| 2014 | PACBB | Retrieval and Discovery of Cell Cycle Literature and Proteins by Means of Machine Learning, Text Mining and Network Analysis. | Martin Krallinger, Florian Leitner, Alfonso Valencia |
| 2012 | ECCB | wKinMut: An integrated tool for the analysis and interpretation of mutations in human protein kinases. | Jos M. G. Izarzugaza, Miguel Vzquez, Angela del Pozo, Alfonso Valencia |
| 2009 | SERVICES | SOA-Based Integration of Text Mining Services. | Johannes Starlinger, Florian Leitner, Alfonso Valencia, Ulf Leser |
| 2008 | APBC | Protein Interactions Extracted from Genomes and Papers. | Alfonso Valencia |
| 2008 | CIKM | Text mining in genomics and systems biology. | Alfonso Valencia |
| 2008 | ISMB | Overview of the Ninth Annual Meeting of the BioLINK SIG at ISMB: Linking Literature, Information and Knowledge for Biology. | Christian Blaschke, Lynette Hirschman, Hagit Shatkay, Alfonso Valencia |
| 2008 | ISMB | Editorial. | Alfonso Valencia, Ildefonso Cases |
| 2005 | ECCB | ECCB/JBI 2005. | Roderic Guig, Federico Morn, Alfonso Valencia, Josep F. Abril |
| 2005 | ECCB | Implementing the iHOP concept for navigation of biomedical literature. | Robert Hoffmann, Alfonso Valencia |
| 2005 | ECCB | A framework for computational and experimental methods: Identifying dimerization residues in CCR chemokine receptors. | David de Juan, Mario Mellado, Jos Miguel Rodrguez-Frade, Patricia Hernanz-Falcn, Antonio Serrano, Antonio del Sol, Alfonso Valencia, Carlos Martnez-A, Ana Mara Rojas |
| 1999 | ISMB | Automatic Extraction of Biological Information from Scientific Text: Protein-Protein Interactions. | Christian Blaschke, Miguel A. Andrade, Christos A. Ouzounis, Alfonso Valencia |
| 1997 | ISMB | Automatic Annotation for Biological Sequences by Etraction of Keywords from MEDLINE Abstracts: Development of a Prototype System. | Miguel A. Andrade, Alfonso Valencia |
| 1994 | ISMB | GeneQuiz: A Workbench for Sequence Analysis. | Michael Scharf, Reinhard Schneider, Georg Casari, Peer Bork, Alfonso Valencia, Christos A. Ouzounis, Chris Sander |