Stop the war!Остановите войну!
for scientists:
default search action
Google
Google Scholar
Semantic Scholar
Internet Archive Scholar
CiteSeerX
ORCIDBibTeX 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 = {Mon, 28 Aug 2023 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 = {Sat, 30 Sep 2023 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, 21 Mar 2023 00:00:00 +0100},
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}
}
a service of 
manage site settings
To protect your privacy, all features that rely on external API calls from your browser are turned off by default. You need to opt-in for them to become active. All settings here will be stored as cookies with your web browser. For more information see our F.A.Q.
last updated on 2024-04-21 17:27 CEST by the dblp team
all metadata released as open data under CC0 1.0 license
see also: Terms of Use | Privacy Policy | Imprint
dblp was originally created in 1993 at:
since 2018, dblp has been operated and maintained by:
the dblp computer science bibliography is funded and supported by:
