Optimizing syntax patterns for discovering protein-protein interactions. - Conrad Plake; Jörg Hakenberg; Ulf Leser (SAC, 2005)

What makes a gene name? Named entity recognition in the biomedical literature. - Ulf Leser; Jörg Hakenberg (Briefings Bioinform., 2005)

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

Collecting a Large Corpus from all of Medline. - Jörg Hakenberg; Ulf Leser; Harald Kirsch; Dietrich Rebholz-Schuhmann (SMBM, 2006)

ALIBABA: PubMed as a graph. - Conrad Plake; Torsten Schiemann; Marcus Pankalla; Jörg Hakenberg; Ulf Leser (Bioinform., 2006)

What's in a gene name? Automated refinement of gene name dictionaries. - Jörg Hakenberg (BioNLP@ACL, 2007)

GoPubMed: Exploring Pubmed with Ontological Background Knowledge. - 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; et al. (Ontologies and Text Mining for Life Sciences, 2008)

Services for annotation of biomedical text. - Jörg Hakenberg (Ontologies and Text Mining for Life Sciences, 2008)

Inter-species normalization of gene mentions with GNAT. - Jörg Hakenberg; Conrad Plake; Robert Leaman; Michael Schroeder 001; Graciela Gonzalez 001 (ECCB, 2008)

Searching Biomedical Literature with Anatomy Ontologies. - Thomas Wächter; Dimitra Alexopoulou; Heiko Dietze; Jörg Hakenberg; Michael Schroeder 001 (Anatomy Ontologies for Bioinformatics, 2008)

Word Sense Disambiguation in Biomedical Applications. - Torsten Schiemann; Ulf Leser; Jörg Hakenberg (Information Retrieval in Biomedicine, 2009)

Molecular event extraction from Link Grammar parse trees. - Jörg Hakenberg; Illés Solt; Domonkos Tikk; Luis Tari; Astrid Rheinländer; Quang Long Nguyen; Graciela Gonzalez 001; Ulf Leser (BioNLP@HLT-NAACL (Shared Task), 2009)

High-performance information extraction with AliBaba. - Peter Palaga; Long Nguyen; Ulf Leser; Jörg Hakenberg (EDBT, 2009)

Towards Effective Sentence Simplification for Automatic Processing of Biomedical Text. - Siddhartha Jonnalagadda; Luis Tari; Jörg Hakenberg; Chitta Baral; Graciela Gonzalez 001 (HLT-NAACL (Short Papers), 2009)

Querying Parse Tree Database of Medline Text to Synthesize User-Specific Biomolecular Networks. - Luis Tari; Jörg Hakenberg; Graciela Gonzalez 001; Chitta Baral (Pacific Symposium on Biocomputing, 2009)

Biomedical word sense disambiguation with ontologies and metadata: automation meets accuracy. - Dimitra Alexopoulou; Bill Andreopoulos; Heiko Dietze; Andreas Doms; Fabien Gandon; Jörg Hakenberg; Khaled Khelif; Michael Schroeder 001; Thomas Wächter (BMC Bioinform., 2009)

GoGene: gene annotation in the fast lane. - Conrad Plake; Loïc Royer; Rainer Winnenburg; Jörg Hakenberg; Michael Schroeder 001 (Nucleic Acids Res., 2009)

Mining relations from the biomedical literature. - Jörg Hakenberg (2009)

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

GenerIE: Information extraction using database queries. - Luis Tari; Phan Huy Tu; Jörg Hakenberg; Yi Chen 001; Tran Cao Son; Graciela Gonzalez 001; Chitta Baral (ICDE, 2010)

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

A Comprehensive Benchmark of Kernel Methods to Extract Protein-Protein Interactions from Literature. - Domonkos Tikk; Philippe Thomas 002; Peter Palaga; Jörg Hakenberg; Ulf Leser (PLoS Comput. Biol., 2010)

Efficient Extraction of Protein-Protein Interactions from Full-Text Articles. - Jörg Hakenberg; Robert Leaman; Nguyen Ha Vo; Siddhartha Jonnalagadda; Ryan Sullivan; Christopher Miller; Luis Tari; Chitta Baral; Graciela Gonzalez 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2010)

The GNAT library for local and remote gene mention normalization. - Jörg Hakenberg; Martin Gerner; Maximilian Haeussler; Illés Solt; Conrad Plake; Michael Schroeder 001; Graciela Gonzalez 001; Goran Nenadic; Casey M. Bergman (Bioinform., 2011)

Molecular Event Extraction from Link Grammar Parse Trees in the BioNLP'09 Shared Task. - Jörg Hakenberg; Illés Solt; Domonkos Tikk; Nguyen Ha Vo; Luis Tari; Quang Long Nguyen; Chitta Baral; Ulf Leser (Comput. Intell., 2011)

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

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

Incremental Information Extraction Using Relational Databases. - Luis Tari; Phan Huy Tu; Jörg Hakenberg; Yi Chen 001; Tran Cao Son; Graciela Gonzalez 001; Chitta Baral (IEEE Trans. Knowl. Data Eng., 2012)

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

An Integrative Pipeline for Multi-Modal Discovery of Disease Relationships. - Benjamin S. Glicksberg; Li Li 062; Wei-Yi Cheng; Khader Shameer; Jörg Hakenberg; Rafael Castellanos; Meng Ma; Lisong Shi; Hardik Shah; Joel T. Dudley; Rong Chen 006 (Pacific Symposium on Biocomputing, 2015)

DIVAS: a centralized genetic variant repository representing 150 000 individuals from multiple disease cohorts. - Wei-Yi Cheng; Jörg Hakenberg; Shuyu Dan Li; Rong Chen 006 (Bioinform., 2016)

Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks. - Benjamin S. Glicksberg; Li Li 062; 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; et al. (Bioinform., 2016)

SETH detects and normalizes genetic variants in text. - Philippe Thomas 002; Tim Rocktäschel; Jörg Hakenberg; Yvonne Lichtblau; Ulf Leser (Bioinform., 2016)

Integrating 400 million variants from 80, 000 human samples with extensive annotations: towards a knowledge base to analyze disease cohorts. - Jörg Hakenberg; Wei-Yi Cheng; Philippe Thomas 002; Ying-Chih Wang; Andrew V. Uzilov; Rong Chen 006 (BMC Bioinform., 2016)