W. John Wilbur

Sun Kim, Dongseop Kwon, Soo-Yong Shin, W. John Wilbur: PIE the search: searching PubMed literature for protein interaction information. Bioinformatics 28(4): 597-598 (2012)

Won Kim, Lana Yeganova, Donald C. Comeau, W. John Wilbur: Identifying well-formed biomedical phrases in MEDLINE® text. Journal of Biomedical Informatics 45(6): 1035-1041 (2012)

Eric W. Sayers, Tanya Barrett, Dennis A. Benson, Evan Bolton, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Scott Federhen, Michael Feolo, Ian M. Fingerman, Lewis Y. Geer, Wolfgang Helmberg, Yuri Kapustin, Sergey Krasnov, David Landsman, David J. Lipman, Zhiyong Lu, Thomas L. Madden, Tom Madej, Donna R. Maglott, Aron Marchler-Bauer, Vadim Miller, Ilene Karsch-Mizrachi, James Ostell, Anna R. Panchenko, Lon Phan, Kim D. Pruitt, Gregory D. Schuler, Edwin Sequeira, Stephen T. Sherry, Martin Shumway, Karl Sirotkin, Douglas J. Slotta, Alexandre Souvorov, Grigory Starchenko, Tatiana A. Tatusova, Lukas Wagner, Yanli Wang, W. John Wilbur, Eugene Yaschenko, Jian Ye: Database resources of the National Center for Biotechnology Information. Nucleic Acids Research 40(Database-Issue): 13-25 (2012)

Aurélie Névéol, W. John Wilbur, Zhiyong Lu: Extraction of data deposition statements from the literature: a method for automatically tracking research results. Bioinformatics 27(23): 3306-3312 (2011)

W. John Wilbur, Won Kim: Improving a gold standard: treating human relevance judgments of MEDLINE document pairs. BMC Bioinformatics 12(S-3): S5 (2011)

Lana Yeganova, Donald C. Comeau, W. John Wilbur: Machine learning with naturally labeled data for identifying abbreviation definitions. BMC Bioinformatics 12(S-3): S6 (2011)

Cecilia N. Arighi, Zhiyong Lu, Martin Krallinger, Kevin Bretonnel Cohen, W. John Wilbur, Alfonso Valencia, Lynette Hirschman, Cathy H. Wu: Overview of the BioCreative III Workshop. BMC Bioinformatics 12(S-8): S1 (2011)

Zhiyong Lu, Hung-Yu Kao, Chih-Hsuan Wei, Minlie Huang, Jingchen Liu, Cheng-Ju Kuo, Chun-Nan Hsu, Richard Tzong-Han Tsai, Hong-Jie Dai, Naoaki Okazaki, Han-Cheol Cho, Martin Gerner, Illés Solt, Shashank Agarwal, Feifan Liu, Dina Vishnyakova, Patrick Ruch, Martin Romacker, Fabio Rinaldi, Sanmitra Bhattacharya, Padmini Srinivasan, Hongfang Liu, Manabu Torii, Sérgio Matos, David Campos, Karin Verspoor, Kevin M. Livingston, W. John Wilbur: The gene normalization task in BioCreative III. BMC Bioinformatics 12(S-8): S2 (2011)

Martin Krallinger, Miguel Vazquez, Florian Leitner, David Salgado, Andrew Chatr-aryamontri, Andrew G. Winter, Livia Perfetto, Leonardo Briganti, Luana Licata, Marta Iannuccelli, Luisa Castagnoli, Gianni Cesareni, Mike Tyers, Gerold Schneider, Fabio Rinaldi, Robert Leaman, Graciela Gonzalez, Sérgio Matos, Sun Kim, W. John Wilbur, Luis Rocha, Hagit Shatkay, Ashish V. Tendulkar, Shashank Agarwal, Feifan Liu, Xinglong Wang, Rafal Rak, Keith Noto, Charles Elkan, Zhiyong Lu: The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. BMC Bioinformatics 12(S-8): S3 (2011)

Sun Kim, W. John Wilbur: Classifying protein-protein interaction articles using word and syntactic features. BMC Bioinformatics 12(S-8): S9 (2011)

Eric W. Sayers, Tanya Barrett, Dennis A. Benson, Evan Bolton, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Scott Federhen, Michael Feolo, Ian M. Fingerman, Lewis Y. Geer, Wolfgang Helmberg, Yuri Kapustin, David Landsman, David J. Lipman, Zhiyong Lu, Thomas L. Madden, Tom Madej, Donna R. Maglott, Aron Marchler-Bauer, Vadim Miller, Ilene Mizrachi, James Ostell, Anna R. Panchenko, Lon Phan, Kim D. Pruitt, Gregory D. Schuler, Edwin Sequeira, Stephen T. Sherry, Martin Shumway, Karl Sirotkin, Douglas J. Slotta, Alexandre Souvorov, Grigory Starchenko, Tatiana A. Tatusova, Lukas Wagner, Yanli Wang, W. John Wilbur, Eugene Yaschenko, Jian Ye: Database resources of the National Center for Biotechnology Information. Nucleic Acids Research 39(Database-Issue): 38-51 (2011)

Sun Kim, W. John Wilbur: An EM Clustering Algorithm which Produces a Dual Representation. ICMLA (2) 2011: 90-95

Lana Yeganova, Won Kim, Donald C. Comeau, W. John Wilbur: Comparison of Two Methods for Finding Biomedical Categories in Medline. ICMLA (2) 2011: 96-99

Larry H. Smith, W. John Wilbur: Finding related sentence pairs in MEDLINE. Inf. Retr. 13(6): 601-617 (2010)

Eric W. Sayers, Tanya Barrett, Dennis A. Benson, Evan Bolton, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Scott Federhen, Michael Feolo, Lewis Y. Geer, Wolfgang Helmberg, Yuri Kapustin, David Landsman, David J. Lipman, Zhiyong Lu, Thomas L. Madden, Tom Madej, Donna R. Maglott, Aron Marchler-Bauer, Vadim Miller, Ilene Mizrachi, James Ostell, Anna R. Panchenko, Kim D. Pruitt, Gregory D. Schuler, Edwin Sequeira, Stephen T. Sherry, Martin Shumway, Karl Sirotkin, Douglas J. Slotta, Alexandre Souvorov, Grigory Starchenko, Tatiana A. Tatusova, Lukas Wagner, Yanli Wang, W. John Wilbur, Eugene Yaschenko, Jian Ye: Database resources of the National Center for Biotechnology Information. Nucleic Acids Research 38(Database-Issue): 5-16 (2010)

Won Kim, W. John Wilbur: Improving a Gold Standard: Treating Human Relevance Judgments of MEDLINE Document Pairs. ICMLA 2010: 491-498

Lana Yeganova, Donald C. Comeau, W. John Wilbur: Identifying Abbreviation Definitions Machine Learning with Naturally Labeled Data. ICMLA 2010: 499-505

Zhiyong Lu, Natalie Xie, W. John Wilbur: Identifying related journals through log analysis. Bioinformatics 25(22): 3038-3039 (2009)

Zhiyong Lu, Won Kim, W. John Wilbur: Evaluation of query expansion using MeSH in PubMed. Inf. Retr. 12(1): 69-80 (2009)

Jimmy J. Lin, W. John Wilbur: Modeling actions of PubMed users with n-gram language models. Inf. Retr. 12(4): 487-503 (2009)

W. John Wilbur, Won Kim: The ineffectiveness of within-document term frequency in text classification. Inf. Retr. 12(5): 509-525 (2009)

Zhiyong Lu, Won Kim, W. John Wilbur: Viewpoint Paper: Evaluating Relevance Ranking Strategies for MEDLINE Retrieval. JAMIA 16(1): 32-36 (2009)

Lana Yeganova, Donald C. Comeau, Won Kim, W. John Wilbur: How to interpret PubMed queries and why it matters. JASIST 60(2): 264-274 (2009)

Zhiyong Lu, W. John Wilbur: Improving accuracy for identifying related PubMed queries by an integrated approach. Journal of Biomedical Informatics 42(5): 831-838 (2009)

Lawrence H. Smith, W. John Wilbur: The value of parsing as feature generation for gene mention recognition. Journal of Biomedical Informatics 42(5): 895-904 (2009)

Andrey Rzhetsky, Hagit Shatkay, W. John Wilbur: How to Get the Most out of Your Curation Effort. PLoS Computational Biology 5(5) (2009)

G. Craig Murray, Jimmy J. Lin, W. John Wilbur, Zhiyong Lu: Users' adjustments to unsuccessful queries in biomedical search. JCDL 2009: 433-434

Hagit Shatkay, Fengxia Pan, Andrey Rzhetsky, W. John Wilbur: Multi-dimensional classification of biomedical text: Toward automated, practical provision of high-utility text to diverse users. Bioinformatics 24(18): 2086-2093 (2008)

Sunghwan Sohn, Donald C. Comeau, Won Kim, W. John Wilbur: Abbreviation definition identification based on automatic precision estimates. BMC Bioinformatics 9 (2008)

Jimmy J. Lin, Michael DiCuccio, Vahan Grigoryan, W. John Wilbur: Navigating information spaces: A case study of related article search in PubMed. Inf. Process. Manage. 44(5): 1771-1783 (2008)

Sunghwan Sohn, Won Kim, Donald C. Comeau, W. John Wilbur: Research Paper: Optimal Training Sets for Bayesian Prediction of MeSH^® Assignment. JAMIA 15(4): 546-553 (2008)

Rezarta Islamaj Dogan, Lise Getoor, W. John Wilbur, Stephen M. Mount: Features generated for computational splice-site prediction correspond to functional elements. BMC Bioinformatics 8 (2007)

Jimmy J. Lin, W. John Wilbur: PubMed related articles: a probabilistic topic-based model for content similarity. BMC Bioinformatics 8 (2007)

Jimmy J. Lin, W. John Wilbur: Syntactic sentence compression in the biomedical domain: facilitating access to related articles. Inf. Retr. 10(4-5): 393-414 (2007)

Hong Yu, Won Kim, Vasileios Hatzivassiloglou, W. John Wilbur: Using MEDLINE as a knowledge source for disambiguating abbreviations and acronyms in full-text biomedical journal articles. Journal of Biomedical Informatics 40(2): 150-159 (2007)

Rezarta Islamaj Dogan, Lise Getoor, W. John Wilbur, Stephen M. Mount: SplicePort - An interactive splice-site analysis tool. Nucleic Acids Research 35(Web-Server-Issue): 285-291 (2007)

Rezarta Islamaj Dogan, Lise Getoor, W. John Wilbur: Characterizing RNA Secondary-Structure Features and Their Effects on Splice-Site Prediction. ICDM Workshops 2007: 89-94

Dina Demner-Fushman, Susanne M. Humphrey, Nicholas C. Ide, Russell F. Loane, James G. Mork, Patrick Ruch, Miguel E. Ruiz, Lawrence H. Smith, W. John Wilbur, Alan R. Aronson: Combining Resources to Find Answers to Biomedical Questions. TREC 2007

W. John Wilbur, Andrey Rzhetsky, Hagit Shatkay: New directions in biomedical text annotation: definitions, guidelines and corpus construction. BMC Bioinformatics 7: 356 (2006)

W. John Wilbur, Won Kim, Natalie Xie: Spelling correction in the PubMed search engine. Inf. Retr. 9(5): 543-564 (2006)

Lawrence H. Smith, Thomas C. Rindflesch, W. John Wilbur: The importance of the lexicon in tagging biological text. Natural Language Engineering 12(4): 335-351 (2006)

Hong Yu, Won Kim, Vasileios Hatzivassiloglou, W. John Wilbur: A large scale, corpus-based approach for automatically disambiguating biomedical abbreviations. ACM Trans. Inf. Syst. 24(3): 380-404 (2006)

Rezarta Islamaj Dogan, Lise Getoor, W. John Wilbur: A Feature Generation Algorithm for Sequences with Application to Splice-Site Prediction. PKDD 2006: 553-560

Dina Demner-Fushman, Susanne M. Humphrey, Nicholas C. Ide, Russell F. Loane, Patrick Ruch, Miguel E. Ruiz, Lawrence H. Smith, Lorraine K. Tanabe, W. John Wilbur, Alan R. Aronson: Finding Relevant Passages in Scientific Articles: Fusion of Automatic Approaches vs. an Interactive Team Effort. TREC 2006

Lorraine K. Tanabe, Natalie Xie, Lynne H. Thom, Wayne Matten, W. John Wilbur: GENETAG: a tagged corpus for gene/protein named entity recognition. BMC Bioinformatics 6(S-1) (2005)

W. John Wilbur, Lana Yeganova, Won Kim: The Synergy Between PAV and AdaBoost. Machine Learning 61(1-3): 71-103 (2005)

Alan R. Aronson, Dina Demner-Fushman, Susanne M. Humphrey, Jimmy J. Lin, Patrick Ruch, Miguel E. Ruiz, Lawrence H. Smith, Lorraine K. Tanabe, W. John Wilbur, Hongfang Liu: Fusion of Knowledge-Intensive and Statistical Approaches for Retrieving and Annotating Textual Genomics Documents. TREC 2005

Lawrence H. Smith, Thomas C. Rindflesch, W. John Wilbur: MedPost: a part-of-speech tagger for bioMedical text. Bioinformatics 20(14): 2320-2321 (2004)

Lana Yeganova, Lawrence H. Smith, W. John Wilbur: Identification of related gene/protein names based on an HMM of name variations. Computational Biology and Chemistry 28(2): 97-107 (2004)

Lawrence H. Smith, W. John Wilbur: Retrieving definitional content for ontology development. Computational Biology and Chemistry 28(5-6): 387-391 (2004)

Donald C. Comeau, W. John Wilbur: Non-word identification or spell checking without a dictionary. JASIST 55(2): 169-177 (2004)

Lorraine K. Tanabe, W. John Wilbur: Generation of a Large Gene/protein Lexicon by Morphological Pattern Analysis. J. Bioinformatics and Computational Biology 1(4): 611-626 (2004)

Andrey Rzhetsky, Ivan Iossifov, Tomohiro Koike, Michael Krauthammer, Pauline Kra, Mitzi Morris, Hong Yu, Pablo Ariel Duboué, Wubin Weng, W. John Wilbur: GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. Journal of Biomedical Informatics 37(1): 43-53 (2004)

Hong Yu, Won Kim, Vasileios Hatzivassiloglou, W. John Wilbur: Using MEDLINE as a Knowledge Source for Disambiguating Abbreviations in Full-Text Biomedical Journal Articles. CBMS 2004: 27-

Alan R. Aronson, Susanne M. Humphrey, Nicholas C. Ide, Won Kim, Russell R. Loane, James G. Mork, Lawrence H. Smith, Lorraine K. Tanabe, W. John Wilbur, Natalie Xie, Dina Demner-Fushman, Hongfang Liu: Knowledge-Intensive and Statistical Approaches to the Retrieval and Annotation of Genomics MEDLINE Citations. TREC 2004

Lawrence H. Smith, Lana Yeganova, W. John Wilbur: Hidden Markov models and optimized sequence alignments. Computational Biology and Chemistry 27(1): 77-84 (2003)

Lorraine K. Tanabe, W. John Wilbur: Tagging gene and protein names in biomedical text. Bioinformatics 18(8): 1124-1132 (2002)

Hong Yu, Vasileios Hatzivassiloglou, Andrey Rzhetsky, W. John Wilbur: Automatically identifying gene/protein terms in MEDLINE abstracts. Journal of Biomedical Informatics 35(5-6): 322-330 (2002)

Lorraine K. Tanabe, W. John Wilbur: Tagging gene and protein names in full text articles. ACL Workshop on Natural Language Processing in the Biomedical Domain 2002: 9-13

W. John Wilbur: A Thematic Analysis of the AIDS Literature. Pacific Symposium on Biocomputing 2002: 386-397

Won Kim, W. John Wilbur: Amino Acid Residue Environments and Predictions of Residue Type. Computers & Chemistry 25(4): 411-422 (2001)

Won Kim, W. John Wilbur: Corpus-based statistical screening for content-bearing terms. JASIST 52(3): 247-259 (2001)

W. John Wilbur, Andrew F. Neuwald: A Theory of Information with Special Application to Search Problems. Computers & Chemistry 24(1): 33-42 (2000)

Won Kim, W. John Wilbur: Research Paper: Corpus-based Statistical Screening for Phrase Identification. JAMIA 7(5): 499-511 (2000)

Hagit Shatkay, W. John Wilbur: Finding Themes in Medline Documents: Probabilistic Similarity Search. ADL 2000: 183-192

Hagit Shatkay, Stephen Edwards, W. John Wilbur, Mark Boguski: Genes, Themes, and Microarrays: Using Information Retrieval for Large-Scale Gene Analysis. ISMB 2000: 317-328

W. John Wilbur: A Comparison of Group and Individual Performance Among Subject Experts and Untrained Workers at the Document Retrieval Task. JASIS 49(6): 517-529 (1998)

W. John Wilbur: The Knowledge in Multiple Human Relevance Judgments. ACM Trans. Inf. Syst. 16(2): 101-126 (1998)

W. John Wilbur: Human Subjectivity and Performance Limits in Document Retrieval. Inf. Process. Manage. 32(5): 515-527 (1996)

Yiming Yang, W. John Wilbur: Using Corpus Statistics to Remove Redundant Words in Text Categorization. JASIS 47(5): 357-369 (1996)

W. John Wilbur, Leona Coffee: The Effectiveness of Document Neighboring in Search Enhancement. Inf. Process. Manage. 30(2): 253-266 (1994)

W. John Wilbur: Retrieval Testing with Hypergeometric Document Models. JASIS 44(6): 340-351 (1993)

W. John Wilbur: An information measure of retrieval performance. Inf. Syst. 17(4): 283-298 (1992)

W. John Wilbur: Retrieval Testing by the Comparison of Statistically Independent Retrieval Methods. JASIS 43(5): 358-370 (1992)

David J. Lipman, W. John Wilbur, Temple F. Smith, Michael S. Waterman: On the statistical significance of nucleic acid similarities. Nucleic Acids Research 12(1): 215-226 (1984)