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2020 – today
- 2024
[i8]Qiao Jin, Zhizheng Wang, Yifan Yang, Qingqing Zhu, Donald Wright, Thomas Huang, W. John Wilbur, Zhe He, Andrew Taylor, Qingyu Chen, Zhiyong Lu:
AgentMD: Empowering Language Agents for Risk Prediction with Large-Scale Clinical Tool Learning. CoRR abs/2402.13225 (2024)- [i7]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:
Ensuring Safety and Trust: Analyzing the Risks of Large Language Models in Medicine. CoRR abs/2411.14487 (2024) - 2023
- [j95]Qiao Jin
, Won Kim, Qingyu Chen, Donald C. Comeau, Lana Yeganova, W. John Wilbur, Zhiyong Lu:
MedCPT: Contrastive Pre-trained Transformers with large-scale PubMed search logs for zero-shot biomedical information retrieval. Bioinform. 39(10) (2023) - [j94]Robert Leaman, Rezarta Islamaj, Alexis Allot, Qingyu Chen, W. John Wilbur, Zhiyong Lu:
Comprehensively identifying Long Covid articles with human-in-the-loop machine learning. Patterns 4(1): 100659 (2023) - [i6]Qiao Jin, Won Kim, Qingyu Chen, Donald C. Comeau, Lana Yeganova, W. John Wilbur, Zhiyong Lu:
BioCPT: Contrastive Pre-trained Transformers with Large-scale PubMed Search Logs for Zero-shot Biomedical Information Retrieval. CoRR abs/2307.00589 (2023) - 2022
- [j93]Won Kim, Lana Yeganova, Donald C. Comeau, W. John Wilbur, Zhiyong Lu:
Towards a unified search: Improving PubMed retrieval with full text. J. Biomed. Informatics 134: 104211 (2022) - [i5]Robert Leaman, Rezarta Islamaj Dogan, Alexis Allot, Qingyu Chen, W. John Wilbur, Zhiyong Lu:
Comprehensive identification of Long Covid articles with human-in-the-loop machine learning. CoRR abs/2209.08124 (2022) - 2021
- [c52]Lana Yeganova, Won Kim, Donald C. Comeau, W. John Wilbur, Zhiyong Lu:
Improving PubMed Retrieval by Integrating Abstract and Full Text Search. AMIA 2021 - [c51]Lana Yeganova, Won Kim, Donald C. Comeau, W. John Wilbur, Zhiyong Lu:
Measuring the relative importance of full text sections for information retrieval from scientific literature. BioNLP@NAACL-HLT 2021: 247-256 - 2020
- [j92]Lana Yeganova, Sun Kim, Qingyu Chen, Grigory Balasanov, W. John Wilbur, Zhiyong Lu:
Better synonyms for enriching biomedical search. J. Am. Medical Informatics Assoc. 27(12): 1894-1902 (2020) - [j91]Qingyu Chen, Jingcheng Du, Sun Kim, W. John Wilbur, Zhiyong Lu:
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. 20-S(1): 73 (2020) - [i4]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:
Navigating the landscape of COVID-19 research through literature analysis: A bird's eye view. CoRR abs/2008.03397 (2020)
2010 – 2019
- 2019
- [j90]Rezarta Islamaj Dogan, W. John Wilbur, Natalie Xie, Noreen R. Gonzales, Narmada Thanki, Roxanne A. Yamashita, Chanjuan Zheng, Aron Marchler-Bauer, Zhiyong Lu:
PubMed Text Similarity Model and its application to curation efforts in the Conserved Domain Database. Database J. Biol. Databases Curation 2019: baz064 (2019) - [j89]Alexis Allot, Qingyu Chen, Sun Kim, Roberto Vera Alvarez, Donald C. Comeau, W. John Wilbur, Zhiyong Lu:
LitSense: making sense of biomedical literature at sentence level. Nucleic Acids Res. 47(Webserver-Issue): W594-W599 (2019) - [c50]Qingyu Chen, Jingcheng Du, Sun Kim, W. John Wilbur, Zhiyong Lu:
Evaluation of Five Sentence Similarity Models on Electronic Medical Records. BCB 2019: 533 - [i3]Qingyu Chen, Jingcheng Du, Sun Kim, W. John Wilbur, Zhiyong Lu:
Deep learning with sentence embeddings pre-trained on biomedical corpora improves the performance of finding similar sentences in electronic medical records. CoRR abs/1909.03044 (2019) - [i2]Rezarta Islamaj Dogan, Lana Yeganova, Won Kim, Natalie Xie, W. John Wilbur:
PDC - a probabilistic distributional clustering algorithm: a case study on suicide articles in PubMed. CoRR abs/1912.02077 (2019) - 2018
- [j88]Lana Yeganova, Won Kim, Donald C. Comeau, W. John Wilbur, Zhiyong Lu:
A Field Sensor: computing the composition and intent of PubMed queries. Database J. Biol. Databases Curation 2018: bay052 (2018) - [j87]Lana Yeganova, Sun Kim, Grigory Balasanov, W. John Wilbur:
Discovering themes in biomedical literature using a projection-based algorithm. BMC Bioinform. 19(1): 269:1-269:12 (2018) - [c49]Qingyu Chen, Sun Kim, W. John Wilbur, Zhiyong Lu:
Sentence Similarity Measures Revisited: Ranking Sentences in PubMed Documents. BCB 2018: 531-532 - [c48]Lana Yeganova, Donald C. Comeau, Won Kim, W. John Wilbur, Zhiyong Lu:
SingleCite: Towards an improved Single Citation Search in PubMed. BioNLP 2018: 151-155 - [c47]Won Kim, Lana Yeganova, Donald C. Comeau, W. John Wilbur, Zhiyong Lu:
MeSH-based dataset for measuring the relevance of text retrieval. BioNLP 2018: 161-165 - 2017
- [j86]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:
The BioC-BioGRID corpus: full text articles annotated for curation of protein-protein and genetic interactions. Database J. Biol. Databases Curation 2017: baw147 (2017) - [j85]Sun Kim, Nicolas Fiorini, W. John Wilbur, Zhiyong Lu:
Bridging the gap: Incorporating a semantic similarity measure for effectively mapping PubMed queries to documents. J. Biomed. Informatics 75: 122-127 (2017) - 2016
- [j84]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:
BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. Database J. Biol. Databases Curation 2016 (2016) - [j83]Soo-Yong Shin, Sun Kim, W. John Wilbur, Dongseop Kwon:
BioC viewer: a web-based tool for displaying and merging annotations in BioC. Database J. Biol. Databases Curation 2016 (2016) - [j82]Sun Kim, Lana Yeganova, W. John Wilbur:
Meshable: searching PubMed abstracts by utilizing MeSH and MeSH-derived topical terms. Bioinform. 32(19): 3044-3046 (2016) - [c46]Lana Yeganova, Won Kim, Sun Kim, Rezarta Islamaj Dogan, Wanli Liu, Donald C. Comeau, Zhiyong Lu, W. John Wilbur:
PubTermVariants: biomedical term variants and their use for PubMed search. BioNLP@ACL 2016: 141-145 - [c45]Donald C. Comeau, Rezarta Islamaj Dogan, Sun Kim, Chih-Hsuan Wei, W. John Wilbur, Zhiyong Lu:
BioCconvert: A Conversion Tool Between BioC and PubAnnotation. ICBO/BioCreative 2016 - [i1]Sun Kim, W. John Wilbur, Zhiyong Lu:
Bridging the Gap: a Semantic Similarity Measure between Queries and Documents. CoRR abs/1608.01972 (2016) - 2015
- [j81]Sun Kim, Zhiyong Lu, W. John Wilbur:
Identifying named entities from PubMed®; for enriching semantic categories. BMC Bioinform. 16: 57:1-57:10 (2015) - [j80]Haibin Liu, Karin Verspoor, Donald C. Comeau, Andrew D. MacKinlay, W. John Wilbur:
Optimizing graph-based patterns to extract biomedical events from the literature. BMC Bioinform. 16(S16): S2 (2015) - [j79]Sun Kim, Haibin Liu, Lana Yeganova, W. John Wilbur:
Extracting drug-drug interactions from literature using a rich feature-based linear kernel approach. J. Biomed. Informatics 55: 23-30 (2015) - [c44]Sun Kim, Lana Yeganova, W. John Wilbur:
Summarizing Topical Contents from PubMed Documents Using a Thematic Analysis. EMNLP 2015: 805-810 - 2014
- [j78]Cecilia N. Arighi, Cathy H. Wu, Kevin Bretonnel Cohen, Lynette Hirschman, Martin Krallinger, Alfonso Valencia, Zhiyong Lu, W. John Wilbur, Thomas C. Wiegers:
BioCreative-IV virtual issue. Database J. Biol. Databases Curation 2014 (2014) - [j77]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:
BioC interoperability track overview. Database J. Biol. Databases Curation 2014 (2014) - [j76]Donald C. Comeau, Haibin Liu, Rezarta Islamaj Dogan, W. John Wilbur:
Natural language processing pipelines to annotate BioC collections with an application to the NCBI disease corpus. Database J. Biol. Databases Curation 2014 (2014) - [j75]Rezarta Islamaj Dogan, Donald C. Comeau, Lana Yeganova, W. John Wilbur:
Finding abbreviations in biomedical literature: three BioC-compatible modules and four BioC-formatted corpora. Database J. Biol. Databases Curation 2014 (2014) - [j74]Dongseop Kwon, Sun Kim, Soo-Yong Shin, Andrew Chatr-aryamontri, W. John Wilbur:
Assisting manual literature curation for protein-protein interactions using BioQRator. Database J. Biol. Databases Curation 2014 (2014) - [j73]Wanli Liu, Rezarta Islamaj Dogan, Dongseop Kwon, Hernani Marques, Fabio Rinaldi, W. John Wilbur, Donald C. Comeau:
BioC implementations in Go, Perl, Python and Ruby. Database J. Biol. Databases Curation 2014 (2014) - [j72]Lana Yeganova, Won Kim, Sun Kim, W. John Wilbur:
Retro: concept-based clustering of biomedical topical sets. Bioinform. 30(22): 3240-3248 (2014) - [j71]Wanli Liu, Rezarta Islamaj Dogan, Sun Kim, Donald C. Comeau, Won Kim, Lana Yeganova, Zhiyong Lu, W. John Wilbur:
Author name disambiguation for PubMed. J. Assoc. Inf. Sci. Technol. 65(4): 765-781 (2014) - [c43]Sun Kim, Haibin Liu, Lana Yeganova, W. John Wilbur:
Extracting drug-drug interactions from literature using a rich feature-based linear kernel approach. AMIA 2014 - [c42]W. John Wilbur, Won Kim:
Stochastic Gradient Descent and the Prediction of MeSH for PubMed Records. AMIA 2014 - 2013
- [j70]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:
An overview of the BioCreative 2012 Workshop Track III: interactive text mining task. Database J. Biol. Databases Curation 2013 (2013) - [j69]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:
BioC: a minimalist approach to interoperability for biomedical text processing. Database J. Biol. Databases Curation 2013 (2013) - [c41]Donald C. Comeau, Rezarta Islamaj Dogan, W. John Wilbur:
BioC: A Minimalist Approach to Interoperability for Biomedical Text Processing. AMIA 2013 - [c40]Andrew MacKinlay, David Martínez, Antonio Jimeno-Yepes, Haibin Liu, W. John Wilbur, Karin Verspoor:
Extracting Biomedical Events and Modifications Using Subgraph Matching with Noisy Training Data. BioNLP@ACL (Shared Task) 2013: 35-44 - [c39]Haibin Liu, Karin Verspoor, Donald C. Comeau, Andrew MacKinlay, W. John Wilbur:
Generalizing an Approximate Subgraph Matching-based System to Extract Events in Molecular Biology and Cancer Genetics. BioNLP@ACL (Shared Task) 2013: 76-85 - [c38]Pontus Stenetorp, Wiktoria Golik, Thierry Hamon, Donald C. Comeau, Rezarta Islamaj Dogan, Haibin Liu, W. John Wilbur:
BioNLP Shared Task 2013: Supporting Resources. BioNLP@ACL (Shared Task) 2013: 99-103 - 2012
- [j68]Sun Kim, Won Kim, Chih-Hsuan Wei, Zhiyong Lu, W. John Wilbur:
Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information. Database J. Biol. Databases Curation 2012 (2012) - [j67]Aurélie Névéol, W. John Wilbur, Zhiyong Lu:
Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE. Database J. Biol. Databases Curation 2012 (2012) - [j66]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:
BioCreative-2012 Virtual Issue. Database J. Biol. Databases Curation 2012 (2012) - [j65]Sun Kim, Dongseop Kwon, Soo-Yong Shin, W. John Wilbur:
PIE the search: searching PubMed literature for protein interaction information. Bioinform. 28(4): 597-598 (2012) - [j64]Lana Yeganova, Won Kim, Donald C. Comeau, W. John Wilbur:
Finding biomedical categories in Medline®. J. Biomed. Semant. 3(S-3): S3 (2012) - [j63]Sun Kim, W. John Wilbur:
Thematic clustering of text documents using an EM-based approach. J. Biomed. Semant. 3(S-3): S6 (2012) - [j62]Won Kim, Lana Yeganova, Donald C. Comeau, W. John Wilbur:
Identifying well-formed biomedical phrases in MEDLINE® text. J. Biomed. Informatics 45(6): 1035-1041 (2012) - [j61]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 Res. 40(Database-Issue): 13-25 (2012) - [c37]Larry H. Smith, Won Kim, W. John Wilbur:
PROBE: Periodic Random Orbiter Algorithm for Machine Learning. AAAI Fall Symposium: Information Retrieval and Knowledge Discovery in Biomedical Text 2012 - [c36]Lana Yeganova, Vahan Grigoryan, Won Kim, W. John Wilbur:
Automatic Identification of Key Concepts in Large PubMed Retrievals. AAAI Fall Symposium: Information Retrieval and Knowledge Discovery in Biomedical Text 2012 - [c35]Sun Kim, Won Kim, Donald C. Comeau, W. John Wilbur:
Classifying Gene Sentences in Biomedical Literature by Combining High-Precision Gene Identifiers. BioNLP@HLT-NAACL 2012: 185-192 - 2011
- [j60]Aurélie Névéol, W. John Wilbur, Zhiyong Lu:
Extraction of data deposition statements from the literature: a method for automatically tracking research results. Bioinform. 27(23): 3306-3312 (2011) - [j59]W. John Wilbur, Won Kim:
Improving a gold standard: treating human relevance judgments of MEDLINE document pairs. BMC Bioinform. 12(S-3): S5 (2011) - [j58]Lana Yeganova, Donald C. Comeau, W. John Wilbur:
Machine learning with naturally labeled data for identifying abbreviation definitions. BMC Bioinform. 12(S-3): S6 (2011) - [j57]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 Bioinform. 12(S-8): S1 (2011) - [j56]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 Bioinform. 12(S-8): S2 (2011) - [j55]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:
The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. BMC Bioinform. 12(S-8): S3 (2011) - [j54]Sun Kim, W. John Wilbur:
Classifying protein-protein interaction articles using word and syntactic features. BMC Bioinform. 12(S-8): S9 (2011) - [j53]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 Res. 39(Database-Issue): 38-51 (2011) - [c34]Aurélie Névéol, W. John Wilbur, Zhiyong Lu:
Automatic extraction of data deposition statements: where do the research results go? BioNLP@ACL 2011: 103-104 - [c33]Lana Yeganova, Donald C. Comeau, Won Kim, W. John Wilbur:
Text Mining Techniques for Leveraging Positively Labeled Data. BioNLP@ACL 2011: 155-163 - [c32]Sun Kim, W. John Wilbur:
An EM Clustering Algorithm which Produces a Dual Representation. ICMLA (2) 2011: 90-95 - [c31]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 - 2010
- [j52]Larry H. Smith, W. John Wilbur:
Finding related sentence pairs in MEDLINE. Inf. Retr. 13(6): 601-617 (2010) - [j51]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 Res. 38(Database-Issue): 5-16 (2010) - [c30]Won Kim, W. John Wilbur:
Improving a Gold Standard: Treating Human Relevance Judgments of MEDLINE Document Pairs. ICMLA 2010: 491-498 - [c29]Lana Yeganova, Donald C. Comeau, W. John Wilbur:
Identifying Abbreviation Definitions Machine Learning with Naturally Labeled Data. ICMLA 2010: 499-505
2000 – 2009
- 2009
- [j50]Zhiyong Lu, Natalie Xie, W. John Wilbur:
Identifying related journals through log analysis. Bioinform. 25(22): 3038-3039 (2009) - [j49]Zhiyong Lu, Won Kim, W. John Wilbur:
Evaluation of query expansion using MeSH in PubMed. Inf. Retr. 12(1): 69-80 (2009) - [j48]Jimmy Lin, W. John Wilbur:
Modeling actions of PubMed users with n-gram language models. Inf. Retr. 12(4): 487-503 (2009) - [j47]W. John Wilbur, Won Kim:
The ineffectiveness of within-document term frequency in text classification. Inf. Retr. 12(5): 509-525 (2009) - [j46]Zhiyong Lu, Won Kim, W. John Wilbur:
Viewpoint Paper: Evaluating Relevance Ranking Strategies for MEDLINE Retrieval. J. Am. Medical Informatics Assoc. 16(1): 32-36 (2009) - [j45]Lana Yeganova, Donald C. Comeau, Won Kim, W. John Wilbur:
How to interpret PubMed queries and why it matters. J. Assoc. Inf. Sci. Technol. 60(2): 264-274 (2009) - [j44]Zhiyong Lu, W. John Wilbur:
Improving accuracy for identifying related PubMed queries by an integrated approach. J. Biomed. Informatics 42(5): 831-838 (2009) - [j43]Lawrence H. Smith, W. John Wilbur:
The value of parsing as feature generation for gene mention recognition. J. Biomed. Informatics 42(5): 895-904 (2009) - [j42]Andrey Rzhetsky, Hagit Shatkay, W. John Wilbur:
How to Get the Most out of Your Curation Effort. PLoS Comput. Biol. 5(5) (2009) - [c28]Zhiyong Lu, W. John Wilbur, Johanna R. McEntyre, Alexey Iskhakov, Lee Szilagyi:
Finding Query Suggestions for PubMed. AMIA 2009 - [c27]Aurélie Névéol, Won Kim, W. John Wilbur, Zhiyong Lu:
Exploring Two Biomedical Text Genres for Disease Recognition. BioNLP@HLT-NAACL 2009: 144-152 - [c26]G. Craig Murray, Jimmy Lin, W. John Wilbur, Zhiyong Lu:
Users' adjustments to unsuccessful queries in biomedical search. JCDL 2009: 433-434 - 2008
- [j41]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. Bioinform. 24(18): 2086-2093 (2008) - [j40]Sunghwan Sohn, Donald C. Comeau, Won Kim, W. John Wilbur:
Abbreviation definition identification based on automatic precision estimates. BMC Bioinform. 9 (2008) - [j39]Jimmy Lin, Michael DiCuccio, Vahan Grigoryan, W. John Wilbur:
Navigating information spaces: A case study of related article search in PubMed. Inf. Process. Manag. 44(5): 1771-1783 (2008) - [j38]Sunghwan Sohn, Won Kim, Donald C. Comeau, W. John Wilbur:
Research Paper: Optimal Training Sets for Bayesian Prediction of MeSH® Assignment. J. Am. Medical Informatics Assoc. 15(4): 546-553 (2008) - [c25]Zhiyong Lu, Won Kim, W. John Wilbur:
Evaluating Relevance Ranking Strategies for MEDLINE Retrieval. AMIA 2008 - 2007
- [j37]Rezarta Islamaj Dogan, Lise Getoor, W. John Wilbur, Stephen M. Mount:
Features generated for computational splice-site prediction correspond to functional elements. BMC Bioinform. 8 (2007) - [j36]Jimmy Lin, W. John Wilbur:
PubMed related articles: a probabilistic topic-based model for content similarity. BMC Bioinform. 8 (2007) - [j35]Jimmy Lin, W. John Wilbur:
Syntactic sentence compression in the biomedical domain: facilitating access to related articles. Inf. Retr. 10(4-5): 393-414 (2007) - [j34]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. J. Biomed. Informatics 40(2): 150-159 (2007) - [j33]Rezarta Islamaj Dogan, Lise Getoor, W. John Wilbur, Stephen M. Mount:
SplicePort - An interactive splice-site analysis tool. Nucleic Acids Res. 35(Web-Server-Issue): 285-291 (2007) - [c24]W. John Wilbur:
Unsupervised Learning of the Morpho-Semantic Relationship in MEDLINE. BioNLP@ACL 2007: 201-208 - [c23]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 - [c22]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 - 2006
- [j32]W. John Wilbur, Andrey Rzhetsky, Hagit Shatkay:
New directions in biomedical text annotation: definitions, guidelines and corpus construction. BMC Bioinform. 7: 356 (2006) - [j31]W. John Wilbur, Won Kim, Natalie Xie:
Spelling correction in the PubMed search engine. Inf. Retr. 9(5): 543-564 (2006) - [j30]Lawrence H. Smith, Thomas C. Rindflesch, W. John Wilbur:
The importance of the lexicon in tagging biological text. Nat. Lang. Eng. 12(4): 335-351 (2006) - [j29]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) - [c21]Lorraine K. Tanabe, Lynne H. Thom, Wayne Matten, Donald C. Comeau, W. John Wilbur:
SemCat: Semantically Categorized Entities for Genomics. AMIA 2006 - [c20]Lorraine K. Tanabe, W. John Wilbur:
A Priority Model for Named Entities. BioNLP@NAACL-HLT 2006: 33-40 - [c19]Rezarta Islamaj Dogan, Lise Getoor, W. John Wilbur:
A Feature Generation Algorithm for Sequences with Application to Splice-Site Prediction. PKDD 2006: 553-560 - [c18]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 - 2005
- [j28]Lorraine K. Tanabe, Natalie Xie, Lynne H. Thom, Wayne Matten, W. John Wilbur:
GENETAG: a tagged corpus for gene/protein named entity recognition. BMC Bioinform. 6(S-1) (2005) - [j27]W. John Wilbur, Lana Yeganova, Won Kim:
The Synergy Between PAV and AdaBoost. Mach. Learn. 61(1-3): 71-103 (2005) - [c17]Won Kim, W. John Wilbur:
A Strategy for Assigning New Concepts in the MEDLINE Database. AMIA 2005 - [c16]Lawrence H. Smith, Lorraine K. Tanabe, Thomas C. Rindflesch, W. John Wilbur:
MedTag: A Collection of Biomedical Annotations. LBLODMBS@IDMB 2005: 32-37 - [c15]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:
Fusion of Knowledge-Intensive and Statistical Approaches for Retrieving and Annotating Textual Genomics Documents. TREC 2005 - 2004
- [j26]Lawrence H. Smith, Thomas C. Rindflesch, W. John Wilbur:
MedPost: a part-of-speech tagger for bioMedical text. Bioinform. 20(14): 2320-2321 (2004) - [j25]Lana Yeganova, Lawrence H. Smith, W. John Wilbur:
Identification of related gene/protein names based on an HMM of name variations. Comput. Biol. Chem. 28(2): 97-107 (2004) - [j24]Lawrence H. Smith, W. John Wilbur:
Retrieving definitional content for ontology development. Comput. Biol. Chem. 28(5-6): 387-391 (2004) - [j23]Donald C. Comeau, W. John Wilbur:
Non-word identification or spell checking without a dictionary. J. Assoc. Inf. Sci. Technol. 55(2): 169-177 (2004) - [j22]Lorraine K. Tanabe, W. John Wilbur:
Generation of a Large Gene/protein Lexicon by Morphological Pattern Analysis. J. Bioinform. Comput. Biol. 1(4): 611-626 (2004) - [j21]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. J. Biomed. Informatics 37(1): 43-53 (2004) - [c14]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- - [c13]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:
Knowledge-Intensive and Statistical Approaches to the Retrieval and Annotation of Genomics MEDLINE Citations. TREC 2004 - 2003
- [j20]Lawrence H. Smith, Lana Yeganova, W. John Wilbur:
Hidden Markov models and optimized sequence alignments. Comput. Biol. Chem. 27(1): 77-84 (2003) - [c12]W. John Wilbur, Won Kim:
The Dimensions of Indexing. AMIA 2003 - 2002
- [j19]Lorraine K. Tanabe, W. John Wilbur:
Tagging gene and protein names in biomedical text. Bioinform. 18(8): 1124-1132 (2002) - [j18]Hong Yu, Vasileios Hatzivassiloglou, Andrey Rzhetsky, W. John Wilbur:
Automatically identifying gene/protein terms in MEDLINE abstracts. J. Biomed. Informatics 35(5-6): 322-330 (2002) - [c11]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 - [c10]Won Kim, W. John Wilbur:
DNA splice site detection: a comparison of specific and general methods. AMIA 2002 - [c9]Hong Yu, Vasileios Hatzivassiloglou, Carol Friedman, Andrey Rzhetsky, W. John Wilbur:
Automatic extraction of gene and protein synonyms from MEDLINE and journal articles. AMIA 2002 - [c8]W. John Wilbur:
A Thematic Analysis of the AIDS Literature. Pacific Symposium on Biocomputing 2002: 386-397 - 2001
- [j17]Won Kim, W. John Wilbur:
Amino Acid Residue Environments and Predictions of Residue Type. Comput. Chem. 25(4): 411-422 (2001) - [j16]Won Kim, W. John Wilbur:
Corpus-based statistical screening for content-bearing terms. J. Assoc. Inf. Sci. Technol. 52(3): 247-259 (2001) - [j15]W. John Wilbur:
Global term weights for document retrieval learned from TREC data. J. Inf. Sci. 27(5): 303-310 (2001) - [c7]Won Kim, Alan R. Aronson, W. John Wilbur:
Automatic MeSH term assignment and quality assessment. AMIA 2001 - 2000
- [j14]W. John Wilbur, Andrew F. Neuwald:
A Theory of Information with Special Application to Search Problems. Comput. Chem. 24(1): 33-42 (2000) - [j13]Won Kim, W. John Wilbur:
Research Paper: Corpus-based Statistical Screening for Phrase Identification. J. Am. Medical Informatics Assoc. 7(5): 499-511 (2000) - [c6]Hagit Shatkay, W. John Wilbur:
Finding Themes in Medline Documents: Probabilistic Similarity Search. ADL 2000: 183-192 - [c5]Alan R. Aronson, Olivier Bodenreider, Florence Chang, Susanne M. Humphrey, James G. Mork, Stuart J. Nelson, Thomas C. Rindflesch, W. John Wilbur:
The NLM Indexing Initiative. AMIA 2000 - [c4]W. John Wilbur:
Boosting naïve Bayesian learning on a large subset of MEDLINE. AMIA 2000 - [c3]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
1990 – 1999
- 1999
- [c2]Stuart J. Nelson, Alan R. Aronson, Tamas E. Doszkocs, W. John Wilbur, Olivier Bodenreider, H. Florence Chang, James G. Mork, Alexa T. McCray:
Automated Assignment of Medical Subject Headings. AMIA 1999 - [c1]W. John Wilbur, George F. Hazard Jr., Guy Divita, James G. Mork, Alan R. Aronson, Allen C. Browne:
Analysis of biomedical text for chemical names: a comparison of three methods. AMIA 1999 - 1998
- [j12]W. John Wilbur:
A Comparison of Group and Individual Performance Among Subject Experts and Untrained Workers at the Document Retrieval Task. J. Am. Soc. Inf. Sci. 49(6): 517-529 (1998) - [j11]W. John Wilbur:
The Knowledge in Multiple Human Relevance Judgments. ACM Trans. Inf. Syst. 16(2): 101-126 (1998) - 1996
- [j10]W. John Wilbur, Yiming Yang:
An analysis of statistical term strength and its use in the indexing and retrieval of molecular biology texts. Comput. Biol. Medicine 26(3): 209-222 (1996) - [j9]W. John Wilbur:
Human Subjectivity and Performance Limits in Document Retrieval. Inf. Process. Manag. 32(5): 515-527 (1996) - [j8]Yiming Yang, W. John Wilbur:
Using Corpus Statistics to Remove Redundant Words in Text Categorization. J. Am. Soc. Inf. Sci. 47(5): 357-369 (1996) - 1994
- [j7]W. John Wilbur, Leona Coffee:
The Effectiveness of Document Neighboring in Search Enhancement. Inf. Process. Manag. 30(2): 253-266 (1994) - [j6]W. John Wilbur:
Non-parametric significance tests of retrieval performance comparisons. J. Inf. Sci. 20(4): 270-284 (1994) - 1993
- [j5]W. John Wilbur:
Retrieval Testing with Hypergeometric Document Models. J. Am. Soc. Inf. Sci. 44(6): 340-351 (1993) - 1992
- [j4]W. John Wilbur:
An information measure of retrieval performance. Inf. Syst. 17(4): 283-298 (1992) - [j3]W. John Wilbur:
Retrieval Testing by the Comparison of Statistically Independent Retrieval Methods. J. Am. Soc. Inf. Sci. 43(5): 358-370 (1992) - [j2]W. John Wilbur, Karl Sirotkin:
The automatic identification of stop words. J. Inf. Sci. 18(1): 45-55 (1992)
1980 – 1989
- 1984
- [j1]David J. Lipman, W. John Wilbur, Temple F. Smith, Michael S. Waterman:
On the statistical significance of nucleic acid similarities. Nucleic Acids Res. 12(1): 215-226 (1984)
Coauthor Index
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