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  Journal articles

• Bui Quoc Chinh, Sophia Katrenko, and Peter Sloot. A Hybrid Approach to Extract Protein-Protein Interactions. Bioinformatics vol. 27(2), pp. 259-265, (impact factor: 4.926), 2011.
• Sophia Katrenko, Pieter Adriaans, and Maarten van Someren. Using Local Alignments for Relation Recognition. In Journal of Artificial Intelligence Research (JAIR), vol. 38, pp. 1-48, (impact factor: 1.981), 2010.
• M. Roos, M. S. Marshall, A. P. Gibson, M. Schuemie, E. Meij, S. Katrenko, W.R. van Hage, K. Krommydas, and P.W. Adriaans. Structuring and Extracting Knowledge for the Support of Hypothesis Generation in Molecular Biology. BMC Bioinformatics, 10(Supplement 10), 2009.
• Larry Smith et al. Overview of BioCreative II Gene Mention Recognition. In Genome Biology, 9(Suppl 2), 2008.
• M. S. Marshall, M. Roos, E. Meij, S. Katrenko, W. R. van Hage, and P. W. Adriaans. De AIDA toolbox: Een gecombineerde aanpak voor het beheren van kennis. In Agro Informatica, 21(4), 5-6. 2008.

  Thesis

• S. Katrenko. A Closer Look at Learning Relations from Text. PhD thesis, University of Amsterdam. ISBN 978-90-9024518-8. 2009.

  Edited volumes

• Maarten van Someren, Sophia Katrenko, and Pieter Adriaans (eds.). Proceedings of the Belgian-Dutch Conference on Machine Learning. Amsterdam, May 2007.
• Janneke Huitink and Sophia Katrenko (eds.). Proceedings of the Eleventh ESSLLI Student Session. University of Malaga, Spain. August 2006.

  Refereed conference and workshop proceedings

• George Lan, Sophia Katrenko and Lei Pan. Analyzing Interdisciplinary Research Along Multiple Dimensions of Research Impact. In SIGMET 2015.
• Assaf Toledo, Stavroula Alexandropoulou, Sophia Katrenko, Heidi Klockmann, Pepijn Kokke, Yoad Winter. Semantic Annotation of Textual Entailment. In IWCS 2013.
• Sophia Katrenko. "Could you make me a favour and do coffee, please?": Implications for Automatic Error Correction in English and Dutch. In Proceedings of the First Joint Conference on Lexical and Computational Semantics (*SEM), 2012. Montreal, Canada.
• Assaf Toledo, Sophia Katrenko, Stavroula Alexandropoulou, Heidi Klockmann, Asher Stern, Ido Dagan, and Yoad Winter. Semantic Annotation for Textual Entailment Recognition. In MICAI 2012.
  
• Sophia Katrenko and Assaf Toledo. A Comparison Study of Lexical and Syntactic Overlap for Textual Entailment Recognition. In Proceedings of BNAIC 2011.
• Sophia Katrenko and Menno van Zaanen. Rademacher Complexity and Grammar Induction: What It May (Not) Tell Us. In ICGI 2010. Valencia, Spain.
• Sophia Katrenko and Pieter Adriaans. Finding Constraints for Semantic Relations via Clustering. In Proceedings of CLIN 2010.
• Sophia Katrenko and Pieter Adriaans. A Local Alignment Kernel in the Context of NLP. In Proceedings of the 22nd International Conference on Computational Linguistics (Coling), 2008. Manchester, UK. [acceptance rate: 25%]
• Sophia Katrenko and Pieter Adriaans. Semantic Types of Some Generic Relation Arguments: Detection and Evaluation. In Proceedings of the 46th Annual Meeting of the Association for Computational Linguistics: Human Language Technologies (ACL/HLT), 2008. Columbus, USA. [acceptance rate: 26,8%]
• Sophia Katrenko and Pieter Adriaans. Qualia Structures and their Impact on the Concrete Noun Categorization Task. In Proceedings of the "Bridging the gap between semantic theory and computational simulations" workshop at ESSLLI 2008, proceedings. Hamburg, Germany.
• Edgar Meij and Sophia Katrenko. Bootstrapping Language Associated with Biomedical Entities. In TREC 2007 Working Notes.
• Willem R. van Hage and Sophia Katrenko. UVAVU: WordNet Similarity and Lexical Patterns for Semantic Relation Classification. In Proceedings of the 4th International Workshop on Semantic Evaluations, ACL, June 2007.
• Sophia Katrenko and P. Adriaans. Named Entity Recognition for Ukrainian: A Resource-Light Approach. In Proceedings of the BSNLP workshop, ACL 2007.
• S. Katrenko and Pieter Adriaans. Using Semi-Supervised Techniques to Detect Gene Mentions. In Proceedings of the Second BioCreative Challenge Workshop, April 2007. Madrid, Spain.
• Sophia Katrenko and Pieter Adriaans. Learning Relations from Biomedical Corpora Using Dependency Trees. Invited paper in KDECB (Knowledge Discovery and Emergent Complexity in BioInformatics), Lecture Notes in Bioinformatics. LNBI, vol. 4366.
• Sophia Katrenko and Pieter Adriaans. Grammatical Inference in Practice: A Case Study in the Biomedical Domain. In Proceedings of the 8th International Colloquium on Grammatical Inference (ICGI). Lecture Notes in Artificial Intelligence, Sakaibara, Y.; Kobayashi, S.; Sato, K.; Nishino, T.; Tomita, E. (Eds.). Tokyo, Japan, September 21, 2006. LNAI, vol. 4201.
  
• Sophia Katrenko and Pieter Adriaans. Pattern Acquisition from the Dependency Paths (Extended Abstract). Presented at the workshop "Ontologies in Text Technology", Osnabrück, Germany, September 28, 2006.
• Sophia Katrenko, M. Scott Marshall, Marco Roos and Pieter Adriaans. Learning Biological Interactions from Medline Abstracts. (Extended Abstract) In Proceedings of the 18th Belgian-Dutch Conference on Artificial Intelligence (BNAIC-2006), Namur, Belgium, October 2006.
• Sophia Katrenko and Pieter Adriaans. Learning Relations from Biomedical Corpora Using Dependency Tree Levels. In Proceedings of the Fifteenth Dutch-Belgian Conference on Machine Learning (Benelearn), Ghent, Belgium, May 12, 2006.
  
• Sophia Katrenko and Pieter Adriaans. Using Maximal Embedded Syntactic Subtrees for Textual Entailment Recognition. In Proceedings of RTE-2 workshop, Venice, Italy, April 10, 2006.
  
• Willem R. van Hage, Sophia Katrenko, and A. Th. Schreiber. A Method to Combine Linguistic Ontology-Mapping Techniques. In Proceedings of ISWC 2005.
  
• Sophia Katrenko, M. Scott Marshall, Marco Roos and Pieter Adriaans. Learning Biological Interactions from Medline Abstracts. In Proceedings of the ICML'05 workshop "Learning Language in Logic", Bonn, 2005.
• Sophia Katrenko. Towards Unsupervised Learning of Morphology Applied to Ukrainian. The 16th European Summer School in Logic, Language and Information (ESSLLI). Nancy, France, pp. 138-149, 2004.
• Sophia Katrenko. Textual data categorization: back to the phrase-based representation. In Proceedings of the 2nd International IEEE Conference "Intelligent systems", Vol. III. Varna, Bulgaria, pp. 64-67, June 22-24, 2004. pdf
• Sophia Katrenko. Die Erkennung der deutschsprachigen Spam-Emails: Naïve-Bayes vs. ähnlichkeitsbasiertes Lernen. FGML'2003 - Treffen der Fachgruppe Maschinelles Lernen, Wissensentdeckung und Data Mining" der Gesellschaft für Informatik. Karlsruhe, pp.110-113.