Jörg Hakenberg

Summary

Affiliation: Humboldt University
Country: Germany

Publications

  1. ncbi Finding kinetic parameters using text mining
    Jörg Hakenberg
    Humboldt Universitat zu Berlin, Department of Computer Science, Berlin, Germany
    OMICS 8:131-52. 2004
  2. ncbi Systematic feature evaluation for gene name recognition
    Jörg Hakenberg
    Computer Science Department, Humboldt Universitat zu Berlin, 10099 Berlin, Germany
    BMC Bioinformatics 6:S9. 2005
  3. ncbi Gene mention normalization and interaction extraction with context models and sentence motifs
    Jörg Hakenberg
    Biotechnological Centre, Technische Universitat Dresden, Dresden, Germany
    Genome Biol 9:S14. 2008
  4. ncbi Biomedical word sense disambiguation with ontologies and metadata: automation meets accuracy
    Dimitra Alexopoulou
    Biotechnology Center BIOTEC, Technische Universitat Dresden, 01062, Dresden, Germany
    BMC Bioinformatics 10:28. 2009
  5. ncbi What makes a gene name? Named entity recognition in the biomedical literature
    Ulf Leser
    Department for Computer Science, Humboldt Universitat zu Berlin, Rudower Chaussee 25, Germany
    Brief Bioinform 6:357-69. 2005
  6. ncbi GoGene: gene annotation in the fast lane
    Conrad Plake
    Biotechnology Center, Technische Universitat Dresden, 01307 Dresden, Germany
    Nucleic Acids Res 37:W300-4. 2009
  7. ncbi A comprehensive benchmark of kernel methods to extract protein-protein interactions from literature
    Domonkos Tikk
    Knowledge Management in Bioinformatics, Computer Science Department, Humboldt Universitat zu Berlin, Berlin, Germany
    PLoS Comput Biol 6:e1000837. 2010
  8. ncbi AliBaba: PubMed as a graph
    Conrad Plake
    Knowledge Management in Bioinformatics, , 10099 Berlin, Germany
    Bioinformatics 22:2444-5. 2006

Detail Information

Publications8

  1. ncbi Finding kinetic parameters using text mining
    Jörg Hakenberg
    Humboldt Universitat zu Berlin, Department of Computer Science, Berlin, Germany
    OMICS 8:131-52. 2004
    ..We evaluated our approach on a manually tagged corpus of 800 documents and found that it outperforms keyword searches in abstracts by a factor of five in terms of precision...
  2. ncbi Systematic feature evaluation for gene name recognition
    Jörg Hakenberg
    Computer Science Department, Humboldt Universitat zu Berlin, 10099 Berlin, Germany
    BMC Bioinformatics 6:S9. 2005
    ..RFE improves the performance by 0.7%, compared to using the complete set of attributes. Moreover, a performance that is only 2.3% below this maximum can be obtained using fewer than 5% of the features...
  3. ncbi Gene mention normalization and interaction extraction with context models and sentence motifs
    Jörg Hakenberg
    Biotechnological Centre, Technische Universitat Dresden, Dresden, Germany
    Genome Biol 9:S14. 2008
    ..We describe a method for identifying genes and relationships between proteins...
  4. ncbi Biomedical word sense disambiguation with ontologies and metadata: automation meets accuracy
    Dimitra Alexopoulou
    Biotechnology Center BIOTEC, Technische Universitat Dresden, 01062, Dresden, Germany
    BMC Bioinformatics 10:28. 2009
    ..Another useful source of information for disambiguation are metadata. Here, we systematically compare three approaches to word sense disambiguation, which use ontologies and metadata, respectively...
  5. ncbi What makes a gene name? Named entity recognition in the biomedical literature
    Ulf Leser
    Department for Computer Science, Humboldt Universitat zu Berlin, Rudower Chaussee 25, Germany
    Brief Bioinform 6:357-69. 2005
    ..In this paper, the problems and resources in NER research are described, the principal algorithms underlying most systems sketched, and the current state-of-the-art in the field surveyed...
  6. ncbi GoGene: gene annotation in the fast lane
    Conrad Plake
    Biotechnology Center, Technische Universitat Dresden, 01307 Dresden, Germany
    Nucleic Acids Res 37:W300-4. 2009
    ..Since all associations of genes to terms are supported by evidence in the literature, the results are transparent and can be verified by the user. GoGene is available at http://gopubmed.org/gogene...
  7. ncbi A comprehensive benchmark of kernel methods to extract protein-protein interactions from literature
    Domonkos Tikk
    Knowledge Management in Bioinformatics, Computer Science Department, Humboldt Universitat zu Berlin, Berlin, Germany
    PLoS Comput Biol 6:e1000837. 2010
    ..Nevertheless, our study shows that three kernels are clearly superior to the other methods...
  8. ncbi AliBaba: PubMed as a graph
    Conrad Plake
    Knowledge Management in Bioinformatics, , 10099 Berlin, Germany
    Bioinformatics 22:2444-5. 2006
    ..Several filter options allow for a more focused search. Thus, researchers can grasp complex networks described in various articles at a glance. AVAILABILITY: http://alibaba.informatik.hu-berlin.de/..