2012

1. Jörg Hakenberg, Dmitry Voronov, Vo Ha Nguyen, Shanshan Liang, Saadat Anwar, Robert Leaman, Luis N Tari, and Chitta Baral:
   A SNPshot of PubMed to find associations between genetic variants, drugs, and diseases.
   J Biomed Info, 2012, in press.
   [PMID: 22564364] - [10.1016/j.jbi.2012.04.006]
2. Jörg Hakenberg, Goran Nenadíc, Dietrich Rebholz-Schuhmann, Jin-Dong Kim (eds.):
   Literature mining solutions for life science research.
   Special issue of Advances in Bioinformatics. To appear 2012.
3. Jörg Hakenberg (field ed.) Text Mining, section in: Werner Dubitzky, Olaf Wolkenhauer, Kwang-Hyun Cho, Hiroki Yokota (eds.) Encyclopedia of Systems Biology, Springer, 2012, in print.
   [Springer Reference Works]

2011

1. Jörg Hakenberg, Martin Gerner, Maximilian Haeussler, Illés Solt, Conrad Plake, Michael Schroeder, Graciela Gonzalez, Goran Nenadic, Casey Bergman:
   The GNAT library for local and remote gene mention normalization.
   Bioinformatics 27(19):2769-2771, 2011.
   [Full paper] - [PubMed: 21813477] - [10.1093/bioinformatics/btr455] - [SourceForge]
2. Vo Ha Nguyen, Jörg Hakenberg, Luis Tari, Chitta Baral, Illés Solt, Domonkos Tikk, Quang Long Nguyen, Ulf Leser:
   Molecular event extraction from Link Grammar parse trees in the BioNLP'09 Shared Task.
   Computational Intelligence (COIN), 27(4):665-680, November 2011.
   [Abstract] - [ToC]

2010

1. Domonkos Tikk, Philippe Thomas, Peter Palaga, Jörg Hakenberg, and Ulf Leser:
   A comprehensive benchmark of kernel methods to extract protein-protein interactions from literature.
   PLoS Computational Biology, 6(7):e1000837, 2010.
   [Open access] - [PubMed: 20617200]
2. Philippe Thomas, Johannes Starlinger, Christoph Jacob, Illés Solt, Jörg Hakenberg, and Ulf Leser:
   GeneView — Gene-Centric Ranking of Biomedical Text.
   In: Proc BioCreative III, Bethesda, USA, 2010. pp 137-142.
3. Luis Tari, Tu Phan Huy, Jörg Hakenberg, Yi Chen, Tran Can Son, Graciela Gonzalez, and Chitta Baral:
   Incremental Information Extraction Using Relational Databases.
   IEEE Transactions on Knowledge and Data Engineering (TKDE), vol. 22, issue 99, Oct 28 2010.
   [10.1109/TKDE.2010.214]
4. 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 Transactions on Computational Biology and Bioinformatics (TCBB), 7(3):481-494, May 20, 2010.
   Selected as Spotlight Paper for the July-September issue of TCBB.
   [PubMed: 20498514]
5. Syed Toufeeq Ali-Ahmed, Radhika Nair, Chintan Patel, Sheela P. Kanwar, Jörg Hakenberg, and Hasan Davulcu:
   Semantic Classification and Dependency Parsing enabled Automated Bio-Molecular Event Extraction from Text.
   Short paper at ACM Int Conf Bioinf and Comp Bio (ACM-BCB), Niagara Falls/NY, August 2-4, 2010.
6. Luis Tari, Phan Huy Tu, Jörg Hakenberg, Yi Chen, Tran Cao Son, Graciela Gonzalez, Chitta Baral:
   GenerIE: Information Extraction Using Database Queries.
   Demo at ICDE 2010, Los Angeles, USA, March 2010.
7. 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.
8. Jörg Hakenberg, Dmitry Voronov, Vo Ha Nguyen, Shanshan Liang, Barry Lumpkin, Saadat Anwar, Robert Leaman, Luis Ng Tari, 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 Pac Symp Biocomput (PSB), Big Island of Hawaii, USA, January 4-8, 2010.
9. 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.
   [PubMed: 19908398]

2009

1. 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.
   In Proc. BioCreative II.5 Workshop, Madrid, Spain, October 7-9 2009.
2. 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: 19465383]
3. Jörg Hakenberg, Illés Solt, Domonkos Tikk, Nguyen Quang Long, Astrid Rheinländer, Luis Tari, Graciela Gonzalez, Ulf Leser:
   Molecular event extraction from Link Grammar parse trees.
   In Proc. Natural Language Processing in Biomedicine (BioNLP), NAACL 2009 Workshop, June 4-5, 2009, Boulder, CO, USA.
4. 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: 19159460]
5. 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.
6. 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.
7. Luis Tari, Jörg Hakenberg, Graciela Gonzalez, Chitta Baral:
   Querying a parse tree database of Medline text to synthesize user-specific biomolecular networks.
   In: Proc Pac Symp Biocomput (PSB), January 5-9, 2009.
   [PubMed: 19209697]
8. 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.
   [Suppl. information]

2008

1. Jörg Hakenberg, Conrad Plake, Robert Leaman, Michael Schroeder, Graciela Gonzalez:
   Inter-species normalization of gene mentions with GNAT.
   Bioinformatics, 24(16):i126-132, 2008.
   Presentation at European Conference on Computational Biology (ECCB), September 22-26, 2008.
   [PubMed: 18689813]
2. Jörg Hakenberg, Conrad Plake, Loic Royer, Hendrik Strobelt, Ulf Leser, Michael Schroeder:
   Gene mention normalization and interaction extraction with context models and sentence motifs.
   Genome Biology, 9(S2):S14, 2008.
   [PubMed: 18834492]
3. 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, Lynette Hirschman:
   Overview of BioCreative II Gene Normalization.
   Genome Biology, 9(S2):S3, 2008.
   [PubMed: 18834494]
4. Florian Leitner, Martin Krallinger, Carlos Rodriguez-Penagos, Jörg Hakenberg, Conrad Plake, et al.:
   Introducing Meta-Services for Biomedical Information Extraction.
   Genome Biology, 9(S2):S6, 2008.
   [PubMed: 18834497]
5. 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.
6. 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.
7. 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, Michael Schroeder:
   GoPubMed: Exploring PubMed with Ontological Background Knowledge.
   In: Stephen A. Krawetz (ed.), Bioinformatics for Systems Biology, Humana Press (2008).

2007

1. Jörg Hakenberg:
   What's in a gene name? Automated refinement of gene name dictionaries.
   In: Proc BioNLP 2007 Workshop at ACL 2007, 153-160, June 29 2007, Prague.
2. Thomas Wächter, Dimitra Alexopoulou, Heiko Dietze, Jörg Hakenberg, 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.
3. Jörg Hakenberg, Michael Schroeder, Ulf Leser:
   Consensus pattern alignment to find protein-protein interactions in text.
   In Proc. 2nd BioCreative Challenge Evaluation Workshop, April 23-25 2007, Madrid, Spain, ISBN 84-933255-6-2.
4. Jörg Hakenberg, Loic Royer, Conrad Plake, Hendrik Strobelt, Michael Schroeder:
   Me and my friends: gene mention normalization with background knowledge.
   In Proc. 2nd BioCreative Challenge Evaluation Workshop, April 23-25 2007, Madrid, Spain, ISBN 84-933255-6-2.

2006

1. 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
2. Conrad Plake, Torsten Schiemann, Marcus Pankalla, Jörg Hakenberg, Ulf Leser:
   AliBaba: PubMed as a graph.
   Bioinformatics, 22(19):2444-2445 (2006).
   [PubMed: 16870931]
3. Jörg Hakenberg, Conrad Plake, Torsten Schiemann, Ulf Leser:
   AliBaba: Accessing PubMed using graphs.
   German Conference on Bioinformatics (GCB), Tübingen, Germany, September 20-22 2006.
4. Jörg Hakenberg, Ulf Leser, Harald Kirsch, Dietrich Rebholz-Schuhmann:
   Collecting a large corpus from all of Medline.
   In Proc. Second International Symposium on Semantic Mining in Biomedicine (SMBM), Jena, Germany, April 2006.

2005

1. 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.
   [PubMed: 16420734]
2. Ulf Leser and Jörg Hakenberg:
   Text Mining: Automatische Analyse biomedizinischer Texte.
   GenomXPress, 4.05:20-22, December 2005.
3. Jörg Hakenberg, Steffen Bickel, Conrad Plake, Ulf Brefeld, Hagen Zahn, Lukas Faulstich, Ulf Leser, Tobias Scheffer:
   Systematic Feature Evaluation for Gene Name Recognition.
   BMC Bioinformatics, 6(Suppl 1):S9, 2005.
   [PubMed: 15960843]
4. Jörg Hakenberg, Juliane Rutsch, Ulf Leser:
   Tuning Text Classification for Hereditary Diseases with Section Weighting.
   In Proc. Int Symp Semantic Mining in Biomedicine (SMBM), pp.34-39. Hinxton, UK, April 2005.
5. Conrad Plake, Jörg Hakenberg, Ulf Leser:
   Optimizing Syntax Patterns for Discovering Protein-Protein Interactions.
   In Proc. ACM Symposium on Applied Computing, Bioinformatics track, 1:195-201. Santa Fe, USA, March 2005.
6. Jörg Hakenberg, Conrad Plake, Ulf Leser, Harald Kirsch, Dietrich Rebholz-Schuhmann:
   LLL'05 Challenge: Genic Interaction Extraction with Alignments and Finite State Automata.
   In Proc. Learning Language in Logic Workshop (LLL'05) at ICML 2005, pp. 38-45. Bonn, Germany, 2005.
7. Conrad Plake, Jörg Hakenberg, Ulf Leser:
   Learning Patterns for Information Extraction from Free Text.
   Workshop Arbeitskreis Knowledge Discovery, Karlsruhe, Germany, March 1st, 2005.
8. Sebastian Schmeier, Jörg Hakenberg, Axel Kowald, Edda Klipp, Ulf Leser:
   Textmining zur Unterstützung von Datenbankkuratoren.
   Workshop Datenbanken im NGFN, March 9, 2005, Cologne, Germany.

2004

1. Jörg Hakenberg, Sebastian Schmeier, Axel Kowald, Edda Klipp, 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.
   [PubMed: 15268772]
2. Steffen Bickel, Ulf Brefeld, Lukas Faulstich, Jörg Hakenberg, Ulf Leser, Conrad Plake, Tobias Scheffer:
   A Support Vector Machine Classifier for Gene Name Recognition.
   In Proc. EMBO Workshop: A critical assessment of text mining methods in molecular biology. Granada, Spain, March 2004

2003

1. 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.
   [PubMed: 15130801]
2. Sebastian Schmeier, Jörg Hakenberg, Axel Kowald, Edda Klipp, and Ulf Leser:
   Text Mining for Systems Biology Using Statistical Learning Methods.
   In Proc. Workshop Arbeitskreis Knowledge Discovery, Karlsruhe, Germany, October 2003.

Posters etc.

• Abhinav Beeravally Nagulapally and Jörg Hakenberg: Genome Browsers for NGS data. Poster at Tenth Annual Research Day, University of the Sciences in Philadelphia, PA/USA, April 2012.
• Syed Toufeeq Ahmed, Sheela Pradeep Kanwar, Jörg Hakenberg, and Hasan Davulcu: BioEve: A Discovery Engine for Life Sciences Literature. Poster at 6th International Symposium on Bioinformatics Research and Applications (ISBRA'10), May 23-26, 2010, Storrs, Connecticut, USA.
• Dimitra Alexopoulou, Bill Andreopoulos, Jörg Hakenberg, Michael Schroeder: Word-sense disambiguation in biomedical ontologies with term co-occurrence analysis. Poster at 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. Poster at Data Integration in the Life Sciences, DILS, Hinxton, UK, 20-22 July 2006
• Sebastian Schmeier, Jörg Hakenberg, Axel Kowald, Ulf Leser, and Edda Klipp: Recognition and Extraction of Entities related to Enzyme Kinetics. Poster at BioText - a biomedical text mining workshop, London, UK, 9 November 2005.
• Sebastian Schmeier, Axel Kowald, Jörg Hakenberg, Ulf Leser, and Edda Klipp: Finding Kinetic Data Using Text Mining. Poster at 5th Int Workshop on Bioinformatics and Systems Biology (IBSB), Berlin, Germany, 22-25 August 2005.
• Sebastian Schmeier, Axel Kowald, Jörg Hakenberg, Ulf Leser, and Edda Klipp: Finding Kinetic Data Using Text Mining. Poster at Workshop Datenbanken im NGFN, Cologne, Germany, March 2005.
• Sebastian Schmeier, Axel Kowald, Jörg Hakenberg, Ulf Leser, and Edda Klipp: Fighting the Data Acquisition Bottleneck. Poster at Int Conf Systems Biology (ICSB), Heidelberg, Germany, October 2004.
• Jörg Hakenberg, Steffen Bickel, Conrad Plake, Ulf Brefeld, Lukas Faulstich, Hagen Zahn, Tobias Scheffer, Ulf Leser: Information Extraction from Biomedical Literature - Gene Name Recognition. Poster, Berlin Center for Bioinformatics (BCB), Feb 2005.
• Sebastian Schmeier, Jörg Hakenberg, Axel Kowald, Edda Klipp, and Ulf Leser: Fighting the Data Acquisition Bottleneck. Poster, Berlin Center for Bioinformatics (BCB), Feb 2005.
• Sebastian Schmeier, Jörg Hakenberg, Axel Kowald, Edda Klipp, and Ulf Leser: Text Mining for Systems Biology Using Statistical Learning Methods. Poster, Berlin Center for Bioinformatics (BCB), Dec 2003.
  
  Et cetera:
• 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.
• Jörg Hakenberg: A Statistical Approach to Identify Positional Dependencies in Protein Domains. Diploma thesis, University of Ulm, 2002.

Talks

• Jörg Hakenberg: Taking a SNPshot of PubMed - a repository of genetic variants and their drug response phenotypes. GPD-Rxn Workshop: Genotype-Phenotype-Drug Relationship Extraction from Text at Pacific Symposium on Biocomputing (PSB), Big Island of Hawaii, USA, January 4-8, 2010.
• Jörg Hakenberg: Online protein interaction extraction and normalization at Arizona State University. BioCreative II.5 Workshop, Madrid, Spain, October 7-9 2009.
• Jörg Hakenberg: Entity Mention Normalization - Taking Another Step Towards Integrating Data Extracted from Literature with Databases. Rocky Mountain Bioinformatics Conference (Rocky 2008), Aspen, CO, USA, December 4-7, 2008.
• Jörg Hakenberg: Inter-species normalization of gene mentions. European Conference on Computational Biology (ECCB), September 22-26, 2008, Cagliari, Italy.
• Jörg Hakenberg: Services for annotation of biomedical text. Dagstuhl Seminar 08131, Ontologies and Text Mining for Life Sciences: Current Status and Future Perspectives, March 24-28, 2008, Dagstuhl, Germany.
• Jörg Hakenberg: Consensus pattern alignment to find protein-protein interactions in text. 2nd BioCreative Challenge Evaluation Workshop, April 23-25 2007, Madrid, Spain.
• Jörg Hakenberg: Me and my friends: gene mention normalization with background knowledge. 2nd BioCreative Challenge Evaluation Workshop, April 23-25 2007, Madrid, Spain.
• Jörg Hakenberg: Collecting a large corpus from all of Medline. Second International Symposium on Semantic Mining in Biomedicine (SMBM). Jena, Germany, April 2006.
• Jörg Hakenberg: Tuning Text Classification for Hereditary Diseases with Section Weighting. Int Symp Semantic Mining in Biomedicine (SMBM), Hinxton, UK, April 2005.
• Jörg Hakenberg: Optimizing Syntax Patterns for Discovering Protein-Protein Interactions. ACM Symposium on Applied Computing, Bioinformatics track, Santa Fe, USA, March 2005.
• Jörg Hakenberg: Text Mining for Systems Biology Using Statistical Learning Methods. Workshop Arbeitskreis Knowledge Discovery. Karlsruhe, Germany, October 2003.

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