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Donald C. Comeau
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Journal Articles
- 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) - 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) - 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) - 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) - 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) - 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) - 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) - 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) - 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) - 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) - 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)
Conference and Workshop Papers
- 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 - 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 - 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
- [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 - 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
- [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
- [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 - 2006
- [c1]Lorraine K. Tanabe, Lynne H. Thom, Wayne Matten, Donald C. Comeau, W. John Wilbur:
SemCat: Semantically Categorized Entities for Genomics. AMIA 2006
Informal and Other Publications
- 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) - 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) - 2018
- [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)
Coauthor Index
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