ASU logo
ASU Sunburst
  • Home
  • Projects
  • Publications
  • CV
  • Links
  • 2009
  • 2008
  • 2007
  • 2006
  • 2005
  • 2004
  • 2003
  • Posters
  • Others
  • Suppl. information

Publications

2010

  • Jörg Hakenberg, Conrad Plake, Ulf Leser: Ali Baba: A Text Mining Tool for Complex Biological Systems. In: Huma Lodhi and Stephen Muggleton (eds.), Elements of Computational Systems Biology, John Wiley & Sons, Inc. (2010). ISBN: 0470180935.
    [Abstract] - [Amazon]

  • Jörg Hakenberg, Dmitry Voronov, Vo Ha Nguyen, Shanshan Liang, Barry Lumpkin, Saadat Anwar, Robert Leaman, Luis Ng Tari, and Chitta Baral: Taking a SNPshot of PubMed - a repository of genetic variants and their drug response phenotypes. In: Proc GPD-Rxn Workshop: Genotype-Phenotype-Drug Relationship Extraction from Text at PSB 2010, Big Island of Hawaii, USA, January 4-8 2010, accepted.
    [Workshop]

  • Luis Tari, Saadat Anwar, Shanshan Liang, Jörg Hakenberg, Chitta Baral: Synthesis of Pharmacokinetic Pathways through Knowledge Acquisition and Automated Reasoning. In Proc Pac Symp Biocomput, Big Island of Hawaii, USA, January 4-8 2010, accepted.
    [PSB 2010] - [Proceedings]

2009

  • Jörg Hakenberg, Robert J. Leaman, Nguyen Ha Vo, Siddhartha Jonnalagadda, Ryan Sullivan, Christopher Miller, Luis Tari, Chitta Baral, Graciela Gonzalez: Online protein interaction extraction and normalization at Arizona State University. Presentation at BioCreative II.5 workshop, Madrid, Spain, October 7-9 2009.
    [Workshop] - [Slides]

  • Luis Tari, Phan Huy Tu, Jörg Hakenberg, Yi Chen, Tran Cao Son, Graciela Gonzalez, and Chitta Baral: GenerIE: Information Extraction Using Database Queries. Demo at ICDE 2010, Los Angeles, USA, March 2010, accepted.

  • Conrad Plake, Loic Royer, Rainer Winnenburg, Jörg Hakenberg, Michael Schroeder: GoGene: gene annotation on the fast lane. Nucl. Acids Res., Web Server Issue, 37(Suppl. 2):W300-304, 2009.
    [PubMed] - [Full text] - [GoGene website]

  • Jörg Hakenberg, Illes Solt, Domonkos Tikk, Nguyen Quang Long, Astrid Rheinländer, Luis Tari, Graciela Gonzalez, Ulf Leser: Molecular event extraction from Link Grammar parse trees. Proc. Natural Language Processing in Biomedicine (BioNLP) NAACL 2009 Workshop, June 4-5, Boulder, CO, USA.
    [PDF] - [NAACL-HLT 2009] - [Workshop] - [Shared Task]

  • 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 Bioinformatics, 10:28, 2009.
    [PubMed] - [Full text]

  • Siddhartha Jonnalagadda, Luis Tari, Jörg Hakenberg, Chitta Baral, Graciela Gonzalez: Towards Effective Sentence Simplification for Automatic Processing of Biomedical Text. In: Proc. NAACL-HLT (short paper), Boulder, Colorado/USA, May 31-June 5, 2009.
    [Conference]

  • Peter Palaga, Long Nguyen, Ulf Leser, Jörg Hakenberg: High-Performance Information Extraction with AliBaba. (Demo). In: Proc EDBT 2009, St. Petersburg, March 23-26, 2009.
    [Conference]

  • Luis Tari, Jörg Hakenberg, Graciela Gonzalez, Chitta Baral: Querying a parse tree database of Medline text to synthesize user-specific biomolecular networks. In: Pacific Symposium on Biocomputing (PSB), January 5-9, 2009.
    [PubMed] - [PDF] - [Electronic proceedings]

  • Torsten Schiemann, Ulf Leser, Jörg Hakenberg: Word Sense Disambiguation in Biomedical Applications: A Machine Learning Approach. In: Violaine Prince and Mathieu Roche (eds.), Information Retrieval in Biomedicine: Natural Language Processing for Knowledge Integration, IGI Global, Hershey PA/USA (March 2009). ISBN: 1605662749.
    [Book's website] - [Abstract] - [Amazon]

2008

  • Jörg Hakenberg, Conrad Plake, Robert Leaman, Michael Schroeder, Graciela Gonzalez: Inter-species normalization of gene mentions. Bioinformatics, 24(16):i126-132, 2008.
    Presentation at European Conference on Computational Biology (ECCB), September 22-26, 2008.
    [PubMed] - [Abstract] - [Full text]

  • Jörg Hakenberg, Conrad Plake, Loic Royer, Hendrik Strobelt, Ulf Leser, and Michael Schroeder: Gene mention normalization and interaction extraction with context models and sentence motifs. Genome Biology, 9(S2):S14, 2008.
    [PubMed] - [Abstract] - [Full text]

  • Alexander A. Morgan, Zhiyong Lu, Xinglong Wang, Aaron A. Cohen, Juliane Fluck, Patrick Ruch, Anna Divoli, Katrin Fundel, Robert Leaman, Jörg Hakenberg, Chenjie Sun, Heng-Hui Liu, Rafael Torres, Michael Krauthammer, William W. Lau, Hongfang Liu, Chun-Nan Hsu, Martijn Schuemie, K. Bretonnel Cohen, and Lynette Hirschman: Overview of BioCreative II Gene Normalization. Genome Biology, 9(S2):S3, 2008.
    [PubMed] - [Full text]

  • Florian Leitner, Martin Krallinger, Carlos Rodriguez-Penagos, Jörg Hakenberg, Conrad Plake, Cheng-Ju Kuo, Chun-Nan Hsu, Richard Tzong-Han Tasi, Hsi-Chuan Hung, William W. Lau, Calvin A. Johnson, Rune Sætre, Kazuhiro Yoshida, Yan Hua Chen, Sun Kim, Soo-Yong Shin, Byoung-Tak Zhang, William A. Baumgartner, Jr., Lawrence Hunter, Barry Haddow, Michael Matthew, Xinglong Wang, Patrick Ruch, Frédéric Ehrler, Arzucan Özgür, Günes Erkan, Dragomir R. Radev, Michael Krauthammer, ThaiBinh Luong, Robert Hoffmann, Chris Sander, and Alfonso Valencia: Introducing Meta-Services for Biomedical Information Extraction. Genome Biology, 9(S2):S6, 2008.
    [PubMed] - [Full text]

  • Jörg Hakenberg: Services for annotation of biomedical text. In: M. Ashburner, U. Leser, D. Rebholz-Schuhmann (eds.), Proc Dagstuhl Seminar 08131, Ontologies and Text Mining for Life Sciences: Current Status and Future Perspectives, March 24-28, 2008.

  • Heiko Dietze, Dimitra Alexopoulou, Michael R. Alvers, Bill Barrio-Alvers, Andreas Doms, Jörg Hakenberg, Jan Mönnich, Conrad Plake, Andreas Reischuk, Loic Royer, Thomas Wächter, Matthias Zschunke, Michael Schroeder: GoPubMed: Exploring Pubmed with Ontological Background Knowledge. In: M. Ashburner, U. Leser, D. Rebholz-Schuhmann (eds.), Proc Dagstuhl Seminar 08131, Ontologies and Text Mining for Life Sciences: Current Status and Future Perspectives, March 24-28, 2008.

  • Heiko Dietze, Dimitra Alexopoulou, Michael R. Alvers, Liliana Barrio-Alvers, Bill Andreopoulos, Andreas Doms, Jörg Hakenberg, Jan Mönnich, Conrad Plake, Andreas Reischuck, Loic Royer, Thomas Wächter, Matthias Zschunke, and Michael Schroeder: GoPubMed: Exploring PubMed with Ontological Background Knowledge. In: Stephen A. Krawetz (ed.), Bioinformatics for Systems Biology, Humana Press (2008).

2007

  • Jörg Hakenberg: What's in a gene name? Automated refinement of gene name dictionaries. Proceedings of the BioNLP 2007 workshop at ACL 2007, 153-160, June 29 2007, Prague.
    [Abstract] - [Supplementary information] - [Workshop]

  • Thomas Wächter, Dimitra Alexopoulou, Heiko Dietze, Jörg Hakenberg, and Michael Schroeder: Searching Biomedical Literature with Anatomy Ontologies. In: Albert Burger, Richard A. Baldock, and Duncan R. Davidson (editors), Anatomy Ontologies for Bioinformatics, Springer Computational Biology Vol. 6, 2007.
    [About this book]

  • Jörg Hakenberg, Michael Schroeder, Ulf Leser: Consensus pattern alignment to find protein-protein interactions in text. Proceedings of the Second BioCreative Challenge Evaluation Workshop, April 23-25 2007, Madrid, Spain, ISBN 84-933255-6-2 (presentation and proceedings).
    [Paper PDF] - [Slides PDF] - [Workshop] - [BioCreAtIvE]

  • Jörg Hakenberg, Loic Royer, Conrad Plake, Hendrik Strobelt, Michael Schroeder: Me and my friends: gene mention normalization with background knowledge. Proceedings of the Second BioCreative Challenge Evaluation Workshop, April 23-25 2007, Madrid, Spain, ISBN 84-933255-6-2 (presentation and proceedings).
    [Paper PDF] - [Slides PDF] - [Workshop] - [BioCreAtIvE]

2006

  • Eric G. Bremer, Jörg Hakenberg, Eui-Hong Han, Daniel Berrar, and Werner Dubitzky (editors): Knowledge Discovery in Life Science Literature. Proceedings of the International Workshop KDLL 2006 in conjunction with PAKDD 2006, Singapore, April 2006. Springer LNCS Series: Lecture Notes in Bioinformatics, Vol. 3886, 2006. ISBN: 3-540-32809-2
    [Information] - [SpringerLink] - [Workshop]

  • Conrad Plake, Torsten Schiemann, Marcus Pankalla, Jörg Hakenberg, Ulf Leser: Ali Baba: PubMed as a graph. Bioinformatics, 22(19):2444-2445 (2006).
    [Abstract] - [Full text] - [PubMed]

  • Jörg Hakenberg, Conrad Plake, Torsten Schiemann, and Ulf Leser: Ali Baba: Accessing PubMed using graphs. German Conference on Bioinformatics (GCB). Tübingen, Germany, September 20-22 2006.
    [Abstract] - [Conference]

  • Jörg Hakenberg, Ulf Leser, Harald Kirsch, and Dietrich Rebholz-Schuhmann: Collecting a large corpus from all of Medline. Proc. of Second International Symposium on Semantic Mining in Biomedicine (SMBM). Jena, Germany, April 2006.
    [Abstract] - [Full text PDF] - [Supplementary Information] - [Proceedings] - [Symposium]

2005

  • Ulf Leser and Jörg Hakenberg: What Makes a Gene Name? Named Entity Recognition in the Biomedical Literature. Briefings in Bioinformatics, 6(4):357-369, December 2005.
    [Abstract] - [Article] - [PubMed]

  • Ulf Leser and Jörg Hakenberg: Text Mining: Automatische Analyse biomedizinischer Texte. GenomXPress, 4.05:20-22, December 2005.
    [ToC] - [Full issue PDF]

  • Jörg Hakenberg, Steffen Bickel, Conrad Plake, Ulf Brefeld, Hagen Zahn, Lukas Faulstich, Ulf Leser, and Tobias Scheffer: Systematic Feature Evaluation for Gene Name Recognition. BMC Bioinformatics, 6(Suppl 1):S9, 2005.
    [Abstract] - [Full text] - [PubMed]

  • Jörg Hakenberg, Juliane Rutsch, and Ulf Leser: Tuning Text Classification for Hereditary Diseases with Section Weighting. Proc. of First International Symposium on Semantic Mining in Biomedicine (SMBM), pp.34-39. Hinxton, UK, April 2005.
    [Abstract] - [Full text PDF] - [Supplementary Information] - [Proceedings] - [Symposium]

  • Conrad Plake, Jörg Hakenberg, and Ulf Leser: Optimizing Syntax Patterns for Discovering Protein-Protein Interactions. Proc. of ACM Symposium on Applied Computing, Bioinformatics track, 1:195-201. Santa Fe, USA, March 2005.
    [Abstract] - [Citation at ACM] - [Full text at ACM PDF] - [Supplementary information] - [Symposium] - [DOI]

  • Jörg Hakenberg, Conrad Plake, Ulf Leser, Harald Kirsch, and Dietrich Rebholz-Schuhmann: LLL'05 Challenge: Genic Interaction Extraction with Alignments and Finite State Automata. Proc Learning Language in Logic Workshop (LLL'05) at ICML 2005, pp. 38-45. Bonn, Germany, 2005.
    [Abstract] - [Full text PDF] - [Workshop] - [Proceedings]

  • Conrad Plake, Jörg Hakenberg, and Ulf Leser: Learning Patterns for Information Extraction from Free Text. Workshop des Arbeitskreises Knowledge Discovery, Karlsruhe, Germany, March 1st, 2005.
    [Abstract] - [Full text PDF] - [Workshop]

  • Sebastian Schmeier, Jörg Hakenberg, Axel Kowald, Edda Klipp, and Ulf Leser: Textmining zur Unterstützung von Datenbankkuratoren. Workshop Datenbanken im NGFN, March 9, 2005, Köln, Germany.
    [Abstract]

2004

  • Jörg Hakenberg, Sebastian Schmeier, Axel Kowald, Edda Klipp, and Ulf Leser: Finding Kinetic Parameters Using Text Mining. OMICS: A Journal of Integrative Biology, 8(2):131-152. Special issue on Data Mining meets Integrative Biology - a Symbiosis in the Making, 2004.
    [Abstract] - [PubMed]

  • Steffen Bickel, Ulf Brefeld, Lukas Faulstich, Jörg Hakenberg, Ulf Leser, Conrad Plake, and Tobias Scheffer: A Support Vector Machine Classifier for Gene Name Recognition. EMBO Workshop: A critical assessment of text mining methods in molecular biology. Granada, Spain, March 2004
    [Abstract] - [Full text PDF] - [Workshop]

2003

  • Jörg Hakenberg, Alexander Nussbaum, Hansjörg Schild, Hans-Georg Rammensee, Christina Kuttler, Hermann-Georg Holzhütter, Peter-M. Kloetzel, Stefan H.E. Kaufmann, and Hans-Joachim Mollenkopf: MAPPP - MHC-I Antigenic Peptide Processing Prediction. Applied Bioinformatics, 2(3):155-158, 2003.
    [Abstract] - [Article] - [PubMed]

  • Sebastian Schmeier, Jörg Hakenberg, Axel Kowald, Edda Klipp, and Ulf Leser: Text Mining for Systems Biology Using Statistical Learning Methods. 3. Workshop des Arbeitskreises Knowledge Discovery. Karlsruhe, Germany, October 2003.
    [    Abstract] - [Full text PDF] - [Workshop]

Posters

  • Dimitra Alexopoulou, Bill Andreopoulos, Jörg Hakenberg, Michael Schroeder: Word-sense disambiguation in biomedical ontologies with term co-occurrence analysis. German Conference on Bioinformatics, Potsdam, September 26-28 2007.

  • Jörg Hakenberg, Conrad Plake, Torsten Schiemann, Ulf Leser: Ali Baba: Visualizing biological networks from PubMed query results. Data Integration in the Life Sciences, DILS, Hinxton, UK, 20-22 July 2006
    [DILS'06]

  • Sebastian Schmeier, Jörg Hakenberg, Axel Kowald, Ulf Leser, and Edda Klipp: Recognition and Extraction of Entities related to Enzyme Kinetics. BioText - a biomedical text mining workshop, London, UK, 9 November 2005.
    [Workshop]

  • Sebastian Schmeier, Axel Kowald, Jörg Hakenberg, Ulf Leser, and Edda Klipp: Finding Kinetic Data Using Text Mining. 5th Int Workshop on Bioinformatics and Systems Biology (IBSB), Berlin, Germany, 22-25 August 2005.
    [Poster PDF] - [Workshop]

  • Sebastian Schmeier, Axel Kowald, Jörg Hakenberg, Ulf Leser, and Edda Klipp: Finding Kinetic Data Using Text Mining. Workshop Datenbanken im NGFN, Cologne, Germany, March 2005.

  • Sebastian Schmeier, Axel Kowald, Jörg Hakenberg, Ulf Leser, and Edda Klipp: Fighting the Data Acquisition Bottleneck. Int Conf Systems Biology (ICSB), Heidelberg, Germany, October 2004.
    [Abstract]

Others

  • Jörg Hakenberg: Entity Mention Normalization - Taking Another Step Towards Integrating Data Extracted from Literature with Databases. Presentation at Rocky Mountain Bioinformatics Conference (Rocky 2008), Aspen/CO, December 4-7, 2008.
    [Abstract] - [Conference]

  • Jörg Hakenberg, Steffen Bickel, Conrad Plake, Ulf Brefeld, Lukas Faulstich, Hagen Zahn, Tobias Scheffer, and Ulf Leser: Information Extraction from Biomedical Literature - Gene Name Recognition. Poster, BCB internal, Feb 2005.

  • Sebastian Schmeier, Jörg Hakenberg, Axel Kowald, Edda Klipp, and Ulf Leser: Fighting the Data Acquisition Bottleneck. Poster, BCB internal, Feb 2005.

  • Sebastian Schmeier, Jörg Hakenberg, Axel Kowald, Edda Klipp, and Ulf Leser: Text Mining for Systems Biology Using Statistical Learning Methods. Poster, BCB internal, Dec 2003.

  • Marc Jacobsen, Helmy Rachman, Andrea Gutschmidt, Jörg Hakenberg, Hans-J. Mollenkopf, Albert Neher, Knut Feldmann, Stefan H.E. Kaufmann: Novel Mycobacterium tuberculosis specific HLA-A*0201 restricted T cell epitopes in Tb patients. MPI internal, 2002.
    [Abstract]

  • Jörg Hakenberg: A Statistical Approach to Identify Positional Dependencies in Protein Domains. Diploma thesis, University of Ulm, 2002.

Supplementary Information

  • Supplementary information for selected publications.

[Google Scholar] - [DBLP] - [PubMed] - [BLIMP] - [ACM Portal] - [BCB] - [BibTeX from BCB] - [BibTex from BibPubMed]