Alfonso Valencia

ORCID

Publication Activity (10 Years)

Years Active: 1994-2023
Publications (10 Years): 36

Top Venues

Bioinform.

Nucleic Acids Res.

Database J. Biol. Databases Curation

PLoS Comput. Biol.

Publications

Antonio Miranda-Escalada, Farrokh Mehryary, Jouni Luoma, Darryl Estrada-Zavala, Luis Gascó, Sampo Pyysalo, Alfonso Valencia, Martin Krallinger
Overview of DrugProt task at BioCreative VII: data and methods for large-scale text mining and knowledge graph generation of heterogenous chemical-protein relations. Database J. Biol. Databases Curation 2023 (2023)
Marc Clascà, Marta Garcia-Gasulla, Arnau Montagud, José Carbonell-Caballero, Alfonso Valencia
Lessons learned from a performance analysis and optimization of a multiscale cellular simulation. CoRR (2023)
Marc Clascà, Marta Garcia-Gasulla, Arnau Montagud, José Carbonell-Caballero, Alfonso Valencia
Lessons Learned from a Performance Analysis and Optimization of a Multiscale Cellular Simulation. PASC (2023)
Eduard Porta-Pardo, Victoria Ruiz-Serra, Samuel Valentini, Alfonso Valencia
The structural coverage of the human proteome before and after AlphaFold. PLoS Comput. Biol. 18 (1) (2022)
Charilaos Akasiadis, Miguel Ponce de Leon, Arnau Montagud, Evangelos Michelioudakis, Alexia Atsidakou, Elias Alevizos, Alexander Artikis, Alfonso Valencia, Georgios Paliouras
Parallel model exploration for tumor treatment simulations. Comput. Intell. 38 (4) (2022)
Casimiro Pio Carrino, Joan Llop, Marc Pàmies, Asier Gutiérrez-Fandiño, Jordi Armengol-Estapé, Joaquín Silveira-Ocampo, Alfonso Valencia, Aitor Gonzalez-Agirre, Marta Villegas
Pretrained Biomedical Language Models for Clinical NLP in Spanish. BioNLP@ACL (2022)
Carlos A. Garcia-Prieto, Francisco Martínez-Jiménez, Alfonso Valencia, Eduard Porta-Pardo
Detection of oncogenic and clinically actionable mutations in cancer genomes critically depends on variant calling tools. Bioinform. 38 (12) (2022)
Charilaos Akasiadis, Miguel Ponce de Leon, Arnau Montagud, Evangelos Michelioudakis, Alexia Atsidakou, Elias Alevizos, Alexander Artikis, Alfonso Valencia, Georgios Paliouras
Parallel Model Exploration for Tumor Treatment Simulations. CoRR (2021)
Alberto Ferrari, Enrico Santus, Davide Cirillo, Miguel Ponce de Leon, Nicola Marino, Maria Teresa Ferretti, Antonella Santuccione Chadha, Nikolaos Mavridis, Alfonso Valencia
Simulating SARS-CoV-2 epidemics by region-specific variables and modeling contact tracing app containment. npj Digit. Medicine 4 (2021)
Gaurav Saxena, Miguel Ponce de Leon, Arnau Montagud, David Vicente Dorca, Alfonso Valencia
BioFVM-X: An MPI+OpenMP 3-D Simulator for Biological Systems. CMSB (2021)
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) (2020)
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) (2020)
Davide Cirillo, Silvina Catuara-Solarz, Czuee Morey, Emre Guney, Laia Subirats, Simona Mellino, Annalisa Gigante, Alfonso Valencia, María-José Rementeria, Antonella Santuccione Chadha, Nikolaos Mavridis
Sex and gender differences and biases in artificial intelligence for biomedicine and healthcare. npj Digit. Medicine 3 (2020)
Marc Josep-Fabregó, Xavier Teruel, Victor Gimenez-Abalos, Davide Cirillo, Dario Garcia-Gasulla, Sergio Álvarez-Napagao, Marta Garcia-Gasulla, Eduard Ayguadé, Alfonso Valencia
GOPHER, an HPC Framework for Large Scale Graph Exploration and Inference. ISC Workshops (2020)
Oriol Canela-Xandri, Samira Anbari, Javier Buceta, Alfonso Valencia
TiFoSi: an efficient tool for mechanobiology simulations of epithelia. Bioinform. 36 (16) (2020)
Anna-Lena Lamprecht, Leyla J. García, Mateusz Kuzak, Carlos Martinez-Ortiz, Ricardo Arcila, Eva Martin Del Pico, Victoria Dominguez Del Angel, Stephanie van de Sandt, Jon C. Ison, Paula Andrea Martínez, Peter McQuilton, Alfonso Valencia, Jennifer L. Harrow, Fotis E. Psomopoulos, Josep Lluis Gelpí, Neil P. Chue Hong, Carole A. Goble, Salvador Capella-Gutiérrez
Towards FAIR principles for research software. Data Sci. 3 (1) (2020)
Sen Li, Qi Yang, Hao Jiang, Jesús A. Cortés-Vecino, Yang Zhang, Alfonso Valencia
Parasitologist-level classification of apicomplexan parasites and host cell with deep cycle transfer learning (DCTL). Bioinform. 36 (16) (2020)
David Salgado, Irina M. Armean, Michael Baudis, Sergi Beltran, Salvador Capella-Gutiérrez, Denise Carvalho-Silva, Victoria Dominguez Del Angel, Joaquín Dopazo, Laura I. Furlong, Bo Gao, Leyla Jael García Castro, Dietlind Gerloff, Ivo Gut, Attila Gyenesei, Nina Habermann, John M. Hancock, Marc Hanauer, Eivind Hovig, Lennart F. Johansson, Thomas Keane, Jan Korbel, Katharina B. Lauer, Steve Laurie, Brane Leskosek, David Lloyd, Tomàs Marquès-Bonet, Hailiang Mei, Katalin Monostory, Janet Piñero, Krzysztof Poterlowicz, Ana Rath, Pubudu Samarakoon, Ferran Sanz, Gary Saunders, Daoud Sie, Morris A. Swertz, Kirill Tsukanov, Alfonso Valencia, Marko Vidak, Cristina Yenyxe González, Bauke Ylstra, Christophe Béroud
The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research. F1000Research 9 (2020)
Mihaly Varadi, John M. Berrisford, Mandar S. Deshpande, Sreenath Nair, Aleksandras Gutmanas, David R. Armstrong, Lukás Pravda, Bissan Al-Lazikani, Stephen Anyango, Geoffrey J. Barton, Karel Berka, Tom L. Blundell, Neera Borkakoti, Jose M. Dana, Sayoni Das, Sucharita Dey, Patrizio Di Micco, Franca Fraternali, Toby J. Gibson, Manuela Helmer-Citterich, David Hoksza, Liang-Chin Huang, Rishabh Jain, Harry Jubb, Christos C. Kannas, Natarajan Kannan, Jaroslav Koca, Radoslav Krivák, Manjeet Kumar, Emmanuel D. Levy, Fábio Madeira, M. S. Madhusudhan, Henry J. Martell, Stuart A. MacGowan, Jake E. McGreig, Saqib Mir, Abhik Mukhopadhyay, Luca Parca, Typhaine Paysan-Lafosse, Leandro G. Radusky, António J. M. Ribeiro, Luis Serrano, Ian Sillitoe, Gulzar Singh, Petr Skoda, Radka Svobodová Vareková, Jonathan D. Tyzack, Alfonso Valencia, Eloy D. Villasclaras-Fernández, Wim F. Vranken, Mark N. Wass, Janet M. Thornton, Michael J. E. Sternberg, Christine A. Orengo, Sameer Velankar
PDBe-KB: a community-driven resource for structural and functional annotations. Nucleic Acids Res. 48 (Database-Issue) (2020)
Miguel Vazquez, Alfonso Valencia
Patient Dossier: Healthcare queries over distributed resources. PLoS Comput. Biol. 15 (10) (2019)
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) (2019)
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) (2019)
Gonzalo Gómez-López, Joaquín Dopazo, Juan C. Cigudosa, Alfonso Valencia, Fátima Al-Shahrour
Precision medicine needs pioneering clinical bioinformaticians. Briefings Bioinform. 20 (3) (2019)
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) (2019)
Jonathan D. Wren, Alfonso Valencia, Janet Kelso
Reviewer-coerced citation: case report, update on journal policy and suggestions for future prevention. Bioinform. 35 (18) (2019)
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) (2019)
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) (2018)
Davide Cirillo, Alfonso Valencia
Algorithmic complexity in Computational Biology. CoRR (2018)
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) (2017)
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)
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) (2017)
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) (2017)
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 J. Biol. Databases Curation 2016 (2016)
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)
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) (2016)
Bonnie Berger, Terry Gaasterland, Thomas Lengauer, Christine A. Orengo, Bruno Gaëta, Scott Markel, Alfonso Valencia
Editorial on Data Sharing. PLoS Comput. Biol. 12 (3) (2016)
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 Comput. Biol. 11 (6) (2015)
David Ochoa, David de Juan, Alfonso Valencia, Florencio Pazos
Detection of significant protein coevolution. Bioinform. 31 (13) (2015)
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) (2015)
Jose Manuel Rodriguez, Angel Carro, Alfonso Valencia, Michael L. Tress
APPRIS WebServer and WebServices. Nucleic Acids Res. 43 (Webserver-Issue) (2015)
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) (2015)
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) (2015)
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) (2015)
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) (2015)
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) (2015)
Karin Verspoor, Hagit Shatkay, Lynette Hirschman, Christian Blaschke, Alfonso Valencia
Summary of the BioLINK SIG 2013 meeting at ISMB/ECCB 2013. Bioinform. 31 (2) (2015)
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 J. Biol. Databases Curation 2014 (2014)
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) (2014)
Anabel Usie, Rui Alves, Francesc Solsona, Miguel Vazquez, Alfonso Valencia
CheNER: chemical named entity recognizer. Bioinform. 30 (7) (2014)
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. Biol. Bioinform. 11 (4) (2014)
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)
Roser Morante, Martin Krallinger, Alfonso Valencia, Walter Daelemans
Machine Reading of Biomedical Texts about Alzheimer's Disease. CLEF (Working Notes) (2013)
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) (2013)
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) (2013)
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 J. Biol. Databases Curation 2013 (2013)
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 (2013)
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) (2013)
Milana Frenkel-Morgenstern, Alfonso Valencia
Novel domain combinations in proteins encoded by chimeric transcripts. Bioinform. 28 (12) (2012)
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) (2012)
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 J. Biol. Databases Curation 2012 (2012)
Miguel Vazquez, Victor de la Torre, Alfonso Valencia
Chapter 14: Cancer Genome Analysis. PLoS Comput. Biol. 8 (12) (2012)
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) (2012)
Roser Morante, Martin Krallinger, Alfonso Valencia, Walter Daelemans
Machine Reading of Biomedical Texts about Alzheimer's Disease. CLEF (Online Working Notes/Labs/Workshop) (2012)
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 J. Biol. Databases Curation 2012 (2012)
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) (2012)
Enrico Glaab, Anaïs Baudot, Natalio Krasnogor, Reinhard Schneider, Alfonso Valencia
EnrichNet: network-based gene set enrichment analysis. Bioinform. 28 (18) (2012)
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 J. Biol. Databases Curation 2012 (2012)
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)
Vivekanand Samant, Arvind Hulgeri, Alfonso Valencia, Ashish V. Tendulkar
Accurate Demarcation of Protein Domain Linkers based on Structural Analysis of Linker Probable Region CoRR (2012)
Hanchuan Peng, Alex Bateman, Alfonso Valencia, Jonathan D. Wren
. Bioinform. 28 (8) (2012)
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 (2011)
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) (2011)
Gonzalo López, Paolo Maietta, Jose Manuel Rodriguez, Alfonso Valencia, Michael L. Tress
- advances in the prediction of functionally important residues. Nucleic Acids Res. 39 (Web-Server-Issue) (2011)
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) (2011)
Iman Hajirasouliha, Alexander Schönhuth, David de Juan, Alfonso Valencia, Süleyman Cenk Sahinalp
Mirroring co-evolving trees in the light of their topologies CoRR (2011)
Olli-P. Kallioniemi, Lodewyk F. A. Wessels, Alfonso Valencia
On the organization of bioinformatics core services in biology-based research institutes. Bioinform. 27 (10) (2011)
José María Fernández, Alfonso Valencia
Bioinformatic Software Developments in Spain. JBI (2010)
Enrico Glaab, Anaïs Baudot, Natalio Krasnogor, Alfonso Valencia
TopoGSA: network topological gene set analysis. Bioinform. 26 (9) (2010)
José María Fernández, Robert Hoffmann, Alfonso Valencia
iHOP Web Services Family. JBI (2010)
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) (2010)
Enrico Glaab, Anaïs Baudot, Natalio Krasnogor, Alfonso Valencia
Extending pathways and processes using molecular interaction networks to analyse cancer genome data. BMC Bioinform. 11 (2010)
Florian Leitner, Scott A. Mardis, Martin Krallinger, Gianni Cesareni, Lynette Hirschman, Alfonso Valencia
An Overview of BioCreative II.5. IEEE ACM Trans. Comput. Biol. Bioinform. 7 (3) (2010)
Guillermo Carbajosa, Almudena Trigo, Alfonso Valencia, Ildefonso Cases
Bionemo: molecular information on biodegradation metabolism. Nucleic Acids Res. 37 (Database-Issue) (2009)
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) (2009)
Eduardo Andrés León, Iakes Ezkurdia, Beatriz García Jiménez, Alfonso Valencia, David de Juan
. Nucleic Acids Res. 37 (Database-Issue) (2009)
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) (2009)
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) (2009)
Johannes Starlinger, Florian Leitner, Alfonso Valencia, Ulf Leser
SOA-Based Integration of Text Mining Services. SERVICES I (2009)
Jaume Bacardit, Michael Stout, Jonathan D. Hirst, Alfonso Valencia, Robert Elliott Smith, Natalio Krasnogor
Automated Alphabet Reduction for Protein Datasets. BMC Bioinform. 10 (2009)
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) (2009)
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)
Alfonso Valencia, Ildefonso Cases
Editorial. ISMB (2008)
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) (2008)
Alfonso Valencia
Text mining in genomics and systems biology. DTMBIO (2008)
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)
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)
Angela del Pozo, Florencio Pazos, Alfonso Valencia
Defining functional distances over Gene Ontology. BMC Bioinform. 9 (2008)
Alfonso Valencia
Protein Interactions Extracted from Genomes and Papers. APBC (2008)
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) (2007)
José María Fernández, Robert Hoffmann, Alfonso Valencia
iHOP web services. Nucleic Acids Res. 35 (Web-Server-Issue) (2007)

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