Jörg Hakenberg
Coordinates
| Work: | Life: | ||
| Hoffmann-La Roche Inc. | Weehawken, NJ | ||
| Pharma Research and Early Development | N40° 46' 46.3", W74° 00' 44" | ||
| 340 Kingsland St, Bldg. 76 |  | ||
| Nutley, NJ 07110, USA | |||
| N40° 50' 03.6", W74° 09' 23.5" | |||
Research
- Exome sequencing and analysis
- Text mining for life sciences
- guest-editing a special issue of Advances in Bioinformatics on "Literature-mining solutions for life science research"
- editing a section on text mining in Springer's Encyclopedia of Systems Biology
- guest-editing a special issue of Advances in Bioinformatics on "Literature-mining solutions for life science research"
News
NGS algorithms
- Papers: recent papers on NGS algorithms
BioNLP
- Proceedings: BMC Bioinfo, supplement on BioCreative III
- Conference: Machine Learning for Biomedical Literature Analysis and Text Retrieval (special session at ICMLA11), December 18-21, 2011, Honolulu, Hawaii
- Papers: recent papers on biomedical text mining
My latest papers:
- Jörg Hakenberg, Dmitry Voronov, Vo Ha Nguyen, Shanshan Liang, Saadat Anwar, Robert Leaman, Luis N Tari, and Chitta Baral: A SNPshot of PubMed to find associations between genetic variants, drugs, and diseases. J Biomed Info, 2012, pre-print available online.
- Jörg Hakenberg, Martin Gerner, Maximilian Haeussler, Illés Solt, Conrad Plake, Michael Schroeder, Graciela Gonzalez, Goran Nenadic, Casey Bergman: The GNAT library for local and remote gene mention normalization. Bioinformatics 27:2769-2771, 2011, DOI: 10.1093/bioinformatics/btr455.
- Vo Ha Nguyen, Jörg Hakenberg, Luis Tari, Chitta Baral, Illes Solt, Domonkos Tikk, Quang Long Nguyen, Ulf Leser: Molecular event extraction from Link Grammar parse trees in the BioNLP'09 Shared Task. Computational Intelligence (COIN), 27(4):665-680, November 2011.
- Domonkos Tikk, Philippe Thomas, Peter Palaga, Jörg Hakenberg, and Ulf Leser: A comprehensive benchmark of kernel methods to extract protein-protein interactions from literature. PLoS Computational Biology, 6(7):e1000837, 2010.
- Luis Tari, Tu Phan Huy, Jörg Hakenberg, Yi Chen, Tran Can Son, Graciela Gonzalez, and Chitta Baral: Incremental Information Extraction Using Relational Databases. IEEE Transactions on Knowledge and Data Engineering (TKDE), vol. 22, issue 99, Oct 28 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 Transactions on Computational Biology and Bioinformatics (TCBB), 7(3):481-494, May 20, 2010. Selected as Spotlight Paper for the July-September issue of TCBB.
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