Publications

Publications related to SCAIView

SCAIView

Malhotra A, Younesi E, Gurulingappa H, Hofmann-Apitius M. 'HypothesisFinder:' a strategy for the detection of speculative statements in scientific text. PLoS Comput Biol. 2013;9(7):e1003117. doi: 10.1371/journal.pcbi.1003117 Link

Younesi E, Toldo L, Müller B, Friedrich CM, Novac N, Scheer A, Hofmann-Apitius M, Fluck J. Mining biomarker information in biomedical literature. BMC Med Inform Decis Mak. 2012 Dec 18;12:148. doi: 10.1186/1472-6947-12-148. Link

Christoph M. Friedrich, Holger Dach, Tobias Gattermayer, Gerhard Engelbrecht, Siegfried Benkner, and Martin Hofmann-Apitius: @neuLink: A Service-oriented Application for Biomedical Knowledge Discovery. In Proceedings of the HealthGrid (2008), pp. 165-172. Link

Martin Hofmann-Apitius, Juliane Fluck, Laura Furlong, Oriol Fornes, Corinna Kolárik, Susanne Hanser, Martin Boeker, Stefan Schulz, Ferran Sanz, Roman Klinger, Heinz-Theodor Mevissen, Tobias Gattermayer, Baldo Oliva, and Christoph M. Friedrich: Knowledge environments representing molecular entities for the virtual physiological human. In: Philosophical Transactions of The Royal Society A Mathematical, Physical & Engineering Sciences 366 (2008), Sep, No. 1878, pp. 3091-3110. - Link

Sudeep Sahadevan, Martin Hofmann-Apitius, Karl Schellander, Dawit Tesfaye, Juliane Fluck and Christoph M. Friedrich: Introducing the potential of text mining to animal sciences. In J ANIM SCI jas.2011-4841; published ahead of print June 4, 2012.

SCAIView related

Younesi E, Hofmann-Apitius M. Biomarker-guided translation of brain imaging into disease pathway models. Sci Rep. 2013 Nov 29;3:3375. doi: 10.1038/srep03375 Link

Harsha Gurulingappa, Bernd Müller, Martin Hofmann-Apitius, and Juliane Fluck: A Semantic Platform for Information Retrieval from E-Health Records. In The Twentieth Text RETrieval Conference (TREC 2011) Proceedings, Gaithersburg, Maryland, USA, November 2011. - Link

Harsha Gurulingappa, Bernd Müller, Martin Hofmann-Apitius, and Juliane Fluck: Information Retrieval Framework for Technology Survey in Biomedical and Chemistry Literature. In The Twentieth Text RETrieval Conference (TREC 2011) Proceedings, Gaithersburg, Maryland, USA, November 2011. - Link

Harsha Gurulingappa, Bernd Müller, Roman Klinger, Heinz-Theo Mevissen, Martin Hofmann-Apitius, Christoph M. Friedrich, and Juliane Fluck: Prior Art Search in Chemistry Patents based on Semantic Concepts and Co-citation Analysis. In The Nineteenth Text RETrieval Conference (TREC 2010) Proceedings, Gaithersburg, Maryland, USA, November 2010. - Link

Bernd Müller, Roman Klinger, Harsha Gurulingappa, Heinz-Theodor Mevissen, Martin Hofmann-Apitius, Juliane Fluck, and Christoph M. Friedrich: Abstracts versus Full Texts and Patents: A Quantitative Analysis of Biomedical Entities. In Proceedings of the 1st IRF Conference, Lecture Notes in Computer Science. Springer, 2010. - Link

Harsha Gurulingappa, Bernd Müller, Roman Klinger, Heinz-Theo Mevissen, Martin Hofmann-Apitius, Juliane Fluck, and Christoph M. Friedrich: Patent Retrieval in Chemistry based on semantically tagged Named Entities. In The Eighteenth Text RETrieval Conference (TREC 2009) Proceedings, Gaithersburg, Maryland, USA, November 2009. - Link

Named Entity Recognition

Corinna Kolářik, Roman Klinger, and Martin Hofmann-Apitius: Identification of Histone Modifications in Biomedical Text for Supporting Epigenomic Research. BMC Bioinformatics, 10(S28), January 2009. Proceedings of the Asia Pacific Bioinformatics Conference (APBC). - Link

Roman Klinger, Corinna Kolářik, Juliane Fluck, Martin Hofmann-Apitius, and Christoph M. Friedrich: Detection of IUPAC and IUPAC-like Chemical Names. Bioinformatics, 24(13):i268-i276, 2008. Proceedings of the International Conference Intelligent Systems for Molecular Biology (ISMB). - Link

Roman Klinger, Laura I. Furlong, Christoph M. Friedrich, Heinz Theodor Mevissen, Juliane Fluck, Ferran Sanz, and Martin Hofmann-Apitius: Identifying gene specific variations in biomedical text. Journal of Bioinformatics and Computational Biology, 5(6):1277-1296, December 2007. - Link

Juliane Fluck, Heinz-Theodor Mevissen, Holger Dach, Marius Oster, and Martin Hofmann-Apitius: ProMiner: recognition of human gene and protein names using regularly updated dictionaries. In: Proceedings of the Second BioCreative Challenge Evaluation Workshop (2007), pp. 149-251. - Link

Ansari, S.; Szostak, J.; Madan, S.; Fluck, J.; Talikka, M.; Iskandar, A.; De Leon, H.; Hofmann-Apitius, M.; Peitsch, M.; Hoeng, J.; (2015) A semi-automated curation workflow to construct biological networks from unstructured information. The Journal of Biological Databases and Curation (DATABASE)

Fluck, J.; Madan, S.; Ansari, S.; Szostak J.; Hoeng, J.; Zimmermann, M.; Hofmann-Apitius, M.; Peitsch, M.; (2014) BELIEF - A semiautomatic workflow for BEL network creation. 6th International Symposium on Semantic Mining in Biomedicine (SMBM 2014), Aveiro, Portugal.

Fluck, J.; Klenner, A.; Madan, S.; Ansari, S.; Bobic, T.; Hoeng, J.; Hofmann-Apitius, M.; Peitsch, M.; (2013) BEL networks derived from qualitative translations of BioNLP Shared Task annotations. The Association for Computational Linguistics (ACL) Sofia 2013.