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2020 – today
- 2023
[j26]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)- [j25]Eric W. Sayers, Evan E. Bolton, J. Rodney Brister, Kathi Canese, Jessica Chan, Donald C. Comeau, Catherine M. Farrell, Michael Feldgarden, Anna M. Fine, Kathryn Funk, Eneida Hatcher, Sivakumar Kannan, Christopher Kelly, Sunghwan Kim, William Klimke, Melissa J. Landrum, Stacy Lathrop, Zhiyong Lu, Thomas L. Madden, Adriana J. Malheiro, Aron Marchler-Bauer, Terence D. Murphy, Lon Phan, Shashikant Pujar, Sanjida H. Rangwala, Valerie A. Schneider, Tony Tse, Jiyao Wang, Jian Ye, Barton W. Trawick, Kim D. Pruitt, Stephen T. Sherry:
Database resources of the National Center for Biotechnology Information in 2023. Nucleic Acids Res. 51(D1): 29-38 (2023) - [i4]Shubo Tian, Qiao Jin, Lana Yeganova, Po-Ting Lai, Qingqing Zhu, Xiuying Chen, Yifan Yang, Qingyu Chen, Won Kim, Donald C. Comeau, Rezarta Islamaj, Aadit Kapoor, Xin Gao, Zhiyong Lu:
Opportunities and Challenges for ChatGPT and Large Language Models in Biomedicine and Health. CoRR abs/2306.10070 (2023) - [i3]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
- [j24]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) - [j23]Eric W. Sayers, Evan E. Bolton, J. Rodney Brister, Kathi Canese, Jessica Chan, Donald C. Comeau, Ryan Connor, Kathryn Funk, Chris Kelly, Sunghwan Kim, Tom Madej, Aron Marchler-Bauer, Christopher J. Lanczycki, Stacy Lathrop, Zhiyong Lu, Françoise Thibaud-Nissen, Terence D. Murphy, Lon Phan, Yuri Skripchenko, Tony Tse, Jiyao Wang, Rebecca Williams, Barton W. Trawick, Kim D. Pruitt, Stephen T. Sherry:
Database resources of the national center for biotechnology information. Nucleic Acids Res. 50(D1): 20-26 (2022) - 2021
- [j22]Eric W. Sayers, Jeffrey Beck, Evan Bolton, Devon Bourexis, James R. Brister, Kathi Canese, Donald C. Comeau, Kathryn Funk, Sunghwan Kim, William Klimke, Aron Marchler-Bauer, Melissa J. Landrum, Stacy Lathrop, Zhiyong Lu, Thomas L. Madden, Nuala A. O'Leary, Lon Phan, Sanjida H. Rangwala, Valerie A. Schneider, Yuri Skripchenko, Jiyao Wang, Jian Ye, Barton W. Trawick, Kim D. Pruitt, Stephen T. Sherry:
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 49(Database-Issue): D10-D17 (2021) - [c15]Lana Yeganova, Won Kim, Donald C. Comeau, W. John Wilbur, Zhiyong Lu:
Improving PubMed Retrieval by Integrating Abstract and Full Text Search. AMIA 2021 - [c14]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
- [j21]Eric W. Sayers, Jeffrey Beck, J. Rodney Brister, Evan Bolton, Kathi Canese, Donald C. Comeau, Kathryn Funk, Anne Ketter, Sunghwan Kim, Avi Kimchi, Paul A. Kitts, Anatoliy Kuznetsov, Stacy Lathrop, Zhiyong Lu, Kelly M. McGarvey, Thomas L. Madden, Terence D. Murphy, Nuala A. O'Leary, Lon Phan, Valerie A. Schneider, Françoise Thibaud-Nissen, Barton W. Trawick, Kim D. Pruitt, James Ostell:
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 48(Database-Issue): D9-D16 (2020) - [i2]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
- [j20]Rezarta Islamaj Dogan, Sun Kim, Andrew Chatr-aryamontri, Chih-Hsuan Wei, Donald C. Comeau, Rui Antunes, Sérgio Matos, Qingyu Chen, Aparna Elangovan, Nagesh C. Panyam, Karin Verspoor, Hongfang Liu, Yanshan Wang, Zhuang Liu, Berna Altinel, Zehra Melce Hüsünbeyi, Arzucan Özgür, Aris Fergadis, Chen-Kai Wang, Hong-Jie Dai, Tung Tran, Ramakanth Kavuluru, Ling Luo, Albert Steppi, Jinfeng Zhang, Jinchan Qu, Zhiyong Lu:
Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine. Database J. Biol. Databases Curation 2019: bay147 (2019) - [j19]Donald C. Comeau, Chih-Hsuan Wei, Rezarta Islamaj Dogan, Zhiyong Lu:
PMC text mining subset in BioC: about three million full-text articles and growing. Bioinform. 35(18): 3533-3535 (2019) - [j18]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) - 2018
- [j17]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) - [c13]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 - [c12]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 - [i1]Donald C. Comeau, Chih-Hsuan Wei, Rezarta Islamaj Dogan, Zhiyong Lu:
PMC text mining subset in BioC: 2.3 million full text articles and growing. CoRR abs/1804.05957 (2018) - 2017
- [j16]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) - [c11]Rezarta Islamaj Dogan, Andrew Chatr-aryamontri, Sun Kim, Chih-Hsuan Wei, Yifan Peng, Donald C. Comeau, Zhiyong Lu:
BioCreative VI Precision Medicine Track: creating a training corpus for mining protein-protein interactions affected by mutations. BioNLP 2017: 171-175 - 2016
- [j15]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) - [c10]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 - [c9]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 - 2015
- [j14]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) - 2014
- [j13]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) - [j12]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) - [j11]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) - [j10]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) - [j9]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) - 2013
- [j8]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) - [c8]Donald C. Comeau, Rezarta Islamaj Dogan, W. John Wilbur:
BioC: A Minimalist Approach to Interoperability for Biomedical Text Processing. AMIA 2013 - [c7]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 - [c6]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
- [j7]Lana Yeganova, Won Kim, Donald C. Comeau, W. John Wilbur:
Finding biomedical categories in Medline®. J. Biomed. Semant. 3(S-3): S3 (2012) - [j6]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) - [c5]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
- [j5]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) - [c4]Lana Yeganova, Donald C. Comeau, Won Kim, W. John Wilbur:
Text Mining Techniques for Leveraging Positively Labeled Data. BioNLP@ACL 2011: 155-163 - [c3]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
- [c2]Lana Yeganova, Donald C. Comeau, W. John Wilbur:
Identifying Abbreviation Definitions Machine Learning with Naturally Labeled Data. ICMLA 2010: 499-505
2000 – 2009
- 2009
- [j4]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) - 2008
- [j3]Sunghwan Sohn, Donald C. Comeau, Won Kim, W. John Wilbur:
Abbreviation definition identification based on automatic precision estimates. BMC Bioinform. 9 (2008) - [j2]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) - 2006
- [c1]Lorraine K. Tanabe, Lynne H. Thom, Wayne Matten, Donald C. Comeau, W. John Wilbur:
SemCat: Semantically Categorized Entities for Genomics. AMIA 2006 - 2004
- [j1]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)
Coauthor Index
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