Jörg Hakenberg

Orcid: 0000-0001-8781-7766

According to our database1, Jörg Hakenberg authored at least 34 papers between 2005 and 2016.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.

Timeline

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Bibliography

2016
Integrating 400 million variants from 80, 000 human samples with extensive annotations: towards a knowledge base to analyze disease cohorts.
BMC Bioinform., 2016

SETH detects and normalizes genetic variants in text.
Bioinform., 2016

Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks.
Bioinform., 2016

DIVAS: a centralized genetic variant repository representing 150 000 individuals from multiple disease cohorts.
Bioinform., 2016

2015
An Integrative Pipeline for Multi-Modal Discovery of Disease Relationships.
Proceedings of the Biocomputing 2015: Proceedings of the Pacific Symposium, 2015

2013
Literature Mining Solutions for Life Science Research.
Adv. Bioinformatics, 2013

2012
Incremental Information Extraction Using Relational Databases.
IEEE Trans. Knowl. Data Eng., 2012

A SNPshot of PubMed to associate genetic variants with drugs, diseases, and adverse reactions.
J. Biomed. Informatics, 2012

A high-throughput analysis pipeline for large next generation DNA sequencing studies.
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine, 2012

2011
Molecular Event Extraction from Link Grammar Parse Trees in the BioNLP'09 Shared Task.
Comput. Intell., 2011

The GNAT library for local and remote gene mention normalization.
Bioinform., 2011

2010
Efficient Extraction of Protein-Protein Interactions from Full-Text Articles.
IEEE ACM Trans. Comput. Biol. Bioinform., 2010

A Comprehensive Benchmark of Kernel Methods to Extract Protein-Protein Interactions from Literature.
PLoS Comput. Biol., 2010

Synthesis of Pharmacokinetic Pathways through Knowledge Acquisition and Automated Reasoning.
Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

GenerIE: Information extraction using database queries.
Proceedings of the 26th International Conference on Data Engineering, 2010

Semantic classification and dependency parsing enabled automated bio-molecular event extraction from text.
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, 2010

2009
Mining relations from the biomedical literature.
PhD thesis, 2009

GoGene: gene annotation in the fast lane.
Nucleic Acids Res., 2009

Biomedical word sense disambiguation with ontologies and metadata: automation meets accuracy.
BMC Bioinform., 2009

Querying Parse Tree Database of Medline Text to Synthesize User-Specific Biomolecular Networks.
Proceedings of the Biocomputing 2009: Proceedings of the Pacific Symposium, 2009

Towards Effective Sentence Simplification for Automatic Processing of Biomedical Text.
Proceedings of the Human Language Technologies: Conference of the North American Chapter of the Association of Computational Linguistics, Proceedings, May 31, 2009

High-performance information extraction with AliBaba.
Proceedings of the EDBT 2009, 2009

Molecular event extraction from Link Grammar parse trees.
Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task, BioNLP@HLT-NAACL 2009, 2009

Word Sense Disambiguation in Biomedical Applications.
Proceedings of the Information Retrieval in Biomedicine, 2009

2008
Searching Biomedical Literature with Anatomy Ontologies.
Proceedings of the Anatomy Ontologies for Bioinformatics, Principles and Practice, 2008

Inter-species normalization of gene mentions with GNAT.
Proceedings of the ECCB'08 Proceedings, 2008

Services for annotation of biomedical text.
Proceedings of the Ontologies and Text Mining for Life Sciences: Current Status and Future Perspectives, 24.03., 2008

GoPubMed: Exploring Pubmed with Ontological Background Knowledge.
Proceedings of the Ontologies and Text Mining for Life Sciences: Current Status and Future Perspectives, 24.03., 2008

2007
What's in a gene name? Automated refinement of gene name dictionaries.
Proceedings of the Biological, translational, and clinical language processing, 2007

2006
ALIBABA: PubMed as a graph.
Bioinform., 2006

Collecting a Large Corpus from all of Medline.
Proceedings of the Second International Symposium on Semantic Mining in Biomedicine, 2006

2005
Systematic feature evaluation for gene name recognition.
BMC Bioinform., 2005

What makes a gene name? Named entity recognition in the biomedical literature.
Briefings Bioinform., 2005

Optimizing syntax patterns for discovering protein-protein interactions.
Proceedings of the 2005 ACM Symposium on Applied Computing (SAC), 2005


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