Alfonso Valencia

168 papers A 5B 1Misc 2Journal 134Unranked 24

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	A novel scalable high performance diffusion solver for multiscale cell simulations. CoRR Jose-Luis Estragues-Muñoz, Carlos Álvarez, Arnau Montagud, Daniel Jiménez-González, Alfonso Valencia
2025	J	`jnl`	PretoxTM: a text mining system for extracting treatment-related findings from preclinical toxicology reports. J. Cheminformatics Javier Corvi, Nicolás Díaz-Roussel, José M. Fernández, Francesco Ronzano, Emilio Centeno, Pablo Accuosto, Celine Ibrahim, Shoji Asakura, Frank Bringezu, Mirjam Fröhlicher, Annika Kreuchwig, Yoko Nogami, Jeong Rih, Raul Rodriguez-Esteban, Nicolas Sajot, Jörg Wichard, Heng-Yi Michael Wu, Philip Drew, Thomas Steger-Hartmann, Alfonso Valencia, Laura I. Furlong, Salvador Capella-Gutiérrez
2024	J	`jnl`	3Dmapper: a command line tool for BioBank-scale mapping of variants to protein structures. Bioinform. Victoria Ruiz-Serra, Samuel Valentini, Sergi Madroñero, Alfonso Valencia, Eduard Porta-Pardo
2023	—	`conf`	Lessons Learned from a Performance Analysis and Optimization of a Multiscale Cellular Simulation. PASC Marc Clascà, Marta Garcia-Gasulla, Arnau Montagud, José Carbonell-Caballero, Alfonso Valencia
2023	J	`jnl`	Lessons learned from a performance analysis and optimization of a multiscale cellular simulation. CoRR Marc Clascà, Marta Garcia-Gasulla, Arnau Montagud, José Carbonell-Caballero, Alfonso Valencia
2023	J	`jnl`	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 Antonio Miranda-Escalada, Farrokh Mehryary, Jouni Luoma, Darryl Estrada-Zavala, Luis Gascó, Sampo Pyysalo, Alfonso Valencia, Martin Krallinger
2022	J	`jnl`	Detection of oncogenic and clinically actionable mutations in cancer genomes critically depends on variant calling tools. Bioinform. Carlos A. Garcia-Prieto, Francisco Martínez-Jiménez, Alfonso Valencia, Eduard Porta-Pardo
2022	J	`jnl`	ECCB2022: the 21st European Conference on Computational Biology. Bioinform. Salvador Capella-Gutiérrez, Eva Alloza, Laura Rubinat-Ripoll, Ana Conesa, Alfonso Valencia
2022	J	`jnl`	Parallel model exploration for tumor treatment simulations. Comput. Intell. Charilaos Akasiadis, Miguel Ponce de Leon, Arnau Montagud, Evangelos Michelioudakis, Alexia Atsidakou, Elias Alevizos, Alexander Artikis, Alfonso Valencia, Georgios Paliouras
2022	—	`conf`	Pretrained Biomedical Language Models for Clinical NLP in Spanish. BioNLP@ACL Casimiro Pio Carrino, Joan Llop, Marc Pàmies, Asier Gutiérrez-Fandiño, Jordi Armengol-Estapé, Joaquín Silveira-Ocampo, Alfonso Valencia, Aitor Gonzalez-Agirre, Marta Villegas
2022	J	`jnl`	The structural coverage of the human proteome before and after AlphaFold. PLoS Comput. Biol. Eduard Porta-Pardo, Victoria Ruiz-Serra, Samuel Valentini, Alfonso Valencia
2021	—	`conf`	BioFVM-X: An MPI+OpenMP 3-D Simulator for Biological Systems. CMSB Gaurav Saxena, Miguel Ponce de Leon, Arnau Montagud, David Vicente Dorca, Alfonso Valencia
2021	J	`jnl`	Parallel Model Exploration for Tumor Treatment Simulations. CoRR Charilaos Akasiadis, Miguel Ponce de Leon, Arnau Montagud, Evangelos Michelioudakis, Alexia Atsidakou, Elias Alevizos, Alexander Artikis, Alfonso Valencia, Georgios Paliouras
2021	J	`jnl`	Simulating SARS-CoV-2 epidemics by region-specific variables and modeling contact tracing app containment. npj Digit. Medicine Alberto Ferrari, Enrico Santus, Davide Cirillo, Miguel Ponce de Leon, Nicola Marino, Maria Teresa Ferretti, Antonella Santuccione Chadha, Nikolaos Mavridis, Alfonso Valencia
2020	J	`jnl`	Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nat. 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 González-Pérez, 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 Glynne Gut, David Haan, Arif Ozgun 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
2020	J	`jnl`	Chromatin network markers of leukemia. Bioinform. Noël Malod-Dognin, Vera Pancaldi, Alfonso Valencia, Natasa Przulj
2020	J	`jnl`	ECCB2020: the 19th European Conference on Computational Biology. Bioinform. Salvador Capella-Gutiérrez, Eva Alloza, Edurne Gallastegui, Ioannis Kavakiotis, Jen Harrow, Alberto Langtry, Alfonso Valencia
2020	—	`conf`	GOPHER, an HPC Framework for Large Scale Graph Exploration and Inference. ISC Workshops Marc Josep-Fabregó, Xavier Teruel, Victor Gimenez-Abalos, Davide Cirillo, Dario Garcia-Gasulla, Sergio Álvarez-Napagao, Marta Garcia-Gasulla, Eduard Ayguadé, Alfonso Valencia
2020	J	`jnl`	On the inconsistent treatment of gene-protein-reaction rules in context-specific metabolic models. Bioinform. Miguel Ponce de Leon, Iñigo Apaolaza, Alfonso Valencia, Francisco J. Planes
2020	J	`jnl`	PDBe-KB: a community-driven resource for structural and functional annotations. Nucleic Acids Res. 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
2020	J	`jnl`	Parasitologist-level classification of apicomplexan parasites and host cell with deep cycle transfer learning (DCTL). Bioinform. Sen Li, Qi Yang, Hao Jiang, Jesús A. Cortés-Vecino, Yang Zhang, Alfonso Valencia
2020	J	`jnl`	Sex and gender differences and biases in artificial intelligence for biomedicine and healthcare. npj Digit. Medicine 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
2020	J	`jnl`	The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research. F1000Research 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 Glynne 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
2020	J	`jnl`	TiFoSi: an efficient tool for mechanobiology simulations of epithelia. Bioinform. Oriol Canela-Xandri, Samira Anbari, Javier Buceta, Alfonso Valencia
2020	J	`jnl`	Towards FAIR principles for research software. Data Sci. Anna-Lena Lamprecht, Leyla J. García, Mateusz Kuzak, Carlos Martinez-Ortiz, Ricardo Arcila, Eva Martín 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 Lluís Gelpí, Neil P. Chue Hong, Carole A. Goble, Salvador Capella-Gutiérrez
2019	J	`jnl`	BIOLITMAP: a web-based geolocated, temporal and thematic visualization of the evolution of bioinformatics publications. Bioinform. Adrián Bazaga, Alfonso Valencia, María-José Rementeria
2019	J	`jnl`	Interactive Extreme: Scale Analytics Towards Battling Cancer. IEEE Technol. Soc. Mag. 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
2019	J	`jnl`	Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm. J. Cheminformatics Martín Pérez-Pérez, Gael Pérez Rodríguez, Aitor Blanco-Míguez, Florentino Fdez-Riverola, Alfonso Valencia, Martin Krallinger, Anália Lourenço
2019	J	`jnl`	Patient Dossier: Healthcare queries over distributed resources. PLoS Comput. Biol. Miguel Vazquez, Alfonso Valencia
2019	J	`jnl`	Precision medicine needs pioneering clinical bioinformaticians. Briefings Bioinform. Gonzalo Gómez-López, Joaquín Dopazo, Juan C. Cigudosa, Alfonso Valencia, Fátima Al-Shahrour
2019	J	`jnl`	Reviewer-coerced citation: case report, update on journal policy and suggestions for future prevention. Bioinform. Jonathan D. Wren, Alfonso Valencia, Janet Kelso
2019	J	`jnl`	vulcanSpot: a tool to prioritize therapeutic vulnerabilities in cancer. Bioinform. 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
2018	J	`jnl`	APPRIS 2017: principal isoforms for multiple gene sets. Nucleic Acids Res. José Manuel Rodriguez, Juan Rodriguez-Rivas, Tomás Di Domenico, Jesús Vázquez, Alfonso Valencia, Michael L. Tress
2018	J	`jnl`	Algorithmic complexity in Computational Biology. CoRR Davide Cirillo, Alfonso Valencia
2017	J	`jnl`	CImbinator: a web-based tool for drug synergy analysis in small- and large-scale datasets. Bioinform. Åsmund Flobak, Miguel Vazquez, Astrid Lægreid, Alfonso Valencia
2017	J	`jnl`	ISCB's initial reaction to New England Journal of Medicine editorial on data sharing. Bioinform. Bonnie Berger, Terry Gaasterland, Thomas Lengauer, Christine A. Orengo, Bruno Gaëta, Scott Markel, Alfonso Valencia
2017	J	`jnl`	LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes. Nucleic Acids Res. Andrés Cañada, Salvador Capella-Gutiérrez, Obdulia Rabal, Julen Oyarzabal, Alfonso Valencia, Martin Krallinger
2017	—	`conf`	The Biomedical Abbreviation Recognition and Resolution (BARR) Track: Benchmarking, Evaluation and Importance of Abbreviation Recognition Systems Applied to Spanish Biomedical Abstracts. IberEval@SEPLN 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
2016	J	`jnl`	A computational approach inspired by simulated annealing to study the stability of protein interaction networks in cancer and neurological disorders. Data Min. Knowl. Discov. Kristina Ibáñez, María Guijarro, Gonzalo Pajares, Alfonso Valencia
2016	—	`conf`	Annotation Process, Guidelines and Text Corpus of Small Non-Coding RNA Molecules: the MiNCor for MicroRNA Annotations. SMBM Jose Camilla Sammartino, Martin Krallinger, Alfonso Valencia
2016	J	`jnl`	ISCB's Initial Reaction to PLoS Comput. Biol. Bonnie Berger, Terry Gaasterland, Thomas Lengauer, Christine A. Orengo, Bruno Gaëta, Scott Markel, Alfonso Valencia
2016	J	`jnl`	The Markyt visualisation, prediction and benchmark platform for chemical and gene entity recognition at BioCreative/CHEMDNER challenge. Database J. Biol. Databases Curation Martín Pérez-Pérez, Gael Pérez Rodríguez, Obdulia Rabal, Miguel Vazquez, Julen Oyarzabal, Florentino Fdez-Riverola, Alfonso Valencia, Martin Krallinger, Anália Lourenço
2015	J	`jnl`	APPRIS WebServer and WebServices. Nucleic Acids Res. José Manuel Rodriguez, Angel Carro, Alfonso Valencia, Michael L. Tress
2015	J	`jnl`	Alternative splicing and co-option of transposable elements: the case of TMPO/LAP2α and ZNF451 in mammals. Bioinform. Federico Abascal, Michael L. Tress, Alfonso Valencia
2015	J	`jnl`	Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level. PLoS Comput. Biol. Federico Abascal, Iakes Ezkurdia, Juan Rodriguez-Rivas, José Manuel Rodriguez, Angela del Pozo, Jesús Vázquez, Alfonso Valencia, Michael L. Tress
2015	J	`jnl`	CHEMDNER: The drugs and chemical names extraction challenge. J. Cheminformatics Martin Krallinger, Florian Leitner, Obdulia Rabal, Miguel Vazquez, Julen Oyarzabal, Alfonso Valencia
2015	J	`jnl`	ChiTaRS 2.1 - an improved database of the chimeric transcripts and RNA-seq data with novel sense-antisense chimeric RNA transcripts. Nucleic Acids Res. Milana Frenkel-Morgenstern, Alessandro Gorohovski, Dunja Vucenovic, Lorena Maestre, Alfonso Valencia
2015	J	`jnl`	Detection of significant protein coevolution. Bioinform. David Ochoa, David de Juan, Alfonso Valencia, Florencio Pazos
2015	J	`jnl`	FUN-L: gene prioritization for RNAi screens. Bioinform. 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
2015	J	`jnl`	Structure-PPi: a module for the annotation of cancer-related single-nucleotide variants at protein-protein interfaces. Bioinform. Miguel Vazquez, Alfonso Valencia, Tirso Pons
2015	J	`jnl`	Summary of the BioLINK SIG 2013 meeting at ISMB/ECCB 2013. Bioinform. Karin Verspoor, Hagit Shatkay, Lynette Hirschman, Christian Blaschke, Alfonso Valencia
2015	J	`jnl`	The CHEMDNER corpus of chemicals and drugs and its annotation principles. J. Cheminformatics 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
2014	J	`jnl`	BioCreative-IV virtual issue. Database J. Biol. Databases Curation Cecilia N. Arighi, Cathy H. Wu, Kevin Bretonnel Cohen, Lynette Hirschman, Martin Krallinger, Alfonso Valencia, Zhiyong Lu, W. John Wilbur, Thomas C. Wiegers
2014	J	`jnl`	CheNER: chemical named entity recognizer. Bioinform. Anabel Usie, Rui Alves, Francesc Solsona, Miguel Vazquez, Alfonso Valencia
2014	J	`jnl`	FireDB: a compendium of biological and pharmacologically relevant ligands. Nucleic Acids Res. Paolo Maietta, Gonzalo López, Angel Carro, Benjamin J. Pingilley, Leticia G. Leon, Alfonso Valencia, Michael L. Tress
2014	J	`jnl`	Predicting Protein Relationshipsto Human Pathways througha Relational Learning ApproachBased on Simple Sequence Features. IEEE ACM Trans. Comput. Biol. Bioinform. Beatriz García Jiménez, Tirso Pons, Araceli Sanchis, Alfonso Valencia
2014	Misc	`conf`	Retrieval and Discovery of Cell Cycle Literature and Proteins by Means of Machine Learning, Text Mining and Network Analysis. PACBB Martin Krallinger, Florian Leitner, Alfonso Valencia
2013	J	`jnl`	APPRIS: annotation of principal and alternative splice isoforms. Nucleic Acids Res. José Manuel Rodriguez, Paolo Maietta, Iakes Ezkurdia, Alessandro Pietrelli, Jan-Jaap Wesselink, Gonzalo López, Alfonso Valencia, Michael L. Tress
2013	J	`jnl`	BioC: a minimalist approach to interoperability for biomedical text processing. Database J. Biol. Databases Curation 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
2013	J	`jnl`	ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data. Nucleic Acids Res. Milana Frenkel-Morgenstern, Alessandro Gorohovski, Vincent Lacroix, Mark F. Rogers, Kristina Ibáñez, Cesar Boullosa, Eduardo Andrés León, Asa Ben-Hur, Alfonso Valencia
2013	—	`conf`	Machine Reading of Biomedical Texts about Alzheimer's Disease. CLEF (Working Notes) Roser Morante, Martin Krallinger, Alfonso Valencia, Walter Daelemans
2013	J	`jnl`	RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses. Bioinform. Miriam Rubio-Camarillo, Gonzalo Gómez-López, José María Fernández, Alfonso Valencia, David G. Pisano
2013	J	`jnl`	wKinMut: An integrated tool for the analysis and interpretation of mutations in human protein kinases. BMC Bioinform. José M. G. Izarzugaza, Miguel Vazquez, Angela del Pozo, Alfonso Valencia
2012	J	`jnl`	Accurate Demarcation of Protein Domain Linkers based on Structural Analysis of Linker Probable Region CoRR Vivekanand Samant, Arvind Hulgeri, Alfonso Valencia, Ashish V. Tendulkar
2012	J	`jnl`	BioCreative-2012 Virtual Issue. Database J. Biol. Databases Curation 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
2012	J	`jnl`	Bioimage informatics: a new category in Bioinform. Hanchuan Peng, Alex Bateman, Alfonso Valencia, Jonathan D. Wren
2012	J	`jnl`	Chapter 14: Cancer Genome Analysis. PLoS Comput. Biol. Miguel Vazquez, Victor de la Torre, Alfonso Valencia
2012	J	`jnl`	EnrichNet: network-based gene set enrichment analysis. Bioinform. Enrico Glaab, Anaïs Baudot, Natalio Krasnogor, Reinhard Schneider, Alfonso Valencia
2012	J	`jnl`	How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience. Database J. Biol. Databases Curation Martin Krallinger, Florian Leitner, Miguel Vazquez, David Salgado, Christophe Marcelle, Mike Tyers, Alfonso Valencia, Andrew Chatr-aryamontri
2012	J	`jnl`	JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures. Bioinform. Thilo Muth, Juan A. García-Martín, Antonio Rausell, David de Juan, Alfonso Valencia, Florencio Pazos
2012	—	`conf`	Machine Reading of Biomedical Texts about Alzheimer's Disease. CLEF (Online Working Notes/Labs/Workshop) Roser Morante, Martin Krallinger, Alfonso Valencia, Walter Daelemans
2012	J	`jnl`	Mirroring co-evolving trees in the light of their topologies. Bioinform. Iman Hajirasouliha, Alexander Schönhuth, David de Juan, Alfonso Valencia, Süleyman Cenk Sahinalp
2012	J	`jnl`	MyMiner: a web application for computer-assisted biocuration and text annotation. Bioinform. David Salgado, Martin Krallinger, Marc Depaule, Elodie Drula, Ashish V. Tendulkar, Florian Leitner, Alfonso Valencia, Christophe Marcelle
2012	J	`jnl`	Novel domain combinations in proteins encoded by chimeric transcripts. Bioinform. Milana Frenkel-Morgenstern, Alfonso Valencia
2012	J	`jnl`	Text mining for the biocuration workflow. Database J. Biol. Databases Curation 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
2012	—	`conf`	wKinMut: An integrated tool for the analysis and interpretation of mutations in human protein kinases. AIMM José M. G. Izarzugaza, Miguel Vazquez, Angela del Pozo, Alfonso Valencia
2011	Misc	`ed.`	5th International Conference on Practical Applications of Computational Biology & Bioinformatics, PACBB 2011, April 6-8, 2011, Salamanca, Spain PACBB Miguel P. Rocha, Juan M. Corchado Rodríguez, Florentino Fdez-Riverola, Alfonso Valencia
2011	J	`jnl`	Characterization of pathogenic germline mutations in human Protein Kinases. BMC Bioinform. José M. G. Izarzugaza, Lisa E. M. Hopcroft, Anja Baresic, Christine A. Orengo, Andrew C. R. Martin, Alfonso Valencia
2011	J	`jnl`	Mirroring co-evolving trees in the light of their topologies CoRR Iman Hajirasouliha, Alexander Schönhuth, David de Juan, Alfonso Valencia, Süleyman Cenk Sahinalp
2011	J	`jnl`	On the organization of bioinformatics core services in biology-based research institutes. Bioinform. Olli-P. Kallioniemi, Lodewyk F. A. Wessels, Alfonso Valencia
2011	J	`jnl`	Overview of the BioCreative III Workshop. BMC Bioinform. Cecilia N. Arighi, Zhiyong Lu, Martin Krallinger, Kevin Bretonnel Cohen, W. John Wilbur, Alfonso Valencia, Lynette Hirschman, Cathy H. Wu
2011	J	`jnl`	Selection of organisms for the co-evolution-based study of protein interactions. BMC Bioinform. Dorota Herman, David Ochoa, David de Juan, Daniel Lopez, Alfonso Valencia, Florencio Pazos
2010	J	`jnl`	An Overview of BioCreative II.5. IEEE ACM Trans. Comput. Biol. Bioinform. Florian Leitner, Scott A. Mardis, Martin Krallinger, Gianni Cesareni, Lynette Hirschman, Alfonso Valencia
2010	—	`conf`	Bioinformatic Software Developments in Spain. JBI José María Fernández, Alfonso Valencia
2010	J	`jnl`	Extending pathways and processes using molecular interaction networks to analyse cancer genome data. BMC Bioinform. Enrico Glaab, Anaïs Baudot, Natalio Krasnogor, Alfonso Valencia
2010	J	`jnl`	The PPI affix dictionary (PPIAD) and BioMethod Lexicon: importance of affixes and tags for recognition of entity mentions and experimental protein interactions. BMC Bioinform. Martin Krallinger, Ashish V. Tendulkar, Florian Leitner, Andrew Chatr-aryamontri, Alfonso Valencia
2010	J	`jnl`	TopoGSA: network topological gene set analysis. Bioinform. Enrico Glaab, Anaïs Baudot, Natalio Krasnogor, Alfonso Valencia
2010	—	`conf`	iHOP Web Services Family. JBI José María Fernández, Robert Hoffmann, Alfonso Valencia
2009	J	`jnl`	An integrated approach to the interpretation of Single Amino Acid Polymorphisms within the framework of CATH and Gene3D. BMC Bioinform. José M. G. Izarzugaza, Anja Baresic, Lisa E. M. McMillan, Corin Yeats, Andrew B. Clegg, Christine A. Orengo, Andrew C. R. Martin, Alfonso Valencia
2009	J	`jnl`	Automated Alphabet Reduction for Protein Datasets. BMC Bioinform. Jaume Bacardit, Michael Stout, Jonathan D. Hirst, Alfonso Valencia, Robert Elliott Smith, Natalio Krasnogor
2009	J	`jnl`	Bionemo: molecular information on biodegradation metabolism. Nucleic Acids Res. Guillermo Carbajosa, Almudena Trigo, Alfonso Valencia, Ildefonso Cases
2009	J	`jnl`	EcID. A database for the inference of functional interactions in Nucleic Acids Res. Eduardo Andrés León, Iakes Ezkurdia, Beatriz García Jiménez, Alfonso Valencia, David de Juan
2009	J	`jnl`	Extraction of human kinase mutations from literature, databases and genotyping studies. BMC Bioinform. Martin Krallinger, José M. G. Izarzugaza, Carlos Rodríguez Penagos, Alfonso Valencia
2009	J	`jnl`	PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction. Nucleic Acids Res. Martin Krallinger, Carlos Rodríguez Penagos, Ashish V. Tendulkar, Alfonso Valencia
2009	J	`jnl`	Progress and challenges in predicting protein-protein interaction sites. Briefings Bioinform. Iakes Ezkurdia, Lisa Bartoli, Piero Fariselli, Rita Casadio, Alfonso Valencia, Michael L. Tress
2009	—	`conf`	SOA-Based Integration of Text Mining Services. SERVICES I Johannes Starlinger, Florian Leitner, Alfonso Valencia, Ulf Leser
2008	—	`ch.`	Computational Methods to Predict Protein Interaction Partners. Protein-protein Interactions and Networks Alfonso Valencia, Florencio Pazos
2008	J	`jnl`	Defining functional distances over Gene Ontology. BMC Bioinform. Angela del Pozo, Florencio Pazos, Alfonso Valencia
2008	J	`jnl`	Determination and validation of principal gene products. Bioinform. 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
2008	A	`conf`	Editorial. ISMB Alfonso Valencia, Ildefonso Cases
2008	J	`jnl`	Enhancing the prediction of protein pairings between interacting families using orthology information. BMC Bioinform. José M. G. Izarzugaza, David de Juan, Carles Pons, Florencio Pazos, Alfonso Valencia
2008	—	`conf`	Overview of the Ninth Annual Meeting of the BioLINK SIG at ISMB: Linking Literature, Information and Knowledge for Biology. BioLINK@ISMB/ECCB Christian Blaschke, Lynette Hirschman, Hagit Shatkay, Alfonso Valencia
2008	B	`conf`	Protein Interactions Extracted from Genomes and Papers. APBC Alfonso Valencia
2008	—	`conf`	Text mining in genomics and systems biology. DTMBIO Alfonso Valencia
2008	—	`conf`	iProLINK: A Framework for Linking Text Mining with Ontology and Systems Biology. BIBM Zhang-Zhi Hu, K. Bretonnel Cohen, Lynette Hirschman, Alfonso Valencia, Hongfang Liu, Michelle G. Giglio, Cathy H. Wu
2007	J	`jnl`	CARGO: a web portal to integrate customized biological information. Nucleic Acids Res. Ildefonso Cases, David G. Pisano, Eduardo Andrés León, Angel Carro, José María Fernández, Gonzalo Gómez-López, José Manuel Rodriguez, Jaime F. Vera, Alfonso Valencia, Ana María Rojas
2007	J	`jnl`	Editorial. Bioinform. Alfonso Valencia, Alex Bateman
2007	J	`jnl`	FireDB - a database of functionally important residues from proteins of known structure. Nucleic Acids Res. Gonzalo López, Alfonso Valencia, Michael L. Tress
2007	J	`jnl`	iHOP web services. Nucleic Acids Res. José María Fernández, Robert Hoffmann, Alfonso Valencia
2006	J	`jnl`	An analysis of the Sargasso Sea resource and the consequences for database composition. BMC Bioinform. Michael L. Tress, Domenico Cozzetto, Anna Tramontano, Alfonso Valencia
2006	J	`jnl`	Bioinformatics in the human interactome project. Bioinform. Trey Ideker, Alfonso Valencia
2006	J	`jnl`	Phylogeny-independent detection of functional residues. Bioinform. Florencio Pazos, Antonio Rausell, Alfonso Valencia
2006	J	`jnl`	Semantic Mining in Biomedicine Bioinform. Udo Hahn, Alfonso Valencia
2006	J	`jnl`	Software patents in Bioinformatics. Bioinform. Alfonso Valencia, Alex Bateman
2006	J	`jnl`	Structural genomics meets computational biology. Bioinform. Alex Bateman, Alfonso Valencia
2006	J	`jnl`	Synthetic Biology: challenges ahead. Bioinform. Victor de Lorenzo, Luis Serrano, Alfonso Valencia
2006	J	`jnl`	TSEMA: interactive prediction of protein pairings between interacting families. Nucleic Acids Res. José M. G. Izarzugaza, David de Juan, Carles Pons, Juan A. G. Ranea, Alfonso Valencia, Florencio Pazos
2006	J	`jnl`	TreeDet: a web server to explore sequence space. Nucleic Acids Res. Angel Carro, Michael L. Tress, David de Juan, Florencio Pazos, Pedro Lopez-Romero, Antonio del Sol, Alfonso Valencia, Ana María Rojas
2005	—	`conf`	A framework for computational and experimental methods: Identifying dimerization residues in CCR chemokine receptors. ECCB/JBI David de Juan, Mario Mellado, José Miguel Rodríguez-Frade, Patricia Hernanz-Falcón, Antonio Serrano, Antonio del Sol, Alfonso Valencia, Carlos Martínez-A, Ana María Rojas
2005	J	`jnl`	A sentence sliding window approach to extract protein annotations from biomedical articles. BMC Bioinform. Martin Krallinger, Maria Padron, Alfonso Valencia
2005	J	`jnl`	Accessible Protein Interaction Data for Network Modeling. Structure of the Information and Available Repositories. Trans. Comp. Sys. Biology Manuel J. Gómez, Ramón Alonso-Allende, Florencio Pazos, Osvaldo Graña, David de Juan, Alfonso Valencia
2005	J	`jnl`	An update from the Bioinform. Alex Bateman, Alfonso Valencia
2005	—	`ch.`	Applications of Text Mining in Molecular Biology, from Name Recognition to Protein Interaction Maps. Data Analysis and Visualization in Genomics and Proteomics Martin Krallinger, Alfonso Valencia
2005	J	`jnl`	Do you do text? Bioinform. Christian Blaschke, Alexander S. Yeh, Evelyn Camon, Marc E. Colosimo, Rolf Apweiler, Lynette Hirschman, Alfonso Valencia
2005	—	`conf`	ECCB/JBI 2005. ECCB/JBI Roderic Guigó, Federico Morán, Alfonso Valencia, Josep F. Abril
2005	J	`jnl`	EVAcon: a protein contact prediction evaluation service. Nucleic Acids Res. Osvaldo Graña, Volker A. Eyrich, Florencio Pazos, Burkhard Rost, Alfonso Valencia
2005	J	`jnl`	Evaluation of BioCreAtIvE assessment of task 2. BMC Bioinform. Christian Blaschke, Eduardo Andrés León, Martin Krallinger, Alfonso Valencia
2005	J	`jnl`	HCAD, closing the gap between breakpoints and genes. Nucleic Acids Res. Robert Hoffmann, Joaquín Dopazo, Juan C. Cigudosa, Alfonso Valencia
2005	—	`conf`	Implementing the iHOP concept for navigation of biomedical literature. ECCB/JBI Robert Hoffmann, Alfonso Valencia
2005	J	`jnl`	Increasing the Impact of Bioinform. Alfonso Valencia, Alex Bateman
2005	J	`jnl`	MetaRouter: bioinformatics for bioremediation. Nucleic Acids Res. Florencio Pazos, David Guijas, Alfonso Valencia, Victor de Lorenzo
2005	J	`jnl`	Overview of BioCreAtIvE: critical assessment of information extraction for biology. BMC Bioinform. Lynette Hirschman, Alexander S. Yeh, Christian Blaschke, Alfonso Valencia
2004	—	`conf`	Assessing the Correlation between Contextual Patterns and Biological Entity Tagging. NLPBA/BioNLP Martin Krallinger, Maria Padron, Christian Blaschke, Alfonso Valencia
2004	—	`conf`	Bioinformatic Analyses of the Dio Family of Proteins. Spanish Bioinformatics Conference Ana María Rojas, Luis Sánchez-Pulido, Agnes Fütterer, Karel H. M. van Wely, Carlos Martínez-A, Alfonso Valencia
2004	J	`jnl`	IntAct: an open source molecular interaction database. Nucleic Acids Res. Henning Hermjakob, Luisa Montecchi-Palazzi, Chris Lewington, Sugath Mudali, Samuel Kerrien, Sandra E. Orchard, Martin Vingron, Bernd Roechert, Peter Roepstorff, Alfonso Valencia, Hanah Margalit, John Armstrong, Amos Bairoch, Gianni Cesareni, David James Sherman, Rolf Apweiler
2004	J	`jnl`	New Leadership for Bioinformatics. Bioinform. Alex Bateman, Alfonso Valencia
2004	J	`jnl`	SIGIR 2003 workshop on text analysis and search for bioinformatics. SIGIR Forum Eric W. Brown, William R. Hersh, Alfonso Valencia
2004	J	`jnl`	SPOC: A widely distributed domain associated with cancer, apoptosis and transcription. BMC Bioinform. Luis Sánchez-Pulido, Ana María Rojas, Karel H. M. van Wely, Carlos Martínez-A, Alfonso Valencia
2004	J	`jnl`	SQUARE-determining reliable regions in sequence alignments. Bioinform. Michael L. Tress, Osvaldo Graña, Alfonso Valencia
2004	—	`conf`	The Biodegradation Network, a New Scenario for Computational Systems Biology Research. CMSB Florencio Pazos, David Guijas, Manuel J. Gómez, Almudena Trigo, Victor de Lorenzo, Alfonso Valencia
2004	—	`conf`	XML Databases, are Ready for Bioinformatics? Spanish Bioinformatics Conference José María Fernández, Alfonso Valencia
2004	J	`jnl`	YAdumper: extracting and translating large information volumes from relational databases to structured flat files. Bioinform. José María Fernández, Alfonso Valencia
2003	J	`jnl`	EVA: evaluation of protein structure prediction servers. Nucleic Acids Res. Ingrid Y. Y. Koh, Volker A. Eyrich, Marc A. Martí-Renom, Dariusz Przybylski, Mallur S. Madhusudhan, Narayanan Eswar, Osvaldo Graña, Florencio Pazos, Alfonso Valencia, Andrej Sali, Burkhard Rost
2003	J	`jnl`	Early bioinformatics: the birth of a discipline - a personal view. Bioinform. Christos A. Ouzounis, Alfonso Valencia
2003	J	`jnl`	Evaluation of annotation strategies using an entire genome sequence. Bioinform. Ioannis Iliopoulos, Sophia Tsoka, Miguel A. Andrade, Anton J. Enright, Mark Carroll, Patrick Poullet, Vasilis J. Promponas, Theodore Liakopoulos, Giorgos Palaios, Claude Pasquier, Stavros J. Hamodrakas, Javier Tamames, Asutosh T. Yagnik, Anna Tramontano, Damien Devos, Christian Blaschke, Alfonso Valencia, David Brett, David M. A. Martin, Christophe Leroy, Isidore Rigoutsos, Chris Sander, Christos A. Ouzounis
2003	J	`jnl`	Meta, Metan and Cyber Servers. Bioinform. Alfonso Valencia
2002	J	`jnl`	Bioinformatics in structural genomics - Editorial. Bioinform. Burkhard Rost, Barry Honig, Alfonso Valencia
2002	J	`jnl`	Bioinformatics: Biology by other means. Bioinform. Alfonso Valencia
2002	J	`jnl`	Clustering of proximal sequence space for the identification of protein families. Bioinform. Federico Abascal, Alfonso Valencia
2002	J	`jnl`	Information extraction in molecular biology. Briefings Bioinform. Christian Blaschke, Lynette Hirschman, Alfonso Valencia
2002	J	`jnl`	The Frame-Based Module of the SUISEKI Information Extraction System. IEEE Intell. Syst. Christian Blaschke, Alfonso Valencia
2001	J	`jnl`	A hierarchical unsupervised growing neural network for clustering gene expression patterns. Bioinform. Javier Herrero, Alfonso Valencia, Joaquín Dopazo
2001	J	`jnl`	Challenges for Intelligent Systems in Biology. IEEE Intell. Syst. Russ B. Altman, Alfonso Valencia, Satoru Miyano, Shoba Ranganathan
2001	J	`jnl`	EVA: continuous automatic evaluation of protein structure prediction servers. Bioinform. Volker A. Eyrich, Marc A. Martí-Renom, Dariusz Przybylski, Mallur S. Madhusudhan, András Fiser, Florencio Pazos, Alfonso Valencia, Andrej Sali, Burkhard Rost
1999	J	`jnl`	A platform for integrating threading results with protein family analyses. Bioinform. Florencio Pazos, Burkhard Rost, Alfonso Valencia
1999	J	`jnl`	Automated genome sequence analysis and annotation. Bioinform. Miguel A. Andrade, Nigel P. Brown, Christophe Leroy, S. Hörsch, Antoine de Daruvar, C. Reich, Angelo Franchini, Javier Tamames, Alfonso Valencia, Christos A. Ouzounis, Chris Sander
1999	A	`conf`	Automatic Extraction of Biological Information from Scientific Text: Protein-Protein Interactions. ISMB Christian Blaschke, Miguel A. Andrade, Christos A. Ouzounis, Alfonso Valencia
1998	J	`jnl`	Automatic extraction of keywords from scientific text: application to the knowledge domain of protein families. Bioinform. Miguel A. Andrade, Alfonso Valencia
1998	J	`jnl`	Computational space reduction and parallelization of a new clustering approach for large groups of sequences. Bioinform. Oswaldo Trelles, Miguel A. Andrade, Alfonso Valencia, Emilio L. Zapata, José María Carazo
1998	J	`jnl`	EUCLID: automatic classification of proteins in functional classes by their database annotations. Bioinform. Javier Tamames, Christos A. Ouzounis, Georg Casari, Chris Sander, Alfonso Valencia
1997	J	`jnl`	A graphical interface for correlated mutations and other protein structure prediction methods. Comput. Appl. Biosci. Florencio Pazos, O. Olmea, Alfonso Valencia
1997	A	`conf`	Automatic Annotation for Biological Sequences by Etraction of Keywords from MEDLINE Abstracts: Development of a Prototype System. ISMB Miguel A. Andrade, Alfonso Valencia
1997	J	`jnl`	Classification of protein families and detection of the determinant residues with an improved self-organizing map. Biol. Cybern. Miguel A. Andrade, Georg Casari, Chris Sander, Alfonso Valencia
1997	—	`conf`	Comparative Analysis of Different Methods for the Detection of Specificity Regions in Protein Families. BCEC Florencio Pazos, Luis Sánchez-Pulido, Juan Antonio Garcia-Ranca, Miguel A. Andrade, Silvia Atrian, Alfonso Valencia
1997	A	`ed.`	Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, Halkidiki, Greece, June 21-26, 1997 ISMB Terry Gaasterland, Peter D. Karp, Kevin Karplus, Christos A. Ouzounis, Chris Sander, Alfonso Valencia
1997	J	`jnl`	Sequence analysis of the Methanococcus jannaschii genome and the prediction of protein function. Comput. Appl. Biosci. Miguel A. Andrade, Georg Casari, Antoine de Daruvar, Chris Sander, Reinhard Schneider, Javier Tamames, Alfonso Valencia, Christos A. Ouzounis
1995	—	`conf`	The Functional Composition of Living Machines as a Design Principle for Artificial Organisms. ECAL Christos A. Ouzounis, Alfonso Valencia, Javier Tamames, Peer Bork, Chris Sander
1994	A	`conf`	GeneQuiz: A Workbench for Sequence Analysis. ISMB Michael Scharf, Reinhard Schneider, Georg Casari, Peer Bork, Alfonso Valencia, Christos A. Ouzounis, Chris Sander