| Year |
Citation |
Score |
| 2024 |
Niarakis A, Ostaszewski M, Mazein A, Kuperstein I, Kutmon M, Gillespie ME, Funahashi A, Acencio ML, Hemedan A, Aichem M, Klein K, Czauderna T, Burtscher F, Yamada TG, Hiki Y, ... ... Valencia A, et al. Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches. Frontiers in Immunology. 14: 1282859. PMID 38414974 DOI: 10.3389/fimmu.2023.1282859 |
0.416 |
|
| 2023 |
Armaos A, Serra F, Núñez-Carpintero I, Seo JH, Baca SC, Gustincich S, Valencia A, Freedman ML, Cirillo D, Giambartolomei C, Tartaglia GG. The PENGUIN approach to reconstruct protein interactions at enhancer-promoter regions and its application to prostate cancer. Nature Communications. 14: 8084. PMID 38057321 DOI: 10.1038/s41467-023-43767-1 |
0.762 |
|
| 2023 |
Ponce-de-Leon M, Montagud A, Noël V, Meert A, Pradas G, Barillot E, Calzone L, Valencia A. PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks. Npj Systems Biology and Applications. 9: 54. PMID 37903760 DOI: 10.1038/s41540-023-00314-4 |
0.776 |
|
| 2023 |
Tomás-Daza L, Rovirosa L, López-Martí P, Nieto-Aliseda A, Serra F, Planas-Riverola A, Molina O, McDonald R, Ghevaert C, Cuatrecasas E, Costa D, Camós M, Bueno C, Menéndez P, Valencia A, et al. Low input capture Hi-C (liCHi-C) identifies promoter-enhancer interactions at high-resolution. Nature Communications. 14: 268. PMID 36650138 DOI: 10.1038/s41467-023-35911-8 |
0.55 |
|
| 2022 |
Harms RL, Ferrari A, Meier IB, Martinkova J, Santus E, Marino N, Cirillo D, Mellino S, Catuara Solarz S, Tarnanas I, Szoeke C, Hort J, Valencia A, Ferretti MT, Seixas A, et al. Digital biomarkers and sex impacts in Alzheimer's disease management - potential utility for innovative 3P medicine approach. The Epma Journal. 13: 299-313. PMID 35719134 DOI: 10.1007/s13167-022-00284-3 |
0.662 |
|
| 2022 |
Ponce-de-Leon M, Montagud A, Akasiadis C, Schreiber J, Ntiniakou T, Valencia A. Optimizing Dosage-Specific Treatments in a Multi-Scale Model of a Tumor Growth. Frontiers in Molecular Biosciences. 9: 836794. PMID 35463947 DOI: 10.3389/fmolb.2022.836794 |
0.683 |
|
| 2022 |
Montagud A, Béal J, Tobalina L, Traynard P, Subramanian V, Szalai B, Alföldi R, Puskás L, Valencia A, Barillot E, Saez-Rodriguez J, Calzone L. Patient-specific Boolean models of signalling networks guide personalised treatments. Elife. 11. PMID 35164900 DOI: 10.7554/eLife.72626 |
0.775 |
|
| 2021 |
Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, ... ... Valencia A, et al. COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Molecular Systems Biology. 17: e10851. PMID 34939300 DOI: 10.15252/msb.202110851 |
0.756 |
|
| 2021 |
Ponce-de-Leon M, Del Valle J, Fernandez JM, Bernardo M, Cirillo D, Sanchez-Valle J, Smith M, Capella-Gutierrez S, Gullón T, Valencia A. COVID-19 Flow-Maps an open geographic information system on COVID-19 and human mobility for Spain. Scientific Data. 8: 310. PMID 34848723 DOI: 10.1038/s41597-021-01093-5 |
0.67 |
|
| 2021 |
Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, ... ... Valencia A, et al. COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Molecular Systems Biology. 17: e10387. PMID 34664389 DOI: 10.15252/msb.202110387 |
0.78 |
|
| 2021 |
Richart L, Lapi E, Pancaldi V, Cuenca-Ardura M, Pau EC, Madrid-Mencía M, Neyret-Kahn H, Radvanyi F, Rodríguez JA, Cuartero Y, Serra F, Le Dily F, Valencia A, Marti-Renom MA, Real FX. STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells. Nucleic Acids Research. PMID 34648034 DOI: 10.1093/nar/gkab864 |
0.574 |
|
| 2021 |
Forés-Martos J, Boullosa C, Rodrigo-Domínguez D, Sánchez-Valle J, Suay-García B, Climent J, Falcó A, Valencia A, Puig-Butillé JA, Puig S, Tabarés-Seisdedos R. Transcriptomic and Genetic Associations between Alzheimer's Disease, Parkinson's Disease, and Cancer. Cancers. 13. PMID 34203763 DOI: 10.3390/cancers13122990 |
0.772 |
|
| 2021 |
Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, ... ... Valencia A, et al. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. PMID 33953289 DOI: 10.1038/s41375-021-01251-z |
0.494 |
|
| 2021 |
Núñez-Carpintero I, Petrizzelli M, Zinovyev A, Cirillo D, Valencia A. The multilayer community structure of medulloblastoma. Iscience. 24: 102365. PMID 33889829 DOI: 10.1016/j.isci.2021.102365 |
0.764 |
|
| 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 |
0.767 |
|
| 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 |
0.683 |
|
| 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 |
0.64 |
|
| 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 |
0.657 |
|
| 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 |
0.305 |
|
| 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 |
0.616 |
|
| 2020 |
Malod-Dognin N, Pancaldi V, Valencia A, Pržulj N. Chromatin network markers of leukemia. Bioinformatics (Oxford, England). 36: i455-i463. PMID 32657405 DOI: 10.1093/Bioinformatics/Btaa445 |
0.319 |
|
| 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 |
0.348 |
|
| 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 |
0.662 |
|
| 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 |
0.617 |
|
| 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 |
0.612 |
|
| 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 |
0.334 |
|
| 2020 |
Porta-Pardo E, Valencia A, Godzik A. Understanding oncogenicity of cancer driver genes and mutations in the cancer genomics era. Febs Letters. PMID 32239503 DOI: 10.1002/1873-3468.13781 |
0.325 |
|
| 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 |
0.305 |
|
| 2019 |
Ponce-de-León M, Apaolaza I, Valencia A, Planes FJ. On the inconsistent treatment of gene-protein-reaction rules in context-specific metabolic models. Bioinformatics (Oxford, England). PMID 31722383 DOI: 10.1093/Bioinformatics/Btz832 |
0.311 |
|
| 2019 |
Saunders G, Baudis M, Becker R, Beltran S, Béroud C, Birney E, Brooksbank C, Brunak S, Van den Bulcke M, Drysdale R, Capella-Gutierrez S, Flicek P, Florindi F, Goodhand P, Gut I, ... ... Valencia A, et al. Leveraging European infrastructures to access 1 million human genomes by 2022. Nature Reviews. Genetics. PMID 31455890 DOI: 10.1038/S41576-019-0156-9 |
0.311 |
|
| 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 |
0.769 |
|
| 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 |
0.624 |
|
| 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 |
0.695 |
|
| 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 |
0.586 |
|
| 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 |
0.529 |
|
| 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 |
0.305 |
|
| 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 |
0.323 |
|
| 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 |
0.655 |
|
| 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 |
0.567 |
|
| 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 |
0.314 |
|
| 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 |
0.612 |
|
| 2017 |
Frenkel-Morgenstern M, Gorohovski A, Tagore S, Sekar V, Vazquez M, Valencia A. ChiPPI: a novel method for mapping chimeric protein-protein interactions uncovers selection principles of protein fusion events in cancer. Nucleic Acids Research. PMID 28549153 DOI: 10.1093/Nar/Gkx423 |
0.353 |
|
| 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 |
0.306 |
|
| 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 |
0.638 |
|
| 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 |
0.53 |
|
| 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 |
0.388 |
|
| 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 |
0.607 |
|
| 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 |
0.594 |
|
| 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 |
0.557 |
|
| 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 |
0.548 |
|
| 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 |
0.509 |
|
| 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 |
0.65 |
|
| 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 |
0.793 |
|
| 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 |
0.351 |
|
| 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 |
0.566 |
|
| 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 |
0.362 |
|
| 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 |
0.313 |
|
| 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 |
0.556 |
|
| 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. Abstract LB-129: Epigenetic regulators to predict docetaxel sensitivity; a guide for treatment choice Cancer Research. 76. DOI: 10.1158/1538-7445.Am2016-Lb-129 |
0.319 |
|
| 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 |
0.569 |
|
| 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 |
0.632 |
|
| 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 |
0.356 |
|
| 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 |
0.394 |
|
| 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 |
0.598 |
|
| 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 |
0.651 |
|
| 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 |
0.539 |
|
| 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 |
0.576 |
|
| 2015 |
Rodriguez JM, Carro A, Valencia A, Tress ML. APPRIS WebServer and WebServices. Nucleic Acids Research. PMID 25990727 DOI: 10.1093/Nar/Gkv512 |
0.669 |
|
| 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 |
0.634 |
|
| 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 |
0.301 |
|
| 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 |
0.359 |
|
| 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 |
0.591 |
|
| 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 |
0.654 |
|
| 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 |
0.654 |
|
| 2015 |
Ochoa D, Juan D, Valencia A, Pazos F. Detection of significant protein coevolution. Bioinformatics (Oxford, England). PMID 25717190 DOI: 10.1093/Bioinformatics/Btv102 |
0.349 |
|
| 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 |
0.317 |
|
| 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 |
0.539 |
|
| 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 |
0.639 |
|
| 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 |
0.348 |
|
| 2015 |
Piñeiro-Yáñez E, Reboiro-Jato M, Perales-Patón J, Glez-Peña D, Tejero H, Shimamura T, Carretero J, Valencia A, Hidalgo M, Al-Shahrour F. Abstract A22: PanDrugsDB: Identifying druggable genetic dependencies for personalized cancer therapy Molecular Cancer Therapeutics. 14. DOI: 10.1158/1535-7163.Targ-15-A22 |
0.347 |
|
| 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 |
0.566 |
|
| 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 |
0.388 |
|
| 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 |
0.55 |
|
| 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 |
0.631 |
|
| 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 |
0.357 |
|
| 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 |
0.638 |
|
| 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 |
0.758 |
|
| 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 |
0.576 |
|
| 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 |
0.779 |
|
| 2014 |
Ferreira PG, Jares P, Rico D, Gómez-López G, MartÃnez-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 |
0.578 |
|
| 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 |
0.787 |
|
| 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 |
0.752 |
|
| 2014 |
Kulis M, Heath S, Castellano G, Beekman R, Merkel A, Raineri E, Esteve A, Queirós AC, Clot G, Schuyler R, Ecker S, Pancaldi V, Rico D, Agueda L, Blanc J, ... ... Valencia A, et al. Characterization of the DNA Methylome during Human B-Cell Differentiation Blood. 124: 4346-4346. DOI: 10.1182/Blood.V124.21.4346.4346 |
0.541 |
|
| 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 |
0.333 |
|
| 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 |
0.528 |
|
| 2013 |
Balbás-MartÃnez 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, DomÃnguez 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 |
0.554 |
|
| 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 |
0.75 |
|
| 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 |
0.621 |
|
| 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/J.Sbi.2013.07.005 |
0.335 |
|
| 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 |
0.593 |
|
| 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 |
0.306 |
|
| 2013 |
de Juan D, Pazos F, Valencia A. Emerging methods in protein co-evolution. Nature Reviews. Genetics. 14: 249-61. PMID 23458856 DOI: 10.7490/F1000Research.1093968.1 |
0.363 |
|
| 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 |
0.34 |
|
| 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 |
0.811 |
|
| 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 |
0.755 |
|
| 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 |
0.364 |
|
| 2013 |
Maietta P, Lopez G, Rodriguez JM, Valencia A, Tress ML. FireDB and firestar - beyond functional annotation F1000research. 4. DOI: 10.7490/F1000Research.1094101.1 |
0.638 |
|
| 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. Correction: An Epistatic Interaction between the PAX8 and STK17B Genes in Papillary Thyroid Cancer Susceptibility Plos One. 8. DOI: 10.1371/Annotation/Cd94C3Eb-70F2-4Dfa-85Be-B3Fc41E495C3 |
0.736 |
|
| 2013 |
Garralda E, Paz K, López-Casas PP, Jones S, Katz A, Kann LM, López-Ríos F, Sarno F, Al-Shahrour F, Vasquez D, Bruckheimer E, Angiuoli SV, Diaz LA, Valencia A, Velculescu VE, et al. Integrated genomics and avatar mouse models for personalized cancer treatment. Journal of Clinical Oncology. 31: 2511-2511. DOI: 10.1200/Jco.2013.31.15_Suppl.2511 |
0.337 |
|
| 2013 |
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, Diaz LA, Valencia A, Velculescu VE, et al. Abstract 2205: Integrated next generation sequencing and patient-derived xenografts to personalized cancer treatment. Cancer Research. 73: 2205-2205. DOI: 10.1158/1538-7445.Am2013-2205 |
0.319 |
|
| 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 |
0.336 |
|
| 2012 |
Kulis M, Heath S, Bibikova M, Queirós AC, Navarro A, Clot G, MartÃnez-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 |
0.545 |
|
| 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 |
0.334 |
|
| 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 |
0.724 |
|
| 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 |
0.647 |
|
| 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 |
0.372 |
|
| 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 |
0.38 |
|
| 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 |
0.367 |
|
| 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 |
0.635 |
|
| 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 |
0.328 |
|
| 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 |
0.327 |
|
| 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 |
0.666 |
|
| 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 |
0.373 |
|
| 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 |
0.312 |
|
| 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 |
0.312 |
|
| 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 |
0.79 |
|
| 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 |
0.635 |
|
| 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 |
0.713 |
|
| 2012 |
Quesada V, Conde L, Villamor N, Ordóñez GR, Jares P, Bassaganyas L, Ramsay AJ, Beà S, Pinyol M, MartÃnez-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 |
0.319 |
|
| 2012 |
Garralda E, Calles A, López-Ríos F, Jones S, Kann LM, Angiuoli SV, Diaz LA, Velculescu VE, López-Casas PP, Sarno F, Martinez R, Gomez-Martin C, Conde E, Belda-Iniesta C, Valencia A, et al. Integrated next-generation sequencing and patient-derived xenografts to personalized cancer treatment. Journal of Clinical Oncology. 30: 3068-3068. DOI: 10.1200/Jco.2012.30.15_Suppl.3068 |
0.3 |
|
| 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 |
0.301 |
|
| 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 |
0.56 |
|
| 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 |
0.305 |
|
| 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 |
0.314 |
|
| 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 |
0.304 |
|
| 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 |
0.788 |
|
| 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 |
0.311 |
|
| 2011 |
Tabarés-Seisdedos R, Dumont N, Baudot A, Valderas JM, Climent J, Valencia A, Crespo-Facorro B, Vieta E, Gómez-Beneyto M, MartÃnez 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 |
0.615 |
|
| 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 |
0.63 |
|
| 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 |
0.552 |
|
| 2011 |
Glaab E, Baudot A, Krasnogor N, Valencia A. PathExpand: Extending biological pathways using molecular interaction networks Nature Precedings. DOI: 10.1038/Npre.2011.5639.1 |
0.601 |
|
| 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 |
0.672 |
|
| 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 |
0.628 |
|
| 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 |
0.316 |
|
| 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 |
0.322 |
|
| 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 |
0.562 |
|
| 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 |
0.609 |
|
| 2010 |
Hudson TJ, Anderson W, Artez A, Barker AD, Bell C, Bernabé RR, Bhan MK, Calvo F, Eerola I, Gerhard DS, Guttmacher A, Guyer M, Hemsley FM, Jennings JL, ... ... Valencia A, ... ... Valencia A, ... ... Valencia A, et al. International network of cancer genome projects. Nature. 464: 993-8. PMID 20393554 DOI: 10.1038/Nature08987 |
0.616 |
|
| 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 |
0.389 |
|
| 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 |
0.624 |
|
| 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 |
0.365 |
|
| 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 |
0.722 |
|
| 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 |
0.384 |
|
| 2010 |
Searle S, Frankish A, Bignell A, Aken B, Derrien T, Diekhans M, Harte R, Howald C, Kokocinski F, Lin M, Tress M, Van Baren M, Barnes I, Hunt T, Carvalho-Silva D, ... ... Valencia A, et al. The GENCODE human gene set Genome Biology. 11: P36. DOI: 10.1186/Gb-2010-11-S1-P36 |
0.629 |
|
| 2010 |
Krallinger M, Tendulkar AV, Leitner F, Chatr-aryamontri A, Valencia A. The PPI affix dictionary (PPIAD) and BioMethod Lexicon: importance of affixes and tags for recognition of entity mentions and experimental protein interactions Bmc Bioinformatics. 11: 1-3. DOI: 10.1186/1471-2105-11-S5-O1 |
0.351 |
|
| 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 |
0.588 |
|
| 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 |
0.34 |
|
| 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 |
0.342 |
|
| 2009 |
Izarzugaza JM, Redfern OC, Orengo CA, Valencia A. Cancer-associated mutations are preferentially distributed in protein kinase functional sites. Proteins. 77: 892-903. PMID 19626714 DOI: 10.1002/Prot.22512 |
0.338 |
|
| 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 |
0.6 |
|
| 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 |
0.327 |
|
| 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 |
0.333 |
|
| 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 |
0.65 |
|
| 2009 |
Fernandez-Ballester G, Beltrao P, Gonzalez JM, Song YH, Wilmanns M, Valencia A, Serrano L. Structure-based prediction of the Saccharomyces cerevisiae SH3-ligand interactions. Journal of Molecular Biology. 388: 902-16. PMID 19324052 DOI: 10.1016/J.Jmb.2009.03.038 |
0.37 |
|
| 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 |
0.64 |
|
| 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 |
0.658 |
|
| 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 |
0.347 |
|
| 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 |
0.327 |
|
| 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 |
0.329 |
|
| 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 |
0.612 |
|
| 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 |
0.303 |
|
| 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 |
0.303 |
|
| 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 |
0.502 |
|
| 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 |
0.32 |
|
| 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 |
0.361 |
|
| 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 |
0.357 |
|
| 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 |
0.3 |
|
| 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 |
0.332 |
|
| 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 |
0.355 |
|
| 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 |
0.322 |
|
| 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 |
0.346 |
|
| 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 |
0.328 |
|
| 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 |
0.38 |
|
| 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 |
0.734 |
|
| 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 |
0.617 |
|
| 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 |
0.691 |
|
| 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 |
0.719 |
|
| 2007 |
Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, ... ... Valencia A, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874 |
0.655 |
|
| 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 |
0.362 |
|
| 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 |
0.337 |
|
| 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 |
0.651 |
|
| 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 |
0.72 |
|
| 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 DOI: 10.11234/Gi1990.17.2_121 |
0.358 |
|
| 2006 |
Izarzugaza JM, Juan D, Pons C, Ranea JA, Valencia A, Pazos F. TSEMA: interactive prediction of protein pairings between interacting families. Nucleic Acids Research. 34: W315-9. PMID 16845017 DOI: 10.1093/Nar/Gkl112 |
0.318 |
|
| 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 |
0.631 |
|
| 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 |
0.631 |
|
| 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 |
0.713 |
|
| 2005 |
Hoffmann R, Valencia A. Implementing the iHOP concept for navigation of biomedical literature Bioinformatics. 21. PMID 16204114 DOI: 10.1093/Bioinformatics/Bti1142 |
0.334 |
|
| 2005 |
de Juan D, Mellado M, Rodríguez-Frade JM, Hernanz-Falcón P, Serrano A, del Sol A, Valencia A, Martínez-A C, Rojas AM. A framework for computational and experimental methods: identifying dimerization residues in CCR chemokine receptors. Bioinformatics (Oxford, England). 21: ii13-8. PMID 16204091 DOI: 10.1093/Bioinformatics/Bti1101 |
0.313 |
|
| 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 |
0.68 |
|
| 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 |
0.703 |
|
| 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 |
0.696 |
|
| 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 |
0.357 |
|
| 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 |
0.321 |
|
| 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 |
0.729 |
|
| 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 |
0.503 |
|
| 2005 |
Krallinger M, Padron M, Valencia A. A sentence sliding window approach to extract protein annotations from biomedical articles. Bmc Bioinformatics. S19. PMID 15960831 DOI: 10.1186/1471-2105-6-S1-S19 |
0.327 |
|
| 2005 |
Blaschke C, Leon EA, Krallinger M, Valencia A. Evaluation of BioCreAtIvE assessment of task 2. Bmc Bioinformatics. S16. PMID 15960828 DOI: 10.1186/1471-2105-6-S1-S16 |
0.373 |
|
| 2005 |
Hirschman L, Yeh A, Blaschke C, Valencia A. Overview of BioCreAtIvE: critical assessment of information extraction for biology. Bmc Bioinformatics. 6: S1. PMID 15960821 DOI: 10.1186/1471-2105-6-S1-S1 |
0.321 |
|
| 2005 |
Valencia A. Automatic annotation of protein function Current Opinion in Structural Biology. 15: 267-274. PMID 15922590 DOI: 10.1016/J.Sbi.2005.05.010 |
0.383 |
|
| 2005 |
Hoffmann R, Krallinger M, Andres E, Tamames J, Blaschke C, Valencia A. Text Mining for Metabolic Pathways, Signaling Cascades, and Protein Networks Science Signaling. 2005. PMID 15886388 DOI: 10.1126/Stke.2832005Pe21 |
0.352 |
|
| 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 |
0.341 |
|
| 2005 |
Contreras-Moreira B, Ezkurdia I, Tress ML, Valencia A. Empirical limits for template-based protein structure prediction: the CASP5 example. Febs Letters. 579: 1203-7. PMID 15710414 DOI: 10.1016/J.Febslet.2005.01.014 |
0.63 |
|
| 2005 |
Pazos F, Guijas D, Valencia A, De Lorenzo V. MetaRouter: bioinformatics for bioremediation. Nucleic Acids Research. 33: D588-92. PMID 15608267 DOI: 10.1093/Nar/Gki068 |
0.331 |
|
| 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 |
0.322 |
|
| 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 |
0.624 |
|
| 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 |
0.327 |
|
| 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 |
0.373 |
|
| 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 |
0.301 |
|
| 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 |
0.375 |
|
| 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 |
0.343 |
|
| 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 |
0.397 |
|
| 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 |
0.519 |
|
| 2003 |
Balsera M, Arellano JB, Pazos F, Devos D, Valencia A, De Las Rivas J. The single tryptophan of the PsbQ protein of photosystem II is at the end of a 4-alpha-helical bundle domain. European Journal of Biochemistry / Febs. 270: 3916-27. PMID 14511373 DOI: 10.1046/J.1432-1033.2003.03774.X |
0.318 |
|
| 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 |
0.63 |
|
| 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 |
0.526 |
|
| 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 |
0.51 |
|
| 2003 |
del Sol A, del Sol Mesa A, Pazos F, Valencia A. Automatic methods for predicting functionally important residues. Journal of Molecular Biology. 326: 1289-302. PMID 12589769 DOI: 10.1016/S0022-2836(02)01451-1 |
0.35 |
|
| 2003 |
Juan D, Graña O, Pazos F, Fariselli P, Casadio R, Valencia A. A neural network approach to evaluate fold recognition results. Proteins. 50: 600-8. PMID 12577266 DOI: 10.1002/Prot.10322 |
0.348 |
|
| 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 |
0.313 |
|
| 2003 |
van Ham RC, Kamerbeek J, Palacios C, Rausell C, Abascal F, Bastolla U, Fernández JM, Jiménez L, Postigo M, Silva FJ, Tamames J, Viguera E, Latorre A, Valencia A, Morán F, et al. Reductive genome evolution in Buchnera aphidicola. Proceedings of the National Academy of Sciences of the United States of America. 100: 581-6. PMID 12522265 DOI: 10.1073/Pnas.0235981100 |
0.35 |
|
| 2003 |
Carettoni D, Gómez-Puertas P, Yim L, Mingorance J, Massidda O, Vicente M, Valencia A, Domenici E, Anderluzzi D. Phage-display and correlated mutations identify an essential region of subdomain 1C involved in homodimerization of Escherichia coli FtsA. Proteins. 50: 192-206. PMID 12486713 DOI: 10.1002/Prot.10244 |
0.329 |
|
| 2003 |
Valencia A, Pazos F. Prediction of protein-protein interactions from evolutionary information. Methods of Biochemical Analysis. 44: 409-426. DOI: 10.1002/0471721204.Ch20 |
0.407 |
|
| 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 |
0.307 |
|
| 2002 |
Garcia-Ranea JA, Mirey G, Camonis J, Valencia A. p23 and HSP20/α-crystallin proteins define a conserved sequence domain present in other eukaryotic protein families Febs Letters. 529: 162-167. PMID 12372593 DOI: 10.1016/S0014-5793(02)03321-5 |
0.306 |
|
| 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 |
0.341 |
|
| 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 |
0.364 |
|
| 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 |
0.343 |
|
| 2002 |
Rost B, Honig B, Valencia A. Bioinformatics in structural genomics Bioinformatics. 18: 897-898. PMID 12117786 DOI: 10.1093/Bioinformatics/18.7.897 |
0.489 |
|
| 2002 |
Sánchez-Pulido L, Devos D, Valencia A. BRICHOS: a conserved domain in proteins associated with dementia, respiratory distress and cancer. Trends in Biochemical Sciences. 27: 329-32. PMID 12114016 DOI: 10.1016/S0968-0004(02)02134-5 |
0.306 |
|
| 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 |
0.312 |
|
| 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 |
0.358 |
|
| 2002 |
Devos D, Garmendia J, De Lorenzo V, Valencia A. Deciphering the action of aromatic effectors on the prokaryotic enhancer-binding protein XylR: A structural model of its N-terminal domain Environmental Microbiology. 4: 29-41. PMID 11966823 DOI: 10.1046/J.1462-2920.2002.00265.X |
0.335 |
|
| 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 |
0.347 |
|
| 2002 |
Fariselli P, Pazos F, Valencia A, Casadio R. Prediction of protein--protein interaction sites in heterocomplexes with neural networks. Febs Journal. 269: 1356-1361. PMID 11874449 DOI: 10.1046/J.1432-1033.2002.02767.X |
0.356 |
|
| 2002 |
Fariselli P, Olmea O, Valencia A, Casadio R. Progress in predicting inter-residue contacts of proteins with neural networks and correlated mutations. Proteins. 157-62. PMID 11835493 DOI: 10.1002/Prot.1173 |
0.362 |
|
| 2002 |
Fariselli P, Olmea O, Valencia A, Casadio R. Prediction of contact maps with neural networks and correlated mutations. Protein Engineering. 14: 835-43. PMID 11742102 DOI: 10.1093/Protein/14.11.835 |
0.351 |
|
| 2002 |
Ligos JM, Lera TLd, Hinderlich S, Guinea B, Sánchez L, Roca R, Valencia A, Bernad A. Functional Interaction between the Ser/Thr Kinase PKL12 and N-Acetylglucosamine Kinase, a Prominent Enzyme Implicated in the Salvage Pathway for GlcNAc Recycling Journal of Biological Chemistry. 277: 6333-6343. PMID 11741987 DOI: 10.1074/Jbc.M105766200 |
0.301 |
|
| 2002 |
Blaschke C, Valencia A. Automatic Ontology Construction from the Literature Genome Informatics. 13: 201-213. DOI: 10.11234/Gi1990.13.201 |
0.352 |
|
| 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 |
0.34 |
|
| 2002 |
Valencia A. Bioinformatics and computational biology at the crossroads of post-genomic technology Phytochemistry Reviews. 1: 209-214. DOI: 10.1023/A:1022563518121 |
0.406 |
|
| 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 |
0.511 |
|
| 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 |
0.345 |
|
| 2001 |
Eyrich VA, Martí-Renom MA, Przybylski D, Madhusudhan MS, Fiser A, Pazos F, Valencia A, Sali A, Rost B. EVA: continuous automatic evaluation of protein structure prediction servers. Bioinformatics (Oxford, England). 17: 1242-3. PMID 11751240 DOI: 10.1093/Bioinformatics/17.12.1242 |
0.531 |
|
| 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 |
0.382 |
|
| 2001 |
Garmendia J, Devos D, Valencia A, De Lorenzo V. À la carte transcriptional regulators: Unlocking responses of the prokaryotic enhancer-binding protein XylR to non-natural effectors Molecular Microbiology. 42: 47-59. PMID 11679066 DOI: 10.1046/J.1365-2958.2001.02633.X |
0.323 |
|
| 2001 |
Devos D, Valencia A. Intrinsic errors in genome annotation Trends in Genetics. 17: 429-431. PMID 11485799 DOI: 10.1016/S0168-9525(01)02348-4 |
0.345 |
|
| 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 |
0.537 |
|
| 2001 |
Blaschke C, Valencia A. The Potential Use of SUISEKI as a Protein Interaction Discovery Tool Genome Informatics. 12: 123-134. DOI: 10.11234/Gi1990.12.123 |
0.333 |
|
| 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 |
0.356 |
|
| 2000 |
Via A, Ferrè F, Brannetti B, Valencia A, Helmer-Citterich M. Three-dimensional view of the surface motif associated with the P-loop structure: cis and trans cases of convergent evolution. Journal of Molecular Biology. 303: 455-65. PMID 11054283 DOI: 10.1006/Jmbi.2000.4151 |
0.342 |
|
| 2000 |
Devos D, Valencia A. Practical limits of function prediction Proteins: Structure, Function and Genetics. 41: 98-107. PMID 10944397 DOI: 10.1002/1097-0134(20001001)41:1<98::Aid-Prot120>3.0.Co;2-S |
0.372 |
|
| 2000 |
Pazos F, Rost B, Valencia A. A platform for integrating threading results with protein family analyses. Bioinformatics (Oxford, England). 15: 1062-3. PMID 10745999 DOI: 10.1093/Bioinformatics/15.12.1062 |
0.527 |
|
| 2000 |
Olmea O, Rost B, Valencia A. Effective use of sequence correlation and conservation in fold recognition. Journal of Molecular Biology. 293: 1221-39. PMID 10547297 DOI: 10.1006/Jmbi.1999.3208 |
0.527 |
|
| 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 |
0.32 |
|
| 1999 |
Andrade MA, Ouzounis C, Sander C, Tamames J, Valencia A. Functional classes in the three domains of life Journal of Molecular Evolution. 49: 551-557. PMID 10552036 DOI: 10.1007/Pl00006576 |
0.492 |
|
| 1999 |
Azuma Y, Renault L, García-Ranea JA, Valencia A, Nishimoto T, Wittinghofer A. Model of the ran-RCC1 interaction using biochemical and docking experiments. Journal of Molecular Biology. 289: 1119-30. PMID 10369786 DOI: 10.1006/Jmbi.1999.2820 |
0.334 |
|
| 1999 |
Andrade MA, Brown NP, Leroy C, Hoersch S, De Daruvar A, Reich C, Franchini A, Tamames J, Valencia A, Ouzounis C, Sander C. Automated genome sequence analysis and annotation Bioinformatics. 15: 391-412. PMID 10366660 DOI: 10.1093/Bioinformatics/15.5.391 |
0.543 |
|
| 1998 |
Garcia-Ranea JA, Valencia A. Distribution and functional diversification of the ras superfamily in Saccharomyces cerevisiae Febs Letters. 434: 219-225. PMID 9742927 DOI: 10.1016/S0014-5793(98)00967-3 |
0.349 |
|
| 1998 |
Andrade MA, Valencia A. Automatic extraction of keywords from scientific text: Application to the knowledge domain of protein families Bioinformatics. 14: 600-607. PMID 9730925 DOI: 10.1093/Bioinformatics/14.7.600 |
0.379 |
|
| 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 |
0.509 |
|
| 1998 |
Trelles O, Andrade MA, Valencia A, Zapata EL, Carazo JM. Computational space reduction and parallelization of a new clustering approach for large groups of sequences. Bioinformatics (Oxford, England). 14: 439-51. PMID 9682057 DOI: 10.1093/Bioinformatics/14.5.439 |
0.305 |
|
| 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 |
0.352 |
|
| 1998 |
Andrade MA, Sander C, Valencia A. Updated catalogue of homologues to human disease-related proteins in the yeast genome Febs Letters. 426: 7-16. PMID 9598968 DOI: 10.1016/S0014-5793(98)00277-4 |
0.534 |
|
| 1998 |
Sancho E, Vilá MR, Sánchez-Pulido L, Lozano JJ, Paciucci R, Nadal M, Fox M, Harvey C, Bercovich B, Loukili N, Ciechanover A, Lin SL, Sanz F, Estivill X, Valencia A, et al. Role of UEV-1, an inactive variant of the E2 ubiquitin-conjugating enzymes, in in vitro differentiation and cell cycle behavior of HT-29-M6 intestinal mucosecretory cells Molecular and Cellular Biology. 18: 576-589. PMID 9418904 DOI: 10.1128/Mcb.18.1.576 |
0.32 |
|
| 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 |
0.617 |
|
| 1997 |
Pazos F, Helmer-Citterich M, Ausiello G, Valencia A. Correlated mutations contain information about protein-protein interaction. Journal of Molecular Biology. 271: 511-23. PMID 9281423 DOI: 10.1006/Jmbi.1997.1198 |
0.37 |
|
| 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 |
0.482 |
|
| 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 |
0.316 |
|
| 1997 |
Voss H, Benes V, Andrade MA, Valencia A, Rechmann S, Teodoru C, Schwager C, Paces V, Sander C, Ansorge W. DNA sequencing and analysis of 130 kb from yeast chromosome XV. Yeast (Chichester, England). 13: 655-72. PMID 9200815 DOI: 10.1002/(Sici)1097-0061(19970615)13:7<655::Aid-Yea120>3.0.Co;2-I |
0.527 |
|
| 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 |
0.361 |
|
| 1996 |
Ouzounis C, Casari G, Sander C, Tamames J, Valencia A. Computational comparisons of model genomes Trends in Biotechnology. 14: 280-285. PMID 8987458 DOI: 10.1016/0167-7799(96)10043-3 |
0.518 |
|
| 1996 |
Ouzounis C, Casari G, Valencia A, Sander C. Novelties from the complete genome of Mycoplasma genitalium [3] Molecular Microbiology. 20: 898-900. PMID 8793887 DOI: 10.1111/J.1365-2958.1996.Tb02529.X |
0.46 |
|
| 1996 |
Rost B, Valencia A. Pitfalls of protein sequence analysis. Commentary Current Opinion in Biotechnology. 7: 457-461. PMID 8768907 DOI: 10.1016/S0958-1669(96)80124-8 |
0.517 |
|
| 1996 |
Tamames J, Ouzounis C, Sander C, Valencia A. Genomes with distinct function composition Febs Letters. 389: 96-101. PMID 8682215 DOI: 10.1016/0014-5793(96)00527-3 |
0.537 |
|
| 1995 |
Voss H, Tamames J, Teodoru C, Valencia A, Sensen C, Wiemann S, Schwager C, Zimmermann J, Sander C, Ansorge W. Nucleotide sequence and analysis of the centromeric region of yeast chromosome IX. Yeast (Chichester, England). 11: 61-78. PMID 7762303 DOI: 10.1002/Yea.320110109 |
0.506 |
|
| 1995 |
Casari G, Sander C, Valencia A. A method to predict functional residues in proteins Nature Structural Biology. 2: 171-178. PMID 7749921 DOI: 10.1038/Nsb0295-171 |
0.524 |
|
| 1995 |
Casari G, Andrade MA, Bork P, Boyle J, Daruvar A, Ouzounis C, Schneider R, Tamames J, Valencia A, Sander C. Challenging times for bioinformatics. Nature. 376: 647-8. PMID 7651513 DOI: 10.1038/376647A0 |
0.55 |
|
| 1994 |
Göbel U, Sander C, Schneider R, Valencia A. Correlated mutations and residue contacts in proteins. Proteins. 18: 309-17. PMID 8208723 DOI: 10.1002/Prot.340180402 |
0.623 |
|
| 1993 |
Holmes KC, Sander C, Valencia A. A new ATP-binding fold in actin, hexokinase and Hsc70. Trends in Cell Biology. 3: 53-9. PMID 14731729 DOI: 10.1016/0962-8924(93)90161-S |
0.68 |
|
| 1993 |
Stouten PFW, Sander C, Wittinghofer A, Valencia A. How Does The Switch-Ii Region Of G-Domains Work Febs Letters. 320: 1-6. PMID 8462668 DOI: 10.1016/0014-5793(93)81644-F |
0.456 |
|
| 1993 |
Bork P, Sander C, Valencia A. Convergent evolution of similar enzymatic function on different protein folds: The hexokinase, ribokinase, and galactokinase families of sugar kinases Protein Science. 2: 31-40. PMID 8382990 DOI: 10.1002/Pro.5560020104 |
0.461 |
|
| 1992 |
Bork P, Sander C, Valencia A. An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins Proceedings of the National Academy of Sciences of the United States of America. 89: 7290-7294. PMID 1323828 DOI: 10.1073/Pnas.89.16.7290 |
0.513 |
|
| 1991 |
Valencia A, Kjeldgaard M, Pai EF, Sander C. GTPase domains of ras p21 oncogene protein and elongation factor Tu: analysis of three-dimensional structures, sequence families, and functional sites. Proceedings of the National Academy of Sciences of the United States of America. 88: 5443-7. PMID 2052624 DOI: 10.1073/Pnas.88.12.5443 |
0.499 |
|
| 1991 |
Valencia A, Chardin P, Wittinghofer A, Sander C. The ras protein family: Evolutionary tree and role of conserved amino acids Biochemistry. 30: 4637-4648. PMID 2029511 DOI: 10.1021/Bi00233A001 |
0.451 |
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