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- 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 Research 46(Database-Issue): D213-D217 (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. Bioinformatics 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. Bioinformatics 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 Research 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. Bioinformatics 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. Bioinformatics 31(12): 2052-2053 (2015) - [j96]David Ochoa, David de Juan, Alfonso Valencia, Florencio Pazos:
Detection of significant protein coevolution. Bioinformatics 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. Bioinformatics 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. Bioinformatics 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 Research 43(Database-Issue): 68-75 (2015) - [j90]Jose Manuel Rodriguez, Angel Carro, Alfonso Valencia, Michael L. Tress:
APPRIS WebServer and WebServices. Nucleic Acids Research 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. Bioinformatics 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 Research 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. Bioinformatics 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 Bioinformatics 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 Research 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 Research 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. Bioinformatics 28(4): 584-586 (2012) - [j75]Hanchuan Peng, Alex Bateman, Alfonso Valencia, Jonathan D. Wren:
Bioimage informatics: a new category in Bioinformatics. Bioinformatics 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. Bioinformatics 28(9): 1202-1208 (2012) - [j73]Milana Frenkel-Morgenstern, Alfonso Valencia:
Novel domain combinations in proteins encoded by chimeric transcripts. Bioinformatics 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. Bioinformatics 28(17): 2285-2287 (2012) - [j71]Enrico Glaab, Anaïs Baudot, Natalio Krasnogor, Reinhard Schneider, Alfonso Valencia:
EnrichNet: network-based gene set enrichment analysis. Bioinformatics 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. Bioinformatics 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 Bioinformatics 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 Bioinformatics 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 Bioinformatics 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 Research 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. Bioinformatics 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 Bioinformatics 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 Bioinformatics 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 in Bioinformatics 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 Bioinformatics 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 Bioinformatics 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 Bioinformatics 10(S-8): 5 (2009) - [j56]Guillermo Carbajosa, Almudena Trigo, Alfonso Valencia, Ildefonso Cases:
Bionemo: molecular information on biodegradation metabolism. Nucleic Acids Research 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 Research 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 Research 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. Bioinformatics 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 Bioinformatics 9 (2008) - [j51]Angela del Pozo, Florencio Pazos, Alfonso Valencia:
Defining functional distances over Gene Ontology. BMC Bioinformatics 9 (2008) - [c17]
- [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]
- [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]
- 2007
- [j50]
- [j49]Gonzalo López, Alfonso Valencia, Michael L. Tress:
FireDB - a database of functionally important residues from proteins of known structure. Nucleic Acids Research 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 Research 35(Web-Server-Issue): 16-20 (2007) - [j47]José María Fernández, Robert Hoffmann, Alfonso Valencia:
iHOP web services. Nucleic Acids Research 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 Research 35(Web-Server-Issue): 573-577 (2007) - 2006
- [j45]Victor de Lorenzo, Luis Serrano, Alfonso Valencia:
Synthetic Biology: challenges ahead. Bioinformatics 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). Bioinformatics 22(6): 643-644 (2006) - [j43]Alfonso Valencia, Alex Bateman:
Software patents in Bioinformatics. Bioinformatics 22(12): 1415 (2006) - [j42]Florencio Pazos, Antonio Rausell, Alfonso Valencia:
Phylogeny-independent detection of functional residues. Bioinformatics 22(12): 1440-1448 (2006) - [j41]Alex Bateman, Alfonso Valencia:
Structural genomics meets computational biology. Bioinformatics 22(19): 2319 (2006) - [j40]Trey Ideker, Alfonso Valencia:
Bioinformatics in the human interactome project. Bioinformatics 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 Bioinformatics 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 Research 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 Research 34(Web-Server-Issue): 315-319 (2006) - 2005
- [j36]Alfonso Valencia, Alex Bateman:
Increasing the Impact of Bioinformatics. Bioinformatics 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? Bioinformatics 21(23): 4199-4200 (2005) - [j34]Alex Bateman, Alfonso Valencia:
An update from the Bioinformatics Editors. Bioinformatics 21(24): 4319 (2005) - [j33]Christian Blaschke, Eduardo Andrés León, Martin Krallinger, Alfonso Valencia:
Evaluation of BioCreAtIvE assessment of task 2. BMC Bioinformatics 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 Bioinformatics 6(S-1) (2005) - [j31]Martin Krallinger, Maria Padron, Alfonso Valencia:
A sentence sliding window approach to extract protein annotations from biomedical articles. BMC Bioinformatics 6(S-1) (2005) - [j30]Robert Hoffmann, Joaquín Dopazo, Juan C. Cigudosa, Alfonso Valencia:
HCAD, closing the gap between breakpoints and genes. Nucleic Acids Research 33(Database-Issue): 511-513 (2005) - [j29]Florencio Pazos, David Guijas, Alfonso Valencia, Victor de Lorenzo:
MetaRouter: bioinformatics for bioremediation. Nucleic Acids Research 33(Database-Issue): 588-592 (2005) - [j28]Osvaldo Graña, Volker A. Eyrich, Florencio Pazos, Burkhard Rost, Alfonso Valencia:
EVAcon: a protein contact prediction evaluation service. Nucleic Acids Research 33(Web-Server-Issue): 347-351 (2005) - [j27]Manuel Gómez, Ramón Alonso-Allende, Florencio Pazos, Osvaldo Graña, David de Juan, Alfonso Valencia:
Accessible Protein Interaction Data for Network Modeling. Structure of the Information and Available Repositories. Trans. Computational Systems Biology 1: 1-13 (2005) - [c12]
- [c11]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:
A framework for computational and experimental methods: Identifying dimerization residues in CCR chemokine receptors. ECCB/JBI 2005: 18 - [c10]Robert Hoffmann, Alfonso Valencia:
Implementing the iHOP concept for navigation of biomedical literature. ECCB/JBI 2005: 258 - 2004
- [j26]Michael L. Tress, Osvaldo Graña, Alfonso Valencia:
SQUARE-determining reliable regions in sequence alignments. Bioinformatics 20(6): 974-975 (2004) - [j25]Alex Bateman, Alfonso Valencia:
New Leadership for Bioinformatics. Bioinformatics 20(12): 1821 (2004) - [j24]José María Fernández, Alfonso Valencia:
YAdumper: extracting and translating large information volumes from relational databases to structured flat files. Bioinformatics 20(15): 2455-2457 (2004) - [j23]Luis Sánchez-Pulido, Ana María Rojas, Karel H. M. van Wely, Carlos Martínez-A, Alfonso Valencia:
SPOC: A widely distributed domain associated with cancer, apoptosis and transcription. BMC Bioinformatics 5: 91 (2004) - [j22]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:
IntAct: an open source molecular interaction database. Nucleic Acids Research 32(Database-Issue): 452-455 (2004) - [j21]Eric W. Brown, William R. Hersh, Alfonso Valencia:
SIGIR 2003 workshop on text analysis and search for bioinformatics. SIGIR Forum 38(2): 31-36 (2004) - [c9]Martin Krallinger, Maria Padron, Christian Blaschke, Alfonso Valencia:
Assessing the Correlation between Contextual Patterns and Biological Entity Tagging. NLPBA/BioNLP 2004 - [c8]Florencio Pazos, David Guijas, Manuel J. Gomez, Almudena Trigo, Victor de Lorenzo, Alfonso Valencia:
The Biodegradation Network, a New Scenario for Computational Systems Biology Research. CMSB 2004: 252-256 - [c7]Ana María Rojas, Luis Sánchez-Pulido, Agnes Fütterer, Karel H. M. van Wely, Carlos Martínez-A, Alfonso Valencia:
Bioinformatic Analyses of the Dio Family of Proteins. Spanish Bioinformatics Conference 2004: 70-71 - [c6]José María Fernández, Alfonso Valencia:
XML Databases, are Ready for Bioinformatics? Spanish Bioinformatics Conference 2004: 166-170 - 2003
- [j20]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:
Evaluation of annotation strategies using an entire genome sequence. Bioinformatics 19(6): 717-726 (2003) - [j19]
- [j18]Christos A. Ouzounis, Alfonso Valencia:
Early bioinformatics: the birth of a discipline - a personal view. Bioinformatics 19(17): 2176-2190 (2003) - [j17]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:
EVA: evaluation of protein structure prediction servers. Nucleic Acids Research 31(13): 3311-3315 (2003) - 2002
- [j16]Christian Blaschke, Lynette Hirschman, Alfonso Valencia:
Information extraction in molecular biology. Briefings in Bioinformatics 3(2): 154-165 (2002) - [j15]Burkhard Rost, Barry Honig, Alfonso Valencia:
Bioinformatics in structural genomics - Editorial. Bioinformatics 18(7): 897 (2002)