant of disease comorbidity relationships. Nature Communications. 11: 2854. PMID 32504002 DOI: 10.1038/s41467-020-16540-x  0.72
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, ... ... Valencia A, 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  0.68
2020 Gaudelet T, Malod-Dognin N, Sánchez-Valle J, Pancaldi V, Valencia A, Pržulj N. Unveiling new disease, pathway, and gene associations via multi-scale neural network. Plos One. 15: e0231059. PMID 32251458 DOI: 10.1371/journal.pone.0231059  0.68
2020 Reyna MA, Haan D, Paczkowska M, Verbeke LPC, Vazquez M, Kahraman A, Pulido-Tamayo S, Barenboim J, Wadi L, Dhingra P, Shrestha R, Getz G, Lawrence MS, Pedersen JS, Rubin MA, ... ... Valencia A, et al. Pathway and network analysis of more than 2500 whole cancer genomes. Nature Communications. 11: 729. PMID 32024854 DOI: 10.1038/s41467-020-14367-0  0.4
2019 Greco A, Sanchez Valle J, Pancaldi V, Baudot A, Barillot E, Caselle M, Valencia A, Zinovyev A, Cantini L. Molecular Inverse Comorbidity between Alzheimer's Disease and Lung Cancer: New Insights from Matrix Factorization. International Journal of Molecular Sciences. 20. PMID 31247897 DOI: 10.3390/ijms20133114  0.72
2019 Pérez-Pérez M, Pérez-Rodríguez G, Blanco-Míguez A, Fdez-Riverola F, Valencia A, Krallinger M, Lourenço A. Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm. Journal of Cheminformatics. 11: 42. PMID 31236786 DOI: 10.1186/s13321-019-0363-6  0.4
2019 Catalá-López F, Forés-Martos J, Driver JA, Page MJ, Hutton B, Ridao M, Alonso-Arroyo A, Macías Saint-Gerons D, Gènova-Maleras R, Valderas JM, Vieta E, Valencia A, Tabarés-Seisdedos R. Association of Anorexia Nervosa With Risk of Cancer: A Systematic Review and Meta-analysis. Jama Network Open. 2: e195313. PMID 31173122 DOI: 10.1001/jamanetworkopen.2019.5313  0.48
2019 Perales-Patón J, Domenico TD, Fustero-Torre C, Piñeiro-Yáñez E, Carretero-Puche C, Tejero H, Valencia A, Gómez-López G, Al-Shahrour F. vulcanSpot: a tool to prioritize therapeutic vulnerabilities in cancer. Bioinformatics (Oxford, England). PMID 31173067 DOI: 10.1093/bioinformatics/btz465  0.64
2019 Forés-Martos J, Catalá-López F, Sánchez-Valle J, Ibáñez K, Tejero H, Palma-Gudiel H, Climent J, Pancaldi V, Fañanás L, Arango C, Parellada M, Baudot A, Vogt D, Rubenstein JL, Valencia A, et al. Transcriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer. Molecular Autism. 10: 17. PMID 31007884 DOI: 10.1186/s13229-019-0262-8  0.72
2019 Cirillo D, Valencia A. Big data analytics for personalized medicine. Current Opinion in Biotechnology. 58: 161-167. PMID 30965188 DOI: 10.1016/j.copbio.2019.03.004  1
2019 Rigau M, Juan D, Valencia A, Rico D. Intronic CNVs and gene expression variation in human populations. Plos Genetics. 15: e1007902. PMID 30677042 DOI: 10.1371/journal.pgen.1007902  0.52
2018 Grassi L, Pourfarzad F, Ullrich S, Merkel A, Were F, Carrillo-de-Santa-Pau E, Yi G, Hiemstra IH, Tool ATJ, Mul E, Perner J, Janssen-Megens E, Berentsen K, Kerstens H, Habibi E, ... ... Valencia A, et al. Dynamics of Transcription Regulation in Human Bone Marrow Myeloid Differentiation to Mature Blood Neutrophils. Cell Reports. 24: 2784-2794. PMID 30184510 DOI: 10.1016/j.celrep.2018.08.018  0.52
2018 Mur P, Jemth AS, Bevc L, Amaral N, Navarro M, Valdés-Mas R, Pons T, Aiza G, Urioste M, Valencia A, Lázaro C, Moreno V, Puente XS, Stenmark P, Warpman-Berglund U, et al. Germline variation in the oxidative DNA repair genes NUDT1 and OGG1 is not associated with hereditary colorectal cancer or polyposis. Human Mutation. PMID 29900613 DOI: 10.1002/humu.23564  0.48
2018 Piñeiro-Yáñez E, Reboiro-Jato M, Gómez-López G, Perales-Patón J, Troulé K, Rodríguez JM, Tejero H, Shimamura T, López-Casas PP, Carretero J, Valencia A, Hidalgo M, Glez-Peña D, Al-Shahrour F. PanDrugs: a novel method to prioritize anticancer drug treatments according to individual genomic data. Genome Medicine. 10: 41. PMID 29848362 DOI: 10.1186/s13073-018-0546-1  0.64
2018 Mur P, De Voer RM, Olivera-Salguero R, Rodríguez-Perales S, Pons T, Setién F, Aiza G, Valdés-Mas R, Bertini A, Pineda M, Vreede L, Navarro M, Iglesias S, González S, Brunet J, ... Valencia A, et al. Germline mutations in the spindle assembly checkpoint genes BUB1 and BUB3 are infrequent in familial colorectal cancer and polyposis. Molecular Cancer. 17: 23. PMID 29448935 DOI: 10.1186/s12943-018-0762-8  0.48
2017 Ecker S, Pancaldi V, Valencia A, Beck S, Paul DS. Epigenetic and Transcriptional Variability Shape Phenotypic Plasticity. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. PMID 29251357 DOI: 10.1002/bies.201700148  0.68
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  0.64
2017 Rodriguez JM, Rodriguez-Rivas J, Di Domenico T, Vázquez J, Valencia A, Tress ML. APPRIS 2017: principal isoforms for multiple gene sets. Nucleic Acids Research. PMID 29069475 DOI: 10.1093/nar/gkx997  0.76
2017 Carrillo-de-Santa-Pau E, Juan D, Pancaldi V, Were F, Martin-Subero I, Rico D, Valencia A. Automatic identification of informative regions with epigenomic changes associated to hematopoiesis. Nucleic Acids Research. 45: 9244-9259. PMID 28934481 DOI: 10.1093/nar/gkx618  0.68
2017 Catalá-López F, Hutton B, Page MJ, Ridao M, Driver JA, Alonso-Arroyo A, Forés-Martos J, Macías Saint-Gerons D, Vieta E, Valencia A, Tabarés-Seisdedos R. Risk of mortality among children, adolescents, and adults with autism spectrum disorder or attention deficit hyperactivity disorder and their first-degree relatives: a protocol for a systematic review and meta-analysis of observational studies. Systematic Reviews. 6: 189. PMID 28915839 DOI: 10.1186/s13643-017-0581-9  0.48
2017 Bellido F, Sowada N, Mur P, Lázaro C, Pons T, Valdés-Mas R, Pineda M, Aiza G, Iglesias S, Soto JL, Urioste M, Caldés T, Balbín M, Blay P, Rueda D, ... ... Valencia A, et al. Association Between Germline Mutations in BRF1, a subunit of the RNA Polymerase III Transcription Complex, and Hereditary Colorectal Cancer. Gastroenterology. PMID 28912018 DOI: 10.1053/j.gastro.2017.09.005  0.48
2017 Porta-Pardo E, Kamburov A, Tamborero D, Pons T, Grases D, Valencia A, Lopez-Bigas N, Getz G, Godzik A. Comparison of algorithms for the detection of cancer drivers at subgene resolution. Nature Methods. PMID 28714987 DOI: 10.1038/nmeth.4364  0.48
2017 Catalá-López F, Hutton B, Driver JA, Ridao M, Valderas JM, Gènova-Maleras R, Forés-Martos J, Alonso-Arroyo A, Saint-Gerons DM, Vieta E, Valencia A, Tabarés-Seisdedos R. Anorexia nervosa and cancer: a protocol for a systematic review and meta-analysis of observational studies. Systematic Reviews. 6: 137. PMID 28693568 DOI: 10.1186/s13643-017-0540-5  0.48
2017 Sánchez-Valle J, Tejero H, Ibáñez K, Portero JL, Krallinger M, Al-Shahrour F, Tabarés-Seisdedos R, Baudot A, Valencia A. A molecular hypothesis to explain direct and inverse co-morbidities between Alzheimer's Disease, Glioblastoma and Lung cancer. Scientific Reports. 7: 4474. PMID 28667284 DOI: 10.1038/s41598-017-04400-6  0.72
2017 Vargas-Parra GM, González-Acosta M, Thompson BA, Gómez C, Fernández A, Dámaso E, Pons T, Morak M, Del Valle J, Iglesias S, Velasco À, Solanes A, Sanjuan X, Padilla N, de la Cruz X, ... Valencia A, et al. Elucidating the molecular basis of msh2-deficient tumors by combined germline and somatic analysis. International Journal of Cancer. PMID 28577310 DOI: 10.1002/ijc.30820  0.48
2017 Cañada A, Capella-Gutierrez S, Rabal O, Oyarzabal J, Valencia A, Krallinger M. LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes. Nucleic Acids Research. PMID 28531339 DOI: 10.1093/nar/gkx462  0.4
2017 Tress ML, Abascal F, Valencia A. Most Alternative Isoforms Are Not Functionally Important. Trends in Biochemical Sciences. 42: 408-410. PMID 28483377 DOI: 10.1016/j.tibs.2017.04.002  0.76
2017 Krallinger M, Rabal O, Lourenço A, Oyarzabal J, Valencia A. Information Retrieval and Text Mining Technologies for Chemistry. Chemical Reviews. PMID 28475312 DOI: 10.1021/acs.chemrev.6b00851  0.4
2017 Catalá-López F, Hutton B, Driver JA, Page MJ, Ridao M, Valderas JM, Alonso-Arroyo A, Forés-Martos J, Martínez S, Gènova-Maleras R, Macías-Saint-Gerons D, Crespo-Facorro B, Vieta E, Valencia A, Tabarés-Seisdedos R. Cancer and central nervous system disorders: protocol for an umbrella review of systematic reviews and updated meta-analyses of observational studies. Systematic Reviews. 6: 69. PMID 28376926 DOI: 10.1186/s13643-017-0466-y  0.48
2017 Ecker S, Chen L, Pancaldi V, Bagger FO, Fernández JM, Carrillo de Santa Pau E, Juan D, Mann AL, Watt S, Casale FP, Sidiropoulos N, Rapin N, Merkel A, Stunnenberg HG, ... ... Valencia A, et al. Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types. Genome Biology. 18: 18. PMID 28126036 DOI: 10.1186/s13059-017-1156-8  0.68
2016 Piccolo P, Attanasio S, Secco I, Sangermano R, Strisciuglio C, Limongelli G, Miele E, Mutarelli M, Banfi S, Nigro V, Pons T, Valencia A, Zentilin L, Campione S, Nardone G, et al. MIB2 variants altering NOTCH signalling result in left ventricle hypertrabeculation/non-compaction and are associated with Ménétrier-like gastropathy. Human Molecular Genetics. PMID 28013292 DOI: 10.1093/hmg/ddw365  0.48
2016 Rodriguez-Rivas J, Marsili S, Juan D, Valencia A. Conservation of coevolving protein interfaces bridges prokaryote-eukaryote homologies in the twilight zone. Proceedings of the National Academy of Sciences of the United States of America. PMID 27965389 DOI: 10.1073/pnas.1611861114  0.52
2016 Abascal F, Corvelo A, Cruz F, Villanueva-Cañas JL, Vlasova A, Marcet-Houben M, Martínez-Cruz B, Cheng JY, Prieto P, Quesada V, Quilez J, Li G, García F, Rubio-Camarillo M, Frias L, ... ... Valencia A, et al. Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx. Genome Biology. 17: 251. PMID 27964752 DOI: 10.1186/s13059-016-1090-1  0.76
2016 Fernández JM, de la Torre V, Richardson D, Royo R, Puiggròs M, Moncunill V, Fragkogianni S, Clarke L, Flicek P, Rico D, Torrents D, Carrillo de Santa Pau E, Valencia A. The BLUEPRINT Data Analysis Portal. Cell Systems. PMID 27863955 DOI: 10.1016/j.cels.2016.10.021  0.72
2016 Astle WJ, Elding H, Jiang T, Allen D, Ruklisa D, Mann AL, Mead D, Bouman H, Riveros-Mckay F, Kostadima MA, Lambourne JJ, Sivapalaratnam S, Downes K, Kundu K, Bomba L, ... ... Valencia A, et al. The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease. Cell. 167: 1415-1429.e19. PMID 27863252 DOI: 10.1016/j.cell.2016.10.042  0.52
2016 Chen L, Ge B, Casale FP, Vasquez L, Kwan T, Garrido-Martín D, Watt S, Yan Y, Kundu K, Ecker S, Datta A, Richardson D, Burden F, Mead D, Mann AL, ... ... Valencia A, et al. Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells. Cell. 167: 1398-1414.e24. PMID 27863251 DOI: 10.1016/j.cell.2016.10.026  0.68
2016 Earl J, Rico D, Carrillo-de-Santa-Pau E, Rodríguez-Santiago B, Méndez-Pertuz M, Auer H, Gómez G, Grossman HB, Pisano DG, Schulz WA, Pérez-Jurado LA, Carrato A, Theodorescu D, Chanock S, Valencia A, et al. Erratum to: The UBC-40 Urothelial Bladder Cancer cell line index: a genomic resource for functional studies. Bmc Genomics. 17: 829. PMID 27782819 DOI: 10.1186/s12864-016-3179-z  0.52
2016 Tress ML, Abascal F, Valencia A. Alternative Splicing May Not Be the Key to Proteome Complexity. Trends in Biochemical Sciences. PMID 27712956 DOI: 10.1016/j.tibs.2016.08.008  0.76
2016 Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, ... ... Valencia A, et al. An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biology. 17: 184. PMID 27604469 DOI: 10.1186/s13059-016-1037-6  0.44
2016 Pérez-Pérez M, Pérez-Rodríguez G, Rabal O, Vazquez M, Oyarzabal J, Fdez-Riverola F, Valencia A, Krallinger M, Lourenço A. The Markyt visualisation, prediction and benchmark platform for chemical and gene entity recognition at BioCreative/CHEMDNER challenge. Database : the Journal of Biological Databases and Curation. 2016. PMID 27542845 DOI: 10.1093/database/baw120  0.4
2016 Pancaldi V, Carrillo-de-Santa-Pau E, Javierre BM, Juan D, Fraser P, Spivakov M, Valencia A, Rico D. Integrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativity. Genome Biology. 17: 152. PMID 27391817 DOI: 10.1186/s13059-016-1003-3  0.68
2016 Pons T, Vazquez M, Matey-Hernandez ML, Brunak S, Valencia A, Izarzugaza JM. KinMutRF: a random forest classifier of sequence variants in the human protein kinase superfamily. Bmc Genomics. 17: 396. PMID 27357839 DOI: 10.1186/s12864-016-2723-1  0.48
2016 Gurard-Levin ZA, Wilson LO, Pancaldi V, Postel-Vinay S, Sousa FG, Reyes C, Marangoni E, Gentien D, Valencia A, Pommier Y, Cottu P, Almouzni G. Chromatin regulators as a guide for cancer treatment choice. Molecular Cancer Therapeutics. PMID 27196757 DOI: 10.1158/1535-7163.MCT-15-1008  1
2016 Toll A, Fernández LC, Pons T, Groesser L, Sagrera A, Carrillo-de Santa Pau E, Vicente A, Baselga E, Vázquez M, Beltrán S, Pisano DG, Rueda D, Gut M, Pujol RM, Hafner C, ... ... Valencia A, et al. Somatic embryonic FGFR2 mutations in keratinocytic epidermal nevi. The Journal of Investigative Dermatology. PMID 27103312 DOI: 10.1016/j.jid.2016.03.040  0.48
2016 Juan D, Perner J, Carrillo de Santa Pau E, Marsili S, Ochoa D, Chung HR, Vingron M, Rico D, Valencia A. Epigenomic Co-localization and Co-evolution Reveal a Key Role for 5hmC as a Communication Hub in the Chromatin Network of ESCs. Cell Reports. PMID 26832418 DOI: 10.1016/j.celrep.2016.01.008  1
2016 Ibáñez K, Guijarro M, Pajares G, Valencia A. A computational approach inspired by simulated annealing to study the stability of protein interaction networks in cancer and neurological disorders Data Mining and Knowledge Discovery. 30: 226-242. DOI: 10.1007/s10618-015-0410-5  1
2015 Earl J, Rico D, Carrillo-de-Santa-Pau E, Rodríguez-Santiago B, Méndez-Pertuz M, Auer H, Gómez G, Grossman HB, Pisano DG, Schulz WA, Pérez-Jurado LA, Carrato A, Theodorescu D, Chanock S, Valencia A, et al. Erratum to: The UBC-40 Urothelial Bladder Cancer Cell Line Index: a genomic resource for functional studies. Bmc Genomics. 16: 1019. PMID 26621286 DOI: 10.1186/s12864-015-2227-4  0.52
2015 Ezkurdia I, Calvo E, Del Pozo A, Vázquez J, Valencia A, Tress ML. The potential clinical impact of the release of two drafts of the human proteome. Expert Review of Proteomics. 12: 579-593. PMID 26496066 DOI: 10.1586/14789450.2015.1103186  1
2015 Sutto L, Marsili S, Valencia A, Gervasio FL. From residue coevolution to protein conformational ensembles and functional dynamics. Proceedings of the National Academy of Sciences of the United States of America. 112: 13567-72. PMID 26487681 DOI: 10.1073/pnas.1508584112  1
2015 Vazquez M, Pons T, Brunak S, Valencia A, Izarzugaza JM. wKinMut-2: Identification and Interpretation of Pathogenic Variants in Human Protein Kinases. Human Mutation. PMID 26443060 DOI: 10.1002/humu.22914  0.48
2015 Puente XS, Beà S, Valdés-Mas R, Villamor N, Gutiérrez-Abril J, Martín-Subero JI, Munar M, Rubio-Pérez C, Jares P, Aymerich M, Baumann T, Beekman R, Belver L, Carrio A, Castellano G, ... ... Valencia A, et al. Non-coding recurrent mutations in chronic lymphocytic leukaemia. Nature. PMID 26200345 DOI: 10.1038/nature14666  1
2015 Bellido F, Pineda M, Aiza G, Valdés-Mas R, Navarro M, Puente DA, Pons T, González S, Iglesias S, Darder E, Piñol V, Soto JL, Valencia A, Blanco I, Urioste M, et al. POLE and POLD1 mutations in 529 kindred with familial colorectal cancer and/or polyposis: review of reported cases and recommendations for genetic testing and surveillance. Genetics in Medicine : Official Journal of the American College of Medical Genetics. PMID 26133394 DOI: 10.1038/gim.2015.75  1
2015 Creixell P, Reimand J, Haider S, Wu G, Shibata T, Vazquez M, Mustonen V, Gonzalez-Perez A, Pearson J, Sander C, Raphael BJ, Marks DS, Ouellette BFF, Valencia A, Bader GD, et al. Pathway and network analysis of cancer genomes. Nature Methods. 12: 615-621. PMID 26125594 DOI: 10.1038/nmeth.3440  0.68
2015 Abascal F, Ezkurdia I, Rodriguez-Rivas J, Rodriguez JM, Del Pozo A, Vázquez J, Valencia A, Tress ML. Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level. Plos Computational Biology. 11: e1004325. PMID 26061177 DOI: 10.1371/journal.pcbi.1004325  1
2015 Kulis M, Merkel A, Heath S, Queirós AC, Schuyler RP, Castellano G, Beekman R, Raineri E, Esteve A, Clot G, Verdaguer-Dot N, Duran-Ferrer M, Russiñol N, Vilarrasa-Blasi R, Ecker S, ... ... Valencia A, et al. Whole-genome fingerprint of the DNA methylome during human B cell differentiation. Nature Genetics. PMID 26053498 DOI: 10.1038/ng.3291  0.68
2015 Seguí N, Mina LB, Lázaro C, Sanz-Pamplona R, Pons T, Navarro M, Bellido F, López-Doriga A, Valdés-Mas R, Pineda M, Guinó E, Vidal A, Soto JL, Caldés T, Durán M, ... ... Valencia A, et al. Germline Mutations in FAN1 Cause Hereditary Colorectal Cancer by Impairing DNA Repair. Gastroenterology. PMID 26052075 DOI: 10.1053/j.gastro.2015.05.056  0.48
2015 Earl J, Rico D, Carrillo-de-Santa-Pau E, Rodríguez-Santiago B, Méndez-Pertuz M, Auer H, Gómez G, Grossman HB, Pisano DG, Schulz WA, Pérez-Jurado LA, Carrato A, Theodorescu D, Chanock S, Valencia A, et al. The UBC-40 Urothelial Bladder Cancer cell line index: a genomic resource for functional studies. Bmc Genomics. 16: 403. PMID 25997541 DOI: 10.1186/s12864-015-1450-3  1
2015 Rodriguez JM, Carro A, Valencia A, Tress ML. APPRIS WebServer and WebServices. Nucleic Acids Research. PMID 25990727 DOI: 10.1093/nar/gkv512  0.76
2015 Abascal F, Tress ML, Valencia A. The evolutionary fate of alternatively spliced homologous exons after gene duplication. Genome Biology and Evolution. 7: 1392-403. PMID 25931610 DOI: 10.1093/gbe/evv076  0.76
2015 Krallinger M, Rabal O, Leitner F, Vazquez M, Salgado D, Lu Z, Leaman R, Lu Y, Ji D, Lowe DM, Sayle RA, Batista-Navarro RT, Rak R, Huber T, Rocktäschel T, ... ... Valencia A, et al. The CHEMDNER corpus of chemicals and drugs and its annotation principles. Journal of Cheminformatics. 7: S2. PMID 25810773 DOI: 10.1186/1758-2946-7-S1-S2  1
2015 Krallinger M, Leitner F, Rabal O, Vazquez M, Oyarzabal J, Valencia A. CHEMDNER: The drugs and chemical names extraction challenge. Journal of Cheminformatics. 7: S1. PMID 25810766 DOI: 10.1186/1758-2946-7-S1-S1  1
2015 Vázquez M, Valencia A, Pons T. Structure-PPi: a module for the annotation of cancer-related single-nucleotide variants at protein-protein interfaces. Bioinformatics (Oxford, England). 31: 2397-9. PMID 25765346 DOI: 10.1093/bioinformatics/btv142  0.48
2015 Ezkurdia I, Vázquez J, Valencia A, Tress M. Correction to "Analyzing the first drafts of the human proteome". Journal of Proteome Research. 14: 1991. PMID 25756922 DOI: 10.1021/acs.jproteome.5b00186  0.64
2015 Abascal F, Tress ML, Valencia A. Alternative splicing and co-option of transposable elements: the case of TMPO/LAP2α and ZNF451 in mammals. Bioinformatics (Oxford, England). PMID 25735770 DOI: 10.1093/bioinformatics/btv132  1
2015 Ezkurdia I, Rodriguez JM, Carrillo-de Santa Pau E, Vázquez J, Valencia A, Tress ML. Most highly expressed protein-coding genes have a single dominant isoform. Journal of Proteome Research. 14: 1880-7. PMID 25732134 DOI: 10.1021/pr501286b  1
2015 Ochoa D, Juan D, Valencia A, Pazos F. Detection of significant protein coevolution. Bioinformatics (Oxford, England). PMID 25717190 DOI: 10.1093/bioinformatics/btv102  1
2015 Lees JG, Hériché JK, Morilla I, Fernández JM, Adler P, Krallinger M, Vilo J, Valencia A, Ellenberg J, Ranea JA, Orengo C. FUN-L: gene prioritization for RNAi screens. Bioinformatics (Oxford, England). 31: 2052-3. PMID 25667547 DOI: 10.1093/bioinformatics/btv073  1
2015 Ecker S, Pancaldi V, Rico D, Valencia A. Higher gene expression variability in the more aggressive subtype of chronic lymphocytic leukemia. Genome Medicine. 7: 8. PMID 25632304 DOI: 10.1186/s13073-014-0125-z  1
2015 Maraver A, Fernandez-Marcos PJ, Cash TP, Mendez-Pertuz M, Dueñas M, Maietta P, Martinelli P, Muñoz-Martin M, Martínez-Fernández M, Cañamero M, Roncador G, Martinez-Torrecuadrada JL, Grivas D, de la Pompa JL, Valencia A, et al. NOTCH pathway inactivation promotes bladder cancer progression. The Journal of Clinical Investigation. 125: 824-30. PMID 25574842 DOI: 10.1172/JCI78185  1
2015 Frenkel-Morgenstern M, Gorohovski A, Vucenovic D, Maestre L, Valencia A. ChiTaRS 2.1--an improved database of the chimeric transcripts and RNA-seq data with novel sense-antisense chimeric RNA transcripts. Nucleic Acids Research. 43: D68-75. PMID 25414346 DOI: 10.1093/nar/gku1199  1
2015 Verspoor K, Shatkay H, Hirschman L, Blaschke C, Valencia A. Summary of the BioLINK SIG 2013 meeting at ISMB/ECCB 2013. Bioinformatics (Oxford, England). 31: 297-8. PMID 25024289 DOI: 10.1093/bioinformatics/btu412  1
2015 Xia J, Wishart DS, Valencia A. MetPA: A web-based metabolomics tool for pathway analysis and visualization Bioinformatics. 27: 2342-2344. DOI: 10.1093/bioinformatics/btq418  1
2015 Creixell P, Reimand J, Haider S, Wu G, Shibata T, Vazquez M, Mustonen V, Gonzalez-Perez A, Pearson J, Sander C, Raphael BJ, Marks DS, Ouellette BFF, Valencia A, Bader GD, et al. Pathway and network analysis of cancer genomes Nature Methods. 12: 615-621. DOI: 10.1038/nmeth.3440  0.68
2014 Garcia-Jimenez B, Pons T, Sanchis A, Valencia A. Predicting Protein Relationships to Human Pathways through a Relational Learning Approach Based on Simple Sequence Features. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 11: 753-65. PMID 26356345 DOI: 10.1109/TCBB.2014.2318730  1
2014 Martinez-Garcia R, Lopez-Casas PP, Rico D, Valencia A, Hidalgo M. Colorectal cancer classification based on gene expression is not associated with FOLFIRI response. Nature Medicine. 20: 1230-1. PMID 25375918 DOI: 10.1038/nm.3701  1
2014 Ezkurdia I, Vázquez J, Valencia A, Tress M. Analyzing the first drafts of the human proteome. Journal of Proteome Research. 13: 3854-5. PMID 25014353 DOI: 10.1021/pr500572z  1
2014 Basilico F, Maffini S, Weir JR, Prumbaum D, Rojas AM, Zimniak T, De Antoni A, Jeganathan S, Voss B, van Gerwen S, Krenn V, Massimiliano L, Valencia A, Vetter IR, Herzog F, et al. The pseudo GTPase CENP-M drives human kinetochore assembly. Elife. 3: e02978. PMID 25006165 DOI: 10.7554/eLife.02978.001  1
2014 Hériché JK, Lees JG, Morilla I, Walter T, Petrova B, Roberti MJ, Hossain MJ, Adler P, Fernández JM, Krallinger M, Haering CH, Vilo J, Valencia A, Ranea JA, Orengo C, et al. Integration of biological data by kernels on graph nodes allows prediction of new genes involved in mitotic chromosome condensation. Molecular Biology of the Cell. 25: 2522-36. PMID 24943848 DOI: 10.1091/mbc.E13-04-0221  1
2014 Ezkurdia I, Juan D, Rodriguez JM, Frankish A, Diekhans M, Harrow J, Vazquez J, Valencia A, Tress ML. Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes. Human Molecular Genetics. 23: 5866-78. PMID 24939910 DOI: 10.1093/hmg/ddu309  1
2014 Arighi CN, Wu CH, Cohen KB, Hirschman L, Krallinger M, Valencia A, Lu Z, Wilbur JW, Wiegers TC. BioCreative-IV virtual issue. Database : the Journal of Biological Databases and Curation. 2014. PMID 24852177 DOI: 10.1093/database/bau039  1
2014 Martinez-Garcia R, Juan D, Rausell A, Muñoz M, Baños N, Menéndez C, Lopez-Casas PP, Rico D, Valencia A, Hidalgo M. Transcriptional dissection of pancreatic tumors engrafted in mice. Genome Medicine. 6: 27. PMID 24739241 DOI: 10.1186/gm544  1
2014 Garralda E, Paz K, López-Casas PP, Jones S, Katz A, Kann LM, López-Rios F, Sarno F, Al-Shahrour F, Vasquez D, Bruckheimer E, Angiuoli SV, Calles A, Diaz LA, Velculescu VE, ... Valencia A, et al. Integrated next-generation sequencing and avatar mouse models for personalized cancer treatment. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 20: 2476-84. PMID 24634382 DOI: 10.1158/1078-0432.CCR-13-3047  1
2014 Juan D, Rico D, Marques-Bonet T, Fernández-Capetillo O, Valencia A. Late-replicating CNVs as a source of new genes. Biology Open. 3. PMID 24596403 DOI: 10.1242/bio.20147815  0.52
2014 Ibáñez K, Boullosa C, Tabarés-Seisdedos R, Baudot A, Valencia A. Molecular evidence for the inverse comorbidity between central nervous system disorders and cancers detected by transcriptomic meta-analyses. Plos Genetics. 10: e1004173. PMID 24586201 DOI: 10.1371/journal.pgen.1004173  1
2014 Catalá-López F, Suárez-Pinilla M, Suárez-Pinilla P, Valderas JM, Gómez-Beneyto M, Martinez S, Balanzá-Martínez V, Climent J, Valencia A, McGrath J, Crespo-Facorro B, Sanchez-Moreno J, Vieta E, Tabarés-Seisdedos R. Inverse and direct cancer comorbidity in people with central nervous system disorders: a meta-analysis of cancer incidence in 577,013 participants of 50 observational studies. Psychotherapy and Psychosomatics. 83: 89-105. PMID 24458030 DOI: 10.1159/000356498  1
2014 Catalá-López F, Crespo-Facorro B, Vieta E, Valderas JM, Valencia A, Tabarés-Seisdedos R. Alzheimer's disease and cancer: current epidemiological evidence for a mutual protection. Neuroepidemiology. 42: 121-2. PMID 24401794 DOI: 10.1159/000355899  1
2014 Ferreira PG, Jares P, Rico D, Gómez-López G, Martínez-Trillos A, Villamor N, Ecker S, González-Pérez A, Knowles DG, Monlong J, Johnson R, Quesada V, Djebali S, Papasaikas P, López-Guerra M, ... ... Valencia A, et al. Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia. Genome Research. 24: 212-26. PMID 24265505 DOI: 10.1101/gr.152132.112  1
2014 Maietta P, Lopez G, Carro A, Pingilley BJ, Leon LG, Valencia A, Tress ML. FireDB: a compendium of biological and pharmacologically relevant ligands. Nucleic Acids Research. 42: D267-72. PMID 24243844 DOI: 10.1093/nar/gkt1127  1
2014 Usié A, Alves R, Solsona F, Vázquez M, Valencia A. CheNER: chemical named entity recognizer. Bioinformatics (Oxford, England). 30: 1039-40. PMID 24227678 DOI: 10.1093/bioinformatics/btt639  1
2014 Pons T, Paramonov I, Boullosa C, Ibáñez K, Rojas AM, Valencia A. A common structural scaffold in CTD phosphatases that supports distinct catalytic mechanisms. Proteins. 82: 103-18. PMID 23900790 DOI: 10.1002/prot.24376  1
2014 Santa Pau ECd, Real FX, Valencia A. Bioinformatics Analysis of Pancreas Cancer Genome in High-Throughput Genomic Technologies Molecular Diagnostics and Treatment of Pancreatic Cancer. 93-131. DOI: 10.1016/B978-0-12-408103-1.00005-4  1
2014 Rojas AM, Valencia A. Evolution of the ras superfamily of GTPases Ras Superfamily Small G Proteins: Biology and Mechanisms 1: General Features, Signaling. 3-23. DOI: 10.1007/978-3-7091-1806-1_1  1
2014 Krallinger M, Leitner F, Valencia A. Retrieval and discovery of cell cycle literature and proteins by means of machine learning, text mining and network analysis Advances in Intelligent Systems and Computing. 294: 285-292. DOI: 10.1007/978-3-319-07581-5_34  1
2013 Izarzugaza JM, Vazquez M, del Pozo A, Valencia A. wKinMut: an integrated tool for the analysis and interpretation of mutations in human protein kinases. Bmc Bioinformatics. 14: 345. PMID 24289158 DOI: 10.1186/1471-2105-14-345  1
2013 Juan D, Rico D, Marques-Bonet T, Fernández-Capetillo O, Valencia A. Late-replicating CNVs as a source of new genes. Biology Open. 2: 1402-11. PMID 24285712 DOI: 10.1242/bio.20136924  1
2013 Balbás-Martínez C, Sagrera A, Carrillo-de-Santa-Pau E, Earl J, Márquez M, Vazquez M, Lapi E, Castro-Giner F, Beltran S, Bayés M, Carrato A, Cigudosa JC, Domínguez O, Gut M, Herranz J, ... ... Valencia A, et al. Recurrent inactivation of STAG2 in bladder cancer is not associated with aneuploidy. Nature Genetics. 45: 1464-9. PMID 24121791 DOI: 10.1038/ng.2799  1
2013 Landa I, Boullosa C, Inglada-Pérez L, Sastre-Perona A, Pastor S, Velázquez A, Mancikova V, Ruiz-Llorente S, Schiavi F, Marcos R, Malats N, Opocher G, Diaz-Uriarte R, Santisteban P, Valencia A, et al. An epistatic interaction between the PAX8 and STK17B genes in papillary thyroid cancer susceptibility. Plos One. 8: e74765. PMID 24086368 DOI: 10.1371/journal.pone.0074765  1
2013 Comeau DC, Islamaj Do?an R, Ciccarese P, Cohen KB, Krallinger M, Leitner F, Lu Z, Peng Y, Rinaldi F, Torii M, Valencia A, Verspoor K, Wiegers TC, Wu CH, Wilbur WJ. BioC: a minimalist approach to interoperability for biomedical text processing. Database : the Journal of Biological Databases and Curation. 2013: bat064. PMID 24048470 DOI: 10.1093/database/bat064  1
2013 Ruz M, Carrasco F, Rojas P, Codoceo J, Inostroza J, Basfi-fer K, Valencia A, Vásquez K, Galgani J, Pérez A, López G, Arredondo M, Perez-Bravo F. Zinc as a potential coadjuvant in therapy for type 2 diabetes. Food and Nutrition Bulletin. 34: 215-21. PMID 23964394  0.64
2013 Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GR, Creixell P, Karchin R, Vazquez M, Fink JL, Kassahn KS, Pearson JV, Bader GD, Boutros PC, Muthuswamy L, Ouellette BF, Reimand J, ... ... Valencia A, et al. Computational approaches to identify functional genetic variants in cancer genomes. Nature Methods. 10: 723-9. PMID 23900255 DOI: 10.1038/nmeth.2562  1
2013 Mosca R, Pons T, Céol A, Valencia A, Aloy P. Towards a detailed atlas of protein-protein interactions. Current Opinion in Structural Biology. 23: 929-40. PMID 23896349 DOI: 10.1016/  1
2013 Cases M, Furlong LI, Albanell J, Altman RB, Bellazzi R, Boyer S, Brand A, Brookes AJ, Brunak S, Clark TW, Gea J, Ghazal P, Graf N, Guigó R, Klein TE, ... ... Valencia A, et al. Improving data and knowledge management to better integrate health care and research. Journal of Internal Medicine. 274: 321-8. PMID 23808970 DOI: 10.1111/joim.12105  1
2013 Abascal F, Corpet A, Gurard-Levin ZA, Juan D, Ochsenbein F, Rico D, Valencia A, Almouzni G. Subfunctionalization via adaptive evolution influenced by genomic context: the case of histone chaperones ASF1a and ASF1b. Molecular Biology and Evolution. 30: 1853-66. PMID 23645555 DOI: 10.1093/molbev/mst086  1
2013 Rubio-Camarillo M, Gómez-López G, Fernández JM, Valencia A, Pisano DG. RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses. Bioinformatics (Oxford, England). 29: 1687-9. PMID 23630175 DOI: 10.1093/bioinformatics/btt203  1
2013 de Juan D, Pazos F, Valencia A. Emerging methods in protein co-evolution. Nature Reviews. Genetics. 14: 249-61. PMID 23458856 DOI: 10.1038/nrg3414  1
2013 Blaschke C, Valencia A. The Functional Genomics Network in the evolution of biological text mining over the past decade. New Biotechnology. 30: 278-85. PMID 23202358 DOI: 10.1016/j.nbt.2012.11.020  1
2013 Rodriguez JM, Maietta P, Ezkurdia I, Pietrelli A, Wesselink JJ, Lopez G, Valencia A, Tress ML. APPRIS: annotation of principal and alternative splice isoforms. Nucleic Acids Research. 41: D110-7. PMID 23161672 DOI: 10.1093/nar/gks1058  1
2013 Frenkel-Morgenstern M, Gorohovski A, Lacroix V, Rogers M, Ibanez K, Boullosa C, Andres Leon E, Ben-Hur A, Valencia A. ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data. Nucleic Acids Research. 41: D142-51. PMID 23143107 DOI: 10.1093/nar/gks1041  1
2013 Ochoa D, García-Gutiérrez P, Juan D, Valencia A, Pazos F. Incorporating information on predicted solvent accessibility to the co-evolution-based study of protein interactions. Molecular Biosystems. 9: 70-6. PMID 23104128 DOI: 10.1039/c2mb25325a  1
2013 Morante R, Krallinger M, Valencia A, Daelemans W. Machine reading of biomedical texts about Alzheimer's disease Ceur Workshop Proceedings. 1179.  1
2013 Morante R, Krallinger M, Valencia A, Daelemans W. Machine reading of biomedical texts about Alzheimer's disease Ceur Workshop Proceedings. 1179.  1
2012 Vazquez M, de la Torre V, Valencia A. Chapter 14: Cancer genome analysis. Plos Computational Biology. 8: e1002824. PMID 23300415 DOI: 10.1371/journal.pcbi.1002824  1
2012 Wu CH, Arighi CN, Cohen KB, Hirschman L, Krallinger M, Lu Z, Mattingly C, Valencia A, Wiegers TC, John Wilbur W. BioCreative-2012 virtual issue. Database : the Journal of Biological Databases and Curation. 2012: bas049. PMID 23221175 DOI: 10.1093/database/bas049  1
2012 Kulis M, Heath S, Bibikova M, Queirós AC, Navarro A, Clot G, Martínez-Trillos A, Castellano G, Brun-Heath I, Pinyol M, Barberán-Soler S, Papasaikas P, Jares P, Beà S, Rico D, ... ... Valencia A, et al. Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia. Nature Genetics. 44: 1236-42. PMID 23064414 DOI: 10.1038/ng.2443  1
2012 Izarzugaza JM, Krallinger M, Valencia A. Interpretation of the consequences of mutations in protein kinases: combined use of bioinformatics and text mining. Frontiers in Physiology. 3: 323. PMID 23055974 DOI: 10.3389/fphys.2012.00323  1
2012 Glaab E, Baudot A, Krasnogor N, Schneider R, Valencia A. EnrichNet: network-based gene set enrichment analysis. Bioinformatics (Oxford, England). 28: i451-i457. PMID 22962466 DOI: 10.1093/bioinformatics/bts389  1
2012 Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, Boychenko V, Hunt T, Kay M, ... ... Valencia A, et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Research. 22: 1760-74. PMID 22955987 DOI: 10.1101/gr.135350.111  1
2012 Valencia A, Hidalgo M. Getting personalized cancer genome analysis into the clinic: the challenges in bioinformatics. Genome Medicine. 4: 61. PMID 22839973 DOI: 10.1186/gm362  1
2012 Salgado D, Krallinger M, Depaule M, Drula E, Tendulkar AV, Leitner F, Valencia A, Marcelle C. MyMiner: a web application for computer-assisted biocuration and text annotation. Bioinformatics (Oxford, England). 28: 2285-7. PMID 22789588 DOI: 10.1093/bioinformatics/bts435  1
2012 Izarzugaza JM, del Pozo A, Vazquez M, Valencia A. Prioritization of pathogenic mutations in the protein kinase superfamily. Bmc Genomics. 13: S3. PMID 22759651 DOI: 10.1186/1471-2164-13-S4-S3  1
2012 Heyn H, Li N, Ferreira HJ, Moran S, Pisano DG, Gomez A, Diez J, Sanchez-Mut JV, Setien F, Carmona FJ, Puca AA, Sayols S, Pujana MA, Serra-Musach J, Iglesias-Platas I, ... ... Valencia A, et al. Distinct DNA methylomes of newborns and centenarians. Proceedings of the National Academy of Sciences of the United States of America. 109: 10522-7. PMID 22689993 DOI: 10.1073/pnas.1120658109  1
2012 Frenkel-Morgenstern M, Valencia A. Novel domain combinations in proteins encoded by chimeric transcripts. Bioinformatics (Oxford, England). 28: i67-74. PMID 22689780 DOI: 10.1093/bioinformatics/bts216  1
2012 Frenkel-Morgenstern M, Lacroix V, Ezkurdia I, Levin Y, Gabashvili A, Prilusky J, Del Pozo A, Tress M, Johnson R, Guigo R, Valencia A. Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts. Genome Research. 22: 1231-42. PMID 22588898 DOI: 10.1101/gr.130062.111  1
2012 Ruiz-Llorente S, Carrillo Santa de Pau E, Sastre-Perona A, Montero-Conde C, Gómez-López G, Fagin JA, Valencia A, Pisano DG, Santisteban P. Genome-wide analysis of Pax8 binding provides new insights into thyroid functions. Bmc Genomics. 13: 147. PMID 22531031 DOI: 10.1186/1471-2164-13-147  1
2012 Hirschman L, Burns GA, Krallinger M, Arighi C, Cohen KB, Valencia A, Wu CH, Chatr-Aryamontri A, Dowell KG, Huala E, Lourenço A, Nash R, Veuthey AL, Wiegers T, Winter AG. Text mining for the biocuration workflow. Database : the Journal of Biological Databases and Curation. 2012: bas020. PMID 22513129 DOI: 10.1093/database/bas020  1
2012 Ezkurdia I, del Pozo A, Frankish A, Rodriguez JM, Harrow J, Ashman K, Valencia A, Tress ML. Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function. Molecular Biology and Evolution. 29: 2265-83. PMID 22446687 DOI: 10.1093/molbev/mss100  1
2012 Krallinger M, Leitner F, Vazquez M, Salgado D, Marcelle C, Tyers M, Valencia A, Chatr-aryamontri A. How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience. Database : the Journal of Biological Databases and Curation. 2012: bas017. PMID 22438567 DOI: 10.1093/database/bas017  1
2012 Rojas AM, Santamaria A, Malik R, Jensen TS, Körner R, Morilla I, de Juan D, Krallinger M, Hansen DA, Hoffmann R, Lees J, Reid A, Yeats C, Wehner A, Elowe S, ... ... Valencia A, et al. Uncovering the molecular machinery of the human spindle--an integration of wet and dry systems biology. Plos One. 7: e31813. PMID 22427808 DOI: 10.1371/journal.pone.0031813  1
2012 Peng H, Bateman A, Valencia A, Wren JD. Bioimage informatics: a new category in Bioinformatics. Bioinformatics (Oxford, England). 28: 1057. PMID 22399678 DOI: 10.1093/bioinformatics/bts111  1
2012 Hajirasouliha I, Schönhuth A, de Juan D, Valencia A, Sahinalp SC. Mirroring co-evolving trees in the light of their topologies. Bioinformatics (Oxford, England). 28: 1202-8. PMID 22399677 DOI: 10.1093/bioinformatics/bts109  1
2012 Adams D, Altucci L, Antonarakis SE, Ballesteros J, Beck S, Bird A, Bock C, Boehm B, Campo E, Caricasole A, Dahl F, Dermitzakis ET, Enver T, Esteller M, Estivill X, ... ... Valencia A, et al. BLUEPRINT to decode the epigenetic signature written in blood. Nature Biotechnology. 30: 224-6. PMID 22398613 DOI: 10.1038/nbt.2153  1
2012 Rojas AM, Fuentes G, Rausell A, Valencia A. The Ras protein superfamily: evolutionary tree and role of conserved amino acids. The Journal of Cell Biology. 196: 189-201. PMID 22270915 DOI: 10.1083/jcb.201103008  1
2012 Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM, Howald C, Foissac S, Ucla C, Chrast J, Ribeca P, Martin D, Murray RR, Yang X, Ghamsari L, ... ... Valencia A, et al. Evidence for transcript networks composed of chimeric RNAs in human cells. Plos One. 7: e28213. PMID 22238572 DOI: 10.1371/journal.pone.0028213  1
2012 Muth T, García-Martín JA, Rausell A, Juan D, Valencia A, Pazos F. JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures. Bioinformatics (Oxford, England). 28: 584-6. PMID 22171333 DOI: 10.1093/bioinformatics/btr688  1
2012 Quesada V, Conde L, Villamor N, Ordóñez GR, Jares P, Bassaganyas L, Ramsay AJ, Beà S, Pinyol M, Martínez-Trillos A, López-Guerra M, Colomer D, Navarro A, Baumann T, Aymerich M, ... ... Valencia A, et al. Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia. Nature Genetics. 44: 47-52. PMID 22158541 DOI: 10.1038/ng.1032  1
2012 Fernández JM, Valencia A. Bioinformatic software developments in Spain Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6620: 108-120. DOI: 10.1007/978-3-642-28062-7_13  1
2012 Fernández JM, Hoffmann R, Valencia A. iHOP web services family Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6620: 102-107. DOI: 10.1007/978-3-642-28062-7_12  1
2011 Vazquez M, Krallinger M, Leitner F, Valencia A. Text Mining for Drugs and Chemical Compounds: Methods, Tools and Applications. Molecular Informatics. 30: 506-19. PMID 27467152 DOI: 10.1002/minf.201100005  0.4
2011 Krallinger M, Vazquez M, Leitner F, Salgado D, Chatr-Aryamontri A, Winter A, Perfetto L, Briganti L, Licata L, Iannuccelli M, Castagnoli L, Cesareni G, Tyers M, Schneider G, Rinaldi F, ... ... Valencia A, et al. The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. Bmc Bioinformatics. 12: S3. PMID 22151929 DOI: 10.1186/1471-2105-12-S8-S3  1
2011 Arighi CN, Lu Z, Krallinger M, Cohen KB, Wilbur WJ, Valencia A, Hirschman L, Wu CH. Overview of the BioCreative III Workshop. Bmc Bioinformatics. 12: S1. PMID 22151647 DOI: 10.1186/1471-2105-12-S8-S1  1
2011 Izarzugaza JM, Hopcroft LE, Baresic A, Orengo CA, Martin AC, Valencia A. Characterization of pathogenic germline mutations in human protein kinases. Bmc Bioinformatics. 12: S1. PMID 21992016 DOI: 10.1186/1471-2105-12-S4-S1  1
2011 Herman D, Ochoa D, Juan D, Lopez D, Valencia A, Pazos F. Selection of organisms for the co-evolution-based study of protein interactions. Bmc Bioinformatics. 12: 363. PMID 21910884 DOI: 10.1186/1471-2105-12-363  1
2011 Javierre BM, Rodriguez-Ubreva J, Al-Shahrour F, Corominas M, Graña O, Ciudad L, Agirre X, Pisano DG, Valencia A, Roman-Gomez J, Calasanz MJ, Prosper F, Esteller M, Gonzalez-Sarmiento R, Ballestar E. Long-range epigenetic silencing associates with deregulation of Ikaros targets in colorectal cancer cells. Molecular Cancer Research : McR. 9: 1139-51. PMID 21737484 DOI: 10.1158/1541-7786.MCR-10-0515  1
2011 Lopez G, Maietta P, Rodriguez JM, Valencia A, Tress ML. firestar--advances in the prediction of functionally important residues. Nucleic Acids Research. 39: W235-41. PMID 21672959 DOI: 10.1093/nar/gkr437  1
2011 Puente XS, Pinyol M, Quesada V, Conde L, Ordóñez GR, Villamor N, Escaramis G, Jares P, Beà S, González-Díaz M, Bassaganyas L, Baumann T, Juan M, López-Guerra M, Colomer D, ... ... Valencia A, et al. Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature. 475: 101-5. PMID 21642962 DOI: 10.1038/nature10113  1
2011 Tabarés-Seisdedos R, Dumont N, Baudot A, Valderas JM, Climent J, Valencia A, Crespo-Facorro B, Vieta E, Gómez-Beneyto M, Martínez S, Rubenstein JL. No paradox, no progress: inverse cancer comorbidity in people with other complex diseases. The Lancet. Oncology. 12: 604-8. PMID 21498115 DOI: 10.1016/S1470-2045(11)70041-9  1
2011 Kallioniemi O, Wessels L, Valencia A. On the organization of bioinformatics core services in biology-based research institutes. Bioinformatics (Oxford, England). 27: 1345. PMID 21402560 DOI: 10.1093/bioinformatics/btr125  1
2011 Wass MN, Fuentes G, Pons C, Pazos F, Valencia A. Towards the prediction of protein interaction partners using physical docking. Molecular Systems Biology. 7: 469. PMID 21326236 DOI: 10.1038/msb.2011.3  1
2011 Marenne G, Rodríguez-Santiago B, Closas MG, Pérez-Jurado L, Rothman N, Rico D, Pita G, Pisano DG, Kogevinas M, Silverman DT, Valencia A, Real FX, Chanock SJ, Génin E, Malats N. Assessment of copy number variation using the Illumina Infinium 1M SNP-array: a comparison of methodological approaches in the Spanish Bladder Cancer/EPICURO study. Human Mutation. 32: 240-8. PMID 21089066 DOI: 10.1002/humu.21398  1
2011 Palczewska M, Casafont I, Ghimire K, Rojas AM, Valencia A, Lafarga M, Mellström B, Naranjo JR. Sumoylation regulates nuclear localization of repressor DREAM. Biochimica Et Biophysica Acta. 1813: 1050-8. PMID 21070824 DOI: 10.1016/j.bbamcr.2010.11.001  1
2011 Vazquez M, Krallinger M, Leitner F, Valencia A. Text mining for drugs and chemical compounds: Methods, tools and applications Molecular Informatics. 30: 506-519. DOI: 10.1002/minf.201100005  1
2010 Glaab E, Baudot A, Krasnogor N, Valencia A. Extending pathways and processes using molecular interaction networks to analyse cancer genome data. Bmc Bioinformatics. 11: 597. PMID 21144022 DOI: 10.1186/1471-2105-11-597  1
2010 Baudot A, de la Torre V, Valencia A. Mutated genes, pathways and processes in tumours. Embo Reports. 11: 805-10. PMID 20847737 DOI: 10.1038/embor.2010.133  1
2010 Leitner F, Chatr-aryamontri A, Mardis SA, Ceol A, Krallinger M, Licata L, Hirschman L, Cesareni G, Valencia A. The FEBS Letters/BioCreative II.5 experiment: making biological information accessible. Nature Biotechnology. 28: 897-9. PMID 20829821 DOI: 10.1038/nbt0910-897  1
2010 Leitner F, Krallinger M, Cesareni G, Valencia A. The FEBS Letters SDA corpus: a collection of protein interaction articles with high quality annotations for the BioCreative II.5 online challenge and the text mining community. Febs Letters. 584: 4129-30. PMID 20728446 DOI: 10.1016/j.febslet.2010.08.026  1
2010 Leitner F, Mardis SA, Krallinger M, Cesareni G, Hirschman LA, Valencia A. An Overview of BioCreative II.5. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 7: 385-99. PMID 20704011 DOI: 10.1109/TCBB.2010.61  1
2010 Rodríguez-Santiago B, Malats N, Rothman N, Armengol L, Garcia-Closas M, Kogevinas M, Villa O, Hutchinson A, Earl J, Marenne G, Jacobs K, Rico D, Tardón A, Carrato A, Thomas G, ... Valencia A, et al. Mosaic uniparental disomies and aneuploidies as large structural variants of the human genome. American Journal of Human Genetics. 87: 129-38. PMID 20598279 DOI: 10.1016/j.ajhg.2010.06.002  1
2010 Tress ML, Valencia A. Predicted residue-residue contacts can help the scoring of 3D models. Proteins. 78: 1980-91. PMID 20408174 DOI: 10.1002/prot.22714  1
2010 Carilla-Latorre S, Gallardo ME, Annesley SJ, Calvo-Garrido J, Graña O, Accari SL, Smith PK, Valencia A, Garesse R, Fisher PR, Escalante R. MidA is a putative methyltransferase that is required for mitochondrial complex I function. Journal of Cell Science. 123: 1674-83. PMID 20406883 DOI: 10.1242/jcs.066076  1
2010 García-Jiménez B, Juan D, Ezkurdia I, Andrés-León E, Valencia A. Inference of functional relations in predicted protein networks with a machine learning approach. Plos One. 5: e9969. PMID 20376314 DOI: 10.1371/journal.pone.0009969  1
2010 Glaab E, Baudot A, Krasnogor N, Valencia A. TopoGSA: network topological gene set analysis. Bioinformatics (Oxford, England). 26: 1271-2. PMID 20335277 DOI: 10.1093/bioinformatics/btq131  1
2010 Tendulkar AV, Krallinger M, de la Torre V, López G, Wangikar PP, Valencia A. FragKB: structural and literature annotation resource of conserved peptide fragments and residues. Plos One. 5: e9679. PMID 20305778 DOI: 10.1371/journal.pone.0009679  1
2010 Rausell A, Juan D, Pazos F, Valencia A. Protein interactions and ligand binding: from protein subfamilies to functional specificity. Proceedings of the National Academy of Sciences of the United States of America. 107: 1995-2000. PMID 20133844 DOI: 10.1073/pnas.0908044107  1
2010 Krallinger M, Leitner F, Valencia A. Analysis of biological processes and diseases using text mining approaches. Methods in Molecular Biology (Clifton, N.J.). 593: 341-82. PMID 19957157 DOI: 10.1007/978-1-60327-194-3_16  1
2009 Fuentes G, Valencia A. Ras classical effectors: new tales from in silico complexes. Trends in Biochemical Sciences. 34: 533-9. PMID 19801192 DOI: 10.1016/j.tibs.2009.07.001  1
2009 Izarzugaza JM, Baresic A, McMillan LE, Yeats C, Clegg AB, Orengo CA, Martin AC, Valencia A. An integrated approach to the interpretation of single amino acid polymorphisms within the framework of CATH and Gene3D. Bmc Bioinformatics. 10: S5. PMID 19758469 DOI: 10.1186/1471-2105-10-S8-S5  1
2009 Krallinger M, Izarzugaza JM, Rodriguez-Penagos C, Valencia A. Extraction of human kinase mutations from literature, databases and genotyping studies. Bmc Bioinformatics. 10: S1. PMID 19758464 DOI: 10.1186/1471-2105-10-S8-S1  0.4
2009 Baudot A, Gómez-López G, Valencia A. Translational disease interpretation with molecular networks. Genome Biology. 10: 221. PMID 19591646 DOI: 10.1186/gb-2009-10-6-221  1
2009 Krallinger M, Rodriguez-Penagos C, Tendulkar A, Valencia A. PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction. Nucleic Acids Research. 37: W160-5. PMID 19520768 DOI: 10.1093/nar/gkp484  0.4
2009 Krallinger M, Rojas AM, Valencia A. Creating reference datasets for systems biology applications using text mining. Annals of the New York Academy of Sciences. 1158: 14-28. PMID 19348628 DOI: 10.1111/j.1749-6632.2008.03750.x  1
2009 Ezkurdia I, Bartoli L, Fariselli P, Casadio R, Valencia A, Tress ML. Progress and challenges in predicting protein-protein interaction sites. Briefings in Bioinformatics. 10: 233-46. PMID 19346321 DOI: 10.1093/bib/bbp021  1
2009 Baudot A, Real FX, Izarzugaza JM, Valencia A. From cancer genomes to cancer models: bridging the gaps. Embo Reports. 10: 359-66. PMID 19305388 DOI: 10.1038/embor.2009.46  1
2009 Juncker AS, Jensen LJ, Pierleoni A, Bernsel A, Tress ML, Bork P, von Heijne G, Valencia A, Ouzounis CA, Casadio R, Brunak S. Sequence-based feature prediction and annotation of proteins. Genome Biology. 10: 206. PMID 19226438 DOI: 10.1186/gb-2009-10-2-206  1
2009 Fernandez AF, Rosales C, Lopez-Nieva P, Graña O, Ballestar E, Ropero S, Espada J, Melo SA, Lujambio A, Fraga MF, Pino I, Javierre B, Carmona FJ, Acquadro F, Steenbergen RD, ... ... Valencia A, et al. The dynamic DNA methylomes of double-stranded DNA viruses associated with human cancer. Genome Research. 19: 438-51. PMID 19208682 DOI: 10.1101/gr.083550.108  1
2009 Bacardit J, Stout M, Hirst JD, Valencia A, Smith RE, Krasnogor N. Automated alphabet reduction for protein datasets. Bmc Bioinformatics. 10: 6. PMID 19126227 DOI: 10.1186/1471-2105-10-6  1
2009 Trigo A, Valencia A, Cases I. Systemic approaches to biodegradation. Fems Microbiology Reviews. 33: 98-108. PMID 19054119 DOI: 10.1111/j.1574-6976.2008.00143.x  1
2009 Andres Leon E, Ezkurdia I, García B, Valencia A, Juan D. EcID. A database for the inference of functional interactions in E. coli. Nucleic Acids Research. 37: D629-35. PMID 19004873 DOI: 10.1093/nar/gkn853  1
2009 Carbajosa G, Trigo A, Valencia A, Cases I. Bionemo: molecular information on biodegradation metabolism. Nucleic Acids Research. 37: D598-602. PMID 18986994 DOI: 10.1093/nar/gkn864  1
2008 Tress ML, Bodenmiller B, Aebersold R, Valencia A. Proteomics studies confirm the presence of alternative protein isoforms on a large scale. Genome Biology. 9: R162. PMID 19017398 DOI: 10.1186/gb-2008-9-11-r162  1
2008 Krallinger M, Valencia A, Hirschman L. Linking genes to literature: text mining, information extraction, and retrieval applications for biology. Genome Biology. 9: S8. PMID 18834499 DOI: 10.1186/gb-2008-9-s2-s8  0.4
2008 Altman RB, Bergman CM, Blake J, Blaschke C, Cohen A, Gannon F, Grivell L, Hahn U, Hersh W, Hirschman L, Jensen LJ, Krallinger M, Mons B, O'Donoghue SI, Peitsch MC, ... ... Valencia A, et al. Text mining for biology--the way forward: opinions from leading scientists. Genome Biology. 9: S7. PMID 18834498 DOI: 10.1186/gb-2008-9-s2-s7  1
2008 Leitner F, Krallinger M, Rodriguez-Penagos C, Hakenberg J, Plake C, Kuo CJ, Hsu CN, Tsai RT, Hung HC, Lau WW, Johnson CA, Saetre R, Yoshida K, Chen YH, Kim S, ... ... Valencia A, et al. Introducing meta-services for biomedical information extraction. Genome Biology. 9: S6. PMID 18834497 DOI: 10.1186/gb-2008-9-s2-s6  1
2008 Krallinger M, Leitner F, Rodriguez-Penagos C, Valencia A. Overview of the protein-protein interaction annotation extraction task of BioCreative II. Genome Biology. 9: S4. PMID 18834495 DOI: 10.1186/gb-2008-9-s2-s4  0.4
2008 Krallinger M, Morgan A, Smith L, Leitner F, Tanabe L, Wilbur J, Hirschman L, Valencia A. Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge. Genome Biology. 9: S1. PMID 18834487 DOI: 10.1186/gb-2008-9-s2-s1  0.4
2008 Pazos F, Valencia A. Protein co-evolution, co-adaptation and interactions. The Embo Journal. 27: 2648-55. PMID 18818697 DOI: 10.1038/emboj.2008.189  1
2008 Pazos F, Juan D, Izarzugaza JM, Leon E, Valencia A. Prediction of protein interaction based on similarity of phylogenetic trees. Methods in Molecular Biology (Clifton, N.J.). 484: 523-35. PMID 18592199 DOI: 10.1007/978-1-59745-398-1_31  1
2008 Valiente PA, Batista PR, Pupo A, Pons T, Valencia A, Pascutti PG. Predicting functional residues in Plasmodium falciparum plasmepsins by combining sequence and structural analysis with molecular dynamics simulations. Proteins. 73: 440-57. PMID 18442137 DOI: 10.1002/prot.22068  0.48
2008 Leitner F, Valencia A. A text-mining perspective on the requirements for electronically annotated abstracts. Febs Letters. 582: 1178-81. PMID 18328824 DOI: 10.1016/j.febslet.2008.02.072  1
2008 Juan D, Pazos F, Valencia A. Co-evolution and co-adaptation in protein networks. Febs Letters. 582: 1225-30. PMID 18282476 DOI: 10.1016/j.febslet.2008.02.017  1
2008 Gómez-López G, Valencia A. Bioinformatics and cancer research: building bridges for translational research. Clinical & Translational Oncology : Official Publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico. 10: 85-95. PMID 18258507 DOI: 10.1007/s12094-008-0161-5  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, ... ... Valencia A, 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 del Pozo A, Pazos F, Valencia A. Defining functional distances over gene ontology. Bmc Bioinformatics. 9: 50. PMID 18221506 DOI: 10.1186/1471-2105-9-50  0.52
2008 Izarzugaza JM, Juan D, Pons C, Pazos F, Valencia A. Enhancing the prediction of protein pairings between interacting families using orthology information. Bmc Bioinformatics. 9: 35. PMID 18215279 DOI: 10.1186/1471-2105-9-35  0.52
2008 Juan D, Pazos F, Valencia A. High-confidence prediction of global interactomes based on genome-wide coevolutionary networks. Proceedings of the National Academy of Sciences of the United States of America. 105: 934-9. PMID 18199838 DOI: 10.1073/pnas.0709671105  1
2008 Tress ML, Wesselink JJ, Frankish A, López G, Goldman N, Löytynoja A, Massingham T, Pardi F, Whelan S, Harrow J, Valencia A. Determination and validation of principal gene products. Bioinformatics (Oxford, England). 24: 11-7. PMID 18006548 DOI: 10.1093/bioinformatics/btm547  1
2008 Hu ZZ, Cohen KB, Hirschman L, Valencia A, Liu H, Giglio MG, Wu CH. iProLINK: A framework for linking text mining with ontology and systems biology Proceedings - Ieee International Conference On Bioinformatics and Biomedicine, Bibm 2008. 467-472. DOI: 10.1109/BIBM.2008.73  1
2008 Frishman D, Valencia A. BioSapiens: A European network of excellence to develop genome annotation resources Modern Genome Annotation: the Biosapiens Network. 1-3. DOI: 10.1007/978-3-211-75123-7_1  1
2008 Frishman D, Valencia A. Modern genome annotation: The biosapiens network Modern Genome Annotation: the Biosapiens Network. 1-490. DOI: 10.1007/978-3-211-75123-7  1
2008 Krallinger M, Valencia A. Mining Information on Protein Function from Text Bioinformatics-From Genomes to Therapies. 3: 1253-1295. DOI: 10.1002/9783527619368.ch34  1
2007 Sanchez-Pulido L, Valencia A, Rojas AM. Are promyelocytic leukaemia protein nuclear bodies a scaffold for caspase-2 programmed cell death? Trends in Biochemical Sciences. 32: 400-6. PMID 17693089 DOI: 10.1016/j.tibs.2007.08.001  1
2007 Izarzugaza JM, Graña O, Tress ML, Valencia A, Clarke ND. Assessment of intramolecular contact predictions for CASP7. Proteins. 69: 152-8. PMID 17671976 DOI: 10.1002/prot.21637  1
2007 López G, Rojas A, Tress M, Valencia A. Assessment of predictions submitted for the CASP7 function prediction category. Proteins. 69: 165-74. PMID 17654548 DOI: 10.1002/prot.21651  1
2007 López G, Valencia A, Tress ML. firestar--prediction of functionally important residues using structural templates and alignment reliability. Nucleic Acids Research. 35: W573-7. PMID 17584799 DOI: 10.1093/nar/gkm297  1
2007 Jiménez-Baranda S, Gómez-Moutón C, Rojas A, Martínez-Prats L, Mira E, Ana Lacalle R, Valencia A, Dimitrov DS, Viola A, Delgado R, Martínez-A C, Mañes S. Filamin-A regulates actin-dependent clustering of HIV receptors. Nature Cell Biology. 9: 838-46. PMID 17572668 DOI: 10.1038/ncb1610  0.64
2007 Gómez MJ, Pazos F, Guijarro FJ, de Lorenzo V, Valencia A. The environmental fate of organic pollutants through the global microbial metabolism. Molecular Systems Biology. 3: 114. PMID 17551509 DOI: 10.1038/msb4100156  0.52
2007 Tamames J, Moya A, Valencia A. Modular organization in the reductive evolution of protein-protein interaction networks. Genome Biology. 8: R94. PMID 17532860 DOI: 10.1186/gb-2007-8-5-r94  0.68
2007 Cases I, Pisano DG, Andres E, Carro A, Fernández JM, Gómez-López G, Rodriguez JM, Vera JF, Valencia A, Rojas AM. CARGO: a web portal to integrate customized biological information. Nucleic Acids Research. 35: W16-20. PMID 17483515 DOI: 10.1093/nar/gkm280  0.96
2007 Tress ML, Martelli PL, Frankish A, Reeves GA, Wesselink JJ, Yeats C, Olason PI, Albrecht M, Hegyi H, Giorgetti A, Raimondo D, Lagarde J, Laskowski RA, López G, Sadowski MI, ... ... Valencia A, et al. The implications of alternative splicing in the ENCODE protein complement. Proceedings of the National Academy of Sciences of the United States of America. 104: 5495-500. PMID 17372197 DOI: 10.1073/pnas.0700800104  1
2007 Lopez G, Valencia A, Tress M. FireDB--a database of functionally important residues from proteins of known structure. Nucleic Acids Research. 35: D219-23. PMID 17132832 DOI: 10.1093/nar/gkl897  1
2006 Krallinger M, Malik R, Valencia A. Text mining and protein annotations: the construction and use of protein description sentences. Genome Informatics. International Conference On Genome Informatics. 17: 121-30. PMID 17503385  1
2006 Ideker T, Valencia A. Bioinformatics in the human interactome project. Bioinformatics (Oxford, England). 22: 2973-4. PMID 17142816 DOI: 10.1093/bioinformatics/btl579  1
2006 Carro A, Tress M, de Juan D, Pazos F, Lopez-Romero P, del Sol A, Valencia A, Rojas AM. TreeDet: a web server to explore sequence space. Nucleic Acids Research. 34: W110-5. PMID 16844971 DOI: 10.1093/nar/gkl203  1
2006 Tress ML, Cozzetto D, Tramontano A, Valencia A. An analysis of the Sargasso Sea resource and the consequences for database composition. Bmc Bioinformatics. 7: 213. PMID 16623953 DOI: 10.1186/1471-2105-7-213  1
2006 Pazos F, Rausell A, Valencia A. Phylogeny-independent detection of functional residues. Bioinformatics (Oxford, England). 22: 1440-8. PMID 16551661 DOI: 10.1093/bioinformatics/btl104  1
2006 Hahn U, Valencia A. Semantic mining in biomedicine (Introduction to the papers selected from the SMBM 2005 Symposium, Hinxton, U.K., April 2005) Bioinformatics. 22: 643-644. PMID 16527834 DOI: 10.1093/bioinformatics/btl084  1
2006 Valencia A, Bateman A. Software patents in Bioinformatics Bioinformatics. 22: 1415. DOI: 10.1093/bioinformatics/btl166  1
2005 Hoffmann R, Valencia A. Implementing the iHOP concept for navigation of biomedical literature Bioinformatics. 21. PMID 16204114 DOI: 10.1093/bioinformatics/bti1142  1
2005 Blaschke C, Yeh A, Camon E, Colosimo M, Apweiler R, Hirschman L, Valencia A. Do you do text? Bioinformatics. 21: 4199-4200. PMID 16195360 DOI: 10.1093/bioinformatics/bti695  1
2005 Graña O, Baker D, MacCallum RM, Meiler J, Punta M, Rost B, Tress ML, Valencia A. CASP6 assessment of contact prediction. Proteins. 61: 214-24. PMID 16187364 DOI: 10.1002/prot.20739  1
2005 Tress M, Ezkurdia I, Graña O, López G, Valencia A. Assessment of predictions submitted for the CASP6 comparative modeling category. Proteins. 61: 27-45. PMID 16187345 DOI: 10.1002/prot.20720  1
2005 Tress M, Tai CH, Wang G, Ezkurdia I, López G, Valencia A, Lee B, Dunbrack RL. Domain definition and target classification for CASP6. Proteins. 61: 8-18. PMID 16187342 DOI: 10.1002/prot.20717  1
2005 Rojas AM, Sanchez-Pulido L, Fütterer A, van Wely KH, Martinez-A C, Valencia A. Death inducer obliterator protein 1 in the context of DNA regulation. Sequence analyses of distant homologues point to a novel functional role. The Febs Journal. 272: 3505-11. PMID 16008551 DOI: 10.1111/j.1742-4658.2005.04759.x  0.96
2005 Krallinger M, Valencia A. Text-mining and information-retrieval services for molecular biology Genome Biology. 6. PMID 15998455 DOI: 10.1186/gb-2005-6-7-224  1
2005 Tress M, de Juan D, Graña O, Gómez MJ, Gómez-Puertas P, González JM, López G, Valencia A. Scoring docking models with evolutionary information. Proteins. 60: 275-80. PMID 15981273 DOI: 10.1002/prot.20570  1
2005 Graña O, Eyrich VA, Pazos F, Rost B, Valencia A. EVAcon: a protein contact prediction evaluation service. Nucleic Acids Research. 33: W347-51. PMID 15980486 DOI: 10.1093/nar/gki411  1
2005 Valencia A. Automatic annotation of protein function Current Opinion in Structural Biology. 15: 267-274. PMID 15922590 DOI: 10.1016/  1
2005 Krallinger M, Erhardt RAA, Valencia A. Text-mining approaches in molecular biology and biomedicine Drug Discovery Today. 10: 439-445. PMID 15808823 DOI: 10.1016/S1359-6446(05)03376-3  1
2005 Valencia A. Protein refinement: A new challenge for CASP in its 10th anniversary Bioinformatics. 21: 277. PMID 15647301 DOI: 10.1093/bioinformatics/bti249  1
2005 Bateman A, Valencia A. An update from the Bioinformatics Editors Bioinformatics. 21: 4319. DOI: 10.1093/bioinformatics/bti768  1
2005 Valencia A, Bateman A. Increasing the impact of Bioinformatics Bioinformatics. 21: 1. DOI: 10.1093/bioinformatics/bti185  1
2005 Krallinger M, Valencia A. Applications of Text Mining in Molecular Biology, from Name Recognition to Protein Interaction Maps Data Analysis and Visualization in Genomics and Proteomics. 41-59. DOI: 10.1002/0470094419.ch4  1
2004 Sanchez-Pulido L, Rojas AM, Valencia A, Martinez-A C, Andrade MA. ACRATA: a novel electron transfer domain associated to apoptosis and cancer. Bmc Cancer. 4: 98. PMID 15623366 DOI: 10.1186/1471-2407-4-98  1
2004 Sánchez-Pulido L, Rojas AM, van Wely KH, Martinez-A C, Valencia A. SPOC: a widely distributed domain associated with cancer, apoptosis and transcription. Bmc Bioinformatics. 5: 91. PMID 15239844 DOI: 10.1186/1471-2105-5-91  0.96
2004 Hoffmann R, Valencia A. A gene network for navigating the literature [2] Nature Genetics. 36: 664. PMID 15226743 DOI: 10.1038/ng0704-664  1
2004 Fernández JM, Valencia A. YAdumper: Extracting and translating large information volumes from relational databases to structured flat files Bioinformatics. 20: 2455-2457. PMID 15117748 DOI: 10.1093/bioinformatics/bth243  1
2004 Tress ML, Graña O, Valencia A. SQUARE--determining reliable regions in sequence alignments. Bioinformatics (Oxford, England). 20: 974-5. PMID 14764569 DOI: 10.1093/bioinformatics/bth032  1
2004 Hermjakob H, Montecchi-Palazzi L, Lewington C, Mudali S, Kerrien S, Orchard S, Vingron M, Roechert B, Roepstorff P, Valencia A, Margalit H, Armstrong J, Bairoch A, Cesareni G, Sherman D, et al. IntAct: an open source molecular interaction database. Nucleic Acids Research. 32: D452-5. PMID 14681455 DOI: 10.1093/nar/gkh052  1
2004 Bateman A, Valencia A. New leadership for Bioinformatics Bioinformatics. 20: 1821. DOI: 10.1093/bioinformatics/bth403  1
2003 Blaschke C, Valencia A. Automatic classification of protein functions from the literature. Comparative and Functional Genomics. 4: 75-9. PMID 18629110 DOI: 10.1002/cfg.241  1
2003 Gomez-Puertas P, Valencia A. ESF Programme on 'Integrated Approaches for Functional Genomics' Workshop on 'Modelling of Molecular Networks'. Comparative and Functional Genomics. 4: 144-7. PMID 18629106 DOI: 10.1002/cfg.224  1
2003 Valencia A. Multiple sequence alignments as tools for protein structure and function prediction. Comparative and Functional Genomics. 4: 424-7. PMID 18629077 DOI: 10.1002/cfg.313  1
2003 Hoffmann R, Valencia A. Protein interaction: Same network, different hubs Trends in Genetics. 19: 681-683. PMID 14642746 DOI: 10.1016/j.tig.2003.10.011  1
2003 Ouzounis CA, Valencia A. Early bioinformatics: the birth of a discipline--a personal view. Bioinformatics (Oxford, England). 19: 2176-90. PMID 14630646 DOI: 10.1093/bioinformatics/btg309  1
2003 Abascal F, Valencia A. Automatic Annotation of Protein Function Based on Family Identification Proteins: Structure, Function and Genetics. 53: 683-692. PMID 14579359 DOI: 10.1002/prot.10449  1
2003 Eyrich VA, Przybylski D, Koh IY, Grana O, Pazos F, Valencia A, Rost B. CAFASP3 in the spotlight of EVA. Proteins. 53: 548-60. PMID 14579345 DOI: 10.1002/prot.10534  1
2003 Tress ML, Jones D, Valencia A. Predicting reliable regions in protein alignments from sequence profiles. Journal of Molecular Biology. 330: 705-18. PMID 12850141 DOI: 10.1016/S0022-2836(03)00622-3  1
2003 Koh IY, Eyrich VA, Marti-Renom MA, Przybylski D, Madhusudhan MS, Eswar N, Graña O, Pazos F, Valencia A, Sali A, Rost B. EVA: Evaluation of protein structure prediction servers. Nucleic Acids Research. 31: 3311-5. PMID 12824315 DOI: 10.1093/nar/gkg619  1
2003 Valencia A. Meta, MetaN and cyber servers Bioinformatics. 19: 795. PMID 12724287 DOI: 10.1093/bioinformatics/btg215  1
2003 Iliopoulos I, Tsoka S, Andrade MA, Enright AJ, Carroll M, Poullet P, Promponas V, Liakopoulos T, Palaios G, Pasquier C, Hamodrakas S, Tamames J, Yagnik AT, Tramontano A, Devos D, ... ... Valencia A, et al. Evaluation of annotation strategies using an entire genome sequence. Bioinformatics (Oxford, England). 19: 717-26. PMID 12691983 DOI: 10.1093/bioinformatics/btg077  1
2003 Hoffmann R, Valencia A. Life cycles of successful genes Trends in Genetics. 19: 79-81. PMID 12547515 DOI: 10.1016/S0168-9525(02)00014-8  1
2002 Alonso-Allende R, Fernández-González JM, Graña O, Valencia A. The REGIA database (RegiaDB): status, limitations and future developments. Comparative and Functional Genomics. 3: 109-14. PMID 18628844 DOI: 10.1002/cfg.144  0.64
2002 Blaschke C, Hirschman L, Valencia A. Information extraction in molecular biology Briefings in Bioinformatics. 3: 154-165. PMID 12139435 DOI: 10.1093/BIB/3.2.154  1
2002 Valencia A, Pazos F. Computational methods for the prediction of protein interactions Current Opinion in Structural Biology. 12: 368-373. PMID 12127457 DOI: 10.1016/S0959-440X(02)00333-0  1
2002 Abascal F, Valencia A. Clustering of proximal sequence space for the identification of protein families Bioinformatics. 18: 908-921. PMID 12117788 DOI: 10.1093/bioinformatics/18.7.908  1
2002 De Daruvar A, Collado-Vides J, Valencia A. Analysis of the cellular functions of Escherichia coli operons and their conservation in Bacillus subtilis Journal of Molecular Evolution. 55: 211-221. PMID 12107597 DOI: 10.1007/s00239-002-2317-1  1
2002 Jensen LJ, Gupta R, Blom N, Devos D, Tamames J, Kesmir C, Nielsen H, Staerfeldt HH, Rapacki K, Workman C, Andersen CA, Knudsen S, Krogh A, Valencia A, Brunak S. Prediction of human protein function from post-translational modifications and localization features. Journal of Molecular Biology. 319: 1257-65. PMID 12079362 DOI: 10.1016/S0022-2836(02)00379-0  1
2002 Pazos F, Valencia A. In silico two-hybrid system for the selection of physically interacting protein pairs Proteins: Structure, Function and Genetics. 47: 219-227. PMID 11933068 DOI: 10.1002/prot.10074  1
2002 Blaschke C, Valencia A. The frame-based module of the SUISEKI information extraction system Ieee Intelligent Systems and Their Applications. 17: 14-20. DOI: 10.1109/5254.999215  1
2002 Valencia A. Search and retrieve. Large-scale data generation is becoming increasingly important in biological research. But how good are the tools to make sense of the data? Embo Reports. 3: 396-400. DOI: 10.1093/embo-reports/kvf104  1
2002 Valencia A. Bioinformatics and computational biology at the crossroads of post-genomic technology Phytochemistry Reviews. 1: 209-214. DOI: 10.1023/A:1022563518121  1
2001 Fischer D, Elofsson A, Rychlewski L, Pazos F, Valencia A, Rost B, Ortiz AR, Dunbrack RL. CAFASP2: the second critical assessment of fully automated structure prediction methods. Proteins. 171-83. PMID 11835495 DOI: 10.1002/prot.10036  1
2001 Blaschke C, Oliveros JC, Valencia A. Mining functional information associated with expression arrays Functional and Integrative Genomics. 1: 256-268. PMID 11793245 DOI: 10.1007/s101420000036  1
2001 Pazos F, Valencia A. Similarity of phylogenetic trees as indicator of protein-protein interaction Protein Engineering. 14: 609-614. PMID 11707606 DOI: 10.1093/PROTEIN/14.9.609  1
2001 Iliopoulos I, Tsoka S, Andrade MA, Janssen P, Audit B, Tramontano A, Valencia A, Leroy C, Sander C, Ouzounis CA. Genome sequences and great expectations. Genome Biology. 2: INTERACTIONS0001. PMID 11178275 DOI: 10.1186/gb-2000-2-1-interactions0001  1
2001 Blaschke C, Valencia A. Can bibliographic pointers for known biological data be found automatically? Protein interactions as a case study Comparative and Functional Genomics. 2: 196-206. DOI: 10.1002/cfg.91  1
1998 Pons T, Olmea O, Chinea G, Beldarraín A, Márquez G, Acosta N, Rodríguez L, Valencia A. Structural model for family 32 of glycosyl-hydrolase enzymes. Proteins. 33: 383-95. PMID 9829697 DOI: 10.1002/(SICI)1097-0134(19981115)33:3<383::AID-PROT7>3.0.CO;2-R  0.48
1998 Tamames J, Ouzounis C, Casari G, Sander C, Valencia A. EUCLID : Automatic classification of proteins in functional classes by their database annotations Bioinformatics. 14: 542-543. PMID 9694995 DOI: 10.1093/bioinformatics/14.6.542  1
1998 Pons T, Chinea G, Olmea O, Beldarraín A, Roca H, Padrón G, Valencia A. Structural model of Dex protein from Penicillium minioluteum and its implications in the mechanism of catalysis. Proteins. 31: 345-54. PMID 9626695 DOI: 10.1002/(SICI)1097-0134(19980601)31:4<345::AID-PROT2>3.0.CO;2-H  0.48
1997 Andrade M, Casari G, de Daruvar A, Sander C, Schneider R, Tamames J, Valencia A, Ouzounis C. Sequence analysis of the Methanococcus jannaschii genome and the prediction of protein function. Computer Applications in the Biosciences : Cabios. 13: 481-3. PMID 9283767 DOI: 10.1093/bioinformatics/13.4.481  1
1997 Andrade MA, Casari G, Sander C, Valencia A. Classification of protein families and detection of the determinant residues with an improved self-organizing map. Biological Cybernetics. 76: 441-50. PMID 9263431 DOI: 10.1007/s004220050357  0.4
1997 Olmea O, Valencia A. Improving contact predictions by the combination of correlated mutations and other sources of sequence information Folding and Design. 2. PMID 9218963 DOI: 10.1016/S1359-0278(97)00060-6  1
1997 Tamames J, Casari G, Ouzounis C, Valencia A. Conserved clusters of functionally related genes in two bacterial genomes Journal of Molecular Evolution. 44: 66-73. PMID 9010137 DOI: 10.1007/PL00006122  1
1995 Ouzounis C, Valencia A, Tamames J, Bork P, Sander C. The functional composition of living machines as a design principle for artificial organisms Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 929: 843-851. DOI: 10.1007/3-540-59496-5_347  1
1994 Buchberger A, Valencia A, McMacken R, Sander C, Bukau B. The chaperone function of DnaK requires the coupling of ATPase activity with substrate binding through residue E171 Embo Journal. 13: 1687-1695. PMID 7908876  1
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