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BibTeX records: Alfonso Valencia
@article{DBLP:journals/biodb/MirandaEscaladaMLEGPVK23, author = {Antonio Miranda{-}Escalada and Farrokh Mehryary and Jouni Luoma and Darryl Estrada{-}Zavala and Luis Gasc{\'{o}} and Sampo Pyysalo and Alfonso Valencia and Martin Krallinger}, title = {Overview of DrugProt task at BioCreative {VII:} data and methods for large-scale text mining and knowledge graph generation of heterogenous chemical-protein relations}, journal = {Database J. Biol. Databases Curation}, volume = {2023}, year = {2023}, url = {https://doi.org/10.1093/database/baad080}, doi = {10.1093/DATABASE/BAAD080}, timestamp = {Sun, 31 Dec 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/biodb/MirandaEscaladaMLEGPVK23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/pasc/ClascaGMCV23, author = {Marc Clasc{\`{a}} and Marta Garcia{-}Gasulla and Arnau Montagud and Jos{\'{e}} Carbonell{-}Caballero and Alfonso Valencia}, editor = {Axel Huebl and Cristina Silvano and Timothy Robinson}, title = {Lessons Learned from a Performance Analysis and Optimization of a Multiscale Cellular Simulation}, booktitle = {Proceedings of the Platform for Advanced Scientific Computing Conference, {PASC} 2023, Davos, Switzerland, June 26-28, 2023}, pages = {4:1--4:10}, publisher = {{ACM}}, year = {2023}, url = {https://doi.org/10.1145/3592979.3593403}, doi = {10.1145/3592979.3593403}, timestamp = {Fri, 07 Jul 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/pasc/ClascaGMCV23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/corr/abs-2306-11544, author = {Marc Clasc{\`{a}} and Marta Garcia{-}Gasulla and Arnau Montagud and Jos{\'{e}} Carbonell{-}Caballero and Alfonso Valencia}, title = {Lessons learned from a performance analysis and optimization of a multiscale cellular simulation}, journal = {CoRR}, volume = {abs/2306.11544}, year = {2023}, url = {https://doi.org/10.48550/arXiv.2306.11544}, doi = {10.48550/ARXIV.2306.11544}, eprinttype = {arXiv}, eprint = {2306.11544}, timestamp = {Fri, 23 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/corr/abs-2306-11544.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/Garcia-PrietoMV22, author = {Carlos A. Garcia{-}Prieto and Francisco Mart{\'{\i}}nez{-}Jim{\'{e}}nez and Alfonso Valencia and Eduard Porta{-}Pardo}, title = {Detection of oncogenic and clinically actionable mutations in cancer genomes critically depends on variant calling tools}, journal = {Bioinform.}, volume = {38}, number = {12}, pages = {3181--3191}, year = {2022}, url = {https://doi.org/10.1093/bioinformatics/btac306}, doi = {10.1093/BIOINFORMATICS/BTAC306}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bioinformatics/Garcia-PrietoMV22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/ci/AkasiadisLMMAAA22, author = {Charilaos Akasiadis and Miguel Ponce de Leon and Arnau Montagud and Evangelos Michelioudakis and Alexia Atsidakou and Elias Alevizos and Alexander Artikis and Alfonso Valencia and Georgios Paliouras}, title = {Parallel model exploration for tumor treatment simulations}, journal = {Comput. Intell.}, volume = {38}, number = {4}, pages = {1379--1401}, year = {2022}, url = {https://doi.org/10.1111/coin.12515}, doi = {10.1111/COIN.12515}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/ci/AkasiadisLMMAAA22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/ploscb/Porta-PardoRVV22, author = {Eduard Porta{-}Pardo and Victoria Ruiz{-}Serra and Samuel Valentini and Alfonso Valencia}, title = {The structural coverage of the human proteome before and after AlphaFold}, journal = {PLoS Comput. Biol.}, volume = {18}, number = {1}, year = {2022}, url = {https://doi.org/10.1371/journal.pcbi.1009818}, doi = {10.1371/JOURNAL.PCBI.1009818}, timestamp = {Mon, 28 Aug 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/ploscb/Porta-PardoRVV22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/bionlp/CarrinoLPGASVGV22, author = {Casimiro Pio Carrino and Joan Llop and Marc P{\`{a}}mies and Asier Guti{\'{e}}rrez{-}Fandi{\~{n}}o and Jordi Armengol{-}Estap{\'{e}} and Joaqu{\'{\i}}n Silveira{-}Ocampo and Alfonso Valencia and Aitor Gonzalez{-}Agirre and Marta Villegas}, editor = {Dina Demner{-}Fushman and Kevin Bretonnel Cohen and Sophia Ananiadou and Junichi Tsujii}, title = {Pretrained Biomedical Language Models for Clinical {NLP} in Spanish}, booktitle = {Proceedings of the 21st Workshop on Biomedical Language Processing, BioNLP@ACL 2022, Dublin, Ireland, May 26, 2022}, pages = {193--199}, publisher = {Association for Computational Linguistics}, year = {2022}, url = {https://doi.org/10.18653/v1/2022.bionlp-1.19}, doi = {10.18653/V1/2022.BIONLP-1.19}, timestamp = {Mon, 01 Aug 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/bionlp/CarrinoLPGASVGV22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/npjdm/FerrariSCLMFCMV21, author = {Alberto Ferrari and Enrico Santus and Davide Cirillo and Miguel Ponce de Leon and Nicola Marino and Maria Teresa Ferretti and Antonella Santuccione Chadha and Nikolaos Mavridis and Alfonso Valencia}, title = {Simulating SARS-CoV-2 epidemics by region-specific variables and modeling contact tracing app containment}, journal = {npj Digit. Medicine}, volume = {4}, year = {2021}, url = {https://doi.org/10.1038/s41746-020-00374-4}, doi = {10.1038/S41746-020-00374-4}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/npjdm/FerrariSCLMFCMV21.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/cmsb/SaxenaLMDV21, author = {Gaurav Saxena and Miguel Ponce de Leon and Arnau Montagud and David Vicente Dorca and Alfonso Valencia}, editor = {Eugenio Cinquemani and Lo{\"{\i}}c Paulev{\'{e}}}, title = {BioFVM-X: An MPI+OpenMP 3-D Simulator for Biological Systems}, booktitle = {Computational Methods in Systems Biology - 19th International Conference, {CMSB} 2021, Bordeaux, France, September 22-24, 2021, Proceedings}, series = {Lecture Notes in Computer Science}, volume = {12881}, pages = {266--279}, publisher = {Springer}, year = {2021}, url = {https://doi.org/10.1007/978-3-030-85633-5\_18}, doi = {10.1007/978-3-030-85633-5\_18}, timestamp = {Thu, 16 Sep 2021 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/cmsb/SaxenaLMDV21.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/corr/abs-2103-14132, author = {Charilaos Akasiadis and Miguel Ponce de Leon and Arnau Montagud and Evangelos Michelioudakis and Alexia Atsidakou and Elias Alevizos and Alexander Artikis and Alfonso Valencia and Georgios Paliouras}, title = {Parallel Model Exploration for Tumor Treatment Simulations}, journal = {CoRR}, volume = {abs/2103.14132}, year = {2021}, url = {https://arxiv.org/abs/2103.14132}, eprinttype = {arXiv}, eprint = {2103.14132}, timestamp = {Wed, 07 Apr 2021 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/corr/abs-2103-14132.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/LeonAVP20, author = {Miguel Ponce de Leon and I{\~{n}}igo Apaolaza and Alfonso Valencia and Francisco J. Planes}, title = {On the inconsistent treatment of gene-protein-reaction rules in context-specific metabolic models}, journal = {Bioinform.}, volume = {36}, number = {6}, pages = {1986--1988}, year = {2020}, url = {https://doi.org/10.1093/bioinformatics/btz832}, doi = {10.1093/BIOINFORMATICS/BTZ832}, timestamp = {Tue, 16 Jun 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bioinformatics/LeonAVP20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/LiYJCZV20, author = {Sen Li and Qi Yang and Hao Jiang and Jes{\'{u}}s A. Cort{\'{e}}s{-}Vecino and Yang Zhang and Alfonso Valencia}, title = {Parasitologist-level classification of apicomplexan parasites and host cell with deep cycle transfer learning {(DCTL)}}, journal = {Bioinform.}, volume = {36}, number = {16}, pages = {4498--4505}, year = {2020}, url = {https://doi.org/10.1093/bioinformatics/btaa513}, doi = {10.1093/BIOINFORMATICS/BTAA513}, timestamp = {Tue, 21 Mar 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/LiYJCZV20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/Canela-XandriAB20, author = {Oriol Canela{-}Xandri and Samira Anbari and Javier Buceta and Alfonso Valencia}, title = {TiFoSi: an efficient tool for mechanobiology simulations of epithelia}, journal = {Bioinform.}, volume = {36}, number = {16}, pages = {4525--4526}, year = {2020}, url = {https://doi.org/10.1093/bioinformatics/btaa592}, doi = {10.1093/BIOINFORMATICS/BTAA592}, timestamp = {Fri, 25 Dec 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/Canela-XandriAB20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/Malod-DogninPVP20, author = {No{\"{e}}l Malod{-}Dognin and Vera Pancaldi and Alfonso Valencia and Natasa Przulj}, title = {Chromatin network markers of leukemia}, journal = {Bioinform.}, volume = {36}, number = {Supplement-1}, pages = {i455--i463}, year = {2020}, url = {https://doi.org/10.1093/bioinformatics/btaa445}, doi = {10.1093/BIOINFORMATICS/BTAA445}, timestamp = {Fri, 01 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bioinformatics/Malod-DogninPVP20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/datasci/LamprechtGKMAPA20, author = {Anna{-}Lena Lamprecht and Leyla J. Garc{\'{\i}}a and Mateusz Kuzak and Carlos Martinez{-}Ortiz and Ricardo Arcila and Eva Martin Del Pico and Victoria Dominguez Del Angel and Stephanie van de Sandt and Jon C. Ison and Paula Andrea Mart{\'{\i}}nez and Peter McQuilton and Alfonso Valencia and Jennifer L. Harrow and Fotis E. Psomopoulos and Josep Lluis Gelp{\'{\i}} and Neil P. Chue Hong and Carole A. Goble and Salvador Capella{-}Guti{\'{e}}rrez}, title = {Towards {FAIR} principles for research software}, journal = {Data Sci.}, volume = {3}, number = {1}, pages = {37--59}, year = {2020}, url = {https://doi.org/10.3233/ds-190026}, doi = {10.3233/DS-190026}, timestamp = {Mon, 20 Sep 2021 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/datasci/LamprechtGKMAPA20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/nar/VaradiBDNGAPAAB20, author = {Mihaly Varadi and John M. Berrisford and Mandar S. Deshpande and Sreenath Nair and Aleksandras Gutmanas and David R. Armstrong and Luk{\'{a}}s Pravda and Bissan Al{-}Lazikani and Stephen Anyango and Geoffrey J. Barton and Karel Berka and Tom L. Blundell and Neera Borkakoti and Jose M. Dana and Sayoni Das and Sucharita Dey and Patrizio Di Micco and Franca Fraternali and Toby J. Gibson and Manuela Helmer{-}Citterich and David Hoksza and Liang{-}Chin Huang and Rishabh Jain and Harry Jubb and Christos C. Kannas and Natarajan Kannan and Jaroslav Koca and Radoslav Kriv{\'{a}}k and Manjeet Kumar and Emmanuel D. Levy and F{\'{a}}bio Madeira and M. S. Madhusudhan and Henry J. Martell and Stuart A. MacGowan and Jake E. McGreig and Saqib Mir and Abhik Mukhopadhyay and Luca Parca and Typhaine Paysan{-}Lafosse and Leandro G. Radusky and Ant{\'{o}}nio J. M. Ribeiro and Luis Serrano and Ian Sillitoe and Gulzar Singh and Petr Skoda and Radka Svobodov{\'{a}} Varekov{\'{a}} and Jonathan D. Tyzack and Alfonso Valencia and Eloy D. Villasclaras{-}Fern{\'{a}}ndez and Wim F. Vranken and Mark N. Wass and Janet M. Thornton and Michael J. E. Sternberg and Christine A. Orengo and Sameer Velankar}, title = {PDBe-KB: a community-driven resource for structural and functional annotations}, journal = {Nucleic Acids Res.}, volume = {48}, number = {Database-Issue}, pages = {D344--D353}, year = {2020}, url = {https://doi.org/10.1093/nar/gkz853}, doi = {10.1093/NAR/GKZ853}, timestamp = {Sun, 02 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/nar/VaradiBDNGAPAAB20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/nature/RheinbayNAWSTHH20, author = {Esther Rheinbay and Morten Muhlig Nielsen and Federico Abascal and Jeremiah Wala and Ofer Shapira and Grace Tiao and Henrik Hornsh{\o}j and Julian M. Hess and Randi Istrup Juul and Ziao Lin and Lars Feuerbach and Radhakrishnan Sabarinathan and Tobias Madsen and Jaegil Kim and Loris Mularoni and Shimin Shuai and Andr{\'{e}}s Lanz{\'{o}}s and Carl Herrmann and Yosef E. Maruvka and Ciyue Shen and Samirkumar B. Amin and Pratiti Bandopadhayay and Johanna Bertl and Keith A. Boroevich and John Busanovich and Joana Carlevaro{-}Fita and Dimple Chakravarty and Calvin Wing Yiu Chan and David Craft and Priyanka Dhingra and Klev Diamanti and Nuno A. Fonseca and Abel Gonzalez{-}Perez and Qianyun Guo and Mark P. Hamilton and Nicholas J. Haradhvala and Chen Hong and Keren Isaev and Todd A. Johnson and Malene Juul and Andr{\'{e}} Kahles and Abdullah Kahraman and Youngwook Kim and Jan Komorowski and Kiran Kumar and Sushant Kumar and Donghoon Lee and Kjong{-}Van Lehmann and Yilong Li and Eric Minwei Liu and Lucas Lochovsky and Keunchil Park and Oriol Pich and Nicola D. Roberts and Gordon Saksena and Steven E. Schumacher and Nikos Sidiropoulos and Lina Sieverling and Nasa Sinnott{-}Armstrong and Chip Stewart and David Tamborero and Jose M. C. Tubio and Husen M. Umer and Liis Uusk{\"{u}}la{-}Reimand and Claes Wadelius and Lina Wadi and Xiaotong Yao and Cheng{-}Zhong Zhang and Jing Zhang and James E. Haber and Asger Hobolth and Marcin Imielinski and Manolis Kellis and Michael S. Lawrence and Christian von Mering and Hidewaki Nakagawa and Benjamin J. Raphael and Mark A. Rubin and Chris Sander and Lincoln D. Stein and Joshua M. Stuart and Tatsuhiko Tsunoda and David A. Wheeler and Rory Johnson and J{\"{u}}ri Reimand and Mark Gerstein and Ekta Khurana and Peter J. Campbell and N{\'{u}}ria L{\'{o}}pez{-}Bigas and Gary D. Bader and Jonathan Barenboim and Rameen Beroukhim and S{\o}ren Brunak and Ken Chen and Jung Kyoon Choi and Jordi Deu{-}Pons and J. Lynn Fink and Joan Frigola and Carlo Gambacorti Passerini and Dale W. Garsed and Gad Getz and Ivo Glynne Gut and David Haan and Arif Ozgun Harmanci and Mohamed Helmy and Ermin Hodzic and Jos{\'{e}} M. G. Izarzugaza and Jong K. Kim and Jan O. Korbel and Erik Larsson and Shantao Li and Xiaotong Li and Shaoke Lou and Kathleen Marchal and I{\~{n}}igo Martincorena and Alexander Mart{\'{\i}}nez{-}Fundichely and Patrick D. McGillivray and William Meyerson and Ferran Mui{\~{n}}os and Marta Paczkowska and Kiejung Park and Jakob Skou Pedersen and Tirso Pons and Sergio Pulido{-}Tamayo and Iker Reyes{-}Salazar and Matthew A. Reyna and Carlota Rubio{-}Perez and S{\"{u}}leyman Cenk Sahinalp and Leonidas Salichos and Mark Shackleton and Raunak Shrestha and Alfonso Valencia and Miguel Vazquez and Lieven P. C. Verbeke and Jiayin Wang and Jonathan Warrell and Sebastian M. Waszak and Joachim Weischenfeldt and Guanming Wu and Jun Yu and Xuanping Zhang and Yan Zhang and Zhongming Zhao and Lihua Zou and Kadir C. Akdemir and Eva G. Alvarez and Adrian Baez{-}Ortega and Paul C. Boutros and David D. L. Bowtell and Benedikt Brors and Kathleen H. Burns and Kin Chan and Isidro Cort{\'{e}}s{-}Ciriano and Ana Dueso{-}Barroso and Andrew J. Dunford and Paul A. Edwards and Xavier Estivill and Dariush Etemadmoghadam and Milana Frenkel{-}Morgenstern and Dmitry A. Gordenin and Barbara Hutter and David T. W. Jones and Young Seok Ju and Marat D. Kazanov and Leszek J. Klimczak and Youngil Koh and Eunjung Alice Lee and Jake June{-}Koo Lee and Andy G. Lynch and Geoff MacIntyre and Florian Markowetz and Matthew Meyerson and Satoru Miyano and Fabio C. P. Navarro and Stephan Ossowski and Peter J. Park and John V. Pearson and Montserrat Puiggr{\`{o}}s and Karsten Rippe and Steven A. Roberts and Bernardo Rodriguez{-}Martin and Ralph Scully and David Torrents and Izar Villasante and Nicola Waddell and Jeremiah A. Wala and Lixing Yang and Sung{-}Soo Yoon and Jorge Zamora}, title = {Analyses of non-coding somatic drivers in 2,658 cancer whole genomes}, journal = {Nat.}, volume = {578}, number = {7793}, pages = {102--111}, year = {2020}, url = {https://doi.org/10.1038/s41586-020-1965-x}, doi = {10.1038/S41586-020-1965-X}, timestamp = {Thu, 11 May 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/nature/RheinbayNAWSTHH20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/npjdm/CirilloCMGSMGVR20, author = {Davide Cirillo and Silvina Catuara{-}Solarz and Czuee Morey and Emre Guney and Laia Subirats and Simona Mellino and Annalisa Gigante and Alfonso Valencia and Mar{\'{\i}}a{-}Jos{\'{e}} Rementeria and Antonella Santuccione Chadha and Nikolaos Mavridis}, title = {Sex and gender differences and biases in artificial intelligence for biomedicine and healthcare}, journal = {npj Digit. Medicine}, volume = {3}, year = {2020}, url = {https://doi.org/10.1038/s41746-020-0288-5}, doi = {10.1038/S41746-020-0288-5}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/npjdm/CirilloCMGSMGVR20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/supercomputer/Josep-FabregoTG20, author = {Marc Josep{-}Fabreg{\'{o}} and Xavier Teruel and Victor Gimenez{-}Abalos and Davide Cirillo and Dario Garcia{-}Gasulla and Sergio {\'{A}}lvarez{-}Napagao and Marta Garcia{-}Gasulla and Eduard Ayguad{\'{e}} and Alfonso Valencia}, editor = {Heike Jagode and Hartwig Anzt and Guido Juckeland and Hatem Ltaief}, title = {GOPHER, an {HPC} Framework for Large Scale Graph Exploration and Inference}, booktitle = {High Performance Computing - {ISC} High Performance 2020 International Workshops, Frankfurt, Germany, June 21-25, 2020, Revised Selected Papers}, series = {Lecture Notes in Computer Science}, volume = {12321}, pages = {211--222}, publisher = {Springer}, year = {2020}, url = {https://doi.org/10.1007/978-3-030-59851-8\_13}, doi = {10.1007/978-3-030-59851-8\_13}, timestamp = {Thu, 14 Oct 2021 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/supercomputer/Josep-FabregoTG20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/f1000research/SalgadoABBCCADFGCGGGHHHHJ20, author = {David Salgado and Irina M. Armean and Michael Baudis and Sergi Beltran and Salvador Capella{-}Guti{\'{e}}rrez and Denise Carvalho{-}Silva and Victoria Dominguez Del Angel and Joaqu{\'{\i}}n Dopazo and Laura I. Furlong and Bo Gao and Leyla Jael Garc{\'{\i}}a Castro and Dietlind Gerloff and Ivo Gut and Attila Gyenesei and Nina Habermann and John M. Hancock and Marc Hanauer and Eivind Hovig and Lennart F. Johansson and Thomas Keane and Jan Korbel and Katharina B. Lauer and Steve Laurie and Brane Leskosek and David Lloyd and Tom{\`{a}}s Marqu{\`{e}}s{-}Bonet and Hailiang Mei and Katalin Monostory and Janet Pi{\~{n}}ero and Krzysztof Poterlowicz and Ana Rath and Pubudu Samarakoon and Ferran Sanz and Gary Saunders and Daoud Sie and Morris A. Swertz and Kirill Tsukanov and Alfonso Valencia and Marko Vidak and Cristina Yenyxe Gonz{\'{a}}lez and Bauke Ylstra and Christophe B{\'{e}}roud}, title = {The {ELIXIR} Human Copy Number Variations Community: building bioinformatics infrastructure for research}, journal = {F1000Research}, volume = {9}, pages = {1229}, year = {2020}, url = {https://doi.org/10.12688/f1000research.24887.1}, doi = {10.12688/F1000RESEARCH.24887.1}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/f1000research/SalgadoABBCCADFGCGGGHHHHJ20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/Gomez-LopezDCVA19, author = {Gonzalo G{\'{o}}mez{-}L{\'{o}}pez and Joaqu{\'{\i}}n Dopazo and Juan C. Cigudosa and Alfonso Valencia and F{\'{a}}tima Al{-}Shahrour}, title = {Precision medicine needs pioneering clinical bioinformaticians}, journal = {Briefings Bioinform.}, volume = {20}, number = {3}, pages = {752--766}, year = {2019}, url = {https://doi.org/10.1093/bib/bbx144}, doi = {10.1093/BIB/BBX144}, timestamp = {Thu, 04 Jun 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/Gomez-LopezDCVA19.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/BazagaVR19, author = {Adri{\'{a}}n Bazaga and Alfonso Valencia and Mar{\'{\i}}a{-}Jos{\'{e}} Rementeria}, title = {{BIOLITMAP:} a web-based geolocated, temporal and thematic visualization of the evolution of bioinformatics publications}, journal = {Bioinform.}, volume = {35}, number = {14}, pages = {2518--2520}, year = {2019}, url = {https://doi.org/10.1093/bioinformatics/bty967}, doi = {10.1093/BIOINFORMATICS/BTY967}, timestamp = {Sat, 30 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bioinformatics/BazagaVR19.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/WrenVK19, author = {Jonathan D. Wren and Alfonso Valencia and Janet Kelso}, title = {Reviewer-coerced citation: case report, update on journal policy and suggestions for future prevention}, journal = {Bioinform.}, volume = {35}, number = {18}, pages = {3217--3218}, year = {2019}, url = {https://doi.org/10.1093/bioinformatics/btz071}, doi = {10.1093/BIOINFORMATICS/BTZ071}, timestamp = {Sat, 30 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bioinformatics/WrenVK19.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/Perales-PatonDT19, author = {Javier Perales{-}Pat{\'{o}}n and Tom{\'{a}}s Di Domenico and Coral Fustero Torre and Elena Pi{\~{n}}eiro{-}Y{\'{a}}{\~{n}}ez and Carlos Carretero{-}Puche and H{\'{e}}ctor Tejero and Alfonso Valencia and Gonzalo G{\'{o}}mez{-}L{\'{o}}pez and F{\'{a}}tima Al{-}Shahrour}, title = {vulcanSpot: a tool to prioritize therapeutic vulnerabilities in cancer}, journal = {Bioinform.}, volume = {35}, number = {22}, pages = {4846--4848}, year = {2019}, url = {https://doi.org/10.1093/bioinformatics/btz465}, doi = {10.1093/BIOINFORMATICS/BTZ465}, timestamp = {Mon, 03 Jan 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/Perales-PatonDT19.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcheminf/Perez-PerezRBFV19, author = {Mart{\'{\i}}n P{\'{e}}rez{-}P{\'{e}}rez and Gael P{\'{e}}rez Rodr{\'{\i}}guez and Aitor Blanco{-}M{\'{\i}}guez and Florentino Fdez{-}Riverola and Alfonso Valencia and Martin Krallinger and An{\'{a}}lia Louren{\c{c}}o}, title = {Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm}, journal = {J. Cheminformatics}, volume = {11}, number = {1}, pages = {42:1--42:16}, year = {2019}, url = {https://doi.org/10.1186/s13321-019-0363-6}, doi = {10.1186/S13321-019-0363-6}, timestamp = {Sat, 30 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcheminf/Perez-PerezRBFV19.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/ploscb/VazquezV19, author = {Miguel Vazquez and Alfonso Valencia}, title = {Patient Dossier: Healthcare queries over distributed resources}, journal = {PLoS Comput. Biol.}, volume = {15}, number = {10}, year = {2019}, url = {https://doi.org/10.1371/journal.pcbi.1007291}, doi = {10.1371/JOURNAL.PCBI.1007291}, timestamp = {Tue, 26 Jan 2021 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/ploscb/VazquezV19.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/tasm/GiatrakosKDAGPA19, author = {Nikos Giatrakos and Nikos Katzouris and Antonios Deligiannakis and Alexander Artikis and Minos N. Garofalakis and George Paliouras and Holger Arndt and Raffaele Grasso and Ralf Klinkenberg and Miguel Ponce de Leon and Gian Gaetano Tartaglia and Alfonso Valencia and Dimitrios Zissis}, title = {Interactive Extreme: Scale Analytics Towards Battling Cancer}, journal = {{IEEE} Technol. Soc. Mag.}, volume = {38}, number = {2}, pages = {54--61}, year = {2019}, url = {https://doi.org/10.1109/MTS.2019.2913071}, doi = {10.1109/MTS.2019.2913071}, timestamp = {Wed, 02 Aug 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/tasm/GiatrakosKDAGPA19.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/nar/RodriguezRDVVT18, author = {Jose Manuel Rodriguez and Juan Rodriguez{-}Rivas and Tom{\'{a}}s Di Domenico and Jes{\'{u}}s V{\'{a}}zquez and Alfonso Valencia and Michael L. Tress}, title = {{APPRIS} 2017: principal isoforms for multiple gene sets}, journal = {Nucleic Acids Res.}, volume = {46}, number = {Database-Issue}, pages = {D213--D217}, year = {2018}, url = {https://doi.org/10.1093/nar/gkx997}, doi = {10.1093/NAR/GKX997}, timestamp = {Mon, 26 Oct 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/nar/RodriguezRDVVT18.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/corr/abs-1811-07312, author = {Davide Cirillo and Alfonso Valencia}, title = {Algorithmic complexity in Computational Biology}, journal = {CoRR}, volume = {abs/1811.07312}, year = {2018}, url = {http://arxiv.org/abs/1811.07312}, eprinttype = {arXiv}, eprint = {1811.07312}, timestamp = {Sun, 25 Nov 2018 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/corr/abs-1811-07312.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/FlobakVLV17, author = {{\AA}smund Flobak and Miguel Vazquez and Astrid L{\ae}greid and Alfonso Valencia}, title = {CImbinator: a web-based tool for drug synergy analysis in small- and large-scale datasets}, journal = {Bioinform.}, volume = {33}, number = {15}, pages = {2410--2412}, year = {2017}, url = {https://doi.org/10.1093/bioinformatics/btx161}, doi = {10.1093/BIOINFORMATICS/BTX161}, timestamp = {Mon, 26 Oct 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/FlobakVLV17.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/BergerGLOGMV17, author = {Bonnie Berger and Terry Gaasterland and Thomas Lengauer and Christine A. Orengo and Bruno Ga{\"{e}}ta and Scott Markel and Alfonso Valencia}, title = {ISCB's initial reaction to New England Journal of Medicine editorial on data sharing}, journal = {Bioinform.}, volume = {33}, number = {18}, pages = {2968}, year = {2017}, url = {https://doi.org/10.1093/bioinformatics/btw090}, doi = {10.1093/BIOINFORMATICS/BTW090}, timestamp = {Thu, 14 Oct 2021 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bioinformatics/BergerGLOGMV17.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/nar/CanadaCROVK17, author = {Andr{\'{e}}s Ca{\~{n}}ada and Salvador Capella{-}Guti{\'{e}}rrez and Obdulia Rabal and Julen Oyarzabal and Alfonso Valencia and Martin Krallinger}, title = {LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes}, journal = {Nucleic Acids Res.}, volume = {45}, number = {Webserver-Issue}, pages = {W484--W489}, year = {2017}, url = {https://doi.org/10.1093/nar/gkx462}, doi = {10.1093/NAR/GKX462}, timestamp = {Thu, 23 Jun 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/nar/CanadaCROVK17.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/sepln/IntxaurrondoPPL17, author = {Ander Intxaurrondo and Mart{\'{\i}}n P{\'{e}}rez{-}P{\'{e}}rez and Gael P{\'{e}}rez Rodr{\'{\i}}guez and Jose Antonio L{\'{o}}pez{-}Mart{\'{\i}}n and Jesus Santamar{\'{\i}}a and Santiago de la Pe{\~{n}}a and Marta Villegas and Saber Ahmad Akhondi and Alfonso Valencia and An{\'{a}}lia Louren{\c{c}}o and Martin Krallinger}, editor = {Raquel Mart{\'{\i}}nez and Julio Gonzalo and Paolo Rosso and Soto Montalvo and Jorge Carrillo de Albornoz}, title = {The Biomedical Abbreviation Recognition and Resolution {(BARR)} Track: Benchmarking, Evaluation and Importance of Abbreviation Recognition Systems Applied to Spanish Biomedical Abstracts}, booktitle = {Proceedings of the Second Workshop on Evaluation of Human Language Technologies for Iberian Languages (IberEval 2017) co-located with 33th Conference of the Spanish Society for Natural Language Processing {(SEPLN} 2017), Murcia, Spain, September 19, 2017}, series = {{CEUR} Workshop Proceedings}, volume = {1881}, pages = {230--246}, publisher = {CEUR-WS.org}, year = {2017}, url = {https://ceur-ws.org/Vol-1881/Overview1.pdf}, timestamp = {Fri, 10 Mar 2023 16:22:59 +0100}, biburl = {https://dblp.org/rec/conf/sepln/IntxaurrondoPPL17.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/biodb/Perez-PerezRRVO16, author = {Mart{\'{\i}}n P{\'{e}}rez{-}P{\'{e}}rez and Gael P{\'{e}}rez Rodr{\'{\i}}guez and Obdulia Rabal and Miguel Vazquez and Julen Oyarzabal and Florentino Fdez{-}Riverola and Alfonso Valencia and Martin Krallinger and An{\'{a}}lia Louren{\c{c}}o}, title = {The Markyt visualisation, prediction and benchmark platform for chemical and gene entity recognition at BioCreative/CHEMDNER challenge}, journal = {Database J. Biol. Databases Curation}, volume = {2016}, year = {2016}, url = {https://doi.org/10.1093/database/baw120}, doi = {10.1093/DATABASE/BAW120}, timestamp = {Thu, 23 Jun 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/biodb/Perez-PerezRRVO16.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/datamine/IbanezGPV16, author = {Kristina Ib{\'{a}}{\~{n}}ez and Mar{\'{\i}}a Guijarro and Gonzalo Pajares and Alfonso Valencia}, title = {A computational approach inspired by simulated annealing to study the stability of protein interaction networks in cancer and neurological disorders}, journal = {Data Min. Knowl. Discov.}, volume = {30}, number = {1}, pages = {226--242}, year = {2016}, url = {https://doi.org/10.1007/s10618-015-0410-5}, doi = {10.1007/S10618-015-0410-5}, timestamp = {Sat, 19 Oct 2019 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/datamine/IbanezGPV16.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/ploscb/BergerGLOGMV16, author = {Bonnie Berger and Terry Gaasterland and Thomas Lengauer and Christine A. Orengo and Bruno Ga{\"{e}}ta and Scott Markel and Alfonso Valencia}, title = {ISCB's Initial Reaction to \emph{The New England Journal of Medicine} Editorial on Data Sharing}, journal = {PLoS Comput. Biol.}, volume = {12}, number = {3}, year = {2016}, url = {https://doi.org/10.1371/journal.pcbi.1004816}, doi = {10.1371/JOURNAL.PCBI.1004816}, timestamp = {Thu, 14 Oct 2021 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/ploscb/BergerGLOGMV16.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/smbm/SammartinoKV16, author = {Jose Camilla Sammartino and Martin Krallinger and Alfonso Valencia}, editor = {Mariana L. Neves and Fabio Rinaldi and Goran Nenadic and Dietrich Rebholz{-}Schuhmann}, title = {Annotation Process, Guidelines and Text Corpus of Small Non-Coding {RNA} Molecules: the MiNCor for MicroRNA Annotations}, booktitle = {Proceedings of the 7th International Symposium on Semantic Mining in Biomedicine, {SMBM} 2016, Potsdam, Germany, August 4-5, 2016}, series = {{CEUR} Workshop Proceedings}, volume = {1650}, pages = {56--63}, publisher = {CEUR-WS.org}, year = {2016}, url = {https://ceur-ws.org/Vol-1650/smbm16Sammartino.pdf}, timestamp = {Fri, 10 Mar 2023 16:22:16 +0100}, biburl = {https://dblp.org/rec/conf/smbm/SammartinoKV16.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/VerspoorSHBV15, author = {Karin Verspoor and Hagit Shatkay and Lynette Hirschman and Christian Blaschke and Alfonso Valencia}, title = {Summary of the BioLINK {SIG} 2013 meeting at {ISMB/ECCB} 2013}, journal = {Bioinform.}, volume = {31}, number = {2}, pages = {297--298}, year = {2015}, url = {https://doi.org/10.1093/bioinformatics/btu412}, doi = {10.1093/BIOINFORMATICS/BTU412}, timestamp = {Thu, 17 Feb 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/VerspoorSHBV15.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/LeesHMFAKVVERO15, author = {Jonathan G. Lees and Jean{-}Karim H{\'{e}}rich{\'{e}} and Ian Morilla and Jos{\'{e}} Mar{\'{\i}}a Fern{\'{a}}ndez and Priit Adler and Martin Krallinger and Jaak Vilo and Alfonso Valencia and Jan Ellenberg and Juan A. G. Ranea and Christine A. Orengo}, title = {{FUN-L:} gene prioritization for RNAi screens}, journal = {Bioinform.}, volume = {31}, number = {12}, pages = {2052--2053}, year = {2015}, url = {https://doi.org/10.1093/bioinformatics/btv073}, doi = {10.1093/BIOINFORMATICS/BTV073}, timestamp = {Fri, 07 Jul 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bioinformatics/LeesHMFAKVVERO15.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/OchoaJVP15, author = {David Ochoa and David de Juan and Alfonso Valencia and Florencio Pazos}, title = {Detection of significant protein coevolution}, journal = {Bioinform.}, volume = {31}, number = {13}, pages = {2166--2173}, year = {2015}, url = {https://doi.org/10.1093/bioinformatics/btv102}, doi = {10.1093/BIOINFORMATICS/BTV102}, timestamp = {Sat, 19 Aug 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bioinformatics/OchoaJVP15.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/AbascalTV15, author = {Federico Abascal and Michael L. Tress and Alfonso Valencia}, title = {Alternative splicing and co-option of transposable elements: the case of TMPO/LAP2{\(\alpha\)} and {ZNF451} in mammals}, journal = {Bioinform.}, volume = {31}, number = {14}, pages = {2257--2261}, year = {2015}, url = {https://doi.org/10.1093/bioinformatics/btv132}, doi = {10.1093/BIOINFORMATICS/BTV132}, timestamp = {Mon, 26 Oct 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/AbascalTV15.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/VazquezVP15, author = {Miguel Vazquez and Alfonso Valencia and Tirso Pons}, title = {Structure-PPi: a module for the annotation of cancer-related single-nucleotide variants at protein-protein interfaces}, journal = {Bioinform.}, volume = {31}, number = {14}, pages = {2397--2399}, year = {2015}, url = {https://doi.org/10.1093/bioinformatics/btv142}, doi = {10.1093/BIOINFORMATICS/BTV142}, timestamp = {Mon, 02 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/VazquezVP15.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcheminf/KrallingerLRVOV15, author = {Martin Krallinger and Florian Leitner and Obdulia Rabal and Miguel Vazquez and Julen Oyarzabal and Alfonso Valencia}, title = {{CHEMDNER:} The drugs and chemical names extraction challenge}, journal = {J. Cheminformatics}, volume = {7}, number = {{S-1}}, pages = {S1}, year = {2015}, url = {https://doi.org/10.1186/1758-2946-7-S1-S1}, doi = {10.1186/1758-2946-7-S1-S1}, timestamp = {Thu, 23 Jun 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcheminf/KrallingerLRVOV15.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcheminf/KrallingerRL15, author = {Martin Krallinger and Obdulia Rabal and Florian Leitner and Miguel Vazquez and David Salgado and Zhiyong Lu and Robert Leaman and Yanan Lu and Donghong Ji and Daniel M. Lowe and Roger A. Sayle and Riza Theresa Batista{-}Navarro and Rafal Rak and Torsten Huber and Tim Rockt{\"{a}}schel and S{\'{e}}rgio Matos and David Campos and Buzhou Tang and Hua Xu and Tsendsuren Munkhdalai and Keun Ho Ryu and S. V. Ramanan and P. Senthil Nathan and Slavko Zitnik and Marko Bajec and Lutz Weber and Matthias Irmer and Saber A. Akhondi and Jan A. Kors and Shuo Xu and Xin An and Utpal Kumar Sikdar and Asif Ekbal and Masaharu Yoshioka and Thaer M. Dieb and Miji Choi and Karin Verspoor and Madian Khabsa and C. Lee Giles and Hongfang Liu and Ravikumar Komandur Elayavilli and Andre Lamurias and Francisco M. Couto and Hong{-}Jie Dai and Richard Tzong{-}Han Tsai and Caglar Ata and Tolga Can and Anabel Usie and Rui Alves and Isabel Segura{-}Bedmar and Paloma Mart{\'{\i}}nez and Julen Oyarzabal and Alfonso Valencia}, title = {The {CHEMDNER} corpus of chemicals and drugs and its annotation principles}, journal = {J. Cheminformatics}, volume = {7}, number = {{S-1}}, pages = {S2}, year = {2015}, url = {https://doi.org/10.1186/1758-2946-7-S1-S2}, doi = {10.1186/1758-2946-7-S1-S2}, timestamp = {Sun, 04 Aug 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcheminf/KrallingerRL15.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/nar/Frenkel-MorgensternGVMV15, author = {Milana Frenkel{-}Morgenstern and Alessandro Gorohovski and Dunja Vucenovic and Lorena Maestre and Alfonso Valencia}, title = {ChiTaRS 2.1 - an improved database of the chimeric transcripts and RNA-seq data with novel sense-antisense chimeric {RNA} transcripts}, journal = {Nucleic Acids Res.}, volume = {43}, number = {Database-Issue}, pages = {68--75}, year = {2015}, url = {https://doi.org/10.1093/nar/gku1199}, doi = {10.1093/NAR/GKU1199}, timestamp = {Sun, 02 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/nar/Frenkel-MorgensternGVMV15.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/nar/RodriguezCVT15, author = {Jose Manuel Rodriguez and Angel Carro and Alfonso Valencia and Michael L. Tress}, title = {{APPRIS} WebServer and WebServices}, journal = {Nucleic Acids Res.}, volume = {43}, number = {Webserver-Issue}, pages = {W455--W459}, year = {2015}, url = {https://doi.org/10.1093/nar/gkv512}, doi = {10.1093/NAR/GKV512}, timestamp = {Mon, 26 Oct 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/nar/RodriguezCVT15.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/ploscb/AbascalERRPVVT15, author = {Federico Abascal and Iakes Ezkurdia and Juan Rodriguez{-}Rivas and Jose Manuel Rodriguez and Angela del Pozo and Jes{\'{u}}s V{\'{a}}zquez and Alfonso Valencia and Michael L. Tress}, title = {Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level}, journal = {PLoS Comput. Biol.}, volume = {11}, number = {6}, year = {2015}, url = {https://doi.org/10.1371/journal.pcbi.1004325}, doi = {10.1371/JOURNAL.PCBI.1004325}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/ploscb/AbascalERRPVVT15.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/biodb/ArighiWCHKVLWW14, author = {Cecilia N. Arighi and Cathy H. Wu and Kevin Bretonnel Cohen and Lynette Hirschman and Martin Krallinger and Alfonso Valencia and Zhiyong Lu and W. John Wilbur and Thomas C. Wiegers}, title = {BioCreative-IV virtual issue}, journal = {Database J. Biol. Databases Curation}, volume = {2014}, year = {2014}, url = {https://doi.org/10.1093/database/bau039}, doi = {10.1093/DATABASE/BAU039}, timestamp = {Thu, 23 Jun 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/biodb/ArighiWCHKVLWW14.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/UsieASVV14, author = {Anabel Usie and Rui Alves and Francesc Solsona and Miguel Vazquez and Alfonso Valencia}, title = {CheNER: chemical named entity recognizer}, journal = {Bioinform.}, volume = {30}, number = {7}, pages = {1039--1040}, year = {2014}, url = {https://doi.org/10.1093/bioinformatics/btt639}, doi = {10.1093/BIOINFORMATICS/BTT639}, timestamp = {Mon, 26 Oct 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/UsieASVV14.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/nar/MaiettaLCPLVT14, author = {Paolo Maietta and Gonzalo L{\'{o}}pez and Angel Carro and Benjamin J. Pingilley and Leticia G. Leon and Alfonso Valencia and Michael L. Tress}, title = {FireDB: a compendium of biological and pharmacologically relevant ligands}, journal = {Nucleic Acids Res.}, volume = {42}, number = {Database-Issue}, pages = {267--272}, year = {2014}, url = {https://doi.org/10.1093/nar/gkt1127}, doi = {10.1093/NAR/GKT1127}, timestamp = {Mon, 26 Oct 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/nar/MaiettaLCPLVT14.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/tcbb/JimenezPSV14, author = {Beatriz Garc{\'{\i}}a Jim{\'{e}}nez and Tirso Pons and Araceli Sanchis and Alfonso Valencia}, title = {Predicting Protein Relationshipsto Human Pathways througha Relational Learning ApproachBased on Simple Sequence Features}, journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.}, volume = {11}, number = {4}, pages = {753--765}, year = {2014}, url = {https://doi.org/10.1109/TCBB.2014.2318730}, doi = {10.1109/TCBB.2014.2318730}, timestamp = {Mon, 03 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/tcbb/JimenezPSV14.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/pacbb/KrallingerLV14, author = {Martin Krallinger and Florian Leitner and Alfonso Valencia}, editor = {Julio Saez{-}Rodriguez and Miguel P. Rocha and Florentino Fdez{-}Riverola and Juan F. De Paz Santana}, title = {Retrieval and Discovery of Cell Cycle Literature and Proteins by Means of Machine Learning, Text Mining and Network Analysis}, booktitle = {8th International Conference on Practical Applications of Computational Biology {\&} Bioinformatics, {PACBB} 2014, 4-6 June, 2014, Salamanca, Spain}, series = {Advances in Intelligent Systems and Computing}, volume = {294}, pages = {285--292}, publisher = {Springer}, year = {2014}, url = {https://doi.org/10.1007/978-3-319-07581-5\_34}, doi = {10.1007/978-3-319-07581-5\_34}, timestamp = {Wed, 12 Oct 2022 08:58:54 +0200}, biburl = {https://dblp.org/rec/conf/pacbb/KrallingerLV14.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/biodb/ComeauDCCKLLPRTVVWWW13, author = {Donald C. Comeau and Rezarta Islamaj Dogan and Paolo Ciccarese and Kevin Bretonnel Cohen and Martin Krallinger and Florian Leitner and Zhiyong Lu and Yifan Peng and Fabio Rinaldi and Manabu Torii and Alfonso Valencia and Karin Verspoor and Thomas C. Wiegers and Cathy H. Wu and W. John Wilbur}, title = {BioC: a minimalist approach to interoperability for biomedical text processing}, journal = {Database J. Biol. Databases Curation}, volume = {2013}, year = {2013}, url = {https://doi.org/10.1093/database/bat064}, doi = {10.1093/DATABASE/BAT064}, timestamp = {Thu, 23 Jun 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/biodb/ComeauDCCKLLPRTVVWWW13.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/Rubio-CamarilloGFVP13, author = {Miriam Rubio{-}Camarillo and Gonzalo G{\'{o}}mez{-}L{\'{o}}pez and Jos{\'{e}} Mar{\'{\i}}a Fern{\'{a}}ndez and Alfonso Valencia and David G. Pisano}, title = {RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses}, journal = {Bioinform.}, volume = {29}, number = {13}, pages = {1687--1689}, year = {2013}, url = {https://doi.org/10.1093/bioinformatics/btt203}, doi = {10.1093/BIOINFORMATICS/BTT203}, timestamp = {Fri, 07 Jul 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bioinformatics/Rubio-CamarilloGFVP13.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bmcbi/IzarzugazaVPV13, author = {Jos{\'{e}} M. G. Izarzugaza and Miguel Vazquez and Angela del Pozo and Alfonso Valencia}, title = {wKinMut: An integrated tool for the analysis and interpretation of mutations in human protein kinases}, journal = {{BMC} Bioinform.}, volume = {14}, pages = {345}, year = {2013}, url = {https://doi.org/10.1186/1471-2105-14-345}, doi = {10.1186/1471-2105-14-345}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bmcbi/IzarzugazaVPV13.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/nar/RodriguezMEPWLVT13, author = {Jose Manuel Rodriguez and Paolo Maietta and Iakes Ezkurdia and Alessandro Pietrelli and Jan{-}Jaap Wesselink and Gonzalo L{\'{o}}pez and Alfonso Valencia and Michael L. Tress}, title = {{APPRIS:} annotation of principal and alternative splice isoforms}, journal = {Nucleic Acids Res.}, volume = {41}, number = {Database-Issue}, pages = {110--117}, year = {2013}, url = {https://doi.org/10.1093/nar/gks1058}, doi = {10.1093/NAR/GKS1058}, timestamp = {Mon, 26 Oct 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/nar/RodriguezMEPWLVT13.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/nar/Frenkel-MorgensternGLRIBLBV13, author = {Milana Frenkel{-}Morgenstern and Alessandro Gorohovski and Vincent Lacroix and Mark F. Rogers and Kristina Ib{\'{a}}{\~{n}}ez and Cesar Boullosa and Eduardo Andr{\'{e}}s Le{\'{o}}n and Asa Ben{-}Hur and Alfonso Valencia}, title = {ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data}, journal = {Nucleic Acids Res.}, volume = {41}, number = {Database-Issue}, pages = {142--151}, year = {2013}, url = {https://doi.org/10.1093/nar/gks1041}, doi = {10.1093/NAR/GKS1041}, timestamp = {Sun, 17 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/nar/Frenkel-MorgensternGLRIBLBV13.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/clef/MoranteKVD13, author = {Roser Morante and Martin Krallinger and Alfonso Valencia and Walter Daelemans}, editor = {Pamela Forner and Roberto Navigli and Dan Tufis and Nicola Ferro}, title = {Machine Reading of Biomedical Texts about Alzheimer's Disease}, booktitle = {Working Notes for {CLEF} 2013 Conference , Valencia, Spain, September 23-26, 2013}, series = {{CEUR} Workshop Proceedings}, volume = {1179}, publisher = {CEUR-WS.org}, year = {2013}, url = {https://ceur-ws.org/Vol-1179/CLEF2013wn-QA4MRE-MoranteEt2013.pdf}, timestamp = {Fri, 10 Mar 2023 16:23:37 +0100}, biburl = {https://dblp.org/rec/conf/clef/MoranteKVD13.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/biodb/HirschmanBKACVWCDHLNVWW12, author = {Lynette Hirschman and Gully A. P. C. Burns and Martin Krallinger and Cecilia N. Arighi and K. Bretonnel Cohen and Alfonso Valencia and Cathy H. Wu and Andrew Chatr{-}aryamontri and Karen G. Dowell and Eva Huala and An{\'{a}}lia Louren{\c{c}}o and Robert S. Nash and Anne{-}Lise Veuthey and Thomas C. Wiegers and Andrew G. Winter}, title = {Text mining for the biocuration workflow}, journal = {Database J. Biol. Databases Curation}, volume = {2012}, year = {2012}, url = {https://doi.org/10.1093/database/bas020}, doi = {10.1093/DATABASE/BAS020}, timestamp = {Thu, 23 Jun 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/biodb/HirschmanBKACVWCDHLNVWW12.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/biodb/KrallingerLVSMTVC12, author = {Martin Krallinger and Florian Leitner and Miguel Vazquez and David Salgado and Christophe Marcelle and Mike Tyers and Alfonso Valencia and Andrew Chatr{-}aryamontri}, title = {How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience}, journal = {Database J. Biol. Databases Curation}, volume = {2012}, year = {2012}, url = {https://doi.org/10.1093/database/bas017}, doi = {10.1093/DATABASE/BAS017}, timestamp = {Thu, 23 Jun 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/biodb/KrallingerLVSMTVC12.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/biodb/WuACHKLMVWW12, author = {Cathy H. Wu and Cecilia N. Arighi and Kevin Bretonnel Cohen and Lynette Hirschman and Martin Krallinger and Zhiyong Lu and Carolyn J. Mattingly and Alfonso Valencia and Thomas C. Wiegers and W. John Wilbur}, title = {BioCreative-2012 Virtual Issue}, journal = {Database J. Biol. Databases Curation}, volume = {2012}, year = {2012}, url = {https://doi.org/10.1093/database/bas049}, doi = {10.1093/DATABASE/BAS049}, timestamp = {Thu, 23 Jun 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/biodb/WuACHKLMVWW12.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/MuthGRJVP12, author = {Thilo Muth and Juan A. Garc{\'{\i}}a{-}Mart{\'{\i}}n and Antonio Rausell and David de Juan and Alfonso Valencia and Florencio Pazos}, title = {JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures}, journal = {Bioinform.}, volume = {28}, number = {4}, pages = {584--586}, year = {2012}, url = {https://doi.org/10.1093/bioinformatics/btr688}, doi = {10.1093/BIOINFORMATICS/BTR688}, timestamp = {Sat, 19 Aug 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bioinformatics/MuthGRJVP12.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/PengBVW12, author = {Hanchuan Peng and Alex Bateman and Alfonso Valencia and Jonathan D. Wren}, title = {Bioimage informatics: a new category in \emph{Bioinformatics}}, journal = {Bioinform.}, volume = {28}, number = {8}, pages = {1057}, year = {2012}, url = {https://doi.org/10.1093/bioinformatics/bts111}, doi = {10.1093/BIOINFORMATICS/BTS111}, timestamp = {Mon, 02 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/PengBVW12.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/HajirasoulihaSJVS12, author = {Iman Hajirasouliha and Alexander Sch{\"{o}}nhuth and David de Juan and Alfonso Valencia and S{\"{u}}leyman Cenk Sahinalp}, title = {Mirroring co-evolving trees in the light of their topologies}, journal = {Bioinform.}, volume = {28}, number = {9}, pages = {1202--1208}, year = {2012}, url = {https://doi.org/10.1093/bioinformatics/bts109}, doi = {10.1093/BIOINFORMATICS/BTS109}, timestamp = {Sun, 02 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bioinformatics/HajirasoulihaSJVS12.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/Frenkel-MorgensternV12, author = {Milana Frenkel{-}Morgenstern and Alfonso Valencia}, title = {Novel domain combinations in proteins encoded by chimeric transcripts}, journal = {Bioinform.}, volume = {28}, number = {12}, pages = {67--74}, year = {2012}, url = {https://doi.org/10.1093/bioinformatics/bts216}, doi = {10.1093/BIOINFORMATICS/BTS216}, timestamp = {Mon, 02 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/Frenkel-MorgensternV12.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/SalgadoKDDTLVM12, author = {David Salgado and Martin Krallinger and Marc Depaule and Elodie Drula and Ashish V. Tendulkar and Florian Leitner and Alfonso Valencia and Christophe Marcelle}, title = {MyMiner: a web application for computer-assisted biocuration and text annotation}, journal = {Bioinform.}, volume = {28}, number = {17}, pages = {2285--2287}, year = {2012}, url = {https://doi.org/10.1093/bioinformatics/bts435}, doi = {10.1093/BIOINFORMATICS/BTS435}, timestamp = {Thu, 23 Jun 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bioinformatics/SalgadoKDDTLVM12.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/GlaabBKSV12, author = {Enrico Glaab and Ana{\"{\i}}s Baudot and Natalio Krasnogor and Reinhard Schneider and Alfonso Valencia}, title = {EnrichNet: network-based gene set enrichment analysis}, journal = {Bioinform.}, volume = {28}, number = {18}, pages = {451--457}, year = {2012}, url = {https://doi.org/10.1093/bioinformatics/bts389}, doi = {10.1093/BIOINFORMATICS/BTS389}, timestamp = {Wed, 07 Dec 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/GlaabBKSV12.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/ploscb/VazquezTV12, author = {Miguel Vazquez and Victor de la Torre and Alfonso Valencia}, title = {Chapter 14: Cancer Genome Analysis}, journal = {PLoS Comput. Biol.}, volume = {8}, number = {12}, year = {2012}, url = {https://doi.org/10.1371/journal.pcbi.1002824}, doi = {10.1371/JOURNAL.PCBI.1002824}, timestamp = {Thu, 10 Sep 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/ploscb/VazquezTV12.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/clef/MoranteKVD12, author = {Roser Morante and Martin Krallinger and Alfonso Valencia and Walter Daelemans}, editor = {Pamela Forner and Jussi Karlgren and Christa Womser{-}Hacker}, title = {Machine Reading of Biomedical Texts about Alzheimer's Disease}, booktitle = {{CLEF} 2012 Evaluation Labs and Workshop, Online Working Notes, Rome, Italy, September 17-20, 2012}, series = {{CEUR} Workshop Proceedings}, volume = {1178}, publisher = {CEUR-WS.org}, year = {2012}, url = {https://ceur-ws.org/Vol-1178/CLEF2012wn-QA4MRE-MoranteEt2012.pdf}, timestamp = {Fri, 10 Mar 2023 16:23:42 +0100}, biburl = {https://dblp.org/rec/conf/clef/MoranteKVD12.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/eccb/IzarzugazaVPV12, author = {Jos{\'{e}} M. G. Izarzugaza and Miguel Vazquez and Angela del Pozo and Alfonso Valencia}, editor = {Christopher J. O. Baker and Dietrich Rebholz{-}Schuhmann}, title = {wKinMut: An integrated tool for the analysis and interpretation of mutations in human protein kinases}, booktitle = {Proceedings of the Workshop on Annotation, Interpretation and Management of Mutations, Basel, Switzerland, September 9, 2012}, series = {{CEUR} Workshop Proceedings}, volume = {916}, publisher = {CEUR-WS.org}, year = {2012}, url = {https://ceur-ws.org/Vol-916/Paper3.pdf}, timestamp = {Fri, 10 Mar 2023 16:22:35 +0100}, biburl = {https://dblp.org/rec/conf/eccb/IzarzugazaVPV12.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/corr/abs-1211-5520, author = {Vivekanand Samant and Arvind Hulgeri and Alfonso Valencia and Ashish V. Tendulkar}, title = {Accurate Demarcation of Protein Domain Linkers based on Structural Analysis of Linker Probable Region}, journal = {CoRR}, volume = {abs/1211.5520}, year = {2012}, url = {http://arxiv.org/abs/1211.5520}, eprinttype = {arXiv}, eprint = {1211.5520}, timestamp = {Mon, 13 Aug 2018 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/corr/abs-1211-5520.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/KallioniemiWV11, author = {Olli{-}P. Kallioniemi and Lodewyk F. A. Wessels and Alfonso Valencia}, title = {On the organization of bioinformatics core services in biology-based research institutes}, journal = {Bioinform.}, volume = {27}, number = {10}, pages = {1345}, year = {2011}, url = {https://doi.org/10.1093/bioinformatics/btr125}, doi = {10.1093/BIOINFORMATICS/BTR125}, timestamp = {Mon, 02 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/KallioniemiWV11.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bmcbi/HermanOJLVP11, author = {Dorota Herman and David Ochoa and David de Juan and Daniel Lopez and Alfonso Valencia and Florencio Pazos}, title = {Selection of organisms for the co-evolution-based study of protein interactions}, journal = {{BMC} Bioinform.}, volume = {12}, pages = {363}, year = {2011}, url = {https://doi.org/10.1186/1471-2105-12-363}, doi = {10.1186/1471-2105-12-363}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bmcbi/HermanOJLVP11.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bmcbi/IzarzugazaHBOMV11, author = {Jos{\'{e}} M. G. Izarzugaza and Lisa E. M. Hopcroft and Anja Baresic and Christine A. Orengo and Andrew C. R. Martin and Alfonso Valencia}, title = {Characterization of pathogenic germline mutations in human Protein Kinases}, journal = {{BMC} Bioinform.}, volume = {12}, number = {{S-4}}, pages = {S1}, year = {2011}, url = {https://doi.org/10.1186/1471-2105-12-S4-S1}, doi = {10.1186/1471-2105-12-S4-S1}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bmcbi/IzarzugazaHBOMV11.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bmcbi/ArighiLKCWVHW11, author = {Cecilia N. Arighi and Zhiyong Lu and Martin Krallinger and Kevin Bretonnel Cohen and W. John Wilbur and Alfonso Valencia and Lynette Hirschman and Cathy H. Wu}, title = {Overview of the BioCreative {III} Workshop}, journal = {{BMC} Bioinform.}, volume = {12}, number = {{S-8}}, pages = {S1}, year = {2011}, url = {https://doi.org/10.1186/1471-2105-12-S8-S1}, doi = {10.1186/1471-2105-12-S8-S1}, timestamp = {Thu, 23 Jun 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bmcbi/ArighiLKCWVHW11.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/nar/LopezMRVT11, author = {Gonzalo L{\'{o}}pez and Paolo Maietta and Jose Manuel Rodriguez and Alfonso Valencia and Michael L. Tress}, title = {\emph{firestar} - advances in the prediction of functionally important residues}, journal = {Nucleic Acids Res.}, volume = {39}, number = {Web-Server-Issue}, pages = {235--241}, year = {2011}, url = {https://doi.org/10.1093/nar/gkr437}, doi = {10.1093/NAR/GKR437}, timestamp = {Mon, 26 Oct 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/nar/LopezMRVT11.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@proceedings{DBLP:conf/pacbb/2011, editor = {Miguel P. Rocha and Juan M. Corchado Rodr{\'{\i}}guez and Florentino Fdez{-}Riverola and Alfonso Valencia}, title = {5th International Conference on Practical Applications of Computational Biology {\&} Bioinformatics, {PACBB} 2011, April 6-8, 2011, Salamanca, Spain}, series = {Advances in Intelligent and Soft Computing}, volume = {93}, publisher = {Springer}, year = {2011}, url = {https://doi.org/10.1007/978-3-642-19914-1}, doi = {10.1007/978-3-642-19914-1}, isbn = {978-3-642-19913-4}, timestamp = {Wed, 12 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/pacbb/2011.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/corr/abs-1110-5704, author = {Iman Hajirasouliha and Alexander Sch{\"{o}}nhuth and David de Juan and Alfonso Valencia and S{\"{u}}leyman Cenk Sahinalp}, title = {Mirroring co-evolving trees in the light of their topologies}, journal = {CoRR}, volume = {abs/1110.5704}, year = {2011}, url = {http://arxiv.org/abs/1110.5704}, eprinttype = {arXiv}, eprint = {1110.5704}, timestamp = {Mon, 13 Aug 2018 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/corr/abs-1110-5704.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/GlaabBKV10, author = {Enrico Glaab and Ana{\"{\i}}s Baudot and Natalio Krasnogor and Alfonso Valencia}, title = {TopoGSA: network topological gene set analysis}, journal = {Bioinform.}, volume = {26}, number = {9}, pages = {1271--1272}, year = {2010}, url = {https://doi.org/10.1093/bioinformatics/btq131}, doi = {10.1093/BIOINFORMATICS/BTQ131}, timestamp = {Mon, 02 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/GlaabBKV10.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bmcbi/GlaabBKV10, author = {Enrico Glaab and Ana{\"{\i}}s Baudot and Natalio Krasnogor and Alfonso Valencia}, title = {Extending pathways and processes using molecular interaction networks to analyse cancer genome data}, journal = {{BMC} Bioinform.}, volume = {11}, pages = {597}, year = {2010}, url = {https://doi.org/10.1186/1471-2105-11-597}, doi = {10.1186/1471-2105-11-597}, timestamp = {Sun, 15 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bmcbi/GlaabBKV10.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bmcbi/KrallingerTLCV10, author = {Martin Krallinger and Ashish V. Tendulkar and Florian Leitner and Andrew Chatr{-}aryamontri and Alfonso Valencia}, title = {The {PPI} affix dictionary {(PPIAD)} and BioMethod Lexicon: importance of affixes and tags for recognition of entity mentions and experimental protein interactions}, journal = {{BMC} Bioinform.}, volume = {11}, number = {{S-5}}, pages = {O1}, year = {2010}, url = {https://doi.org/10.1186/1471-2105-11-S5-O1}, doi = {10.1186/1471-2105-11-S5-O1}, timestamp = {Sun, 15 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bmcbi/KrallingerTLCV10.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/tcbb/LeitnerMKCHV10, author = {Florian Leitner and Scott A. Mardis and Martin Krallinger and Gianni Cesareni and Lynette Hirschman and Alfonso Valencia}, title = {An Overview of BioCreative {II.5}}, journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.}, volume = {7}, number = {3}, pages = {385--399}, year = {2010}, url = {https://doi.org/10.1109/TCBB.2010.61}, doi = {10.1109/TCBB.2010.61}, timestamp = {Mon, 28 Aug 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/tcbb/LeitnerMKCHV10.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/jbi/FernandezHV10, author = {Jos{\'{e}} Mar{\'{\i}}a Fern{\'{a}}ndez and Robert Hoffmann and Alfonso Valencia}, editor = {Ana T. Freitas and Arcadi Navarro}, title = {iHOP Web Services Family}, booktitle = {Bioinformatics for Personalized Medicine - 10th Spanish Symposium, {JBI} 2010, Torremolinos, Spain, October 27-29, 2010. Revised Selected Papers}, series = {Lecture Notes in Computer Science}, volume = {6620}, pages = {102--107}, publisher = {Springer}, year = {2010}, url = {https://doi.org/10.1007/978-3-642-28062-7\_12}, doi = {10.1007/978-3-642-28062-7\_12}, timestamp = {Fri, 07 Jul 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/jbi/FernandezHV10.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/jbi/FernandezV10, author = {Jos{\'{e}} Mar{\'{\i}}a Fern{\'{a}}ndez and Alfonso Valencia}, editor = {Ana T. Freitas and Arcadi Navarro}, title = {Bioinformatic Software Developments in Spain}, booktitle = {Bioinformatics for Personalized Medicine - 10th Spanish Symposium, {JBI} 2010, Torremolinos, Spain, October 27-29, 2010. Revised Selected Papers}, series = {Lecture Notes in Computer Science}, volume = {6620}, pages = {108--120}, publisher = {Springer}, year = {2010}, url = {https://doi.org/10.1007/978-3-642-28062-7\_13}, doi = {10.1007/978-3-642-28062-7\_13}, timestamp = {Fri, 07 Jul 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/jbi/FernandezV10.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/EzkurdiaBFCVT09, author = {Iakes Ezkurdia and Lisa Bartoli and Piero Fariselli and Rita Casadio and Alfonso Valencia and Michael L. Tress}, title = {Progress and challenges in predicting protein-protein interaction sites}, journal = {Briefings Bioinform.}, volume = {10}, number = {3}, pages = {233--246}, year = {2009}, url = {https://doi.org/10.1093/bib/bbp021}, doi = {10.1093/BIB/BBP021}, timestamp = {Mon, 05 Feb 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/EzkurdiaBFCVT09.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bmcbi/BacarditSHVSK09, author = {Jaume Bacardit and Michael Stout and Jonathan D. Hirst and Alfonso Valencia and Robert Elliott Smith and Natalio Krasnogor}, title = {Automated Alphabet Reduction for Protein Datasets}, journal = {{BMC} Bioinform.}, volume = {10}, year = {2009}, url = {https://doi.org/10.1186/1471-2105-10-6}, doi = {10.1186/1471-2105-10-6}, timestamp = {Sun, 15 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bmcbi/BacarditSHVSK09.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bmcbi/KrallingerIPV09, author = {Martin Krallinger and Jos{\'{e}} M. G. Izarzugaza and Carlos Rodr{\'{\i}}guez Penagos and Alfonso Valencia}, title = {Extraction of human kinase mutations from literature, databases and genotyping studies}, journal = {{BMC} Bioinform.}, volume = {10}, number = {{S-8}}, pages = {1}, year = {2009}, url = {https://doi.org/10.1186/1471-2105-10-S8-S1}, doi = {10.1186/1471-2105-10-S8-S1}, timestamp = {Thu, 23 Jun 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bmcbi/KrallingerIPV09.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bmcbi/IzarzugazaBMYCOMV09, author = {Jos{\'{e}} M. G. Izarzugaza and Anja Baresic and Lisa E. M. McMillan and Corin Yeats and Andrew B. Clegg and Christine A. Orengo and Andrew C. R. Martin and Alfonso Valencia}, title = {An integrated approach to the interpretation of Single Amino Acid Polymorphisms within the framework of {CATH} and Gene3D}, journal = {{BMC} Bioinform.}, volume = {10}, number = {{S-8}}, pages = {5}, year = {2009}, url = {https://doi.org/10.1186/1471-2105-10-S8-S5}, doi = {10.1186/1471-2105-10-S8-S5}, timestamp = {Fri, 09 Apr 2021 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bmcbi/IzarzugazaBMYCOMV09.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/nar/CarbajosaTVC09, author = {Guillermo Carbajosa and Almudena Trigo and Alfonso Valencia and Ildefonso Cases}, title = {Bionemo: molecular information on biodegradation metabolism}, journal = {Nucleic Acids Res.}, volume = {37}, number = {Database-Issue}, pages = {598--602}, year = {2009}, url = {https://doi.org/10.1093/nar/gkn864}, doi = {10.1093/NAR/GKN864}, timestamp = {Sun, 17 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/nar/CarbajosaTVC09.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/nar/LeonEGVJ09, author = {Eduardo Andr{\'{e}}s Le{\'{o}}n and Iakes Ezkurdia and Beatriz Garc{\'{\i}}a Jim{\'{e}}nez and Alfonso Valencia and David de Juan}, title = {EcID. {A} database for the inference of functional interactions in \emph{E. coli}}, journal = {Nucleic Acids Res.}, volume = {37}, number = {Database-Issue}, pages = {629--635}, year = {2009}, url = {https://doi.org/10.1093/nar/gkn853}, doi = {10.1093/NAR/GKN853}, timestamp = {Sun, 02 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/nar/LeonEGVJ09.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/nar/KrallingerPTV09, author = {Martin Krallinger and Carlos Rodr{\'{\i}}guez Penagos and Ashish V. Tendulkar and Alfonso Valencia}, title = {{PLAN2L:} a web tool for integrated text mining and literature-based bioentity relation extraction}, journal = {Nucleic Acids Res.}, volume = {37}, number = {Web-Server-Issue}, pages = {160--165}, year = {2009}, url = {https://doi.org/10.1093/nar/gkp484}, doi = {10.1093/NAR/GKP484}, timestamp = {Thu, 23 Jun 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/nar/KrallingerPTV09.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/services/StarlingerLVL09, author = {Johannes Starlinger and Florian Leitner and Alfonso Valencia and Ulf Leser}, title = {SOA-Based Integration of Text Mining Services}, booktitle = {2009 {IEEE} Congress on Services, Part I, {SERVICES} {I} 2009, Los Angeles, CA, USA, July 6-10, 2009}, pages = {99--106}, publisher = {{IEEE} Computer Society}, year = {2009}, url = {https://doi.org/10.1109/SERVICES-I.2009.100}, doi = {10.1109/SERVICES-I.2009.100}, timestamp = {Fri, 24 Mar 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/conf/services/StarlingerLVL09.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/TressWFLGLMPWHV08, author = {Michael L. Tress and Jan{-}Jaap Wesselink and Adam Frankish and Gonzalo L{\'{o}}pez and Nick Goldman and Ari L{\"{o}}ytynoja and Tim Massingham and Fabio Pardi and Simon Whelan and Jennifer L. Harrow and Alfonso Valencia}, title = {Determination and validation of principal gene products}, journal = {Bioinform.}, volume = {24}, number = {1}, pages = {11--17}, year = {2008}, url = {https://doi.org/10.1093/bioinformatics/btm547}, doi = {10.1093/BIOINFORMATICS/BTM547}, timestamp = {Sat, 09 Apr 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bioinformatics/TressWFLGLMPWHV08.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bmcbi/IzarzugazaJPPV08, author = {Jos{\'{e}} M. G. Izarzugaza and David de Juan and Carles Pons and Florencio Pazos and Alfonso Valencia}, title = {Enhancing the prediction of protein pairings between interacting families using orthology information}, journal = {{BMC} Bioinform.}, volume = {9}, year = {2008}, url = {https://doi.org/10.1186/1471-2105-9-35}, doi = {10.1186/1471-2105-9-35}, timestamp = {Sat, 19 Aug 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bmcbi/IzarzugazaJPPV08.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bmcbi/PozoPV08, author = {Angela del Pozo and Florencio Pazos and Alfonso Valencia}, title = {Defining functional distances over Gene Ontology}, journal = {{BMC} Bioinform.}, volume = {9}, year = {2008}, url = {https://doi.org/10.1186/1471-2105-9-50}, doi = {10.1186/1471-2105-9-50}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bmcbi/PozoPV08.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/apbc/Valencia08, author = {Alfonso Valencia}, editor = {Alvis Brazma and Satoru Miyano and Tatsuya Akutsu}, title = {Protein Interactions Extracted from Genomes and Papers}, booktitle = {Proceedings of the 6th Asia-Pacific Bioinformatics Conference, {APBC} 2008, 14-17 January 2008, Kyoto, Japan}, series = {Advances in Bioinformatics and Computational Biology}, volume = {6}, pages = {7}, publisher = {Imperial College Press}, year = {2008}, url = {http://www.comp.nus.edu.sg/\%7Ewongls/psZ/apbc2008/keynote003.pdf}, timestamp = {Thu, 12 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/conf/apbc/Valencia08.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/bibm/HuCHVLGW08, author = {Zhang{-}Zhi Hu and K. Bretonnel Cohen and Lynette Hirschman and Alfonso Valencia and Hongfang Liu and Michelle G. Giglio and Cathy H. Wu}, editor = {Xue{-}wen Chen and Xiaohua Hu and Sun Kim}, title = {iProLINK: {A} Framework for Linking Text Mining with Ontology and Systems Biology}, booktitle = {2008 {IEEE} International Conference on Bioinformatics and Biomedicine, {BIBM} 2008, Philadephia, Pennsylvania, USA, November 3-5, 2008}, pages = {467--472}, publisher = {{IEEE} Computer Society}, year = {2008}, url = {https://doi.org/10.1109/BIBM.2008.73}, doi = {10.1109/BIBM.2008.73}, timestamp = {Fri, 24 Mar 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/conf/bibm/HuCHVLGW08.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/cikm/Valencia08, author = {Alfonso Valencia}, editor = {Min Song and Doheon Kim and Luke Huan}, title = {Text mining in genomics and systems biology}, booktitle = {Proceeding of the 2nd International Workshop on Data and Text Mining in Bioinformatics, {DTMBIO} 2008, Napa Valley, California, USA, October 30, 2008}, pages = {3--4}, publisher = {{ACM}}, year = {2008}, url = {https://doi.org/10.1145/1458449.1458453}, doi = {10.1145/1458449.1458453}, timestamp = {Tue, 06 Nov 2018 16:57:48 +0100}, biburl = {https://dblp.org/rec/conf/cikm/Valencia08.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/ismb/BlaschkeHSV08, author = {Christian Blaschke and Lynette Hirschman and Hagit Shatkay and Alfonso Valencia}, editor = {Christian Blaschke and Hagit Shatkay}, title = {Overview of the Ninth Annual Meeting of the BioLINK {SIG} at {ISMB:} Linking Literature, Information and Knowledge for Biology}, booktitle = {Linking Literature, Information, and Knowledge for Biology - Workshop of the BioLink Special Interest Group, {ISMB/ECCB} 2009, Stockholm, Sweden, June 28-29, 2009, Revised Selected Papers}, series = {Lecture Notes in Computer Science}, volume = {6004}, pages = {1--7}, publisher = {Springer}, year = {2008}, url = {https://doi.org/10.1007/978-3-642-13131-8\_1}, doi = {10.1007/978-3-642-13131-8\_1}, timestamp = {Tue, 14 May 2019 10:00:52 +0200}, biburl = {https://dblp.org/rec/conf/ismb/BlaschkeHSV08.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/ismb/ValenciaC08, author = {Alfonso Valencia and Ildefonso Cases}, title = {Editorial}, booktitle = {Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), Toronto, Canada, July 19-23, 2008}, year = {2008}, url = {https://doi.org/10.1093/bioinformatics/btn204}, doi = {10.1093/BIOINFORMATICS/BTN204}, timestamp = {Wed, 24 May 2017 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/ismb/ValenciaC08.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@incollection{DBLP:books/sp/08/ValenciaP08, author = {Alfonso Valencia and Florencio Pazos}, editor = {Anna R. Panchenko and Teresa M. Przytycka}, title = {Computational Methods to Predict Protein Interaction Partners}, booktitle = {Protein-protein Interactions and Networks: Identification, Computer Analysis, and Prediction}, series = {Computational Biology}, volume = {9}, pages = {67--81}, publisher = {Springer}, year = {2008}, url = {https://doi.org/10.1007/978-1-84800-125-1\_4}, doi = {10.1007/978-1-84800-125-1\_4}, timestamp = {Thu, 28 May 2020 13:10:24 +0200}, biburl = {https://dblp.org/rec/books/sp/08/ValenciaP08.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/ValenciaB07, author = {Alfonso Valencia and Alex Bateman}, title = {Editorial}, journal = {Bioinform.}, volume = {23}, number = {2}, pages = {133}, year = {2007}, url = {https://doi.org/10.1093/bioinformatics/btl635}, doi = {10.1093/BIOINFORMATICS/BTL635}, timestamp = {Mon, 02 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/ValenciaB07.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/nar/LopezVT07, author = {Gonzalo L{\'{o}}pez and Alfonso Valencia and Michael L. Tress}, title = {FireDB - a database of functionally important residues from proteins of known structure}, journal = {Nucleic Acids Res.}, volume = {35}, number = {Database-Issue}, pages = {219--223}, year = {2007}, url = {https://doi.org/10.1093/nar/gkl897}, doi = {10.1093/NAR/GKL897}, timestamp = {Mon, 26 Oct 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/nar/LopezVT07.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/nar/CasesPACFGRVVR07, author = {Ildefonso Cases and David G. Pisano and Eduardo Andr{\'{e}}s Le{\'{o}}n and Angel Carro and Jos{\'{e}} Mar{\'{\i}}a Fern{\'{a}}ndez and Gonzalo G{\'{o}}mez{-}L{\'{o}}pez and Jose Manuel Rodriguez and Jaime F. Vera and Alfonso Valencia and Ana Mar{\'{\i}}a Rojas}, title = {{CARGO:} a web portal to integrate customized biological information}, journal = {Nucleic Acids Res.}, volume = {35}, number = {Web-Server-Issue}, pages = {16--20}, year = {2007}, url = {https://doi.org/10.1093/nar/gkm280}, doi = {10.1093/NAR/GKM280}, timestamp = {Fri, 07 Jul 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/nar/CasesPACFGRVVR07.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/nar/FernandezHV07, author = {Jos{\'{e}} Mar{\'{\i}}a Fern{\'{a}}ndez and Robert Hoffmann and Alfonso Valencia}, title = {iHOP web services}, journal = {Nucleic Acids Res.}, volume = {35}, number = {Web-Server-Issue}, pages = {21--26}, year = {2007}, url = {https://doi.org/10.1093/nar/gkm298}, doi = {10.1093/NAR/GKM298}, timestamp = {Fri, 07 Jul 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/nar/FernandezHV07.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/nar/LopezVT07a, author = {Gonzalo L{\'{o}}pez and Alfonso Valencia and Michael L. Tress}, title = {\emph{firestar} - prediction of functionally important residues using structural templates and alignment reliability}, journal = {Nucleic Acids Res.}, volume = {35}, number = {Web-Server-Issue}, pages = {573--577}, year = {2007}, url = {https://doi.org/10.1093/nar/gkm297}, doi = {10.1093/NAR/GKM297}, timestamp = {Mon, 26 Oct 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/nar/LopezVT07a.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/LorenzoSV06, author = {Victor de Lorenzo and Luis Serrano and Alfonso Valencia}, title = {Synthetic Biology: challenges ahead}, journal = {Bioinform.}, volume = {22}, number = {2}, pages = {127--128}, year = {2006}, url = {https://doi.org/10.1093/bioinformatics/btk018}, doi = {10.1093/BIOINFORMATICS/BTK018}, timestamp = {Mon, 02 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/LorenzoSV06.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/HahnV06, author = {Udo Hahn and Alfonso Valencia}, title = {Semantic Mining in Biomedicine \emph{(Introduction to the papers selected from the {SMBM} 2005 Symposium, Hinxton, U.K., April 2005)}}, journal = {Bioinform.}, volume = {22}, number = {6}, pages = {643--644}, year = {2006}, url = {https://doi.org/10.1093/bioinformatics/btl084}, doi = {10.1093/BIOINFORMATICS/BTL084}, timestamp = {Mon, 02 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/HahnV06.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/ValenciaB06, author = {Alfonso Valencia and Alex Bateman}, title = {Software patents in Bioinformatics}, journal = {Bioinform.}, volume = {22}, number = {12}, pages = {1415}, year = {2006}, url = {https://doi.org/10.1093/bioinformatics/btl166}, doi = {10.1093/BIOINFORMATICS/BTL166}, timestamp = {Mon, 02 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/ValenciaB06.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/PazosRV06, author = {Florencio Pazos and Antonio Rausell and Alfonso Valencia}, title = {Phylogeny-independent detection of functional residues}, journal = {Bioinform.}, volume = {22}, number = {12}, pages = {1440--1448}, year = {2006}, url = {https://doi.org/10.1093/bioinformatics/btl104}, doi = {10.1093/BIOINFORMATICS/BTL104}, timestamp = {Sat, 19 Aug 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bioinformatics/PazosRV06.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/BatemanV06, author = {Alex Bateman and Alfonso Valencia}, title = {Structural genomics meets computational biology}, journal = {Bioinform.}, volume = {22}, number = {19}, pages = {2319}, year = {2006}, url = {https://doi.org/10.1093/bioinformatics/btl426}, doi = {10.1093/BIOINFORMATICS/BTL426}, timestamp = {Mon, 02 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/BatemanV06.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/IdekerV06, author = {Trey Ideker and Alfonso Valencia}, title = {Bioinformatics in the human interactome project}, journal = {Bioinform.}, volume = {22}, number = {24}, pages = {2973--2974}, year = {2006}, url = {https://doi.org/10.1093/bioinformatics/btl579}, doi = {10.1093/BIOINFORMATICS/BTL579}, timestamp = {Sun, 02 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bioinformatics/IdekerV06.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bmcbi/TressCTV06, author = {Michael L. Tress and Domenico Cozzetto and Anna Tramontano and Alfonso Valencia}, title = {An analysis of the Sargasso Sea resource and the consequences for database composition}, journal = {{BMC} Bioinform.}, volume = {7}, pages = {213}, year = {2006}, url = {https://doi.org/10.1186/1471-2105-7-213}, doi = {10.1186/1471-2105-7-213}, timestamp = {Mon, 26 Oct 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bmcbi/TressCTV06.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/nar/CarroTJPLSVR06, author = {Angel Carro and Michael L. Tress and David de Juan and Florencio Pazos and Pedro Lopez{-}Romero and Antonio del Sol and Alfonso Valencia and Ana Mar{\'{\i}}a Rojas}, title = {TreeDet: a web server to explore sequence space}, journal = {Nucleic Acids Res.}, volume = {34}, number = {Web-Server-Issue}, pages = {110--115}, year = {2006}, url = {https://doi.org/10.1093/nar/gkl203}, doi = {10.1093/NAR/GKL203}, timestamp = {Sat, 19 Aug 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/nar/CarroTJPLSVR06.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/nar/IzarzugazaJPRVP06, author = {Jos{\'{e}} M. G. Izarzugaza and David de Juan and Carles Pons and Juan A. G. Ranea and Alfonso Valencia and Florencio Pazos}, title = {{TSEMA:} interactive prediction of protein pairings between interacting families}, journal = {Nucleic Acids Res.}, volume = {34}, number = {Web-Server-Issue}, pages = {315--319}, year = {2006}, url = {https://doi.org/10.1093/nar/gkl112}, doi = {10.1093/NAR/GKL112}, timestamp = {Sat, 19 Aug 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/nar/IzarzugazaJPRVP06.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/ValenciaB05, author = {Alfonso Valencia and Alex Bateman}, title = {Increasing the Impact of \emph{Bioinformatics}}, journal = {Bioinform.}, volume = {21}, number = {1}, pages = {1--1}, year = {2005}, url = {https://doi.org/10.1093/bioinformatics/bti185}, doi = {10.1093/BIOINFORMATICS/BTI185}, timestamp = {Mon, 02 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/ValenciaB05.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/BlaschkeYCCAHV05, author = {Christian Blaschke and Alexander S. Yeh and Evelyn Camon and Marc E. Colosimo and Rolf Apweiler and Lynette Hirschman and Alfonso Valencia}, title = {Do you do text?}, journal = {Bioinform.}, volume = {21}, number = {23}, pages = {4199--4200}, year = {2005}, url = {https://doi.org/10.1093/bioinformatics/bti695}, doi = {10.1093/BIOINFORMATICS/BTI695}, timestamp = {Mon, 02 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/BlaschkeYCCAHV05.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/BatemanV05, author = {Alex Bateman and Alfonso Valencia}, title = {An update from the \emph{Bioinformatics} Editors}, journal = {Bioinform.}, volume = {21}, number = {24}, pages = {4319}, year = {2005}, url = {https://doi.org/10.1093/bioinformatics/bti768}, doi = {10.1093/BIOINFORMATICS/BTI768}, timestamp = {Mon, 02 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/BatemanV05.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bmcbi/BlaschkeLKV05, author = {Christian Blaschke and Eduardo Andr{\'{e}}s Le{\'{o}}n and Martin Krallinger and Alfonso Valencia}, title = {Evaluation of BioCreAtIvE assessment of task 2}, journal = {{BMC} Bioinform.}, volume = {6}, number = {{S-1}}, year = {2005}, url = {https://doi.org/10.1186/1471-2105-6-S1-S16}, doi = {10.1186/1471-2105-6-S1-S16}, timestamp = {Mon, 26 Sep 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bmcbi/BlaschkeLKV05.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bmcbi/HirschmanYBV05, author = {Lynette Hirschman and Alexander S. Yeh and Christian Blaschke and Alfonso Valencia}, title = {Overview of BioCreAtIvE: critical assessment of information extraction for biology}, journal = {{BMC} Bioinform.}, volume = {6}, number = {{S-1}}, year = {2005}, url = {https://doi.org/10.1186/1471-2105-6-S1-S1}, doi = {10.1186/1471-2105-6-S1-S1}, timestamp = {Mon, 26 Sep 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bmcbi/HirschmanYBV05.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bmcbi/KrallingerPV05, author = {Martin Krallinger and Maria Padron and Alfonso Valencia}, title = {A sentence sliding window approach to extract protein annotations from biomedical articles}, journal = {{BMC} Bioinform.}, volume = {6}, number = {{S-1}}, year = {2005}, url = {https://doi.org/10.1186/1471-2105-6-S1-S19}, doi = {10.1186/1471-2105-6-S1-S19}, timestamp = {Thu, 23 Jun 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bmcbi/KrallingerPV05.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/nar/HoffmannDCV05, author = {Robert Hoffmann and Joaqu{\'{\i}}n Dopazo and Juan C. Cigudosa and Alfonso Valencia}, title = {HCAD, closing the gap between breakpoints and genes}, journal = {Nucleic Acids Res.}, volume = {33}, number = {Database-Issue}, pages = {511--513}, year = {2005}, url = {https://doi.org/10.1093/nar/gki061}, doi = {10.1093/NAR/GKI061}, timestamp = {Sun, 17 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/nar/HoffmannDCV05.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/nar/PazosGVL05, author = {Florencio Pazos and David Guijas and Alfonso Valencia and Victor de Lorenzo}, title = {MetaRouter: bioinformatics for bioremediation}, journal = {Nucleic Acids Res.}, volume = {33}, number = {Database-Issue}, pages = {588--592}, year = {2005}, url = {https://doi.org/10.1093/nar/gki068}, doi = {10.1093/NAR/GKI068}, timestamp = {Sat, 19 Aug 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/nar/PazosGVL05.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/nar/GranaEPRV05, author = {Osvaldo Gra{\~{n}}a and Volker A. Eyrich and Florencio Pazos and Burkhard Rost and Alfonso Valencia}, title = {EVAcon: a protein contact prediction evaluation service}, journal = {Nucleic Acids Res.}, volume = {33}, number = {Web-Server-Issue}, pages = {347--351}, year = {2005}, url = {https://doi.org/10.1093/nar/gki411}, doi = {10.1093/NAR/GKI411}, timestamp = {Sat, 19 Aug 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/nar/GranaEPRV05.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/tcsb/GomezAPGJV05, author = {Manuel J. G{\'{o}}mez and Ram{\'{o}}n Alonso{-}Allende and Florencio Pazos and Osvaldo Gra{\~{n}}a and David de Juan and Alfonso Valencia}, title = {Accessible Protein Interaction Data for Network Modeling. Structure of the Information and Available Repositories}, journal = {Trans. Comp. Sys. Biology}, volume = {1}, pages = {1--13}, year = {2005}, url = {https://doi.org/10.1007/978-3-540-32126-2\_1}, doi = {10.1007/978-3-540-32126-2\_1}, timestamp = {Sat, 19 Aug 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/tcsb/GomezAPGJV05.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/eccb/GuigoMVA05, author = {Roderic Guig{\'{o}} and Federico Mor{\'{a}}n and Alfonso Valencia and Josep F. Abril}, title = {{ECCB/JBI} 2005}, booktitle = {ECCB/JBI'05 Proceedings, Fourth European Conference on Computational Biology/Sixth Meeting of the Spanish Bioinformatics Network (Jornadas de BioInform{\'{a}}tica), Palacio de Congresos, Madrid, Spain, September 28 - October 1, 2005}, pages = {2}, year = {2005}, url = {https://doi.org/10.1093/bioinformatics/bti1145}, doi = {10.1093/BIOINFORMATICS/BTI1145}, timestamp = {Wed, 14 Nov 2018 00:00:00 +0100}, biburl = {https://dblp.org/rec/conf/eccb/GuigoMVA05.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/eccb/JuanMRHSSVMR05, author = {David de Juan and Mario Mellado and Jos{\'{e}} Miguel Rodr{\'{\i}}guez{-}Frade and Patricia Hernanz{-}Falc{\'{o}}n and Antonio Serrano and Antonio del Sol and Alfonso Valencia and Carlos Mart{\'{\i}}nez{-}A and Ana Mar{\'{\i}}a Rojas}, title = {A framework for computational and experimental methods: Identifying dimerization residues in {CCR} chemokine receptors}, booktitle = {ECCB/JBI'05 Proceedings, Fourth European Conference on Computational Biology/Sixth Meeting of the Spanish Bioinformatics Network (Jornadas de BioInform{\'{a}}tica), Palacio de Congresos, Madrid, Spain, September 28 - October 1, 2005}, pages = {18}, year = {2005}, url = {https://doi.org/10.1093/bioinformatics/bti1101}, doi = {10.1093/BIOINFORMATICS/BTI1101}, timestamp = {Sun, 02 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/eccb/JuanMRHSSVMR05.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/eccb/HoffmannV05, author = {Robert Hoffmann and Alfonso Valencia}, title = {Implementing the iHOP concept for navigation of biomedical literature}, booktitle = {ECCB/JBI'05 Proceedings, Fourth European Conference on Computational Biology/Sixth Meeting of the Spanish Bioinformatics Network (Jornadas de BioInform{\'{a}}tica), Palacio de Congresos, Madrid, Spain, September 28 - October 1, 2005}, pages = {258}, year = {2005}, url = {https://doi.org/10.1093/bioinformatics/bti1142}, doi = {10.1093/BIOINFORMATICS/BTI1142}, timestamp = {Wed, 14 Nov 2018 00:00:00 +0100}, biburl = {https://dblp.org/rec/conf/eccb/HoffmannV05.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@incollection{DBLP:books/wi/05/KrallingerV05, author = {Martin Krallinger and Alfonso Valencia}, editor = {Francisco Azuaje and Joaqu{\'{\i}}n Dopazo}, title = {Applications of Text Mining in Molecular Biology, from Name Recognition to Protein Interaction Maps}, booktitle = {Data Analysis and Visualization in Genomics and Proteomics}, pages = {41--59}, publisher = {Wiley}, year = {2005}, url = {https://doi.org/10.1002/0470094419.ch4}, doi = {10.1002/0470094419.CH4}, timestamp = {Thu, 25 Jun 2020 14:30:22 +0200}, biburl = {https://dblp.org/rec/books/wi/05/KrallingerV05.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/TressGV04, author = {Michael L. Tress and Osvaldo Gra{\~{n}}a and Alfonso Valencia}, title = {SQUARE-determining reliable regions in sequence alignments}, journal = {Bioinform.}, volume = {20}, number = {6}, pages = {974--975}, year = {2004}, url = {https://doi.org/10.1093/bioinformatics/bth032}, doi = {10.1093/BIOINFORMATICS/BTH032}, timestamp = {Sun, 02 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bioinformatics/TressGV04.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/BatemanV04, author = {Alex Bateman and Alfonso Valencia}, title = {New Leadership for Bioinformatics}, journal = {Bioinform.}, volume = {20}, number = {12}, pages = {1821}, year = {2004}, url = {https://doi.org/10.1093/bioinformatics/bth403}, doi = {10.1093/BIOINFORMATICS/BTH403}, timestamp = {Mon, 02 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/BatemanV04.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/FernandezV04, author = {Jos{\'{e}} Mar{\'{\i}}a Fern{\'{a}}ndez and Alfonso Valencia}, title = {YAdumper: extracting and translating large information volumes from relational databases to structured flat files}, journal = {Bioinform.}, volume = {20}, number = {15}, pages = {2455--2457}, year = {2004}, url = {https://doi.org/10.1093/bioinformatics/bth243}, doi = {10.1093/BIOINFORMATICS/BTH243}, timestamp = {Fri, 07 Jul 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bioinformatics/FernandezV04.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bmcbi/Sanchez-PulidoRWMV04, author = {Luis S{\'{a}}nchez{-}Pulido and Ana Mar{\'{\i}}a Rojas and Karel H. M. van Wely and Carlos Mart{\'{\i}}nez{-}A and Alfonso Valencia}, title = {{SPOC:} {A} widely distributed domain associated with cancer, apoptosis and transcription}, journal = {{BMC} Bioinform.}, volume = {5}, pages = {91}, year = {2004}, url = {https://doi.org/10.1186/1471-2105-5-91}, doi = {10.1186/1471-2105-5-91}, timestamp = {Sun, 15 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bmcbi/Sanchez-PulidoRWMV04.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/nar/HermjakobMLMKOVRRVMABCSA04, author = {Henning Hermjakob and Luisa Montecchi{-}Palazzi and Chris Lewington and Sugath Mudali and Samuel Kerrien and Sandra E. Orchard and Martin Vingron and Bernd Roechert and Peter Roepstorff and Alfonso Valencia and Hanah Margalit and John Armstrong and Amos Bairoch and Gianni Cesareni and David James Sherman and Rolf Apweiler}, title = {IntAct: an open source molecular interaction database}, journal = {Nucleic Acids Res.}, volume = {32}, number = {Database-Issue}, pages = {452--455}, year = {2004}, url = {https://doi.org/10.1093/nar/gkh052}, doi = {10.1093/NAR/GKH052}, timestamp = {Sun, 02 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/nar/HermjakobMLMKOVRRVMABCSA04.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/sigir/BrownHV04, author = {Eric W. Brown and William R. Hersh and Alfonso Valencia}, title = {{SIGIR} 2003 workshop on text analysis and search for bioinformatics}, journal = {{SIGIR} Forum}, volume = {38}, number = {2}, pages = {31--36}, year = {2004}, url = {https://doi.org/10.1145/1041394.1041401}, doi = {10.1145/1041394.1041401}, timestamp = {Tue, 06 Nov 2018 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/sigir/BrownHV04.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/bionlp/KrallingerPBV04, author = {Martin Krallinger and Maria Padron and Christian Blaschke and Alfonso Valencia}, editor = {Nigel Collier and Patrick Ruch and Adeline Nazarenko}, title = {Assessing the Correlation between Contextual Patterns and Biological Entity Tagging}, booktitle = {Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications, NLPBA/BioNLP 2004, Geneva, Switzerland, August 28-29, 2004}, year = {2004}, url = {https://aclanthology.org/W04-1206/}, timestamp = {Fri, 06 Aug 2021 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/bionlp/KrallingerPBV04.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/cmsb/PazosGGTLV04, author = {Florencio Pazos and David Guijas and Manuel J. G{\'{o}}mez and Almudena Trigo and Victor de Lorenzo and Alfonso Valencia}, editor = {Vincent Danos and Vincent Sch{\"{a}}chter}, title = {The Biodegradation Network, a New Scenario for Computational Systems Biology Research}, booktitle = {Computational Methods in Systems Biology, International Conference, {CMSB} 2004, Paris, France, May 26-28, 2004, Revised Selected Papers}, series = {Lecture Notes in Computer Science}, volume = {3082}, pages = {252--256}, publisher = {Springer}, year = {2004}, url = {https://doi.org/10.1007/978-3-540-25974-9\_23}, doi = {10.1007/978-3-540-25974-9\_23}, timestamp = {Sat, 19 Aug 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/cmsb/PazosGGTLV04.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/jbi/RojasSFWMV04, author = {Ana Mar{\'{\i}}a Rojas and Luis S{\'{a}}nchez{-}Pulido and Agnes F{\"{u}}tterer and Karel H. M. van Wely and Carlos Mart{\'{\i}}nez{-}A and Alfonso Valencia}, editor = {Xavier Messeguer and Gabriel Valiente}, title = {Bioinformatic Analyses of the Dio Family of Proteins}, booktitle = {Proceedings of the 5th Annual Spanish Bioinformatics Conference, Barcelona, Catalonia, Spain, November 29-30, 2004}, pages = {70--71}, publisher = {Technical University of Catalonia, Barcelona}, year = {2004}, timestamp = {Fri, 02 Feb 2007 00:00:00 +0100}, biburl = {https://dblp.org/rec/conf/jbi/RojasSFWMV04.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/jbi/FernandezV04, author = {Jos{\'{e}} Mar{\'{\i}}a Fern{\'{a}}ndez and Alfonso Valencia}, editor = {Xavier Messeguer and Gabriel Valiente}, title = {{XML} Databases, are Ready for Bioinformatics?}, booktitle = {Proceedings of the 5th Annual Spanish Bioinformatics Conference, Barcelona, Catalonia, Spain, November 29-30, 2004}, pages = {166--170}, publisher = {Technical University of Catalonia, Barcelona}, year = {2004}, timestamp = {Fri, 07 Jul 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/jbi/FernandezV04.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/IliopoulosTAECPPLPPHTYTDBVBMLRSO03, author = {Ioannis Iliopoulos and Sophia Tsoka and Miguel A. Andrade and Anton J. Enright and Mark Carroll and Patrick Poullet and Vasilis J. Promponas and Theodore Liakopoulos and Giorgos Palaios and Claude Pasquier and Stavros J. Hamodrakas and Javier Tamames and Asutosh T. Yagnik and Anna Tramontano and Damien Devos and Christian Blaschke and Alfonso Valencia and David Brett and David M. A. Martin and Christophe Leroy and Isidore Rigoutsos and Chris Sander and Christos A. Ouzounis}, title = {Evaluation of annotation strategies using an entire genome sequence}, journal = {Bioinform.}, volume = {19}, number = {6}, pages = {717--726}, year = {2003}, url = {https://doi.org/10.1093/bioinformatics/btg077}, doi = {10.1093/BIOINFORMATICS/BTG077}, timestamp = {Mon, 26 Oct 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/IliopoulosTAECPPLPPHTYTDBVBMLRSO03.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/Valencia03, author = {Alfonso Valencia}, title = {Meta, Metan and Cyber Servers}, journal = {Bioinform.}, volume = {19}, number = {7}, pages = {795}, year = {2003}, url = {https://doi.org/10.1093/bioinformatics/btg215}, doi = {10.1093/BIOINFORMATICS/BTG215}, timestamp = {Mon, 02 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/Valencia03.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/OuzounisV03, author = {Christos A. Ouzounis and Alfonso Valencia}, title = {Early bioinformatics: the birth of a discipline - a personal view}, journal = {Bioinform.}, volume = {19}, number = {17}, pages = {2176--2190}, year = {2003}, url = {https://doi.org/10.1093/bioinformatics/btg309}, doi = {10.1093/BIOINFORMATICS/BTG309}, timestamp = {Mon, 26 Oct 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/OuzounisV03.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/nar/KohEMPMEGPVSR03, author = {Ingrid Y. Y. Koh and Volker A. Eyrich and Marc A. Mart{\'{\i}}{-}Renom and Dariusz Przybylski and Mallur S. Madhusudhan and Narayanan Eswar and Osvaldo Gra{\~{n}}a and Florencio Pazos and Alfonso Valencia and Andrej Sali and Burkhard Rost}, title = {{EVA:} evaluation of protein structure prediction servers}, journal = {Nucleic Acids Res.}, volume = {31}, number = {13}, pages = {3311--3315}, year = {2003}, url = {https://doi.org/10.1093/nar/gkg619}, doi = {10.1093/NAR/GKG619}, timestamp = {Sat, 19 Aug 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/nar/KohEMPMEGPVSR03.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BlaschkeHV02, author = {Christian Blaschke and Lynette Hirschman and Alfonso Valencia}, title = {Information extraction in molecular biology}, journal = {Briefings Bioinform.}, volume = {3}, number = {2}, pages = {154--165}, year = {2002}, url = {https://doi.org/10.1093/bib/3.2.154}, doi = {10.1093/BIB/3.2.154}, timestamp = {Thu, 04 Jun 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/BlaschkeHV02.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/RostHV02, author = {Burkhard Rost and Barry Honig and Alfonso Valencia}, title = {Bioinformatics in structural genomics - Editorial}, journal = {Bioinform.}, volume = {18}, number = {7}, pages = {897}, year = {2002}, url = {https://doi.org/10.1093/bioinformatics/18.7.897}, doi = {10.1093/BIOINFORMATICS/18.7.897}, timestamp = {Tue, 07 May 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bioinformatics/RostHV02.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/AbascalV02, author = {Federico Abascal and Alfonso Valencia}, title = {Clustering of proximal sequence space for the identification of protein families}, journal = {Bioinform.}, volume = {18}, number = {7}, pages = {908--921}, year = {2002}, url = {https://doi.org/10.1093/bioinformatics/18.7.908}, doi = {10.1093/BIOINFORMATICS/18.7.908}, timestamp = {Mon, 02 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/AbascalV02.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/Valencia02, author = {Alfonso Valencia}, title = {Bioinformatics: Biology by other means}, journal = {Bioinform.}, volume = {18}, number = {12}, pages = {1551--1552}, year = {2002}, url = {https://doi.org/10.1093/bioinformatics/18.12.1551}, doi = {10.1093/BIOINFORMATICS/18.12.1551}, timestamp = {Sat, 30 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bioinformatics/Valencia02.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/expert/BlaschkeV02, author = {Christian Blaschke and Alfonso Valencia}, title = {The Frame-Based Module of the {SUISEKI} Information Extraction System}, journal = {{IEEE} Intell. Syst.}, volume = {17}, number = {2}, pages = {14--20}, year = {2002}, url = {https://doi.org/10.1109/MIS.2002.999215}, doi = {10.1109/MIS.2002.999215}, timestamp = {Fri, 06 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/expert/BlaschkeV02.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/HerreroVD01, author = {Javier Herrero and Alfonso Valencia and Joaqu{\'{\i}}n Dopazo}, title = {A hierarchical unsupervised growing neural network for clustering gene expression patterns}, journal = {Bioinform.}, volume = {17}, number = {1}, pages = {126--136}, year = {2001}, url = {https://doi.org/10.1093/bioinformatics/17.2.126}, doi = {10.1093/BIOINFORMATICS/17.2.126}, timestamp = {Mon, 02 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/HerreroVD01.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/EyrichMPMFPVSR01, author = {Volker A. Eyrich and Marc A. Mart{\'{\i}}{-}Renom and Dariusz Przybylski and Mallur S. Madhusudhan and Andr{\'{a}}s Fiser and Florencio Pazos and Alfonso Valencia and Andrej Sali and Burkhard Rost}, title = {{EVA:} continuous automatic evaluation of protein structure prediction servers}, journal = {Bioinform.}, volume = {17}, number = {12}, pages = {1242--1243}, year = {2001}, url = {https://doi.org/10.1093/bioinformatics/17.12.1242}, doi = {10.1093/BIOINFORMATICS/17.12.1242}, timestamp = {Sat, 19 Aug 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bioinformatics/EyrichMPMFPVSR01.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/expert/AltmanVMR01, author = {Russ B. Altman and Alfonso Valencia and Satoru Miyano and Shoba Ranganathan}, title = {Challenges for Intelligent Systems in Biology}, journal = {{IEEE} Intell. Syst.}, volume = {16}, number = {6}, pages = {14--20}, year = {2001}, url = {https://doi.org/10.1109/5254.972065}, doi = {10.1109/5254.972065}, timestamp = {Fri, 06 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/expert/AltmanVMR01.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/AndradeBLHDRFTVOS99, author = {Miguel A. Andrade and Nigel P. Brown and Christophe Leroy and S. H{\"{o}}rsch and Antoine de Daruvar and C. Reich and Angelo Franchini and Javier Tamames and Alfonso Valencia and Christos A. Ouzounis and Chris Sander}, title = {Automated genome sequence analysis and annotation}, journal = {Bioinform.}, volume = {15}, number = {5}, pages = {391--412}, year = {1999}, url = {https://doi.org/10.1093/bioinformatics/15.5.391}, doi = {10.1093/BIOINFORMATICS/15.5.391}, timestamp = {Wed, 01 Mar 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/AndradeBLHDRFTVOS99.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/PazosRV99, author = {Florencio Pazos and Burkhard Rost and Alfonso Valencia}, title = {A platform for integrating threading results with protein family analyses}, journal = {Bioinform.}, volume = {15}, number = {12}, pages = {1062--1063}, year = {1999}, url = {https://doi.org/10.1093/bioinformatics/15.12.1062}, doi = {10.1093/BIOINFORMATICS/15.12.1062}, timestamp = {Sat, 19 Aug 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bioinformatics/PazosRV99.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/ismb/BlaschkeAOV99, author = {Christian Blaschke and Miguel A. Andrade and Christos A. Ouzounis and Alfonso Valencia}, editor = {Thomas Lengauer and Reinhard Schneider and Peer Bork and Douglas L. Brutlag and Janice I. Glasgow and Hans{-}Werner Mewes and Ralf Zimmer}, title = {Automatic Extraction of Biological Information from Scientific Text: Protein-Protein Interactions}, booktitle = {Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology, August 6-10, 1999, Heidelberg, Germany}, pages = {60--67}, publisher = {{AAAI}}, year = {1999}, url = {http://www.aaai.org/Library/ISMB/1999/ismb99-008.php}, timestamp = {Mon, 24 Jun 2013 09:48:15 +0200}, biburl = {https://dblp.org/rec/conf/ismb/BlaschkeAOV99.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/TrellesAVZC98, author = {Oswaldo Trelles and Miguel A. Andrade and Alfonso Valencia and Emilio L. Zapata and Jos{\'{e}} Mar{\'{\i}}a Carazo}, title = {Computational space reduction and parallelization of a new clustering approach for large groups of sequences}, journal = {Bioinform.}, volume = {14}, number = {5}, pages = {439--451}, year = {1998}, url = {https://doi.org/10.1093/bioinformatics/14.5.439}, doi = {10.1093/BIOINFORMATICS/14.5.439}, timestamp = {Mon, 02 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/TrellesAVZC98.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/TamamesOCSV98, author = {Javier Tamames and Christos A. Ouzounis and Georg Casari and Chris Sander and Alfonso Valencia}, title = {{EUCLID:} automatic classification of proteins in functional classes by their database annotations}, journal = {Bioinform.}, volume = {14}, number = {6}, pages = {542--543}, year = {1998}, url = {https://doi.org/10.1093/bioinformatics/14.6.542}, doi = {10.1093/BIOINFORMATICS/14.6.542}, timestamp = {Mon, 26 Oct 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/TamamesOCSV98.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/AndradeV98, author = {Miguel A. Andrade and Alfonso Valencia}, title = {Automatic extraction of keywords from scientific text: application to the knowledge domain of protein families}, journal = {Bioinform.}, volume = {14}, number = {7}, pages = {600--607}, year = {1998}, url = {https://doi.org/10.1093/bioinformatics/14.7.600}, doi = {10.1093/BIOINFORMATICS/14.7.600}, timestamp = {Mon, 02 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/AndradeV98.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bc/AndradeCSV97, author = {Miguel A. Andrade and Georg Casari and Chris Sander and Alfonso Valencia}, title = {Classification of protein families and detection of the determinant residues with an improved self-organizing map}, journal = {Biol. Cybern.}, volume = {76}, number = {6}, pages = {441--450}, year = {1997}, url = {https://doi.org/10.1007/s004220050357}, doi = {10.1007/S004220050357}, timestamp = {Thu, 17 Sep 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bc/AndradeCSV97.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/PazosOV97, author = {Florencio Pazos and O. Olmea and Alfonso Valencia}, title = {A graphical interface for correlated mutations and other protein structure prediction methods}, journal = {Comput. Appl. Biosci.}, volume = {13}, number = {3}, pages = {319--321}, year = {1997}, timestamp = {Fri, 15 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bioinformatics/PazosOV97.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/AndradeCDSSTVO97, author = {Miguel A. Andrade and Georg Casari and Antoine de Daruvar and Chris Sander and Reinhard Schneider and Javier Tamames and Alfonso Valencia and Christos A. Ouzounis}, title = {Sequence analysis of the Methanococcus jannaschii genome and the prediction of protein function}, journal = {Comput. Appl. Biosci.}, volume = {13}, number = {4}, pages = {481--483}, year = {1997}, url = {https://doi.org/10.1093/bioinformatics/13.4.481}, doi = {10.1093/BIOINFORMATICS/13.4.481}, timestamp = {Mon, 26 Oct 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/AndradeCDSSTVO97.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/bcec/PasosSGAAV97, author = {Florencio Pazos and Luis S{\'{a}}nchez{-}Pulido and Juan Antonio Garcia{-}Ranca and Miguel A. Andrade and Silvia Atrian and Alfonso Valencia}, editor = {Dan Lundh and Bj{\"{o}}rn Olsson and Ajit Narayanan}, title = {Comparative Analysis of Different Methods for the Detection of Specificity Regions in Protein Families}, booktitle = {Biocomputing and emergent computation: Proceedings of {BCEC97}}, pages = {132--145}, publisher = {World Scientific}, year = {1997}, timestamp = {Sun, 14 Mar 2021 00:00:00 +0100}, biburl = {https://dblp.org/rec/conf/bcec/PasosSGAAV97.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/ismb/AndradeV97, author = {Miguel A. Andrade and Alfonso Valencia}, editor = {Terry Gaasterland and Peter D. Karp and Kevin Karplus and Christos A. Ouzounis and Chris Sander and Alfonso Valencia}, title = {Automatic Annotation for Biological Sequences by Etraction of Keywords from {MEDLINE} Abstracts: Development of a Prototype System}, booktitle = {Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, Halkidiki, Greece, June 21-26, 1997}, pages = {25--32}, publisher = {{AAAI}}, year = {1997}, url = {http://www.aaai.org/Library/ISMB/1997/ismb97-003.php}, timestamp = {Thu, 13 Dec 2012 00:00:00 +0100}, biburl = {https://dblp.org/rec/conf/ismb/AndradeV97.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@proceedings{DBLP:conf/ismb/1997, editor = {Terry Gaasterland and Peter D. Karp and Kevin Karplus and Christos A. Ouzounis and Chris Sander and Alfonso Valencia}, title = {Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, Halkidiki, Greece, June 21-26, 1997}, publisher = {{AAAI}}, year = {1997}, isbn = {1-57735-022-7}, timestamp = {Tue, 01 Jul 2003 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/ismb/1997.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/ecal/OuzounisVTBS95, author = {Christos A. Ouzounis and Alfonso Valencia and Javier Tamames and Peer Bork and Chris Sander}, editor = {Federico Mor{\'{a}}n and Alvaro Moreno and Juan Juli{\'{a}}n Merelo Guerv{\'{o}}s and Pablo Chac{\'{o}}n}, title = {The Functional Composition of Living Machines as a Design Principle for Artificial Organisms}, booktitle = {Advances in Artificial Life, Third European Conference on Artificial Life, Granada, Spain, June 4-6, 1995, Proceedings}, series = {Lecture Notes in Computer Science}, volume = {929}, pages = {843--851}, publisher = {Springer}, year = {1995}, url = {https://doi.org/10.1007/3-540-59496-5\_347}, doi = {10.1007/3-540-59496-5\_347}, timestamp = {Sun, 25 Oct 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/ecal/OuzounisVTBS95.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/ismb/ScharfSCBVOS94, author = {Michael Scharf and Reinhard Schneider and Georg Casari and Peer Bork and Alfonso Valencia and Christos A. Ouzounis and Chris Sander}, editor = {Russ B. Altman and Douglas L. Brutlag and Peter D. Karp and Richard H. Lathrop and David B. Searls}, title = {GeneQuiz: {A} Workbench for Sequence Analysis}, booktitle = {Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, August 14-17, 1994, Stanford University, Stanford, California, {USA}}, pages = {348--353}, publisher = {{AAAI}}, year = {1994}, url = {http://www.aaai.org/Library/ISMB/1994/ismb94-043.php}, timestamp = {Mon, 24 Jun 2013 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/ismb/ScharfSCBVOS94.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
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