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Semantic ScholarAlfonso Valencia
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- affiliation: Barcelona Supercomputing Centre, Life Sciences Department, Spain
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2020 – today
- 2020
[j114]Miguel Ponce de Leon
, Iñigo Apaolaza, Alfonso Valencia, Francisco J. Planes:
On the inconsistent treatment of gene-protein-reaction rules in context-specific metabolic models. Bioinform. 36(6): 1986-1988 (2020)- [j113]Esther Rheinbay, Morten Muhlig Nielsen, Federico Abascal, Jeremiah Wala, Ofer Shapira, Grace Tiao, Henrik Hornshøj, Julian M. Hess, Randi Istrup Juul, Ziao Lin, Lars Feuerbach, Radhakrishnan Sabarinathan, Tobias Madsen, Jaegil Kim, Loris Mularoni, Shimin Shuai, Andrés Lanzós, Carl Herrmann, Yosef E. Maruvka, Ciyue Shen, Samirkumar B. Amin, Pratiti Bandopadhayay, Johanna Bertl, Keith A. Boroevich, John Busanovich, Joana Carlevaro-Fita, Dimple Chakravarty, Calvin Wing Yiu Chan, David Craft, Priyanka Dhingra, Klev Diamanti, Nuno A. Fonseca, Abel Gonzalez-Perez, Qianyun Guo, Mark P. Hamilton, Nicholas J. Haradhvala, Chen Hong, Keren Isaev, Todd A. Johnson, Malene Juul, André Kahles, Abdullah Kahraman, Youngwook Kim, Jan Komorowski, Kiran Kumar, Sushant Kumar, Donghoon Lee, Kjong-Van Lehmann, Yilong Li, Eric Minwei Liu, Lucas Lochovsky, Keunchil Park, Oriol Pich, Nicola D. Roberts, Gordon Saksena, Steven E. Schumacher, Nikos Sidiropoulos, Lina Sieverling, Nasa Sinnott-Armstrong, Chip Stewart, David Tamborero, Jose M. C. Tubio, Husen M. Umer, Liis Uusküla-Reimand, Claes Wadelius, Lina Wadi, Xiaotong Yao, Cheng-Zhong Zhang, Jing Zhang, James E. Haber, Asger Hobolth, Marcin Imielinski, Manolis Kellis, Michael S. Lawrence, Christian von Mering, Hidewaki Nakagawa, Benjamin J. Raphael, Mark A. Rubin, Chris Sander, Lincoln D. Stein, Joshua M. Stuart, Tatsuhiko Tsunoda, David A. Wheeler, Rory Johnson, Jüri Reimand, Mark Gerstein, Ekta Khurana, Peter J. Campbell, Núria López-Bigas, Gary D. Bader, Jonathan Barenboim, Rameen Beroukhim, Søren Brunak, Ken Chen, Jung Kyoon Choi, Jordi Deu-Pons, J. Lynn Fink, Joan Frigola, Carlo Gambacorti Passerini, Dale W. Garsed, Gad Getz, Ivo G. Gut, David Haan, Arif O. Harmanci, Mohamed Helmy, Ermin Hodzic, José M. G. Izarzugaza, Jong K. Kim, Jan O. Korbel, Erik Larsson, Shantao Li, Xiaotong Li, Shaoke Lou, Kathleen Marchal, Iñigo Martincorena, Alexander Martínez-Fundichely, Patrick D. McGillivray, William Meyerson, Ferran Muiños, Marta Paczkowska, Kiejung Park, Jakob Skou Pedersen, Tirso Pons, Sergio Pulido-Tamayo, Iker Reyes-Salazar, Matthew A. Reyna, Carlota Rubio-Perez, Süleyman Cenk Sahinalp, Leonidas Salichos, Mark Shackleton, Raunak Shrestha, Alfonso Valencia, Miguel Vazquez, Lieven P. C. Verbeke, Jiayin Wang, Jonathan Warrell, Sebastian M. Waszak, Joachim Weischenfeldt, Guanming Wu, Jun Yu, Xuanping Zhang, Yan Zhang, Zhongming Zhao, Lihua Zou, Kadir C. Akdemir, Eva G. Alvarez, Adrian Baez-Ortega, Paul C. Boutros, David D. L. Bowtell, Benedikt Brors, Kathleen H. Burns, Kin Chan, Isidro Cortés-Ciriano, Ana Dueso-Barroso, Andrew J. Dunford, Paul A. Edwards, Xavier Estivill, Dariush Etemadmoghadam, Milana Frenkel-Morgenstern, Dmitry A. Gordenin, Barbara Hutter, David T. W. Jones, Young Seok Ju, Marat D. Kazanov, Leszek J. Klimczak, Youngil Koh, Eunjung Alice Lee, Jake June-Koo Lee, Andy G. Lynch, Geoff MacIntyre, Florian Markowetz, Matthew Meyerson, Satoru Miyano, Fabio C. P. Navarro, Stephan Ossowski, Peter J. Park, John V. Pearson, Montserrat Puiggròs, Karsten Rippe, Steven A. Roberts, Bernardo Rodriguez-Martin, Ralph Scully, David Torrents, Izar Villasante, Nicola Waddell, Jeremiah A. Wala, Lixing Yang, Sung-Soo Yoon, Jorge Zamora:
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nat. 578(7793): 102-111 (2020)
2010 – 2019
- 2019
- [j112]Gonzalo Gómez-López, Joaquín Dopazo, Juan C. Cigudosa, Alfonso Valencia, Fátima Al-Shahrour:
Precision medicine needs pioneering clinical bioinformaticians. Briefings Bioinform. 20(3): 752-766 (2019) - [j111]Adrián Bazaga, Alfonso Valencia, María-José Rementeria:
BIOLITMAP: a web-based geolocated, temporal and thematic visualization of the evolution of bioinformatics publications. Bioinform. 35(14): 2518-2520 (2019) - [j110]Jonathan D. Wren, Alfonso Valencia, Janet Kelso:
Reviewer-coerced citation: case report, update on journal policy and suggestions for future prevention. Bioinform. 35(18): 3217-3218 (2019) - [j109]Javier Perales-Patón, Tomás Di Domenico, Coral Fustero Torre, Elena Piñeiro-Yáñez, Carlos Carretero-Puche, Héctor Tejero, Alfonso Valencia, Gonzalo Gómez-López, Fátima Al-Shahrour:
vulcanSpot: a tool to prioritize therapeutic vulnerabilities in cancer. Bioinform. 35(22): 4846-4848 (2019) - [j108]Martín Pérez-Pérez, Gael Pérez Rodríguez, Aitor Blanco-Míguez, Florentino Fdez-Riverola, Alfonso Valencia, Martin Krallinger, Anália Lourenço:
Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm. J. Cheminformatics 11(1): 42:1-42:16 (2019) - [j107]Miguel Vazquez, Alfonso Valencia:
Patient Dossier: Healthcare queries over distributed resources. PLoS Computational Biology 15(10) (2019) - [j106]Nikos Giatrakos, Nikos Katzouris, Antonios Deligiannakis, Alexander Artikis, Minos N. Garofalakis, George Paliouras, Holger Arndt, Raffaele Grasso, Ralf Klinkenberg, Miguel Ponce de Leon, Gian Gaetano Tartaglia, Alfonso Valencia, Dimitrios Zissis:
Interactive Extreme: Scale Analytics Towards Battling Cancer. IEEE Technol. Soc. Mag. 38(2): 54-61 (2019) - 2018
- [j105]Jose Manuel Rodriguez, Juan Rodriguez-Rivas, Tomás Di Domenico, Jesús Vázquez, Alfonso Valencia, Michael L. Tress:
APPRIS 2017: principal isoforms for multiple gene sets. Nucleic Acids Res. 46(Database-Issue): D213-D217 (2018) - [i3]Davide Cirillo, Alfonso Valencia:
Algorithmic complexity in Computational Biology. CoRR abs/1811.07312 (2018) - 2017
- [j104]Åsmund Flobak, Miguel Vazquez, Astrid Lægreid, Alfonso Valencia:
CImbinator: a web-based tool for drug synergy analysis in small- and large-scale datasets. Bioinform. 33(15): 2410-2412 (2017) - [j103]Bonnie Berger, Terry Gaasterland, Thomas Lengauer, Christine A. Orengo, Bruno Gaëta, Scott Markel, Alfonso Valencia:
ISCB's initial reaction to New England Journal of Medicine editorial on data sharing. Bioinform. 33(18): 2968 (2017) - [j102]Andrés Cañada, Salvador Capella-Gutiérrez, Obdulia Rabal, Julen Oyarzabal, Alfonso Valencia, Martin Krallinger:
LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes. Nucleic Acids Res. 45(Webserver-Issue): W484-W489 (2017) - [c26]Ander Intxaurrondo, Martín Pérez-Pérez, Gael Pérez Rodríguez, Jose Antonio López-Martín, Jesus Santamaría, Santiago de la Peña, Marta Villegas, Saber Ahmad Akhondi, Alfonso Valencia, Anália Lourenço, Martin Krallinger:
The Biomedical Abbreviation Recognition and Resolution (BARR) Track: Benchmarking, Evaluation and Importance of Abbreviation Recognition Systems Applied to Spanish Biomedical Abstracts. IberEval@SEPLN 2017: 230-246 - 2016
- [j101]Martín Pérez-Pérez, Gael Pérez Rodríguez, Obdulia Rabal, Miguel Vazquez, Julen Oyarzabal, Florentino Fdez-Riverola, Alfonso Valencia, Martin Krallinger, Anália Lourenço:
The Markyt visualisation, prediction and benchmark platform for chemical and gene entity recognition at BioCreative/CHEMDNER challenge. Database 2016 (2016) - [j100]Kristina Ibáñez, María Guijarro, Gonzalo Pajares, Alfonso Valencia:
A computational approach inspired by simulated annealing to study the stability of protein interaction networks in cancer and neurological disorders. Data Min. Knowl. Discov. 30(1): 226-242 (2016) - [j99]Bonnie Berger, Terry Gaasterland, Thomas Lengauer, Christine A. Orengo, Bruno Gaëta, Scott Markel, Alfonso Valencia:
ISCB's Initial Reaction to The New England Journal of Medicine Editorial on Data Sharing. PLoS Computational Biology 12(3) (2016) - [c25]Jose Camilla Sammartino, Martin Krallinger, Alfonso Valencia:
Annotation Process, Guidelines and Text Corpus of Small Non-Coding RNA Molecules: the MiNCor for MicroRNA Annotations. SMBM 2016: 56-63 - 2015
- [j98]Karin Verspoor, Hagit Shatkay, Lynette Hirschman, Christian Blaschke, Alfonso Valencia:
Summary of the BioLINK SIG 2013 meeting at ISMB/ECCB 2013. Bioinform. 31(2): 297-298 (2015) - [j97]Jonathan G. Lees, Jean-Karim Hériché, Ian Morilla, José María Fernández, Priit Adler, Martin Krallinger, Jaak Vilo, Alfonso Valencia, Jan Ellenberg, Juan A. G. Ranea, Christine A. Orengo:
FUN-L: gene prioritization for RNAi screens. Bioinform. 31(12): 2052-2053 (2015) - [j96]David Ochoa, David de Juan, Alfonso Valencia, Florencio Pazos:
Detection of significant protein coevolution. Bioinform. 31(13): 2166-2173 (2015) - [j95]Federico Abascal, Michael L. Tress, Alfonso Valencia:
Alternative splicing and co-option of transposable elements: the case of TMPO/LAP2α and ZNF451 in mammals. Bioinform. 31(14): 2257-2261 (2015) - [j94]Miguel Vazquez, Alfonso Valencia, Tirso Pons:
Structure-PPi: a module for the annotation of cancer-related single-nucleotide variants at protein-protein interfaces. Bioinform. 31(14): 2397-2399 (2015) - [j93]Martin Krallinger, Florian Leitner, Obdulia Rabal, Miguel Vazquez, Julen Oyarzabal, Alfonso Valencia:
CHEMDNER: The drugs and chemical names extraction challenge. J. Cheminformatics 7(S-1): S1 (2015) - [j92]Martin Krallinger, Obdulia Rabal, Florian Leitner, Miguel Vazquez, David Salgado, Zhiyong Lu, Robert Leaman, Yanan Lu, Donghong Ji, Daniel M. Lowe, Roger A. Sayle, Riza Theresa Batista-Navarro, Rafal Rak, Torsten Huber, Tim Rocktäschel, Sérgio Matos, David Campos, Buzhou Tang, Hua Xu, Tsendsuren Munkhdalai, Keun Ho Ryu, S. V. Ramanan, P. Senthil Nathan, Slavko Zitnik, Marko Bajec, Lutz Weber, Matthias Irmer, Saber A. Akhondi, Jan A. Kors, Shuo Xu, Xin An, Utpal Kumar Sikdar, Asif Ekbal, Masaharu Yoshioka, Thaer M. Dieb, Miji Choi, Karin Verspoor, Madian Khabsa, C. Lee Giles, Hongfang Liu, Ravikumar Komandur Elayavilli, Andre Lamurias, Francisco M. Couto, Hong-Jie Dai, Richard Tzong-Han Tsai, Caglar Ata, Tolga Can, Anabel Usie, Rui Alves, Isabel Segura-Bedmar, Paloma Martínez, Julen Oyarzabal, Alfonso Valencia:
The CHEMDNER corpus of chemicals and drugs and its annotation principles. J. Cheminformatics 7(S-1): S2 (2015) - [j91]Milana Frenkel-Morgenstern, Alessandro Gorohovski, Dunja Vucenovic, Lorena Maestre, Alfonso Valencia:
ChiTaRS 2.1 - an improved database of the chimeric transcripts and RNA-seq data with novel sense-antisense chimeric RNA transcripts. Nucleic Acids Res. 43(Database-Issue): 68-75 (2015) - [j90]Jose Manuel Rodriguez, Angel Carro, Alfonso Valencia, Michael L. Tress:
APPRIS WebServer and WebServices. Nucleic Acids Res. 43(Webserver-Issue): W455-W459 (2015) - [j89]Federico Abascal, Iakes Ezkurdia, Juan Rodriguez-Rivas, Jose Manuel Rodriguez, Angela del Pozo, Jesús Vázquez, Alfonso Valencia, Michael L. Tress:
Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level. PLoS Computational Biology 11(6) (2015) - 2014
- [j88]Cecilia N. Arighi, Cathy H. Wu, Kevin Bretonnel Cohen, Lynette Hirschman, Martin Krallinger, Alfonso Valencia, Zhiyong Lu, W. John Wilbur, Thomas C. Wiegers:
BioCreative-IV virtual issue. Database 2014 (2014) - [j87]Anabel Usie, Rui Alves, Francesc Solsona, Miguel Vazquez, Alfonso Valencia:
CheNER: chemical named entity recognizer. Bioinform. 30(7): 1039-1040 (2014) - [j86]Paolo Maietta, Gonzalo López, Angel Carro, Benjamin J. Pingilley, Leticia G. Leon, Alfonso Valencia, Michael L. Tress:
FireDB: a compendium of biological and pharmacologically relevant ligands. Nucleic Acids Res. 42(Database-Issue): 267-272 (2014) - [j85]Beatriz García Jiménez, Tirso Pons, Araceli Sanchis, Alfonso Valencia:
Predicting Protein Relationshipsto Human Pathways througha Relational Learning ApproachBased on Simple Sequence Features. IEEE/ACM Trans. Comput. Biology Bioinform. 11(4): 753-765 (2014) - [c24]Martin Krallinger, Florian Leitner, Alfonso Valencia:
Retrieval and Discovery of Cell Cycle Literature and Proteins by Means of Machine Learning, Text Mining and Network Analysis. PACBB 2014: 285-292 - 2013
- [j84]Donald C. Comeau, Rezarta Islamaj Dogan, Paolo Ciccarese, Kevin Bretonnel Cohen, Martin Krallinger, Florian Leitner, Zhiyong Lu, Yifan Peng, Fabio Rinaldi, Manabu Torii, Alfonso Valencia, Karin Verspoor, Thomas C. Wiegers, Cathy H. Wu, W. John Wilbur:
BioC: a minimalist approach to interoperability for biomedical text processing. Database 2013 (2013) - [j83]Miriam Rubio-Camarillo, Gonzalo Gómez-López, José María Fernández, Alfonso Valencia, David G. Pisano:
RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses. Bioinform. 29(13): 1687-1689 (2013) - [j82]José M. G. Izarzugaza, Miguel Vazquez, Angela del Pozo, Alfonso Valencia:
wKinMut: An integrated tool for the analysis and interpretation of mutations in human protein kinases. BMC Bioinform. 14: 345 (2013) - [j81]Jose Manuel Rodriguez, Paolo Maietta, Iakes Ezkurdia, Alessandro Pietrelli, Jan-Jaap Wesselink, Gonzalo López, Alfonso Valencia, Michael L. Tress:
APPRIS: annotation of principal and alternative splice isoforms. Nucleic Acids Res. 41(Database-Issue): 110-117 (2013) - [j80]Milana Frenkel-Morgenstern, Alessandro Gorohovski, Vincent Lacroix, Mark F. Rogers, Kristina Ibáñez, Cesar Boullosa, Eduardo Andrés León, Asa Ben-Hur, Alfonso Valencia:
ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data. Nucleic Acids Res. 41(Database-Issue): 142-151 (2013) - [c23]Roser Morante, Martin Krallinger, Alfonso Valencia, Walter Daelemans:
Machine Reading of Biomedical Texts about Alzheimer's Disease. CLEF (Working Notes) 2013 - 2012
- [j79]Lynette Hirschman, Gully A. P. C. Burns, Martin Krallinger, Cecilia N. Arighi, K. Bretonnel Cohen, Alfonso Valencia, Cathy H. Wu, Andrew Chatr-aryamontri, Karen G. Dowell, Eva Huala, Anália Lourenço, Robert S. Nash, Anne-Lise Veuthey, Thomas C. Wiegers, Andrew G. Winter:
Text mining for the biocuration workflow. Database 2012 (2012) - [j78]Martin Krallinger, Florian Leitner, Miguel Vazquez, David Salgado, Christophe Marcelle, Mike Tyers, Alfonso Valencia, Andrew Chatr-aryamontri:
How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience. Database 2012 (2012) - [j77]Cathy H. Wu, Cecilia N. Arighi, Kevin Bretonnel Cohen, Lynette Hirschman, Martin Krallinger, Zhiyong Lu, Carolyn J. Mattingly, Alfonso Valencia, Thomas C. Wiegers, W. John Wilbur:
BioCreative-2012 Virtual Issue. Database 2012 (2012) - [j76]Thilo Muth, Juan A. García-Martín, Antonio Rausell, David de Juan, Alfonso Valencia, Florencio Pazos:
JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures. Bioinform. 28(4): 584-586 (2012) - [j75]Hanchuan Peng, Alex Bateman, Alfonso Valencia, Jonathan D. Wren:
Bioimage informatics: a new category in Bioinformatics. Bioinform. 28(8): 1057 (2012) - [j74]Iman Hajirasouliha, Alexander Schönhuth, David de Juan, Alfonso Valencia, Süleyman Cenk Sahinalp:
Mirroring co-evolving trees in the light of their topologies. Bioinform. 28(9): 1202-1208 (2012) - [j73]Milana Frenkel-Morgenstern, Alfonso Valencia:
Novel domain combinations in proteins encoded by chimeric transcripts. Bioinform. 28(12): 67-74 (2012) - [j72]David Salgado, Martin Krallinger, Marc Depaule, Elodie Drula, Ashish V. Tendulkar, Florian Leitner, Alfonso Valencia, Christophe Marcelle:
MyMiner: a web application for computer-assisted biocuration and text annotation. Bioinform. 28(17): 2285-2287 (2012) - [j71]Enrico Glaab, Anaïs Baudot, Natalio Krasnogor, Reinhard Schneider, Alfonso Valencia:
EnrichNet: network-based gene set enrichment analysis. Bioinform. 28(18): 451-457 (2012) - [j70]Miguel Vazquez, Victor de la Torre, Alfonso Valencia:
Chapter 14: Cancer Genome Analysis. PLoS Computational Biology 8(12) (2012) - [c22]Roser Morante, Martin Krallinger, Alfonso Valencia, Walter Daelemans:
Machine Reading of Biomedical Texts about Alzheimer's Disease. CLEF (Online Working Notes/Labs/Workshop) 2012 - [c21]José M. G. Izarzugaza, Miguel Vazquez, Angela del Pozo, Alfonso Valencia:
wKinMut: An integrated tool for the analysis and interpretation of mutations in human protein kinases. AIMM 2012 - [i2]Vivekanand Samant, Arvind Hulgeri, Alfonso Valencia, Ashish V. Tendulkar:
Accurate Demarcation of Protein Domain Linkers based on Structural Analysis of Linker Probable Region. CoRR abs/1211.5520 (2012) - 2011
- [j69]Olli-P. Kallioniemi, Lodewyk F. A. Wessels, Alfonso Valencia:
On the organization of bioinformatics core services in biology-based research institutes. Bioinform. 27(10): 1345 (2011) - [j68]Dorota Herman, David Ochoa, David de Juan, Daniel Lopez, Alfonso Valencia, Florencio Pazos:
Selection of organisms for the co-evolution-based study of protein interactions. BMC Bioinform. 12: 363 (2011) - [j67]José M. G. Izarzugaza, Lisa E. M. Hopcroft, Anja Baresic, Christine A. Orengo, Andrew C. R. Martin, Alfonso Valencia:
Characterization of pathogenic germline mutations in human Protein Kinases. BMC Bioinform. 12(S-4): S1 (2011) - [j66]Cecilia N. Arighi, Zhiyong Lu, Martin Krallinger, Kevin Bretonnel Cohen, W. John Wilbur, Alfonso Valencia, Lynette Hirschman, Cathy H. Wu:
Overview of the BioCreative III Workshop. BMC Bioinform. 12(S-8): S1 (2011) - [j65]Gonzalo López, Paolo Maietta, Jose Manuel Rodriguez, Alfonso Valencia, Michael L. Tress:
firestar - advances in the prediction of functionally important residues. Nucleic Acids Res. 39(Web-Server-Issue): 235-241 (2011) - [e2]Miguel P. Rocha, Juan M. Corchado Rodríguez, Florentino Fdez-Riverola, Alfonso Valencia:
5th International Conference on Practical Applications of Computational Biology & Bioinformatics, PACBB 2011, April 6-8, 2011, Salamanca, Spain. Advances in Intelligent and Soft Computing 93, Springer 2011, ISBN 978-3-642-19913-4 [contents] - [i1]Iman Hajirasouliha, Alexander Schönhuth, David de Juan, Alfonso Valencia, Süleyman Cenk Sahinalp:
Mirroring co-evolving trees in the light of their topologies. CoRR abs/1110.5704 (2011) - 2010
- [j64]Enrico Glaab, Anaïs Baudot, Natalio Krasnogor, Alfonso Valencia:
TopoGSA: network topological gene set analysis. Bioinform. 26(9): 1271-1272 (2010) - [j63]Enrico Glaab, Anaïs Baudot, Natalio Krasnogor, Alfonso Valencia:
Extending pathways and processes using molecular interaction networks to analyse cancer genome data. BMC Bioinform. 11: 597 (2010) - [j62]Martin Krallinger, Ashish V. Tendulkar, Florian Leitner, Andrew Chatr-aryamontri, Alfonso Valencia:
The PPI affix dictionary (PPIAD) and BioMethod Lexicon: importance of affixes and tags for recognition of entity mentions and experimental protein interactions. BMC Bioinform. 11(S-5): O1 (2010) - [j61]Florian Leitner, Scott A. Mardis, Martin Krallinger, Gianni Cesareni, Lynette Hirschman, Alfonso Valencia:
An Overview of BioCreative II.5. IEEE/ACM Trans. Comput. Biology Bioinform. 7(3): 385-399 (2010) - [c20]José María Fernández, Robert Hoffmann, Alfonso Valencia:
iHOP Web Services Family. JBI 2010: 102-107 - [c19]José María Fernández, Alfonso Valencia:
Bioinformatic Software Developments in Spain. JBI 2010: 108-120
2000 – 2009
- 2009
- [j60]Iakes Ezkurdia, Lisa Bartoli, Piero Fariselli, Rita Casadio, Alfonso Valencia, Michael L. Tress:
Progress and challenges in predicting protein-protein interaction sites. Briefings Bioinform. 10(3): 233-246 (2009) - [j59]Jaume Bacardit, Michael Stout, Jonathan D. Hirst, Alfonso Valencia, Robert Elliott Smith, Natalio Krasnogor:
Automated Alphabet Reduction for Protein Datasets. BMC Bioinform. 10 (2009) - [j58]Martin Krallinger, José M. G. Izarzugaza, Carlos Rodríguez Penagos, Alfonso Valencia:
Extraction of human kinase mutations from literature, databases and genotyping studies. BMC Bioinform. 10(S-8): 1 (2009) - [j57]José M. G. Izarzugaza, Anja Baresic, Lisa E. M. McMillan, Corin Yeats, Andrew B. Clegg, Christine A. Orengo, Andrew C. R. Martin, Alfonso Valencia:
An integrated approach to the interpretation of Single Amino Acid Polymorphisms within the framework of CATH and Gene3D. BMC Bioinform. 10(S-8): 5 (2009) - [j56]Guillermo Carbajosa, Almudena Trigo, Alfonso Valencia, Ildefonso Cases:
Bionemo: molecular information on biodegradation metabolism. Nucleic Acids Res. 37(Database-Issue): 598-602 (2009) - [j55]Eduardo Andrés León, Iakes Ezkurdia, Beatriz García Jiménez, Alfonso Valencia, David de Juan:
EcID. A database for the inference of functional interactions in E. coli. Nucleic Acids Res. 37(Database-Issue): 629-635 (2009) - [j54]Martin Krallinger, Carlos Rodríguez Penagos, Ashish V. Tendulkar, Alfonso Valencia:
PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction. Nucleic Acids Res. 37(Web-Server-Issue): 160-165 (2009) - [c18]Johannes Starlinger, Florian Leitner, Alfonso Valencia, Ulf Leser:
SOA-Based Integration of Text Mining Services. SERVICES I 2009: 99-106 - 2008
- [j53]Michael L. Tress, Jan-Jaap Wesselink, Adam Frankish, Gonzalo López, Nick Goldman, Ari Löytynoja, Tim Massingham, Fabio Pardi, Simon Whelan, Jennifer L. Harrow, Alfonso Valencia:
Determination and validation of principal gene products. Bioinform. 24(1): 11-17 (2008) - [j52]José M. G. Izarzugaza, David de Juan, Carles Pons, Florencio Pazos, Alfonso Valencia:
Enhancing the prediction of protein pairings between interacting families using orthology information. BMC Bioinform. 9 (2008) - [j51]Angela del Pozo, Florencio Pazos, Alfonso Valencia:
Defining functional distances over Gene Ontology. BMC Bioinform. 9 (2008) - [c17]Alfonso Valencia:
Protein Interactions Extracted from Genomes and Papers. APBC 2008: 7 - [c16]Zhang-Zhi Hu, K. Bretonnel Cohen, Lynette Hirschman, Alfonso Valencia, Hongfang Liu, Michelle G. Giglio, Cathy H. Wu:
iProLINK: A Framework for Linking Text Mining with Ontology and Systems Biology. BIBM 2008: 467-472 - [c15]Alfonso Valencia:
Text mining in genomics and systems biology. DTMBIO 2008: 3-4 - [c14]Christian Blaschke, Lynette Hirschman, Hagit Shatkay, Alfonso Valencia:
Overview of the Ninth Annual Meeting of the BioLINK SIG at ISMB: Linking Literature, Information and Knowledge for Biology. BioLINK@ISMB/ECCB 2008: 1-7 - [c13]Alfonso Valencia, Ildefonso Cases:
Editorial. ISMB 2008 - [p2]Alfonso Valencia, Florencio Pazos:
Computational Methods to Predict Protein Interaction Partners. Protein-protein Interactions and Networks 2008: 67-81 - 2007
- [j50]Alfonso Valencia, Alex Bateman:
Editorial. Bioinform. 23(2): 133 (2007) - [j49]Gonzalo López, Alfonso Valencia, Michael L. Tress:
FireDB - a database of functionally important residues from proteins of known structure. Nucleic Acids Res. 35(Database-Issue): 219-223 (2007) - [j48]Ildefonso Cases, David G. Pisano, Eduardo Andrés León, Angel Carro, José María Fernández, Gonzalo Gómez-López, Jose Manuel Rodriguez, Jaime F. Vera, Alfonso Valencia, Ana María Rojas:
CARGO: a web portal to integrate customized biological information. Nucleic Acids Res. 35(Web-Server-Issue): 16-20 (2007) - [j47]José María Fernández, Robert Hoffmann, Alfonso Valencia:
iHOP web services. Nucleic Acids Res. 35(Web-Server-Issue): 21-26 (2007) - [j46]Gonzalo López, Alfonso Valencia, Michael L. Tress:
firestar - prediction of functionally important residues using structural templates and alignment reliability. Nucleic Acids Res. 35(Web-Server-Issue): 573-577 (2007) - 2006
- [j45]Victor de Lorenzo, Luis Serrano, Alfonso Valencia:
Synthetic Biology: challenges ahead. Bioinform. 22(2): 127-128 (2006) - [j44]Udo Hahn, Alfonso Valencia:
Semantic Mining in Biomedicine (Introduction to the papers selected from the SMBM 2005 Symposium, Hinxton, U.K., April 2005). Bioinform. 22(6): 643-644 (2006) - [j43]Alfonso Valencia, Alex Bateman:
Software patents in Bioinformatics. Bioinform. 22(12): 1415 (2006) - [j42]Florencio Pazos, Antonio Rausell, Alfonso Valencia:
Phylogeny-independent detection of functional residues. Bioinform. 22(12): 1440-1448 (2006) - [j41]Alex Bateman, Alfonso Valencia:
Structural genomics meets computational biology. Bioinform. 22(19): 2319 (2006) - [j40]Trey Ideker, Alfonso Valencia:
Bioinformatics in the human interactome project. Bioinform. 22(24): 2973-2974 (2006) - [j39]Michael L. Tress, Domenico Cozzetto, Anna Tramontano, Alfonso Valencia:
An analysis of the Sargasso Sea resource and the consequences for database composition. BMC Bioinform. 7: 213 (2006) - [j38]Angel Carro, Michael L. Tress, David de Juan, Florencio Pazos, Pedro Lopez-Romero, Antonio del Sol, Alfonso Valencia, Ana María Rojas:
TreeDet: a web server to explore sequence space. Nucleic Acids Res. 34(Web-Server-Issue): 110-115 (2006) - [j37]José M. G. Izarzugaza, David de Juan, Carles Pons, Juan A. G. Ranea, Alfonso Valencia, Florencio Pazos:
TSEMA: interactive prediction of protein pairings between interacting families. Nucleic Acids Res. 34(Web-Server-Issue): 315-319 (2006) - 2005
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Increasing the Impact of Bioinformatics. Bioinform. 21(1): 1-1 (2005) - [j35]Christian Blaschke, Alexander S. Yeh, Evelyn Camon, Marc E. Colosimo, Rolf Apweiler, Lynette Hirschman, Alfonso Valencia:
Do you do text? Bioinform. 21(23): 4199-4200 (2005) - [j34]Alex Bateman, Alfonso Valencia:
An update from the Bioinformatics Editors. Bioinform. 21(24): 4319 (2005) - [j33]Christian Blaschke, Eduardo Andrés León, Martin Krallinger, Alfonso Valencia:
Evaluation of BioCreAtIvE assessment of task 2. BMC Bioinform. 6(S-1) (2005) - [j32]Lynette Hirschman, Alexander S. Yeh, Christian Blaschke, Alfonso Valencia:
Overview of BioCreAtIvE: critical assessment of information extraction for biology. BMC Bioinform. 6(S-1) (2005) - [j31]Martin Krallinger, Maria Padron, Alfonso Valencia:
A sentence sliding window approach to extract protein annotations from biomedical articles. BMC Bioinform. 6(S-1) (2005) - [j30]