W. John Wilbur

156 papers A* 1A 1B 1C 2Misc 17Journal 104Unranked 30
YearRankTypeTitle / Venue / Authors
2026 J jnl
Exploring Anti-Aging Literature via ConvexTopics and Large Language Models.
CoRR
Lana Yeganova, Won Kim, Shubo Tian, Natalie Xie, Donald C. Comeau, W. John Wilbur, Zhiyong Lu
2024 J jnl
AgentMD: Empowering Language Agents for Risk Prediction with Large-Scale Clinical Tool Learning.
CoRR
Qiao Jin, Zhizheng Wang, Yifan Yang, Qingqing Zhu, Donald Wright, Thomas Huang, W. John Wilbur, Zhe He, Andrew Taylor, Qingyu Chen, Zhiyong Lu
2024 J jnl
Ensuring Safety and Trust: Analyzing the Risks of Large Language Models in Medicine.
CoRR
Yifan Yang, Qiao Jin, Robert Leaman, Xiaoyu Liu, Guangzhi Xiong, Maame Sarfo-Gyamfi, Changlin Gong, Santiago Ferrière-Steinert, W. John Wilbur, Xiaojun Li, Jiaxin Yuan, Bang An, Kelvin S. Castro, Francisco Erramuspe Álvarez, Matías Stockle, Aidong Zhang, Furong Huang, Zhiyong Lu
2024 J jnl
PubMed Computed Authors in 2024: an open resource of disambiguated author names in biomedical literature.
Bioinform.
Shubo Tian, Qingyu Chen, Donald C. Comeau, W. John Wilbur, Zhiyong Lu
2023 J jnl
BioCPT: Contrastive Pre-trained Transformers with Large-scale PubMed Search Logs for Zero-shot Biomedical Information Retrieval.
CoRR
Qiao Jin, Won Kim, Qingyu Chen, Donald C. Comeau, Lana Yeganova, W. John Wilbur, Zhiyong Lu
2023 J jnl
Comprehensively identifying Long Covid articles with human-in-the-loop machine learning.
Patterns
Robert Leaman, Rezarta Islamaj, Alexis Allot, Qingyu Chen, W. John Wilbur, Zhiyong Lu
2023 J jnl
MedCPT: Contrastive Pre-trained Transformers with large-scale PubMed search logs for zero-shot biomedical information retrieval.
Bioinform.
Qiao Jin, Won Kim, Qingyu Chen, Donald C. Comeau, Lana Yeganova, W. John Wilbur, Zhiyong Lu
2022 J jnl
Comprehensive identification of Long Covid articles with human-in-the-loop machine learning.
CoRR
Robert Leaman, Rezarta Islamaj Dogan, Alexis Allot, Qingyu Chen, W. John Wilbur, Zhiyong Lu
2022 J jnl
Towards a unified search: Improving PubMed retrieval with full text.
J. Biomed. Informatics
Won Kim, Lana Yeganova, Donald C. Comeau, W. John Wilbur, Zhiyong Lu
2021 Misc conf
Improving PubMed Retrieval by Integrating Abstract and Full Text Search.
AMIA
Lana Yeganova, Won Kim, Donald C. Comeau, W. John Wilbur, Zhiyong Lu
2021 — conf
Measuring the relative importance of full text sections for information retrieval from scientific literature.
BioNLP@NAACL-HLT
Lana Yeganova, Won Kim, Donald C. Comeau, W. John Wilbur, Zhiyong Lu
2020 J jnl
Better synonyms for enriching biomedical search.
J. Am. Medical Informatics Assoc.
Lana Yeganova, Sun Kim, Qingyu Chen, Grigory Balasanov, W. John Wilbur, Zhiyong Lu
2020 J jnl
Deep learning with sentence embeddings pre-trained on biomedical corpora improves the performance of finding similar sentences in electronic medical records.
BMC Medical Informatics Decis. Mak.
Qingyu Chen, Jingcheng Du, Sun Kim, W. John Wilbur, Zhiyong Lu
2020 J jnl
Navigating the landscape of COVID-19 research through literature analysis: A bird's eye view.
CoRR
Lana Yeganova, Rezarta Islamaj Dogan, Qingyu Chen, Robert Leaman, Alexis Allot, Chih-Hsuan Wei, Donald C. Comeau, Won Kim, Yifan Peng, W. John Wilbur, Zhiyong Lu
2019 J jnl
Deep learning with sentence embeddings pre-trained on biomedical corpora improves the performance of finding similar sentences in electronic medical records.
CoRR
Qingyu Chen, Jingcheng Du, Sun Kim, W. John Wilbur, Zhiyong Lu
2019 — conf
Evaluation of Five Sentence Similarity Models on Electronic Medical Records.
BCB
Qingyu Chen, Jingcheng Du, Sun Kim, W. John Wilbur, Zhiyong Lu
2019 J jnl
LitSense: making sense of biomedical literature at sentence level.
Nucleic Acids Res.
Alexis Allot, Qingyu Chen, Sun Kim, Roberto Vera Alvarez, Donald C. Comeau, W. John Wilbur, Zhiyong Lu
2019 J jnl
PDC - a probabilistic distributional clustering algorithm: a case study on suicide articles in PubMed.
CoRR
Rezarta Islamaj Dogan, Lana Yeganova, Won Kim, Natalie Xie, W. John Wilbur
2019 J jnl
PubMed Text Similarity Model and its application to curation efforts in the Conserved Domain Database.
Database J. Biol. Databases Curation
Rezarta Islamaj Dogan, W. John Wilbur, Natalie Xie, Noreen R. Gonzales, Narmada Thanki, Roxanne A. Yamashita, Chanjuan Zheng, Aron Marchler-Bauer, Zhiyong Lu
2018 J jnl
A Field Sensor: computing the composition and intent of PubMed queries.
Database J. Biol. Databases Curation
Lana Yeganova, Won Kim, Donald C. Comeau, W. John Wilbur, Zhiyong Lu
2018 J jnl
Discovering themes in biomedical literature using a projection-based algorithm.
BMC Bioinform.
Lana Yeganova, Sun Kim, Grigory Balasanov, W. John Wilbur
2018 — conf
MeSH-based dataset for measuring the relevance of text retrieval.
BioNLP
Won Kim, Lana Yeganova, Donald C. Comeau, W. John Wilbur, Zhiyong Lu
2018 — conf
Sentence Similarity Measures Revisited: Ranking Sentences in PubMed Documents.
BCB
Qingyu Chen, Sun Kim, W. John Wilbur, Zhiyong Lu
2018 — conf
SingleCite: Towards an improved Single Citation Search in PubMed.
BioNLP
Lana Yeganova, Donald C. Comeau, Won Kim, W. John Wilbur, Zhiyong Lu
2017 J jnl
Bridging the gap: Incorporating a semantic similarity measure for effectively mapping PubMed queries to documents.
J. Biomed. Informatics
Sun Kim, Nicolas Fiorini, W. John Wilbur, Zhiyong Lu
2017 J jnl
The BioC-BioGRID corpus: full text articles annotated for curation of protein-protein and genetic interactions.
Database J. Biol. Databases Curation
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
2016 J jnl
BioC viewer: a web-based tool for displaying and merging annotations in BioC.
Database J. Biol. Databases Curation
Soo-Yong Shin, Sun Kim, W. John Wilbur, Dongseop Kwon
2016 — conf
BioCconvert: A Conversion Tool Between BioC and PubAnnotation.
ICBO/BioCreative
Donald C. Comeau, Rezarta Islamaj Dogan, Sun Kim, Chih-Hsuan Wei, W. John Wilbur, Zhiyong Lu
2016 J jnl
BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID.
Database J. Biol. Databases Curation
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, José Luís Oliveira, Onkar Singh, Jitendra Jonnagaddala, Hong-Jie Dai, Emily Chia-Yu Su, Yung-Chun Chang, Yu-Chen Su, Chun-Han Chu, Chien Chin Chen, Wen-Lian Hsu, Yifan Peng, Cecilia N. Arighi, Cathy H. Wu, K. Vijay-Shanker, Ferhat Aydin, Zehra Melce Hüsünbeyi, Arzucan Özgür, Soo-Yong Shin, Dongseop Kwon, Kara Dolinski, Mike Tyers, W. John Wilbur, Donald C. Comeau
2016 J jnl
Bridging the Gap: a Semantic Similarity Measure between Queries and Documents.
CoRR
Sun Kim, W. John Wilbur, Zhiyong Lu
2016 — conf
PubTermVariants: biomedical term variants and their use for PubMed search.
BioNLP@ACL
Lana Yeganova, Won Kim, Sun Kim, Rezarta Islamaj Dogan, Wanli Liu, Donald C. Comeau, Zhiyong Lu, W. John Wilbur
2015 J jnl
Extracting drug-drug interactions from literature using a rich feature-based linear kernel approach.
J. Biomed. Informatics
Sun Kim, Haibin Liu, Lana Yeganova, W. John Wilbur
2015 J jnl
Identifying named entities from PubMed®; for enriching semantic categories.
BMC Bioinform.
Sun Kim, Zhiyong Lu, W. John Wilbur
2015 J jnl
Optimizing graph-based patterns to extract biomedical events from the literature.
BMC Bioinform.
Haibin Liu, Karin Verspoor, Donald C. Comeau, Andrew D. MacKinlay, W. John Wilbur
2015 A* conf
Summarizing Topical Contents from PubMed Documents Using a Thematic Analysis.
EMNLP
Sun Kim, Lana Yeganova, W. John Wilbur
2014 J jnl
Assisting manual literature curation for protein-protein interactions using BioQRator.
Database J. Biol. Databases Curation
Dongseop Kwon, Sun Kim, Soo-Yong Shin, Andrew Chatr-aryamontri, W. John Wilbur
2014 J jnl
Author name disambiguation for PubMed.
J. Assoc. Inf. Sci. Technol.
Wanli Liu, Rezarta Islamaj Dogan, Sun Kim, Donald C. Comeau, Won Kim, Lana Yeganova, Zhiyong Lu, W. John Wilbur
2014 J jnl
BioC implementations in Go, Perl, Python and Ruby.
Database J. Biol. Databases Curation
Wanli Liu, Rezarta Islamaj Dogan, Dongseop Kwon, Hernani Marques, Fabio Rinaldi, W. John Wilbur, Donald C. Comeau
2014 J jnl
BioC interoperability track overview.
Database J. Biol. Databases Curation
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, Rafal Rak, Fabio Rinaldi, Richard Tzong-Han Tsai, Karin Verspoor, Thomas C. Wiegers, Cathy H. Wu, W. John Wilbur
2014 J jnl
BioCreative-IV virtual issue.
Database J. Biol. Databases Curation
Cecilia N. Arighi, Cathy H. Wu, Kevin Bretonnel Cohen, Lynette Hirschman, Martin Krallinger, Alfonso Valencia, Zhiyong Lu, W. John Wilbur, Thomas C. Wiegers
2014 Misc conf
Extracting drug-drug interactions from literature using a rich feature-based linear kernel approach.
AMIA
Sun Kim, Haibin Liu, Lana Yeganova, W. John Wilbur
2014 J jnl
Finding abbreviations in biomedical literature: three BioC-compatible modules and four BioC-formatted corpora.
Database J. Biol. Databases Curation
Rezarta Islamaj Dogan, Donald C. Comeau, Lana Yeganova, W. John Wilbur
2014 J jnl
Natural language processing pipelines to annotate BioC collections with an application to the NCBI disease corpus.
Database J. Biol. Databases Curation
Donald C. Comeau, Haibin Liu, Rezarta Islamaj Dogan, W. John Wilbur
2014 J jnl
Retro: concept-based clustering of biomedical topical sets.
Bioinform.
Lana Yeganova, Won Kim, Sun Kim, W. John Wilbur
2014 Misc conf
Stochastic Gradient Descent and the Prediction of MeSH for PubMed Records.
AMIA
W. John Wilbur, Won Kim
2013 J jnl
An overview of the BioCreative 2012 Workshop Track III: interactive text mining task.
Database J. Biol. Databases Curation
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, Bethany R. Harris, Marc Gillespie, Silvia Jimenez, Phoebe M. Roberts, Lisa Matthews, Kevin G. Becker, Harold J. Drabkin, Susan M. Bello, Luana Licata, Andrew Chatr-aryamontri, Mary L. Schaeffer, Julie Park, Melissa A. Haendel, Kimberly Van Auken, Yuling Li, Juancarlos Chan, Hans-Michael Müller, Hong Cui, James P. Balhoff, Chi-Yang Wu, Zhiyong Lu, Chih-Hsuan Wei, Catalina O. Tudor, Kalpana Raja, Suresh Subramani, Jeyakumar Natarajan, Juan Miguel Cejuela, Pratibha Dubey, Cathy H. Wu
2013 Misc conf
BioC: A Minimalist Approach to Interoperability for Biomedical Text Processing.
AMIA
Donald C. Comeau, Rezarta Islamaj Dogan, W. John Wilbur
2013 J jnl
BioC: a minimalist approach to interoperability for biomedical text processing.
Database J. Biol. Databases Curation
Donald C. Comeau, Rezarta Islamaj Dogan, Paolo Ciccarese, Kevin Bretonnel Cohen, Martin Krallinger, Florian Leitner, Zhiyong Lu, Yifan Peng, Fabio Rinaldi, Manabu Torii, Alfonso Valencia, Karin Verspoor, Thomas C. Wiegers, Cathy H. Wu, W. John Wilbur
2013 — conf
BioNLP Shared Task 2013: Supporting Resources.
BioNLP@ACL (Shared Task)
Pontus Stenetorp, Wiktoria Golik, Thierry Hamon, Donald C. Comeau, Rezarta Islamaj Dogan, Haibin Liu, W. John Wilbur
2013 — conf
Extracting Biomedical Events and Modifications Using Subgraph Matching with Noisy Training Data.
BioNLP@ACL (Shared Task)
Andrew MacKinlay, David Martínez, Antonio Jimeno-Yepes, Haibin Liu, W. John Wilbur, Karin Verspoor
2013 — conf
Generalizing an Approximate Subgraph Matching-based System to Extract Events in Molecular Biology and Cancer Genetics.
BioNLP@ACL (Shared Task)
Haibin Liu, Karin Verspoor, Donald C. Comeau, Andrew MacKinlay, W. John Wilbur
2012 — conf
Automatic Identification of Key Concepts in Large PubMed Retrievals.
AAAI Fall Symposium: Information Retrieval and Knowledge Discovery in Biomedical Text
Lana Yeganova, Vahan Grigoryan, Won Kim, W. John Wilbur
2012 J jnl
BioCreative-2012 Virtual Issue.
Database J. Biol. Databases Curation
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
2012 — conf
Classifying Gene Sentences in Biomedical Literature by Combining High-Precision Gene Identifiers.
BioNLP@HLT-NAACL
Sun Kim, Won Kim, Donald C. Comeau, W. John Wilbur
2012 J jnl
Database resources of the National Center for Biotechnology Information.
Nucleic Acids Res.
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
2012 J jnl
Finding biomedical categories in Medline
J. Biomed. Semant.
Lana Yeganova, Won Kim, Donald C. Comeau, W. John Wilbur
2012 J jnl
Identifying well-formed biomedical phrases in MEDLINE® text.
J. Biomed. Informatics
Won Kim, Lana Yeganova, Donald C. Comeau, W. John Wilbur
2012 J jnl
Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE.
Database J. Biol. Databases Curation
Aurélie Névéol, W. John Wilbur, Zhiyong Lu
2012 J jnl
PIE
Bioinform.
Sun Kim, Dongseop Kwon, Soo-Yong Shin, W. John Wilbur
2012 — conf
PROBE: Periodic Random Orbiter Algorithm for Machine Learning.
AAAI Fall Symposium: Information Retrieval and Knowledge Discovery in Biomedical Text
Larry H. Smith, Won Kim, W. John Wilbur
2012 J jnl
Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information.
Database J. Biol. Databases Curation
Sun Kim, Won Kim, Chih-Hsuan Wei, Zhiyong Lu, W. John Wilbur
2012 J jnl
Thematic clustering of text documents using an EM-based approach.
J. Biomed. Semant.
Sun Kim, W. John Wilbur
2011 — conf
An EM Clustering Algorithm which Produces a Dual Representation.
ICMLA (2)
Sun Kim, W. John Wilbur
2011 — conf
Automatic extraction of data deposition statements: where do the research results go?
BioNLP@ACL
Aurélie Névéol, W. John Wilbur, Zhiyong Lu
2011 J jnl
Classifying protein-protein interaction articles using word and syntactic features.
BMC Bioinform.
Sun Kim, W. John Wilbur
2011 — conf
Comparison of Two Methods for Finding Biomedical Categories in Medline.
ICMLA (2)
Lana Yeganova, Won Kim, Donald C. Comeau, W. John Wilbur
2011 J jnl
Database resources of the National Center for Biotechnology Information.
Nucleic Acids Res.
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
2011 J jnl
Extraction of data deposition statements from the literature: a method for automatically tracking research results.
Bioinform.
Aurélie Névéol, W. John Wilbur, Zhiyong Lu
2011 J jnl
Improving a gold standard: treating human relevance judgments of MEDLINE document pairs.
BMC Bioinform.
W. John Wilbur, Won Kim
2011 J jnl
Machine learning with naturally labeled data for identifying abbreviation definitions.
BMC Bioinform.
Lana Yeganova, Donald C. Comeau, W. John Wilbur
2011 J jnl
Overview of the BioCreative III Workshop.
BMC Bioinform.
Cecilia N. Arighi, Zhiyong Lu, Martin Krallinger, Kevin Bretonnel Cohen, W. John Wilbur, Alfonso Valencia, Lynette Hirschman, Cathy H. Wu
2011 — conf
Text Mining Techniques for Leveraging Positively Labeled Data.
BioNLP@ACL
Lana Yeganova, Donald C. Comeau, Won Kim, W. John Wilbur
2011 J jnl
The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text.
BMC Bioinform.
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 M. Rocha, Hagit Shatkay, Ashish V. Tendulkar, Shashank Agarwal, Feifan Liu, Xinglong Wang, Rafal Rak, Keith Noto, Charles Elkan, Zhiyong Lu
2011 J jnl
The gene normalization task in BioCreative III.
BMC Bioinform.
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
2010 J jnl
Database resources of the National Center for Biotechnology Information.
Nucleic Acids Res.
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
2010 J jnl
Finding related sentence pairs in MEDLINE.
Inf. Retr.
Larry H. Smith, W. John Wilbur
2010 C conf
Identifying Abbreviation Definitions Machine Learning with Naturally Labeled Data.
ICMLA
Lana Yeganova, Donald C. Comeau, W. John Wilbur
2010 C conf
Improving a Gold Standard: Treating Human Relevance Judgments of MEDLINE Document Pairs.
ICMLA
Won Kim, W. John Wilbur
2009 J jnl
Evaluation of query expansion using MeSH in PubMed.
Inf. Retr.
Zhiyong Lu, Won Kim, W. John Wilbur
2009 — conf
Exploring Two Biomedical Text Genres for Disease Recognition.
BioNLP@HLT-NAACL
Aurélie Névéol, Won Kim, W. John Wilbur, Zhiyong Lu
2009 Misc conf
Finding Query Suggestions for PubMed.
AMIA
Zhiyong Lu, W. John Wilbur, Johanna R. McEntyre, Alexey Iskhakov, Lee Szilagyi
2009 J jnl
How to Get the Most out of Your Curation Effort.
PLoS Comput. Biol.
Andrey Rzhetsky, Hagit Shatkay, W. John Wilbur
2009 J jnl
How to interpret PubMed queries and why it matters.
J. Assoc. Inf. Sci. Technol.
Lana Yeganova, Donald C. Comeau, Won Kim, W. John Wilbur
2009 J jnl
Identifying related journals through log analysis.
Bioinform.
Zhiyong Lu, Natalie Xie, W. John Wilbur
2009 J jnl
Improving accuracy for identifying related PubMed queries by an integrated approach.
J. Biomed. Informatics
Zhiyong Lu, W. John Wilbur
2009 J jnl
Modeling actions of PubMed users with
Inf. Retr.
Jimmy Lin, W. John Wilbur
2009 J jnl
The ineffectiveness of within-document term frequency in text classification.
Inf. Retr.
W. John Wilbur, Won Kim
2009 J jnl
The value of parsing as feature generation for gene mention recognition.
J. Biomed. Informatics
Lawrence H. Smith, W. John Wilbur
2009 — conf
Users' adjustments to unsuccessful queries in biomedical search.
JCDL
G. Craig Murray, Jimmy Lin, W. John Wilbur, Zhiyong Lu
2009 J jnl
Viewpoint Paper: Evaluating Relevance Ranking Strategies for MEDLINE Retrieval.
J. Am. Medical Informatics Assoc.
Zhiyong Lu, Won Kim, W. John Wilbur
2008 J jnl
Abbreviation definition identification based on automatic precision estimates.
BMC Bioinform.
Sunghwan Sohn, Donald C. Comeau, Won Kim, W. John Wilbur
2008 Misc conf
Evaluating Relevance Ranking Strategies for MEDLINE Retrieval.
AMIA
Zhiyong Lu, Won Kim, W. John Wilbur
2008 J jnl
Multi-dimensional classification of biomedical text: Toward automated, practical provision of high-utility text to diverse users.
Bioinform.
Hagit Shatkay, Fengxia Pan, Andrey Rzhetsky, W. John Wilbur
2008 J jnl
Navigating information spaces: A case study of related article search in PubMed.
Inf. Process. Manag.
Jimmy Lin, Michael DiCuccio, Vahan Grigoryan, W. John Wilbur
2008 J jnl
Research Paper: Optimal Training Sets for Bayesian Prediction of MeSH
J. Am. Medical Informatics Assoc.
Sunghwan Sohn, Won Kim, Donald C. Comeau, W. John Wilbur
2007 — conf
Characterizing RNA Secondary-Structure Features and Their Effects on Splice-Site Prediction.
ICDM Workshops
Rezarta Islamaj Dogan, Lise Getoor, W. John Wilbur
2007 — conf
Combining Resources to Find Answers to Biomedical Questions.
TREC
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
2007 J jnl
Features generated for computational splice-site prediction correspond to functional elements.
BMC Bioinform.
Rezarta Islamaj Dogan, Lise Getoor, W. John Wilbur, Stephen M. Mount
2007 J jnl
PubMed related articles: a probabilistic topic-based model for content similarity.
BMC Bioinform.
Jimmy Lin, W. John Wilbur
2007 J jnl
SplicePort - An interactive splice-site analysis tool.
Nucleic Acids Res.
Rezarta Islamaj Dogan, Lise Getoor, W. John Wilbur, Stephen M. Mount
2007 J jnl
Syntactic sentence compression in the biomedical domain: facilitating access to related articles.
Inf. Retr.
Jimmy Lin, W. John Wilbur
2007 — conf
Unsupervised Learning of the Morpho-Semantic Relationship in MEDLINE.
BioNLP@ACL
W. John Wilbur
2007 J jnl
Using MEDLINE as a knowledge source for disambiguating abbreviations and acronyms in full-text biomedical journal articles.
J. Biomed. Informatics
Hong Yu, Won Kim, Vasileios Hatzivassiloglou, W. John Wilbur
2006 — conf
A Feature Generation Algorithm for Sequences with Application to Splice-Site Prediction.
PKDD
Rezarta Islamaj Dogan, Lise Getoor, W. John Wilbur
2006 — conf
A Priority Model for Named Entities.
BioNLP@NAACL-HLT
Lorraine K. Tanabe, W. John Wilbur
2006 J jnl
A large scale, corpus-based approach for automatically disambiguating biomedical abbreviations.
ACM Trans. Inf. Syst.
Hong Yu, Won Kim, Vasileios Hatzivassiloglou, W. John Wilbur
2006 — conf
Finding Relevant Passages in Scientific Articles: Fusion of Automatic Approaches vs. an Interactive Team Effort.
TREC
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
2006 J jnl
New directions in biomedical text annotation: definitions, guidelines and corpus construction.
BMC Bioinform.
W. John Wilbur, Andrey Rzhetsky, Hagit Shatkay
2006 Misc conf
SemCat: Semantically Categorized Entities for Genomics.
AMIA
Lorraine K. Tanabe, Lynne H. Thom, Wayne Matten, Donald C. Comeau, W. John Wilbur
2006 J jnl
Spelling correction in the PubMed search engine.
Inf. Retr.
W. John Wilbur, Won Kim, Natalie Xie
2006 J jnl
The importance of the lexicon in tagging biological text.
Nat. Lang. Eng.
Lawrence H. Smith, Thomas C. Rindflesch, W. John Wilbur
2005 Misc conf
A Strategy for Assigning New Concepts in the MEDLINE Database.
AMIA
Won Kim, W. John Wilbur
2005 — conf
Fusion of Knowledge-Intensive and Statistical Approaches for Retrieving and Annotating Textual Genomics Documents.
TREC
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
2005 J jnl
GENETAG: a tagged corpus for gene/protein named entity recognition.
BMC Bioinform.
Lorraine K. Tanabe, Natalie Xie, Lynne H. Thom, Wayne Matten, W. John Wilbur
2005 — conf
MedTag: A Collection of Biomedical Annotations.
LBLODMBS@IDMB
Lawrence H. Smith, Lorraine K. Tanabe, Thomas C. Rindflesch, W. John Wilbur
2005 J jnl
The Synergy Between PAV and AdaBoost.
Mach. Learn.
W. John Wilbur, Lana Yeganova, Won Kim
2004 J jnl
GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data.
J. Biomed. Informatics
Andrey Rzhetsky, Ivan Iossifov, Tomohiro Koike, Michael Krauthammer, Pauline Kra, Mitzi Morris, Hong Yu, Pablo Ariel Duboué, Wubin Weng, W. John Wilbur
2004 J jnl
Generation of a Large Gene/protein Lexicon by Morphological Pattern Analysis.
J. Bioinform. Comput. Biol.
Lorraine K. Tanabe, W. John Wilbur
2004 J jnl
Identification of related gene/protein names based on an HMM of name variations.
Comput. Biol. Chem.
Lana Yeganova, Lawrence H. Smith, W. John Wilbur
2004 — conf
Knowledge-Intensive and Statistical Approaches to the Retrieval and Annotation of Genomics MEDLINE Citations.
TREC
Alan R. Aronson, Susanne M. Humphrey, Nicholas C. Ide, Won Kim, Russell F. Loane, James G. Mork, Lawrence H. Smith, Lorraine K. Tanabe, W. John Wilbur, Natalie Xie, Dina Demner-Fushman, Hongfang Liu
2004 J jnl
MedPost: a part-of-speech tagger for bioMedical text.
Bioinform.
Lawrence H. Smith, Thomas C. Rindflesch, W. John Wilbur
2004 J jnl
Non-word identification or spell checking without a dictionary.
J. Assoc. Inf. Sci. Technol.
Donald C. Comeau, W. John Wilbur
2004 J jnl
Retrieving definitional content for ontology development.
Comput. Biol. Chem.
Lawrence H. Smith, W. John Wilbur
2004 B conf
Using MEDLINE as a Knowledge Source for Disambiguating Abbreviations in Full-Text Biomedical Journal Articles.
CBMS
Hong Yu, Won Kim, Vasileios Hatzivassiloglou, W. John Wilbur
2003 J jnl
Hidden Markov models and optimized sequence alignments.
Comput. Biol. Chem.
Lawrence H. Smith, Lana Yeganova, W. John Wilbur
2003 Misc conf
The Dimensions of Indexing.
AMIA
W. John Wilbur, Won Kim
2002 Misc conf
A Thematic Analysis of the AIDS Literature.
Pacific Symposium on Biocomputing
W. John Wilbur
2002 Misc conf
Automatic extraction of gene and protein synonyms from MEDLINE and journal articles.
AMIA
Hong Yu, Vasileios Hatzivassiloglou, Carol Friedman, Andrey Rzhetsky, W. John Wilbur
2002 J jnl
Automatically identifying gene/protein terms in MEDLINE abstracts.
J. Biomed. Informatics
Hong Yu, Vasileios Hatzivassiloglou, Andrey Rzhetsky, W. John Wilbur
2002 Misc conf
DNA splice site detection: a comparison of specific and general methods.
AMIA
Won Kim, W. John Wilbur
2002 J jnl
Tagging gene and protein names in biomedical text.
Bioinform.
Lorraine K. Tanabe, W. John Wilbur
2002 — conf
Tagging gene and protein names in full text articles.
ACL Workshop on Natural Language Processing in the Biomedical Domain
Lorraine K. Tanabe, W. John Wilbur
2001 J jnl
Amino Acid Residue Environments and Predictions of Residue Type.
Comput. Chem.
Won Kim, W. John Wilbur
2001 Misc conf
Automatic MeSH term assignment and quality assessment.
AMIA
Won Kim, Alan R. Aronson, W. John Wilbur
2001 J jnl
Corpus-based statistical screening for content-bearing terms.
J. Assoc. Inf. Sci. Technol.
Won Kim, W. John Wilbur
2001 J jnl
Global term weights for document retrieval learned from TREC data.
J. Inf. Sci.
W. John Wilbur
2000 J jnl
A Theory of Information with Special Application to Search Problems.
Comput. Chem.
W. John Wilbur, Andrew F. Neuwald
2000 Misc conf
Boosting naïve Bayesian learning on a large subset of MEDLINE.
AMIA
W. John Wilbur
2000 — conf
Finding Themes in Medline Documents: Probabilistic Similarity Search.
ADL
Hagit Shatkay, W. John Wilbur
2000 A conf
Genes, Themes, and Microarrays: Using Information Retrieval for Large-Scale Gene Analysis.
ISMB
Hagit Shatkay, Stephen Edwards, W. John Wilbur, Mark Boguski
2000 J jnl
Research Paper: Corpus-based Statistical Screening for Phrase Identification.
J. Am. Medical Informatics Assoc.
Won Kim, W. John Wilbur
2000 Misc conf
The NLM Indexing Initiative.
AMIA
Alan R. Aronson, Olivier Bodenreider, Florence Chang, Susanne M. Humphrey, James G. Mork, Stuart J. Nelson, Thomas C. Rindflesch, W. John Wilbur
1999 Misc conf
Analysis of biomedical text for chemical names: a comparison of three methods.
AMIA
W. John Wilbur, George F. Hazard Jr., Guy Divita, James G. Mork, Alan R. Aronson, Allen C. Browne
1999 Misc conf
Automated Assignment of Medical Subject Headings.
AMIA
Stuart J. Nelson, Alan R. Aronson, Tamas E. Doszkocs, W. John Wilbur, Olivier Bodenreider, H. Florence Chang, James G. Mork, Alexa T. McCray
1998 J jnl
A Comparison of Group and Individual Performance Among Subject Experts and Untrained Workers at the Document Retrieval Task.
J. Am. Soc. Inf. Sci.
W. John Wilbur
1998 J jnl
The Knowledge in Multiple Human Relevance Judgments.
ACM Trans. Inf. Syst.
W. John Wilbur
1996 J jnl
An analysis of statistical term strength and its use in the indexing and retrieval of molecular biology texts.
Comput. Biol. Medicine
W. John Wilbur, Yiming Yang
1996 J jnl
Human Subjectivity and Performance Limits in Document Retrieval.
Inf. Process. Manag.
W. John Wilbur
1996 J jnl
Using Corpus Statistics to Remove Redundant Words in Text Categorization.
J. Am. Soc. Inf. Sci.
Yiming Yang, W. John Wilbur
1994 J jnl
Non-parametric significance tests of retrieval performance comparisons.
J. Inf. Sci.
W. John Wilbur
1994 J jnl
The Effectiveness of Document Neighboring in Search Enhancement.
Inf. Process. Manag.
W. John Wilbur, Leona Coffee
1993 J jnl
Retrieval Testing with Hypergeometric Document Models.
J. Am. Soc. Inf. Sci.
W. John Wilbur
1992 J jnl
An information measure of retrieval performance.
Inf. Syst.
W. John Wilbur
1992 J jnl
Retrieval Testing by the Comparison of Statistically Independent Retrieval Methods.
J. Am. Soc. Inf. Sci.
W. John Wilbur
1992 J jnl
The automatic identification of stop words.
J. Inf. Sci.
W. John Wilbur, Karl Sirotkin
1984 J jnl
On the statistical significance of nucleic acid similarities.
Nucleic Acids Res.
David J. Lipman, W. John Wilbur, Temple F. Smith, Michael S. Waterman