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  1. Gerold Schneider. Extracting and Using Trace-Free Functional Dependencies from the Penn Treebank to Reduce Parsing Complexity. In: Joakim Nivre and Erhard Hinrichs, eds.: Proceedings of Treebanks and Linguistic Theories (TLT) 2003. Växjö University Press, Series: Mathematical Modelling in Physics, Engineering and Cognitive Sciences, v. 9, Växjö, Sweden: 153-164 Download as pdf
  2. James Dowdall, Fabio Rinaldi, Andreas Persidis, Kaarel Kaljurand, Gerold Schneider, Michael Hess. Terminology expansion and relation identification between genes and pathways. Workshop on Terminology, Ontology and Knowledge Representation. Universite Jean Moulin (Lyon 3). 22-23 January 2004. Download as pdf
  3. Fabio Rinaldi, James Dowdall, Gerold Schneider, Andreas Persidis. Answering Questions in the Genomics Domain. ACL-2004 workshop on Question Answering in Restricted Domains, July 2004, Barcelona, Spain. Download as pdf
  4. Gerold Schneider. Combining Shallow and Deep Processing for a Robust, Fast, Deep-Linguistic Dependency Parser. European Summer School in Logic, Language and Information ESSLLI 2004, Nancy, France. pdf
  5. Gerold Schneider, James Dowdall, Fabio Rinaldi. A Robust and Hybrid Deep-Linguistic Theory Applied to Large Scale Parsing. COLING-2004 workshop on Robust Methods in Analysis of Natural language Data, August 2004, Geneva, Switzerland. Download as pdf
  6. Gerold Schneider, Fabio Rinaldi, James Dowdall. Fast, Deep-Linguistic Statistical Minimalist Dependency Parsing. COLING-2004 workshop on Recent Advances in Dependency Grammars, August 2004, Geneva, Switzerland. Download as pdf
  7. Fabio Rinaldi, Gerold Schneider, Kaarel Kaljurand, James Dowdall and Andreas Persidis. Mining Relations in the GENIA corpus. Second European Workshop on Data Mining and Text Mining for Bioinformatics, at ECML/PKDD 2004, September 2004, Pisa, Italy. Download as pdf
  8. Gerold Schneider, Fabio Rinaldi, Kaarel Kaljurand, Michael Hess. Steps towards a GENIA Dependency Treebank. In Treebanks and Linguistic Theories (TLT) 2004, Tübingen, December 2004. Download as pdf
  9. Eric SanJuan, James Dowdall, Fidelia Ibekwe-SanJuan, Fabio Rinaldi. A symbolic approach to Automatic MultiWord Term Structuring. Computer Speech and Language, Special Issue on Multiword Expressions. Elsevier Science.
  10. Julie Weeds, James Dowdall, Gerold Schneider, Bill Keller, David Weir. Using Distributional Similarity to Organise BioMedical Terminology. Terminology: Special issue on Application-driven Terminology engineering. Ed. Maria-Teresa Cabré, Annes Condamines, Fidelia Ibekwe-SanJuan. John Benjamins, Amsterdam.
  11. Fabio Rinaldi, Elia Yuste, Gerold Schneider, Michael Hess. Exploiting Technical Terminology for Knowledge Management. In Ontology Learning and Population, Paul Buitelaar, Philipp Cimiano, Bernardo Magnini (editors). IOS Press, 2005.
  12. Gerold Schneider, Fabio Rinaldi, Kaarel Kaljurand, Michael Hess, 2005. "Closing the Gap: Cognitively Adequate, Fast Broad-Coverage Grammatical Role Parsing". Proceedings of the 2nd International Workshop on Natural Language and Cognitive Science (NLUCS-2005). May 24-25, Miami.
  13. Fabio Rinaldi, Gerold Schneider, Kaarel Kaljurand, Michael Hess, Christos Andronis, Andreas Persidis, Ourania Konstanti. Relation Mining over a Corpus of Scientific Literature. In Proceedings of Artificial Intelligence in Medicine: AIME 2005, July 2005, Aberdeen, Scotland. Springer Verlag, LNAI 3581, pp. 550-559.
  14. Kaarel Kaljurand, Fabio Rinaldi, Gerold Schneider. Prolog-based query interface to syntactic dependencies extracted from biomedical literature. IFI Technical Report, ifi-2006.04.
  15. Fabio Rinaldi, Gerold Schneider, Kaarel Kaljurand, Michael Hess, Martin Romacker. An Environment for Relation Mining over Richly Annotated Corpora: the case of GENIA. Accepted for publication at SMBM 2006: 2nd International Symposium on Semantic Mining in Biomedicine. Jena, Germany, April 9th-12th 2006.
  16. Fabio Rinaldi, Gerold Schneider, Kaarel Kaljurand, Michael Hess. Tools for Text Mining over Biomedical Literature. Poster to be presented at ECAI2006.
  17. Fabio Rinaldi, Gerold Schneider, Kaarel Kaljurand, Michael Hess, Christos Andronis, Ourania Konstandi, Andreas Persidis. Mining of Functional Relations between Genes and Proteins over Biomedical Scientific Literature using a Deep-Linguistic Approach. Accepted for publication in the journal of Artificial Intelligence in Medicine
  18. Fabio Rinaldi, Gerold Schneider, Kaarel Kaljurand, Michael Hess, Martin Romacker. An environment for relation mining over richly annotated corpora: the case of GENIA. BMC Bioinformatics 2006, 7(Suppl 3):S3. doi:10.1186/1471-2105-7-S3-S3
  19. Fabio Rinaldi, Thomas Kappeler, Kaarel Kaljurand, Gerold Schneider, Manfred Klenner, Michael Hess, Jean-Marc von Allmen, Martin Romacker, Therese Vachon. OntoGene in Biocreative II. Proceedings of the Second BioCreative Challenge Evaluation Workshop. Madrid, Spain, April 2007 (ISBN 84-933255-6-2).  
  20. Gerold Schneider, Kaarel Kaljurand, Fabio Rinaldi, Tobias Kuhn. Pro3Gres Parser in the CoNLL Domain Adaptation Shared Task. Proceedings of the ACL Conference, Workshop on Computational Natural Language Learning (CoNLL-XI) Shared Task, Prague, June 2007. 
  21. Fabio Rinaldi, Gerold Schneider, Kaarel Kaljurand. Tools for detection of Protein Interactions in Biomedical Literature. Genome to Systems, Manchester, UK. 17-19 March 2008.  
  22. Fabio Rinaldi, Gerold Schneider, Kaarel Kaljurand, Michael Hess. Dependency-Based Relation Mining for Biomedical Literature. LREC 2008, Marrakech, Morocco. May 2008. 
  23.  Fabio Rinaldi, Thomas Kappeler, Kaarel Kaljurand, Gerold Schneider, Manfred Klenner, Simon Clematide, Michael Hess, Jean-Marc von Allmen, Pierre Parisot, Martin Romacker, Therese Vachon. OntoGene in BioCreative II. Genome Biology, 2008, 9:S13.
  24. Thomas Kappeler, Simon Clematide, Kaarel Kaljurand, Gerold Schneider, Fabio Rinaldi. Towards Automatic Detection of Experimental Methods from Biomedical Literature. Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008). 
  25. Kaarel Kaljurand. ACE View — an ontology and rule editor based on Attempto Controlled English. 5th OWL Experiences and Directions Workshop (OWLED 2008).
  26. Kaarel Kaljurand. ACE View — an ontology and rule editor based on controlled English. Proceedings of the Poster and Demonstration Session at the 7th International Semantic Web Conference (ISWC2008), CEUR Workshop Proceedings, 2008.
  27. Kaarel Kaljurand, Thomas Kappeler, Gerold Schneider, Fabio Rinaldi.
    Detecting and grounding terms in biomedical literature. CICLING 2009. 
  28. Gerold Schneider, Kaarel Kaljurand, Thomas Kappeler, Fabio Rinaldi.Detecting protein-protein interactions in biomedical texts using a parser and linguistic resources. CICLING 2009.
  29. Thomas Kappeler, Kaarel Kaljurand, Fabio Rinaldi. TX Task: Automatic Detection of Focus Organisms in Biomedical Publications. BioNLP workshop, NAACL/HLT, Boulder, Colorado 2009.
  30. Kaarel Kaljurand, Gerold Schneider and Fabio Rinaldi. UZurich in the BioNLP 2009 Shared Task. BioNLP workshop, NAACL/HLT, Boulder, Colorado, 2009.
  31. Kaarel Kaljurand, Fabio Rinaldi, Thomas Kappeler, Gerold Schneider. Using existing biomedical resources to detect and ground terms in biomedical literature. Artificial Intelligence in Medicine, Verona, July 2009.
  32. Fabio Rinaldi, Gerold Schneider, Kaarel Kaljurand, Simon Clematide. Effective Mining of Protein Interactions. LBM 2009: The 3rd International Symposium on Languages in Biology and Medicine. Jeju Island, South Korea, November 8-10, 2009.
  33. Fabio Rinaldi, Dietrich Rebholz-Schuhmann. Support tools for literature-based information access in the genomics domain. 3rd International Universal Communication Symposium. Tokyo, December 2009.