@Book{BioNLP:2006,
  editor    = {Karin Verspoor  and  Kevin Bretonnel Cohen  and  Ben Goertzel  and  Inderjeet Mani},
  title     = {Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology},
  month     = {June},
  year      = {2006},
  address   = {New York, New York},
  publisher = {Association for Computational Linguistics},
  url       = {http://www.aclweb.org/anthology/W/W06/W06-17}
}

@InProceedings{yu-wei:2006:BioNLP,
  author    = {Yu, Hong  and  Wei, Ying},
  title     = {The Semantics of a Definiendum Constrains both the Lexical Semantics and the Lexicosyntactic Patterns in the Definiens},
  booktitle = {Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology},
  month     = {June},
  year      = {2006},
  address   = {New York, New York},
  publisher = {Association for Computational Linguistics},
  pages     = {1--8},
  url       = {http://www.aclweb.org/anthology/W/W06/W06-17 1}
}

@InProceedings{liang-EtAl:2006:BioNLP,
  author    = {Liang, Jisheng  and  Nguyen, Thien  and  Koperski, Krzysztof  and  Marchisio, Giovanni},
  title     = {Ontology-Based Natural Language Query Processing for the Biological Domain},
  booktitle = {Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology},
  month     = {June},
  year      = {2006},
  address   = {New York, New York},
  publisher = {Association for Computational Linguistics},
  pages     = {9--16},
  url       = {http://www.aclweb.org/anthology/W/W06/W06-17 2}
}

@InProceedings{fyshe-szafron:2006:BioNLP,
  author    = {Fyshe, Alona  and  Szafron, Duane},
  title     = {Term Generalization and Synonym Resolution for Biological Abstracts: Using the Gene Ontology for Subcellular Localization Prediction},
  booktitle = {Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology},
  month     = {June},
  year      = {2006},
  address   = {New York, New York},
  publisher = {Association for Computational Linguistics},
  pages     = {17--24},
  url       = {http://www.aclweb.org/anthology/W/W06/W06-17 3}
}

@InProceedings{sanfilippo-EtAl:2006:BioNLP,
  author    = {Sanfilippo, Antonio  and  Posse, Christian  and  Gopalan, Banu  and  Tratz, Stephen  and  Gregory, Michelle},
  title     = {Integrating Ontological Knowledge and Textual Evidence in Estimating Gene and Gene Product Similarity},
  booktitle = {Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology},
  month     = {June},
  year      = {2006},
  address   = {New York, New York},
  publisher = {Association for Computational Linguistics},
  pages     = {25--32},
  url       = {http://www.aclweb.org/anthology/W/W06/W06-17 4}
}

@InProceedings{tanabe-wilbur:2006:BioNLP,
  author    = {Tanabe, Lorraine  and  Wilbur, W.\ John},
  title     = {A Priority Model for Named Entities},
  booktitle = {Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology},
  month     = {June},
  year      = {2006},
  address   = {New York, New York},
  publisher = {Association for Computational Linguistics},
  pages     = {33--40},
  url       = {http://www.aclweb.org/anthology/W/W06/W06-17 5}
}

@InProceedings{fang-EtAl:2006:BioNLP,
  author    = {Fang, Haw-ren  and  Murphy, Kevin  and  Jin, Yang  and  Kim, Jessica  and  White, Peter},
  title     = {Human Gene Name Normalization using Text Matching with Automatically Extracted Synonym Dictionaries},
  booktitle = {Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology},
  month     = {June},
  year      = {2006},
  address   = {New York, New York},
  publisher = {Association for Computational Linguistics},
  pages     = {41--48},
  url       = {http://www.aclweb.org/anthology/W/W06/W06-17 6}
}

@InProceedings{bunescu-EtAl:2006:BioNLP,
  author    = {Bunescu, Razvan  and  Mooney, Raymond  and  Ramani, Arun  and  Marcotte, Edward},
  title     = {Integrating Co-occurrence Statistics with Information Extraction for Robust Retrieval of Protein Interactions from Medline},
  booktitle = {Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology},
  month     = {June},
  year      = {2006},
  address   = {New York, New York},
  publisher = {Association for Computational Linguistics},
  pages     = {49--56},
  url       = {http://www.aclweb.org/anthology/W/W06/W06-17 7}
}

@InProceedings{tsai-EtAl:2006:BioNLP,
  author    = {Tsai, Richard Tzong-Han  and  Chou, Wen-Chi  and  Lin, Yu-Chun  and  Sung, Cheng-Lung  and  Ku, Wei  and  Su, Ying-Shan  and  Sung, Ting-Yi  and  Hsu, Wen-Lian},
  title     = {BIOSMILE: Adapting Semantic Role Labeling for Biomedical Verbs:},
  booktitle = {Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology},
  month     = {June},
  year      = {2006},
  address   = {New York, New York},
  publisher = {Association for Computational Linguistics},
  pages     = {57--64},
  url       = {http://www.aclweb.org/anthology/W/W06/W06-17 8}
}

@InProceedings{lin-EtAl:2006:BioNLP,
  author    = {Lin, Jimmy  and  Karakos, Damianos  and  Demner-Fushman, Dina  and  Khudanpur, Sanjeev},
  title     = {Generative Content Models for Structural Analysis of Medical Abstracts},
  booktitle = {Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology},
  month     = {June},
  year      = {2006},
  address   = {New York, New York},
  publisher = {Association for Computational Linguistics},
  pages     = {65--72},
  url       = {http://www.aclweb.org/anthology/W/W06/W06-17 9}
}

@InProceedings{rafkind-EtAl:2006:BioNLP,
  author    = {Rafkind, Barry  and  Lee, Minsuk  and  Chang, Shih-Fu  and  Yu, Hong},
  title     = {Exploring Text and Image Features to Classify Images in Bioscience Literature},
  booktitle = {Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology},
  month     = {June},
  year      = {2006},
  address   = {New York, New York},
  publisher = {Association for Computational Linguistics},
  pages     = {73--80},
  url       = {http://www.aclweb.org/anthology/W/W06/W06-1710}
}

@InProceedings{rzhetsky:2006:BioNLP,
  author    = {Rzhetsky, Andrey},
  title     = {Mining biomedical texts for disease-related pathways},
  booktitle = {Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology},
  month     = {June},
  year      = {2006},
  address   = {New York, New York},
  publisher = {Association for Computational Linguistics},
  pages     = {81},
  url       = {http://www.aclweb.org/anthology/W/W06/W06-1711}
}

@InProceedings{schuman-bergler:2006:BioNLP,
  author    = {Schuman, Jonathan  and  Bergler, Sabine},
  title     = {Postnominal Prepositional Phrase Attachment in Proteomics},
  booktitle = {Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology},
  month     = {June},
  year      = {2006},
  address   = {New York, New York},
  publisher = {Association for Computational Linguistics},
  pages     = {82--89},
  url       = {http://www.aclweb.org/anthology/W/W06/W06-1712}
}

@InProceedings{bergler-EtAl:2006:BioNLP,
  author    = {Bergler, Sabine  and  Schuman, Jonathan  and  Dubuc, Julien  and  Lebedev, Alexandr},
  title     = {BioKI:Enzymes - an adaptable system to locate low-frequency information in full-text proteomics articles},
  booktitle = {Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology},
  month     = {June},
  year      = {2006},
  address   = {New York, New York},
  publisher = {Association for Computational Linguistics},
  pages     = {91--92},
  url       = {http://www.aclweb.org/anthology/W/W06/W06-1714}
}

@InProceedings{cohen:2006:BioNLP,
  author    = {Cohen, William},
  title     = {A Graph-Search Framework for GeneId Ranking},
  booktitle = {Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology},
  month     = {June},
  year      = {2006},
  address   = {New York, New York},
  publisher = {Association for Computational Linguistics},
  pages     = {93--95},
  url       = {http://www.aclweb.org/anthology/W/W06/W06-1715}
}

@InProceedings{gasperin:2006:BioNLP,
  author    = {Gasperin, Caroline},
  title     = {Semi-supervised anaphora resolution in biomedical texts},
  booktitle = {Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology},
  month     = {June},
  year      = {2006},
  address   = {New York, New York},
  publisher = {Association for Computational Linguistics},
  pages     = {96--103},
  url       = {http://www.aclweb.org/anthology/W/W06/W06-1716}
}

@InProceedings{goertzel-EtAl:2006:BioNLP,
  author    = {Goertzel, Ben  and  Pinto, Hugo  and  Heljakka, Ari  and  Ross, Michael  and  Pennachin, Cassio  and  Goertzel, Izabela},
  title     = {Using Dependency Parsing and Probabilistic Inference to Extract Relationships between Genes, Proteins and Malignancies Implicit Among Multiple Biomedical Research Abstracts},
  booktitle = {Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology},
  month     = {June},
  year      = {2006},
  address   = {New York, New York},
  publisher = {Association for Computational Linguistics},
  pages     = {104--111},
  url       = {http://www.aclweb.org/anthology/W/W06/W06-1717}
}

@InProceedings{gu:2006:BioNLP,
  author    = {Gu, Baohua},
  title     = {Recognizing Nested Named Entities in GENIA corpus},
  booktitle = {Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology},
  month     = {June},
  year      = {2006},
  address   = {New York, New York},
  publisher = {Association for Computational Linguistics},
  pages     = {112--113},
  url       = {http://www.aclweb.org/anthology/W/W06/W06-1718}
}

@InProceedings{jiampojamarn-kondrak-cherry:2006:BioNLP,
  author    = {Jiampojamarn, Sittichai  and  Kondrak, Grzegorz  and  Cherry, Colin},
  title     = {Biomedical Term Recognition with the Perceptron HMM Algorithm},
  booktitle = {Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology},
  month     = {June},
  year      = {2006},
  address   = {New York, New York},
  publisher = {Association for Computational Linguistics},
  pages     = {114--115},
  url       = {http://www.aclweb.org/anthology/W/W06/W06-1719}
}

@InProceedings{johnson-EtAl:2006:BioNLP,
  author    = {Johnson, Helen L.  and  Baumgartner, Jr., William A.  and  Krallinger, Martin  and  Cohen, K. Bretonnel  and  Hunter, Lawrence},
  title     = {Refactoring Corpora},
  booktitle = {Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology},
  month     = {June},
  year      = {2006},
  address   = {New York, New York},
  publisher = {Association for Computational Linguistics},
  pages     = {116--117},
  url       = {http://www.aclweb.org/anthology/W/W06/W06-1720}
}

@InProceedings{miller-EtAl:2006:BioNLP,
  author    = {Miller, John E.  and  Bloodgood, Michael  and  Torii, Manabu  and  Vijay-Shanker, K.},
  title     = {Rapid Adaptation of POS Tagging for Domain Specific Uses},
  booktitle = {Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology},
  month     = {June},
  year      = {2006},
  address   = {New York, New York},
  publisher = {Association for Computational Linguistics},
  pages     = {118--119},
  url       = {http://www.aclweb.org/anthology/W/W06/W06-1721}
}

@InProceedings{nielsen:2006:BioNLP,
  author    = {Nielsen, Leif Arda},
  title     = {Extracting Protein-Protein interactions using simple contextual features},
  booktitle = {Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology},
  month     = {June},
  year      = {2006},
  address   = {New York, New York},
  publisher = {Association for Computational Linguistics},
  pages     = {120--121},
  url       = {http://www.aclweb.org/anthology/W/W06/W06-1722}
}

@InProceedings{oberoi-struble-sugg:2006:BioNLP,
  author    = {Oberoi, Meeta  and  Struble, Craig A.  and  Sugg, Sonia L.},
  title     = {Identifying Experimental Techniques in Biomedical Literature},
  booktitle = {Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology},
  month     = {June},
  year      = {2006},
  address   = {New York, New York},
  publisher = {Association for Computational Linguistics},
  pages     = {122--123},
  url       = {http://www.aclweb.org/anthology/W/W06/W06-1723}
}

@InProceedings{rosemblat-graham:2006:BioNLP,
  author    = {Rosemblat, Graciela  and  Graham, Laurel},
  title     = {A Pragmatic Approach to Summary Extraction in Clinical Trials},
  booktitle = {Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology},
  month     = {June},
  year      = {2006},
  address   = {New York, New York},
  publisher = {Association for Computational Linguistics},
  pages     = {124--125},
  url       = {http://www.aclweb.org/anthology/W/W06/W06-1724}
}

@InProceedings{sautter-bohm:2006:BioNLP,
  author    = {Sautter, Guido  and  B\"{o}hm, Klemens},
  title     = {The Difficulties of Taxonomic Name Extraction and a Solution},
  booktitle = {Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology},
  month     = {June},
  year      = {2006},
  address   = {New York, New York},
  publisher = {Association for Computational Linguistics},
  pages     = {126--133},
  url       = {http://www.aclweb.org/anthology/W/W06/W06-1725}
}

@InProceedings{schwartz-hearst:2006:BioNLP,
  author    = {Schwartz, Ariel S.  and  Hearst, Marti},
  title     = {Summarizing Key Concepts using Citation Sentences},
  booktitle = {Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology},
  month     = {June},
  year      = {2006},
  address   = {New York, New York},
  publisher = {Association for Computational Linguistics},
  pages     = {134--135},
  url       = {http://www.aclweb.org/anthology/W/W06/W06-1726}
}

@InProceedings{tateisi-tsuruoka-tsujii:2006:BioNLP,
  author    = {Tateisi, Yuka  and  Tsuruoka, Yoshimasa  and  Tsujii, Jun'ichi},
  title     = {Subdomain adaptation of a POS tagger with a small corpus},
  booktitle = {Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology},
  month     = {June},
  year      = {2006},
  address   = {New York, New York},
  publisher = {Association for Computational Linguistics},
  pages     = {136--137},
  url       = {http://www.aclweb.org/anthology/W/W06/W06-1727}
}

@InProceedings{vlachos-gasperin:2006:BioNLP,
  author    = {Vlachos, Andreas  and  Gasperin, Caroline},
  title     = {Bootstrapping and Evaluating Named Entity Recognition in the Biomedical Domain},
  booktitle = {Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology},
  month     = {June},
  year      = {2006},
  address   = {New York, New York},
  publisher = {Association for Computational Linguistics},
  pages     = {138--145},
  url       = {http://www.aclweb.org/anthology/W/W06/W06-1728}
}