selected publications
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academic article
- Controlled vocabularies and semantics in systems biology. Molecular Systems Biology. 7:543-543. 2014
- Evaluation of research in biomedical ontologies. Briefings in bioinformatics. 14:696-712. 2013
- State of the art and open challenges in community-driven knowledge curation. Journal of biomedical informatics. 46:1-4. 2013
- Aptamer base: a collaborative knowledge base to describe aptamers and SELEX experiments. Database. 2012:bas006-bas006. 2012
- Building an HIV data mashup using Bio2RDF. Briefings in bioinformatics. 13:98-106. 2012
- Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics. Bioinformatics (Oxford, England). 28:2169-2175. 2012
- Linked Data in Drug Discovery. IEEE internet computing. 16:68-71. 2012
- Self-organizing ontology of biochemically relevant small molecules. BMC Bioinformatics. 13:3. 2012
- A common layer of interoperability for biomedical ontologies based on OWL EL. Bioinformatics (Oxford, England). 27:1001-1008. 2011
- Chemical Entity Semantic Specification: Knowledge representation for efficient semantic cheminformatics and facile data integration. Journal of Cheminformatics. 3:20. 2011
- Integrating systems biology models and biomedical ontologies. BMC Systems Biology. 5:124. 2011
- MoSuMo: A Semantic Web service to generate electrostatic potentials across solvent excluded protein surfaces and binding pockets. Computers & graphics. 35:823-830. 2011
- Prototype semantic infrastructure for automated small molecule classification and annotation in lipidomics. BMC Bioinformatics. 12:303. 2011
- Semantic Web integration of Cheminformatics resources with the SADI framework. Journal of Cheminformatics. 3:16. 2011
- Computational approaches toward the design of pools for the in vitro selection of complex aptamers. RNA (New York, N.Y.). 16:2252-2262. 2010
- Integrating findings of traditional medicine with modern pharmaceutical research: the potential role of linked open data. Chinese Medicine. 5:43. 2010
- Modeling and querying graphical representations of statistical data. Web semantics (Online). 8:241-254. 2010
- Towards pharmacogenomics knowledge discovery with the semantic web. Briefings in bioinformatics. 10:153-163. 2009
- Global investigation of protein-protein interactions in yeast Saccharomyces cerevisiae using re-occurring short polypeptide sequences. Nucleic acids research. 36:4286-4294. 2008
- Armadillo: Domain Boundary Prediction by Amino Acid Composition. Journal of molecular biology. 350:1061-1073. 2005
- CO: A chemical ontology for identification of functional groups and semantic comparison of small molecules. FEBS letters. 579:4685-4691. 2005
- The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Research. 33:D418-D424. 2004
- Taking flight with OWL2. Semantic web. 2:67-70.
- The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data. Applied ontology. 6:53-89.
- Towards an Interoperable Information Infrastructure Providing Decision Support for Genomic Medicine. Studies in health technology and informatics. 169:165-169.
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chapter
- Evaluating Scientific Hypotheses Using the SPARQL Inferencing Notation. Lecture Notes in Computer Science. 647-658. 2012
- Development of Small-Molecule Ligands and Inhibitors. Protein Targeting with Small Molecules. 115-147.
- Target Profiling of Small Molecules. Protein Targeting with Small Molecules. 11-38.
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conference paper