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ORCIDJörg Hakenberg
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2010 – 2019
- 2016
[j16]Wei-Yi Cheng, Jörg Hakenberg
, Shuyu Dan Li, Rong Chen:
DIVAS: a centralized genetic variant repository representing 150 000 individuals from multiple disease cohorts. Bioinform. 32(1): 151-153 (2016)- [j15]Benjamin S. Glicksberg, Li Li, Marcus A. Badgeley, Khader Shameer, Roman Kosoy, Noam D. Beckmann, Nam Pho, Jörg Hakenberg, Meng Ma, Kristin L. Ayers, Gabriel E. Hoffman, Shuyu Dan Li, Eric E. Schadt, Chirag J. Patel, Rong Chen, Joel T. Dudley:
Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks. Bioinform. 32(12): 101-110 (2016) - [j14]Philippe Thomas, Tim Rocktäschel, Jörg Hakenberg, Yvonne Lichtblau, Ulf Leser:
SETH detects and normalizes genetic variants in text. Bioinform. 32(18): 2883-2885 (2016) - [j13]Jörg Hakenberg, Wei-Yi Cheng, Philippe Thomas, Ying-Chih Wang, Andrew V. Uzilov, Rong Chen:
Integrating 400 million variants from 80, 000 human samples with extensive annotations: towards a knowledge base to analyze disease cohorts. BMC Bioinform. 17: 24 (2016) - 2015
- [c13]Benjamin S. Glicksberg, Li Li, Wei-Yi Cheng, Khader Shameer, Jörg Hakenberg, Rafael Castellanos, Meng Ma, Lisong Shi, Hardik Shah, Joel T. Dudley, Rong Chen:
An Integrative Pipeline for Multi-Modal Discovery of Disease Relationships. Pacific Symposium on Biocomputing 2015: 407-418 - 2013
- [j12]Jörg Hakenberg, Goran Nenadic, Dietrich Rebholz-Schuhmann, Jin-Dong Kim:
Literature Mining Solutions for Life Science Research. Adv. Bioinformatics 2013: 320436:1-320436:2 (2013) - 2012
- [j11]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. J. Biomed. Informatics 45(5): 842-850 (2012) - [j10]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) - [c12]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 - 2011
- [j9]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. Bioinform. 27(19): 2769-2771 (2011) - [j8]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. Comput. Intell. 27(4): 665-680 (2011) - 2010
- [j7]Domonkos Tikk, Philippe Thomas, Peter Palaga, Jörg Hakenberg, Ulf Leser:
A Comprehensive Benchmark of Kernel Methods to Extract Protein-Protein Interactions from Literature. PLoS Comput. Biol. 6(7) (2010) - [j6]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. Biol. Bioinform. 7(3): 481-494 (2010) - [c11]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 - [c10]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 - [c9]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 - [i3]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)
2000 – 2009
- 2009
- [b1]Jörg Hakenberg:
Mining relations from the biomedical literature. Humboldt University of Berlin, 2009 - [j5]Dimitra Alexopoulou, Bill Andreopoulos, Heiko Dietze, Andreas Doms, Fabien Gandon, Jörg Hakenberg, Khaled Khelif, Michael Schroeder, Thomas Wächter:
Biomedical word sense disambiguation with ontologies and metadata: automation meets accuracy. BMC Bioinform. 10 (2009) - [j4]Conrad Plake, Loïc Royer, Rainer Winnenburg, Jörg Hakenberg, Michael Schroeder:
GoGene: gene annotation in the fast lane. Nucleic Acids Res. 37(Web-Server-Issue): 300-304 (2009) - [c8]Jörg Hakenberg, Illés Solt, Domonkos Tikk, Luis Tari, Astrid Rheinländer, Quang Long Nguyen, Graciela Gonzalez, Ulf Leser:
Molecular event extraction from Link Grammar parse trees. BioNLP@HLT-NAACL (Shared Task) 2009: 86-94 - [c7]Peter Palaga, Long Nguyen, Ulf Leser, Jörg Hakenberg:
High-performance information extraction with AliBaba. EDBT 2009: 1140-1143 - [c6]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 - [c5]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 - [p2]Torsten Schiemann, Ulf Leser, Jörg Hakenberg:
Word Sense Disambiguation in Biomedical Applications. Information Retrieval in Biomedicine 2009: 142-161 - 2008
- [c4]Jörg Hakenberg, Conrad Plake, Robert Leaman, Michael Schroeder, Graciela Gonzalez:
Inter-species normalization of gene mentions with GNAT. ECCB 2008: 126-132 - [p1]Thomas Wächter, Dimitra Alexopoulou, Heiko Dietze, Jörg Hakenberg, Michael Schroeder:
Searching Biomedical Literature with Anatomy Ontologies. Anatomy Ontologies for Bioinformatics 2008: 177-194 - [i2]Heiko Dietze, Dimitra Alexopoulou, Michael R. Alvers, Bill Barrio-Alvers, Andreas Doms, Jörg Hakenberg, Jan Mönnich, Conrad Plake, Andreas Reischuck, Loïc Royer, Thomas Wächter, Matthias Zschunke, Michael Schroeder:
GoPubMed: Exploring Pubmed with Ontological Background Knowledge. Ontologies and Text Mining for Life Sciences 2008 - [i1]Jörg Hakenberg:
Services for annotation of biomedical text. Ontologies and Text Mining for Life Sciences 2008 - 2007
- [c3]Jörg Hakenberg:
What's in a gene name? Automated refinement of gene name dictionaries. BioNLP@ACL 2007: 153-160 - 2006
- [j3]Conrad Plake, Torsten Schiemann, Marcus Pankalla, Jörg Hakenberg, Ulf Leser:
ALIBABA: PubMed as a graph. Bioinform. 22(19): 2444-2445 (2006) - [c2]Jörg Hakenberg, Ulf Leser, Harald Kirsch, Dietrich Rebholz-Schuhmann:
Collecting a Large Corpus from all of Medline. SMBM 2006 - [e1]Eric G. Bremer, Jörg Hakenberg, Eui-Hong Han, Daniel P. Berrar, Werner Dubitzky:
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 [contents] - 2005
- [j2]Ulf Leser, Jörg Hakenberg:
What makes a gene name? Named entity recognition in the biomedical literature. Briefings Bioinform. 6(4): 357-369 (2005) - [j1]Jörg Hakenberg, Steffen Bickel, Conrad Plake, Ulf Brefeld, Hagen Zahn, Lukas Faulstich, Ulf Leser, Tobias Scheffer:
Systematic feature evaluation for gene name recognition. BMC Bioinform. 6(S-1) (2005) - [c1]Conrad Plake, Jörg Hakenberg, Ulf Leser:
Optimizing syntax patterns for discovering protein-protein interactions. SAC 2005: 195-201
Coauthor Index
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