Jörg Hakenberg

Jörg Hakenberg, Goran Nenadic, Dietrich Rebholz-Schuhmann, Jin-Dong Kim: Literature Mining Solutions for Life Science Research. Adv. Bioinformatics 2013 (2013)

Jörg Hakenberg, Dmitry Voronov, Nguyen Ha Vo, Shanshan Liang, Saadat Anwar, Barry Lumpkin, Robert Leaman, Luis Tari, Chitta Baral: A SNPshot of PubMed to associate genetic variants with drugs, diseases, and adverse reactions. Journal of Biomedical Informatics 45(5): 842-850 (2012)

Luis Tari, Phan Huy Tu, Jörg Hakenberg, Yi Chen, Tran Cao Son, Graciela Gonzalez, Chitta Baral: Incremental Information Extraction Using Relational Databases. IEEE Trans. Knowl. Data Eng. 24(1): 86-99 (2012)

Zayed Albertyn, Jörg Hakenberg, Hongjin Bian, Huifeng Niu, James Cai: A high-throughput analysis pipeline for large next generation DNA sequencing studies. BIBM 2012: 1

Jörg Hakenberg, Martin Gerner, Maximilian Haeussler, Illés Solt, Conrad Plake, Michael Schroeder, Graciela Gonzalez, Goran Nenadic, Casey M. Bergman: The GNAT library for local and remote gene mention normalization. Bioinformatics 27(19): 2769-2771 (2011)

Jörg Hakenberg, Illés Solt, Domonkos Tikk, Nguyen Ha Vo, Luis Tari, Quang Long Nguyen, Chitta Baral, Ulf Leser: Molecular Event Extraction from Link Grammar Parse Trees in the BioNLP'09 Shared Task. Computational Intelligence 27(4): 665-680 (2011)

Domonkos Tikk, Philippe E. Thomas, Peter Palaga, Jörg Hakenberg, Ulf Leser: A Comprehensive Benchmark of Kernel Methods to Extract Protein-Protein Interactions from Literature. PLoS Computational Biology 6(7) (2010)

Jörg Hakenberg, Robert Leaman, Nguyen Ha Vo, Siddhartha Jonnalagadda, Ryan Sullivan, Christopher Miller, Luis Tari, Chitta Baral, Graciela Gonzalez: Efficient Extraction of Protein-Protein Interactions from Full-Text Articles. IEEE/ACM Trans. Comput. Biology Bioinform. 7(3): 481-494 (2010)

Syed Toufeeq Ahmed, Radhika Nair, Chintan Patel, Sheela P. Kanwar, Jörg Hakenberg, Hasan Davulcu: Semantic classification and dependency parsing enabled automated bio-molecular event extraction from text. BCB 2010: 370-373

Luis Tari, Phan Huy Tu, Jörg Hakenberg, Yi Chen, Tran Cao Son, Graciela Gonzalez, Chitta Baral: GenerIE: Information extraction using database queries. ICDE 2010: 1121-1124

Luis Tari, Saadat Anwar, Shanshan Liang, Jörg Hakenberg, Chitta Baral: Synthesis of Pharmacokinetic Pathways through Knowledge Acquisition and Automated Reasoning. Pacific Symposium on Biocomputing 2010: 465-476

Siddhartha Jonnalagadda, Luis Tari, Jörg Hakenberg, Chitta Baral, Graciela Gonzalez: Towards Effective Sentence Simplification for Automatic Processing of Biomedical Text. CoRR abs/1001.4277 (2010)

Jörg Hakenberg: Mining relations from the biomedical literature. Humboldt University of Berlin 2009

Dimitra Alexopoulou, Bill Andreopoulos, Heiko Dietze, Andreas Doms, Fabien L. Gandon, Jörg Hakenberg, Khaled Khelif, Michael Schroeder, Thomas Wächter: Biomedical word sense disambiguation with ontologies and metadata: automation meets accuracy. BMC Bioinformatics 10 (2009)

Conrad Plake, Loïc Royer, Rainer Winnenburg, Jörg Hakenberg, Michael Schroeder: GoGene: gene annotation in the fast lane. Nucleic Acids Research 37(Web-Server-Issue): 300-304 (2009)

Peter Palaga, Long Nguyen, Ulf Leser, Jörg Hakenberg: High-performance information extraction with AliBaba. EDBT 2009: 1140-1143

Siddhartha Jonnalagadda, Luis Tari, Jörg Hakenberg, Chitta Baral, Graciela Gonzalez: Towards Effective Sentence Simplification for Automatic Processing of Biomedical Text. HLT-NAACL (Short Papers) 2009: 177-180

Luis Tari, Jörg Hakenberg, Graciela Gonzalez, Chitta Baral: Querying Parse Tree Database of Medline Text to Synthesize User-Specific Biomolecular Networks. Pacific Symposium on Biocomputing 2009: 87-98

Heiko Dietze, Dimitra Alexopoulou, Michael R. Alvers, Bill Barrio-Alvers, Andreas Doms, Jörg Hakenberg, Jan Mönnich, Conrad Plake, Andreas Reischuk, Loïc Royer, Thomas Wächter, Matthias Zschunke, Michael Schroeder: GoPubMed: Exploring Pubmed with Ontological Background Knowledge. Ontologies and Text Mining for Life Sciences 2008

Jörg Hakenberg: Services for annotation of biomedical text. Ontologies and Text Mining for Life Sciences 2008

Jörg Hakenberg, Conrad Plake, Robert Leaman, Michael Schroeder, Graciela Gonzalez: Inter-species normalization of gene mentions with GNAT. ECCB 2008: 126-132

Conrad Plake, Torsten Schiemann, Marcus Pankalla, Jörg Hakenberg, Ulf Leser: ALIBABA: PubMed as a graph. Bioinformatics 22(19): 2444-2445 (2006)

Eric G. Bremer, Jörg Hakenberg, Eui-Hong Han, Daniel P. Berrar, Werner Dubitzky (Eds.): Knowledge Discovery in Life Science Literature, PAKDD 2006 International Workshop, KDLL 2006, Singapore, April 9, 2006, Proceedings. Lecture Notes in Computer Science 3886, Springer 2006, isbn 3-540-32809-2

Ulf Leser, Jörg Hakenberg: What makes a gene name? Named entity recognition in the biomedical literature. Briefings in Bioinformatics 6(4): 357-369 (2005)

Jörg Hakenberg, Steffen Bickel, Conrad Plake, Ulf Brefeld, Hagen Zahn, Lukas Faulstich, Ulf Leser, Tobias Scheffer: Systematic feature evaluation for gene name recognition. BMC Bioinformatics 6(S-1) (2005)

Conrad Plake, Jörg Hakenberg, Ulf Leser: Optimizing syntax patterns for discovering protein-protein interactions. SAC 2005: 195-201