Jörg Hakenberg

ORCID

Publication Activity (10 Years)

Years Active: 2005-2016
Publications (10 Years): 4

Top Venues

Humboldt University of Berlin (PHD)

Education History

Humboldt University of Berlin

PHD

Publications

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) (2016)
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 (2016)
Philippe Thomas, Tim Rocktäschel, Jörg Hakenberg, Yvonne Lichtblau, Ulf Leser
SETH detects and normalizes genetic variants in text. Bioinform. 32 (18) (2016)
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) (2016)
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)
Jörg Hakenberg, Goran Nenadic, Dietrich Rebholz-Schuhmann, Jin-Dong Kim
Literature Mining Solutions for Life Science Research. Adv. Bioinformatics 2013 (2013)
Zayed Albertyn, Jörg Hakenberg, Hongjin Bian, Huifeng Niu, James Cai
A high-throughput analysis pipeline for large next generation DNA sequencing studies. BIBM (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) (2012)
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) (2012)
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) (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. Comput. Intell. 27 (4) (2011)
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)
Luis Tari, Phan Huy Tu, Jörg Hakenberg, Yi Chen, Tran Cao Son, Graciela Gonzalez, Chitta Baral
GenerIE: Information extraction using database queries. ICDE (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. Biol. Bioinform. 7 (3) (2010)
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)
Siddhartha Jonnalagadda, Luis Tari, Jörg Hakenberg, Chitta Baral, Graciela Gonzalez
Towards Effective Sentence Simplification for Automatic Processing of Biomedical Text CoRR (2010)
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)
Conrad Plake, Loïc Royer, Rainer Winnenburg, Jörg Hakenberg, Michael Schroeder
GoGene: gene annotation in the fast lane. Nucleic Acids Res. 37 (Web-Server-Issue) (2009)
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)
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)
Peter Palaga, Long Nguyen, Ulf Leser, Jörg Hakenberg
High-performance information extraction with AliBaba. EDBT (2009)
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)
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)
Jörg Hakenberg, Conrad Plake, Robert Leaman, Michael Schroeder, Graciela Gonzalez
Inter-species normalization of gene mentions with GNAT. ECCB (2008)
Jörg Hakenberg
Services for annotation of biomedical text. Ontologies and Text Mining for Life Sciences (2008)
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)
Jörg Hakenberg
What's in a gene name? Automated refinement of gene name dictionaries. BioNLP@ACL (2007)
Jörg Hakenberg, Ulf Leser, Harald Kirsch, Dietrich Rebholz-Schuhmann
Collecting a Large Corpus from all of Medline. SMBM (2006)
Conrad Plake, Torsten Schiemann, Marcus Pankalla, Jörg Hakenberg, Ulf Leser
ALIBABA: PubMed as a graph. Bioinform. 22 (19) (2006)
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)
Ulf Leser, Jörg Hakenberg
What makes a gene name? Named entity recognition in the biomedical literature. Briefings Bioinform. 6 (4) (2005)
Conrad Plake, Jörg Hakenberg, Ulf Leser
Optimizing syntax patterns for discovering protein-protein interactions. SAC (2005)

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Publication Activity (10 Years)

Top Topics

Top Venues

Jörg Hakenberg