Erik Fäßler

[Overview] | [Research] | Publications

2020

• Erik Faessler, Luise Modersohn, Christina Lohr and Udo Hahn: ProGene - A Large-scale, High-Quality Protein-Gene Annotated Benchmark Corpus. In: Proceedings of the Twelfth International Conference on Language Resources and Evaluation (LREC 2020), Marseille, France, May 11 - 16, 2020, pp. 4585–4596.
• Ahmed Sadik, Luis F. Somarribas Patterson, Selcen Öztürk, Soumya R. Mohapatra, Verena Panitz, Philipp F. Secker, Pauline Pfänder, Stefanie Loth, Heba Salem, Mirja Tamara Prentzell, Bianca Berdel, Murat Iskar, Erik Faessler, Friederike Reuter, Isabelle Kirst, Verena Kalter, Kathrin I. Foerster, Evelyn Jäger, Carina Ramallo Guevara, Mansour Sobeh, Thomas Hielscher, Gernot Poschet, Annekathrin Reinhardt, Jessica C. Hassel, Marc Zapatka, Udo Hahn, Andreas von Deimling, Carsten Hopf, Rita Schlichting, Beate I. Escher, Jürgen Burhenne, Walter E. Haefeli, Naveed Ishaque, Alexander Böhme, Sascha Schäuble, Kathrin Thedieck, Saskia Trump, Martina Seiffert, Christiane A. Opitz: IL4I1 Is a Metabolic Immune Checkpoint that Activates the AHR and Promotes Tumor Progression. In: Cell, 182(5) (2020), DOI:https://doi.org/10.1016/j.cell.2020.07.038
• Erik Faessler, Michel Oleynik and Udo Hahn: What Makes a Top-Performing Precision Medicine Search Engine? Tracing Main System Features in a Systematic Way. In: Proceedings of the 43rd International ACM SIGIR Conference on Research and Development in Information Retrieval (SIGIR ’20), Xi’an, China, July 25 - 30, 2020, DOI:10.1145/3397271.3401048
• Lena Reimann, Anja N. Schwäble, Anna L. Fricke, Wignand W. D. Mühlhäuser, Yvonne Leber, Keerthika Lohanadan, Martin G. Puchinger, Sascha Schäuble, Erik Faessler, Heike Wiese, Christa Reichenbach, Bettina Knapp, Christian D. Peikert, Friedel Drepper, Udo Hahn, Clemens Kreutz, Peter F. M. van der Ven, Gerald Radziwill, Kristina Djinović-Carugo, Dieter O. Fürst & Bettina Warscheid: Phosphoproteomics identifies dual-site phosphorylation in an extended basophilic motif regulating FILIP1-mediated degradation of filamin-C. In: Communications Biology 3, 253 (2020), DOI:10.1038/s42003-020-0982-5
• Erik Faessler, Michel Oleynik and Udo Hahn: JULIE Lab & Med Uni Graz @ TREC 2019 Precision Medicine Track. In: Proceedings of the Twenty-Eighth Text REtrieval Conference (TREC 2019), Gaithersburg, Washington, USA, November 13 - 15, 2019

2019

• Michel Oleynik, Erik Faessler, Ariane Morassi Sasso, Arpita Kappattanavar, Benjamin Bergner, Harry Freitas da Cruz, Jan-Philipp Sachs, Suparno Datta and Erwin Bottinger: HPI-DHC at TREC 2018 Precision Medicine Track. In: Proceedings of the Twenty-Seventh Text REtrieval Conference (TREC 2018), Gaithersburg, Washington, USA, November 14 - 16, 2018

2018

• Erik Faessler and Udo Hahn: Annotation Data Management with JeDIS. In: The 18th ACM Symposium on Document Engineering, Halifax, Nova Scotia, Canada, August 28 - 31, 2018, DOI:10.1145/3209280.3229102

2017

• Erik Faessler and Udo Hahn: Semedico: A Comprehensive Semantic Search Engine for the Life Sciences. In: ACL 2017, System Demonstrations. System Demonstrations. Vancouver, Canada, July 30 - August 4, 2017, pp. 91-96. [Link]
• Friederike Klan, Erik Faessler, Alsayed Algergawy, Birgitta König-Ries, Udo Hahn: Integrated Semantic Search on Structured and Unstructured Data in the ADOnIS System. In: Proceedings of the 2nd International Workshop on Semantics for Biodiversity co-located with 16th International Semantic Web Conference (ISWC 2017), Vienna, Austria, October 21 - 25, 2017.

2016

• Piero Dalle Pezze, Stefanie Ruf, Annika G. Sonntag, Miriam Langelaar-Makkinje, Philip Hall, Alexander M. Heberle, Patricia Razquin Navas, Karen van Eunen, Regine C. Tölle, Jennifer J. Schwarz, Heike Wiese, Bettina Warscheid, Jana Deitersen, Björn Stork, Erik Fäßler, Sascha Schäuble, Udo Hahn, Peter Horvatovich, Daryl P. Shanley, Kathrin Thedieck: A systems study reveals concurrent activation of AMPK and mTOR by amino acids. In: Nature Communications November 21, 2016; 7:13254., DOI:10.1038/ncomms13254

• Erik Faessler, Friederike Klan, Alsayed Algergawy, Birgitta König-Ries and Udo Hahn: Selecting and Tailoring Ontologies with Joyce. In: EKAW 2016 - 20th International Conference on Knowledge Engineering and Knowledge Management, Systems Demonstrations. Bologna, Italy, November 19 - 23, 2016.

• Udo Hahn, Franz Matthies, Erik Faessler and Johannes Hellrich: UIMA-Based JCoRe 2.0 Goes GitHub and Maven Central ― State-of-the-Art Software Resource Engineering and Distribution of NLP Pipelines. In: Nicoletta Calzolari (Conference Chair), Khalid Choukri, Thierry Declerck, Marko Grobelnik, Bente Maegaard, Joseph Mariani, Asuncion Moreno, Jan Odijk, Stelios Piperidis (Eds.): Proceedings of the Tenth International Conference on Language Resources and Evaluation (LREC 2016), Portorož, Slovenia. 2016, pp. 2502-2509.

2015

• Johannes Hellrich, Franz Matthies, Erik Faessler and Udo Hahn: Sharing Models and Tools for Processing German Clinical Text. In: Ronald Cornet, Lăcrămioara Stoicu-Tivadar, Alexander Hörbst, Carlos Luis Parra Calderón, Stig Kjær Andersen, Mira Hercigonja-Szekeres (Eds.): Digital Healthcare Empowering Europeans [= Proceedings of MIE2015]. 2015, pp. 734-738 (Studies in Health Technology and Informatics, 210).

2014

• Erik Faessler, Johannes Hellrich and Udo Hahn. [Disclose Models, Hide the Data-How to Make Use of Confidential Corpora without Seeing Sensitive Raw Data]. In: Calzolari N., Choukri K., Declerck T., Loftsson H., Maegaard B., Mariani J., Moreno A., Odijk J. and Piperidis S (Eds.): Proceedings of the Ninth International Conference on Language Resources and Evaluation (LREC’14), 26-31 May, Reykjavik, Iceland, 2014. pp. 4230-4237.

2012

• Johannes Hellrich, Erik Faessler, Ekaterina Buyko and Udo Hahn: Visualizing Semantic Metadata from Biological Publications. In: International Workshop on Intelligent Exploration of Semantic Data @ EKAW 2012, Galway City, Ireland, October 2012.
• Udo Hahn, Elena Beisswanger, Ekaterina Buyko, Erik Faessler: Active Learning-Based Corpus Annotation—The PathoJen Experience. In: AMIA 2012, Annual Symposium proceedings, AMIA Symposium. Chicago, Illinois, November 3 - 7, 2012, pp. 301-10.
• Udo Hahn, Elena Beisswanger, Ekaterina Buyko, Erik Faessler, Jenny Traumüller, Susann Schröder and Kerstin Hornbostel: Iterative Refinement and Quality Checking of Annotation Guidelines — How to Deal Effectively with Semantically Sloppy Named Entity Types, such as Pathological Phenomena. In: International Conference on Language Resources and Evaluation, Istanbul, Turkey, May, 2012.

2010

• Udo Hahn, Katrin Tomanek, Elena Beisswanger and Erik Faessler. A Proposal for a Configurable Silver Standard. In The LAW at ACL’10 Proceedings of the Fourth Linguistic Annotation Workshop, 2010.

• Ekaterina Buyko, Erik Faessler, Joachim Wermter and Udo Hahn. Syntactic Simplification and Semantic Enrichment - Trimming Dependency Graphs for Event Extraction. Computational Intelligence.

2009

• Ekaterina Buyko, Erik Faessler, Joachim Wermter and Udo Hahn. Event Extraction from Trimmed Dependency Graphs. Proceedings of Natural Language Processing in Biomedicine (BioNLP) NAACL 2009 Workshop, 2009.

• Erik Faessler, Rico Landefeld, Katrin Tomanek and Udo Hahn. LuCas - A Lucene CAS Indexer. Proceedings of the Biennial GSCL Conference, 2009.

• Erik Fäßler. Automatische Extraktion von Protein-Protein-Interaktionen in biomedizinischen Texten unter Verwendung von Supportvektormaschinen. Master Thesis, Friedrich-Schiller-Universtität Jena, 2009. [Download PDF, 1.3 MB]

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