On the statistical significance of nucleic acid similarities. - David J. Lipman; W. John Wilbur; Temple F. Smith; Michael S. Waterman (Nucleic Acids Res., 1984)

An information measure of retrieval performance. - W. John Wilbur (Inf. Syst., 1992)

Retrieval Testing by the Comparison of Statistically Independent Retrieval Methods. - W. John Wilbur (J. Am. Soc. Inf. Sci., 1992)

The automatic identification of stop words. - W. John Wilbur; Karl Sirotkin (J. Inf. Sci., 1992)

Retrieval Testing with Hypergeometric Document Models. - W. John Wilbur (J. Am. Soc. Inf. Sci., 1993)

The Effectiveness of Document Neighboring in Search Enhancement. - W. John Wilbur; Leona Coffee (Inf. Process. Manag., 1994)

Non-parametric significance tests of retrieval performance comparisons. - W. John Wilbur (J. Inf. Sci., 1994)

An analysis of statistical term strength and its use in the indexing and retrieval of molecular biology texts. - W. John Wilbur; Yiming Yang (Comput. Biol. Medicine, 1996)

Human Subjectivity and Performance Limits in Document Retrieval. - W. John Wilbur (Inf. Process. Manag., 1996)

Using Corpus Statistics to Remove Redundant Words in Text Categorization. - Yiming Yang; W. John Wilbur (J. Am. Soc. Inf. Sci., 1996)

A Comparison of Group and Individual Performance Among Subject Experts and Untrained Workers at the Document Retrieval Task. - W. John Wilbur (J. Am. Soc. Inf. Sci., 1998)

The Knowledge in Multiple Human Relevance Judgments. - W. John Wilbur (ACM Trans. Inf. Syst., 1998)

Automated Assignment of Medical Subject Headings. - Stuart J. Nelson; Alan R. Aronson; Tamas E. Doszkocs; W. John Wilbur; Olivier Bodenreider; H. Florence Chang; James G. Mork; Alexa T. McCray (AMIA, 1999)

Analysis of biomedical text for chemical names: a comparison of three methods. - W. John Wilbur; George F. Hazard Jr.; Guy Divita; James G. Mork; Alan R. Aronson; Allen C. Browne (AMIA, 1999)

Finding Themes in Medline Documents: Probabilistic Similarity Search. - Hagit Shatkay; W. John Wilbur (ADL, 2000)

The NLM Indexing Initiative. - Alan R. Aronson; Olivier Bodenreider; Florence Chang; Susanne M. Humphrey; James G. Mork; Stuart J. Nelson; Thomas C. Rindflesch; W. John Wilbur (AMIA, 2000)

Boosting naïve Bayesian learning on a large subset of MEDLINE. - W. John Wilbur (AMIA, 2000)

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

A Theory of Information with Special Application to Search Problems. - W. John Wilbur; Andrew F. Neuwald (Comput. Chem., 2000)

Research Paper: Corpus-based Statistical Screening for Phrase Identification. - Won Kim 003; W. John Wilbur (J. Am. Medical Informatics Assoc., 2000)

Automatic MeSH term assignment and quality assessment. - Won Kim 003; Alan R. Aronson; W. John Wilbur (AMIA, 2001)

Amino Acid Residue Environments and Predictions of Residue Type. - Won Kim 003; W. John Wilbur (Comput. Chem., 2001)

Corpus-based statistical screening for content-bearing terms. - Won Kim 003; W. John Wilbur (J. Assoc. Inf. Sci. Technol., 2001)

Global term weights for document retrieval learned from TREC data. - W. John Wilbur (J. Inf. Sci., 2001)

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

DNA splice site detection: a comparison of specific and general methods. - Won Kim 003; W. John Wilbur (AMIA, 2002)

Automatic extraction of gene and protein synonyms from MEDLINE and journal articles. - Hong Yu 001; Vasileios Hatzivassiloglou; Carol Friedman; Andrey Rzhetsky; W. John Wilbur (AMIA, 2002)

A Thematic Analysis of the AIDS Literature. - W. John Wilbur (Pacific Symposium on Biocomputing, 2002)

Tagging gene and protein names in biomedical text. - Lorraine K. Tanabe; W. John Wilbur (Bioinform., 2002)

Automatically identifying gene/protein terms in MEDLINE abstracts. - Hong Yu 001; Vasileios Hatzivassiloglou; Andrey Rzhetsky; W. John Wilbur (J. Biomed. Informatics, 2002)

The Dimensions of Indexing. - W. John Wilbur; Won Kim 003 (AMIA, 2003)

Hidden Markov models and optimized sequence alignments. - Lawrence H. Smith; Lana Yeganova; W. John Wilbur (Comput. Biol. Chem., 2003)

Using MEDLINE as a Knowledge Source for Disambiguating Abbreviations in Full-Text Biomedical Journal Articles. - Hong Yu 001; Won Kim 003; Vasileios Hatzivassiloglou; W. John Wilbur (CBMS, 2004)

Knowledge-Intensive and Statistical Approaches to the Retrieval and Annotation of Genomics MEDLINE Citations. - Alan R. Aronson; Susanne M. Humphrey; Nicholas C. Ide; Won Kim 003; Russell F. Loane; James G. Mork; Lawrence H. Smith; Lorraine K. Tanabe; W. John Wilbur; Natalie Xie; Dina Demner-Fushman; Hongfang Liu (TREC, 2004)

MedPost: a part-of-speech tagger for bioMedical text. - Lawrence H. Smith; Thomas C. Rindflesch; W. John Wilbur (Bioinform., 2004)

Retrieving definitional content for ontology development. - Lawrence H. Smith; W. John Wilbur (Comput. Biol. Chem., 2004)

Identification of related gene/protein names based on an HMM of name variations. - Lana Yeganova; Lawrence H. Smith; W. John Wilbur (Comput. Biol. Chem., 2004)

Non-word identification or spell checking without a dictionary. - Donald C. Comeau; W. John Wilbur (J. Assoc. Inf. Sci. Technol., 2004)

Generation of a Large Gene/protein Lexicon by Morphological Pattern Analysis. - Lorraine K. Tanabe; W. John Wilbur (J. Bioinform. Comput. Biol., 2004)

GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. - Andrey Rzhetsky; Ivan Iossifov; Tomohiro Koike; Michael Krauthammer; Pauline Kra; Mitzi Morris; Hong Yu 001; Pablo Ariel Duboué; Wubin Weng; W. John Wilbur (J. Biomed. Informatics, 2004)

A Strategy for Assigning New Concepts in the MEDLINE Database. - Won Kim 003; W. John Wilbur (AMIA, 2005)

MedTag: A Collection of Biomedical Annotations. - Lawrence H. Smith; Lorraine K. Tanabe; Thomas C. Rindflesch; W. John Wilbur (LBLODMBS@IDMB, 2005)

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

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

The Synergy Between PAV and AdaBoost. - W. John Wilbur; Lana Yeganova; Won Kim 003 (Mach. Learn., 2005)

SemCat: Semantically Categorized Entities for Genomics. - Lorraine K. Tanabe; Lynne H. Thom; Wayne Matten; Donald C. Comeau; W. John Wilbur (AMIA, 2006)

A Priority Model for Named Entities. - Lorraine K. Tanabe; W. John Wilbur (BioNLP@NAACL-HLT, 2006)

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

Finding Relevant Passages in Scientific Articles: Fusion of Automatic Approaches vs. an Interactive Team Effort. - 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 (TREC, 2006)

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

Spelling correction in the PubMed search engine. - W. John Wilbur; Won Kim 003; Natalie Xie (Inf. Retr., 2006)

The importance of the lexicon in tagging biological text. - Lawrence H. Smith; Thomas C. Rindflesch; W. John Wilbur (Nat. Lang. Eng., 2006)

A large scale, corpus-based approach for automatically disambiguating biomedical abbreviations. - Hong Yu 001; Won Kim 003; Vasileios Hatzivassiloglou; W. John Wilbur (ACM Trans. Inf. Syst., 2006)

Unsupervised Learning of the Morpho-Semantic Relationship in MEDLINE. - W. John Wilbur (BioNLP@ACL, 2007)

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

Combining Resources to Find Answers to Biomedical Questions. - 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 (TREC, 2007)

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

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

Syntactic sentence compression in the biomedical domain: facilitating access to related articles. - Jimmy Lin; W. John Wilbur (Inf. Retr., 2007)

Using MEDLINE as a knowledge source for disambiguating abbreviations and acronyms in full-text biomedical journal articles. - Hong Yu 001; Won Kim 003; Vasileios Hatzivassiloglou; W. John Wilbur (J. Biomed. Informatics, 2007)

SplicePort - An interactive splice-site analysis tool. - Rezarta Islamaj Dogan; Lise Getoor; W. John Wilbur; Stephen M. Mount (Nucleic Acids Res., 2007)

Evaluating Relevance Ranking Strategies for MEDLINE Retrieval. - Zhiyong Lu; Won Kim 003; W. John Wilbur (AMIA, 2008)

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

Abbreviation definition identification based on automatic precision estimates. - Sunghwan Sohn; Donald C. Comeau; Won Kim 003; W. John Wilbur (BMC Bioinform., 2008)

Navigating information spaces: A case study of related article search in PubMed. - Jimmy Lin; Michael DiCuccio; Vahan Grigoryan; W. John Wilbur (Inf. Process. Manag., 2008)

Research Paper: Optimal Training Sets for Bayesian Prediction of MeSH® Assignment. - Sunghwan Sohn; Won Kim 003; Donald C. Comeau; W. John Wilbur (J. Am. Medical Informatics Assoc., 2008)

Finding Query Suggestions for PubMed. - Zhiyong Lu; W. John Wilbur; Johanna R. McEntyre; Alexey Iskhakov; Lee Szilagyi (AMIA, 2009)

Exploring Two Biomedical Text Genres for Disease Recognition. - Aurélie Névéol; Won Kim 003; W. John Wilbur; Zhiyong Lu (BioNLP@HLT-NAACL, 2009)

Users' adjustments to unsuccessful queries in biomedical search. - G. Craig Murray; Jimmy Lin; W. John Wilbur; Zhiyong Lu (JCDL, 2009)

Identifying related journals through log analysis. - Zhiyong Lu; Natalie Xie; W. John Wilbur (Bioinform., 2009)

Modeling actions of PubMed users with n-gram language models. - Jimmy Lin; W. John Wilbur (Inf. Retr., 2009)

Evaluation of query expansion using MeSH in PubMed. - Zhiyong Lu; Won Kim 003; W. John Wilbur (Inf. Retr., 2009)

The ineffectiveness of within-document term frequency in text classification. - W. John Wilbur; Won Kim 003 (Inf. Retr., 2009)

Viewpoint Paper: Evaluating Relevance Ranking Strategies for MEDLINE Retrieval. - Zhiyong Lu; Won Kim 003; W. John Wilbur (J. Am. Medical Informatics Assoc., 2009)

How to interpret PubMed queries and why it matters. - Lana Yeganova; Donald C. Comeau; Won Kim 003; W. John Wilbur (J. Assoc. Inf. Sci. Technol., 2009)

Improving accuracy for identifying related PubMed queries by an integrated approach. - Zhiyong Lu; W. John Wilbur (J. Biomed. Informatics, 2009)

The value of parsing as feature generation for gene mention recognition. - Lawrence H. Smith; W. John Wilbur (J. Biomed. Informatics, 2009)

How to Get the Most out of Your Curation Effort. - Andrey Rzhetsky; Hagit Shatkay; W. John Wilbur (PLoS Comput. Biol., 2009)

Identifying Abbreviation Definitions Machine Learning with Naturally Labeled Data. - Lana Yeganova; Donald C. Comeau; W. John Wilbur (ICMLA, 2010)

Finding related sentence pairs in MEDLINE. - Larry H. Smith; W. John Wilbur (Inf. Retr., 2010)

Database resources of the National Center for Biotechnology Information. - 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; et al. (Nucleic Acids Res., 2010)

Automatic extraction of data deposition statements: where do the research results go? - Aurélie Névéol; W. John Wilbur; Zhiyong Lu (BioNLP@ACL, 2011)

Text Mining Techniques for Leveraging Positively Labeled Data. - Lana Yeganova; Donald C. Comeau; Won Kim 003; W. John Wilbur (BioNLP@ACL, 2011)

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

Comparison of Two Methods for Finding Biomedical Categories in Medline. - Lana Yeganova; Won Kim 003; Donald C. Comeau; W. John Wilbur (ICMLA (2), 2011)

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

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

Classifying protein-protein interaction articles using word and syntactic features. - Sun Kim; W. John Wilbur (BMC Bioinform., 2011)

The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. - 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; et al. (BMC Bioinform., 2011)

The gene normalization task in BioCreative III. - 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; et al. (BMC Bioinform., 2011)

Improving a gold standard: treating human relevance judgments of MEDLINE document pairs. - W. John Wilbur; Won Kim 003 (BMC Bioinform., 2011)

Machine learning with naturally labeled data for identifying abbreviation definitions. - Lana Yeganova; Donald C. Comeau; W. John Wilbur (BMC Bioinform., 2011)

Database resources of the National Center for Biotechnology Information. - 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; et al. (Nucleic Acids Res., 2011)

PROBE: Periodic Random Orbiter Algorithm for Machine Learning. - Larry H. Smith; Won Kim 003; W. John Wilbur (AAAI Fall Symposium: Information Retrieval and Knowledge Discovery in Biomedical Text, 2012)

Automatic Identification of Key Concepts in Large PubMed Retrievals. - Lana Yeganova; Vahan Grigoryan; Won Kim 003; W. John Wilbur (AAAI Fall Symposium: Information Retrieval and Knowledge Discovery in Biomedical Text, 2012)

Classifying Gene Sentences in Biomedical Literature by Combining High-Precision Gene Identifiers. - Sun Kim; Won Kim 003; Donald C. Comeau; W. John Wilbur (BioNLP@HLT-NAACL, 2012)

Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information. - Sun Kim; Won Kim 003; Chih-Hsuan Wei; Zhiyong Lu; W. John Wilbur (Database J. Biol. Databases Curation, 2012)

Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE. - Aurélie Névéol; W. John Wilbur; Zhiyong Lu (Database J. Biol. Databases Curation, 2012)

BioCreative-2012 Virtual Issue. - Cathy H. Wu; Cecilia N. Arighi; Kevin Bretonnel Cohen; Lynette Hirschman; Martin Krallinger; Zhiyong Lu; Carolyn J. Mattingly; Alfonso Valencia; Thomas C. Wiegers; W. John Wilbur (Database J. Biol. Databases Curation, 2012)

PIE the search: searching PubMed literature for protein interaction information. - Sun Kim; Dongseop Kwon; Soo-Yong Shin; W. John Wilbur (Bioinform., 2012)

Thematic clustering of text documents using an EM-based approach. - Sun Kim; W. John Wilbur (J. Biomed. Semant., 2012)

Finding biomedical categories in Medline®. - Lana Yeganova; Won Kim 003; Donald C. Comeau; W. John Wilbur (J. Biomed. Semant., 2012)

Identifying well-formed biomedical phrases in MEDLINE® text. - Won Kim 003; Lana Yeganova; Donald C. Comeau; W. John Wilbur (J. Biomed. Informatics, 2012)

Database resources of the National Center for Biotechnology Information. - 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; et al. (Nucleic Acids Res., 2012)

BioC: A Minimalist Approach to Interoperability for Biomedical Text Processing. - Donald C. Comeau; Rezarta Islamaj Dogan; W. John Wilbur (AMIA, 2013)

Generalizing an Approximate Subgraph Matching-based System to Extract Events in Molecular Biology and Cancer Genetics. - Haibin Liu; Karin Verspoor; Donald C. Comeau; Andrew MacKinlay; W. John Wilbur (BioNLP@ACL (Shared Task), 2013)

Extracting Biomedical Events and Modifications Using Subgraph Matching with Noisy Training Data. - Andrew MacKinlay; David Martínez 001; Antonio Jimeno-Yepes; Haibin Liu; W. John Wilbur; Karin Verspoor (BioNLP@ACL (Shared Task), 2013)

BioNLP Shared Task 2013: Supporting Resources. - Pontus Stenetorp; Wiktoria Golik; Thierry Hamon; Donald C. Comeau; Rezarta Islamaj Dogan; Haibin Liu; W. John Wilbur (BioNLP@ACL (Shared Task), 2013)

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task. - Cecilia N. Arighi; Ben Carterette; K. Bretonnel Cohen; Martin Krallinger; W. John Wilbur; Petra Fey; Robert J. Dodson; Laurel Cooper; Ceri E. Van Slyke; Wasila M. Dahdul; Paula M. Mabee; Donghui Li; et al. (Database J. Biol. Databases Curation, 2013)

BioC: a minimalist approach to interoperability for biomedical text processing. - Donald C. Comeau; Rezarta Islamaj Dogan; Paolo Ciccarese; Kevin Bretonnel Cohen; Martin Krallinger; Florian Leitner; Zhiyong Lu; Yifan Peng 002; Fabio Rinaldi 001; Manabu Torii; Alfonso Valencia; Karin Verspoor; et al. (Database J. Biol. Databases Curation, 2013)

Stochastic Gradient Descent and the Prediction of MeSH for PubMed Records. - W. John Wilbur; Won Kim 003 (AMIA, 2014)

BioCreative-IV virtual issue. - Cecilia N. Arighi; Cathy H. Wu; Kevin Bretonnel Cohen; Lynette Hirschman; Martin Krallinger; Alfonso Valencia; Zhiyong Lu; W. John Wilbur; Thomas C. Wiegers (Database J. Biol. Databases Curation, 2014)

BioC interoperability track overview. - Donald C. Comeau; Riza Theresa Batista-Navarro; Hong-Jie Dai; Rezarta Islamaj Dogan; Antonio Jimeno-Yepes; Ritu Khare; Zhiyong Lu; Hernani Marques; Carolyn J. Mattingly; Mariana L. Neves; Yifan Peng 002; Rafal Rak; et al. (Database J. Biol. Databases Curation, 2014)

Natural language processing pipelines to annotate BioC collections with an application to the NCBI disease corpus. - Donald C. Comeau; Haibin Liu; Rezarta Islamaj Dogan; W. John Wilbur (Database J. Biol. Databases Curation, 2014)

Finding abbreviations in biomedical literature: three BioC-compatible modules and four BioC-formatted corpora. - Rezarta Islamaj Dogan; Donald C. Comeau; Lana Yeganova; W. John Wilbur (Database J. Biol. Databases Curation, 2014)

Assisting manual literature curation for protein-protein interactions using BioQRator. - Dongseop Kwon; Sun Kim; Soo-Yong Shin; Andrew Chatr-aryamontri; W. John Wilbur (Database J. Biol. Databases Curation, 2014)

BioC implementations in Go, Perl, Python and Ruby. - Wanli Liu; Rezarta Islamaj Dogan; Dongseop Kwon; Hernani Marques; Fabio Rinaldi 001; W. John Wilbur; Donald C. Comeau (Database J. Biol. Databases Curation, 2014)

Retro: concept-based clustering of biomedical topical sets. - Lana Yeganova; Won Kim 003; Sun Kim; W. John Wilbur (Bioinform., 2014)

Author name disambiguation for PubMed. - Wanli Liu; Rezarta Islamaj Dogan; Sun Kim; Donald C. Comeau; Won Kim 003; Lana Yeganova; Zhiyong Lu; W. John Wilbur (J. Assoc. Inf. Sci. Technol., 2014)

Summarizing Topical Contents from PubMed Documents Using a Thematic Analysis. - Sun Kim; Lana Yeganova; W. John Wilbur (EMNLP, 2015)

Identifying named entities from PubMed®; for enriching semantic categories. - Sun Kim; Zhiyong Lu; W. John Wilbur (BMC Bioinform., 2015)

Extracting drug-drug interactions from literature using a rich feature-based linear kernel approach. - Sun Kim; Haibin Liu; Lana Yeganova; W. John Wilbur (J. Biomed. Informatics, 2015)

Optimizing graph-based patterns to extract biomedical events from the literature. - Haibin Liu; Karin Verspoor; Donald C. Comeau; Andrew D. MacKinlay; W. John Wilbur (BMC Bioinform., 2015)

PubTermVariants: biomedical term variants and their use for PubMed search. - Lana Yeganova; Won Kim 003; Sun Kim; Rezarta Islamaj Dogan; Wanli Liu; Donald C. Comeau; Zhiyong Lu; W. John Wilbur (BioNLP@ACL, 2016)

BioCconvert: A Conversion Tool Between BioC and PubAnnotation. - Donald C. Comeau; Rezarta Islamaj Dogan; Sun Kim; Chih-Hsuan Wei; W. John Wilbur; Zhiyong Lu (ICBO/BioCreative, 2016)

BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. - Sun Kim; Rezarta Islamaj Dogan; Andrew Chatr-aryamontri; Christie S. Chang; Rose Oughtred; Jennifer M. Rust; Riza Batista-Navarro; Jacob Carter; Sophia Ananiadou; Sérgio Matos; André Santos; David Campos 001; et al. (Database J. Biol. Databases Curation, 2016)

BioC viewer: a web-based tool for displaying and merging annotations in BioC. - Soo-Yong Shin; Sun Kim; W. John Wilbur; Dongseop Kwon (Database J. Biol. Databases Curation, 2016)

Meshable: searching PubMed abstracts by utilizing MeSH and MeSH-derived topical terms. - Sun Kim; Lana Yeganova; W. John Wilbur (Bioinform., 2016)

Bridging the Gap: a Semantic Similarity Measure between Queries and Documents. - Sun Kim; W. John Wilbur; Zhiyong Lu (CoRR, 2016)

The BioC-BioGRID corpus: full text articles annotated for curation of protein-protein and genetic interactions. - Rezarta Islamaj Dogan; Sun Kim; Andrew Chatr-aryamontri; Christie S. Chang; Rose Oughtred; Jennifer M. Rust; W. John Wilbur; Donald C. Comeau; Kara Dolinski; Mike Tyers (Database J. Biol. Databases Curation, 2017)

Bridging the gap: Incorporating a semantic similarity measure for effectively mapping PubMed queries to documents. - Sun Kim; Nicolas Fiorini; W. John Wilbur; Zhiyong Lu (J. Biomed. Informatics, 2017)

Sentence Similarity Measures Revisited: Ranking Sentences in PubMed Documents. - Qingyu Chen 001; Sun Kim; W. John Wilbur; Zhiyong Lu (BCB, 2018)

MeSH-based dataset for measuring the relevance of text retrieval. - Won Kim 003; Lana Yeganova; Donald C. Comeau; W. John Wilbur; Zhiyong Lu (BioNLP, 2018)

SingleCite: Towards an improved Single Citation Search in PubMed. - Lana Yeganova; Donald C. Comeau; Won Kim 003; W. John Wilbur; Zhiyong Lu (BioNLP, 2018)

A Field Sensor: computing the composition and intent of PubMed queries. - Lana Yeganova; Won Kim 003; Donald C. Comeau; W. John Wilbur; Zhiyong Lu (Database J. Biol. Databases Curation, 2018)

Discovering themes in biomedical literature using a projection-based algorithm. - Lana Yeganova; Sun Kim; Grigory Balasanov; W. John Wilbur (BMC Bioinform., 2018)

Evaluation of Five Sentence Similarity Models on Electronic Medical Records. - Qingyu Chen 001; Jingcheng Du; Sun Kim; W. John Wilbur; Zhiyong Lu (BCB, 2019)

PubMed Text Similarity Model and its application to curation efforts in the Conserved Domain Database. - Rezarta Islamaj Dogan; W. John Wilbur; Natalie Xie; Noreen R. Gonzales; Narmada Thanki; Roxanne A. Yamashita; Chanjuan Zheng; Aron Marchler-Bauer; Zhiyong Lu (Database J. Biol. Databases Curation, 2019)

PDC - a probabilistic distributional clustering algorithm: a case study on suicide articles in PubMed. - Rezarta Islamaj Dogan; Lana Yeganova; Won Kim 003; Natalie Xie; W. John Wilbur (CoRR, 2019)

LitSense: making sense of biomedical literature at sentence level. - Alexis Allot; Qingyu Chen 001; Sun Kim; Roberto Vera Alvarez; Donald C. Comeau; W. John Wilbur; Zhiyong Lu (Nucleic Acids Res., 2019)

Navigating the landscape of COVID-19 research through literature analysis: A bird's eye view. - Lana Yeganova; Rezarta Islamaj Dogan; Qingyu Chen 001; Robert Leaman; Alexis Allot; Chih-Hsuan Wei; Donald C. Comeau; Won Kim 003; Yifan Peng 002; W. John Wilbur; Zhiyong Lu (CoRR, 2020)

Better synonyms for enriching biomedical search. - Lana Yeganova; Sun Kim; Qingyu Chen 001; Grigory Balasanov; W. John Wilbur; Zhiyong Lu (J. Am. Medical Informatics Assoc., 2020)

Deep learning with sentence embeddings pre-trained on biomedical corpora improves the performance of finding similar sentences in electronic medical records. - Qingyu Chen 001; Jingcheng Du; Sun Kim; W. John Wilbur; Zhiyong Lu (BMC Medical Informatics Decis. Mak., 2020)

Improving PubMed Retrieval by Integrating Abstract and Full Text Search. - Lana Yeganova; Won Kim 003; Donald C. Comeau; W. John Wilbur; Zhiyong Lu (AMIA, 2021)

Measuring the relative importance of full text sections for information retrieval from scientific literature. - Lana Yeganova; Won Kim 003; Donald C. Comeau; W. John Wilbur; Zhiyong Lu (BioNLP@NAACL-HLT, 2021)

Comprehensive identification of Long Covid articles with human-in-the-loop machine learning. - Robert Leaman; Rezarta Islamaj Dogan; Alexis Allot; Qingyu Chen 001; W. John Wilbur; Zhiyong Lu (CoRR, 2022)

Towards a unified search: Improving PubMed retrieval with full text. - Won Kim 003; Lana Yeganova; Donald C. Comeau; W. John Wilbur; Zhiyong Lu (J. Biomed. Informatics, 2022)

BioCPT: Contrastive Pre-trained Transformers with Large-scale PubMed Search Logs for Zero-shot Biomedical Information Retrieval. - Qiao Jin 001; Won Kim 003; Qingyu Chen 001; Donald C. Comeau; Lana Yeganova; W. John Wilbur; Zhiyong Lu (CoRR, 2023)

Comprehensively identifying Long Covid articles with human-in-the-loop machine learning. - Robert Leaman; Rezarta Islamaj; Alexis Allot; Qingyu Chen 001; W. John Wilbur; Zhiyong Lu (Patterns, 2023)

MedCPT: Contrastive Pre-trained Transformers with large-scale PubMed search logs for zero-shot biomedical information retrieval. - Qiao Jin 001; Won Kim 003; Qingyu Chen 001; Donald C. Comeau; Lana Yeganova; W. John Wilbur; Zhiyong Lu (Bioinform., 2023)

AgentMD: Empowering Language Agents for Risk Prediction with Large-Scale Clinical Tool Learning. - Qiao Jin 001; Zhizheng Wang; Yifan Yang 006; Qingqing Zhu; Donald Wright; Thomas Huang 003; W. John Wilbur; Zhe He 001; Andrew Taylor; Qingyu Chen 001; Zhiyong Lu (CoRR, 2024)

Ensuring Safety and Trust: Analyzing the Risks of Large Language Models in Medicine. - Yifan Yang 006; Qiao Jin 001; Robert Leaman; Xiaoyu Liu 003; Guangzhi Xiong; Maame Sarfo-Gyamfi; Changlin Gong; Santiago Ferrière-Steinert; W. John Wilbur; Xiaojun Li; Jiaxin Yuan; Bang An 001; et al. (CoRR, 2024)