Donald C. Comeau

Publication Activity (10 Years)

Years Active: 2004-2023
Publications (10 Years): 23

Top Topics

Training Corpus

Medline Abstracts

Biomedical Literature

Biomedical Information Retrieval

Top Venues

Database J. Biol. Databases Curation

Nucleic Acids Res.

Publications

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 (2023)
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 (2023)
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)
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) (2023)
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) (2022)
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 (2022)
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)
Lana Yeganova, Won Kim, Donald C. Comeau, W. John Wilbur, Zhiyong Lu
Improving PubMed Retrieval by Integrating Abstract and Full Text Search. AMIA (2021)
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) (2021)
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 (2020)
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) (2020)
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) (2019)
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 (2019)
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) (2019)
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 (2018)
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 (2018)
Won Kim, Lana Yeganova, Donald C. Comeau, W. John Wilbur, Zhiyong Lu
MeSH-based dataset for measuring the relevance of text retrieval. BioNLP (2018)
Lana Yeganova, Donald C. Comeau, Won Kim, W. John Wilbur, Zhiyong Lu
SingleCite: Towards an improved Single Citation Search in PubMed. BioNLP (2018)
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 (2017)
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)
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)
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)
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)
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) (2015)
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)
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)
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)
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) (2014)
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)
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)
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)
Donald C. Comeau, Rezarta Islamaj Dogan, W. John Wilbur
BioC: A Minimalist Approach to Interoperability for Biomedical Text Processing. AMIA (2013)
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)
Won Kim, Lana Yeganova, Donald C. Comeau, W. John Wilbur
Identifying well-formed biomedical phrases in MEDLINE® text. J. Biomed. Informatics 45 (6) (2012)
Lana Yeganova, Won Kim, Donald C. Comeau, W. John Wilbur
. J. Biomed. Semant. 3 (S-3) (2012)
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)
Lana Yeganova, Donald C. Comeau, Won Kim, W. John Wilbur
Text Mining Techniques for Leveraging Positively Labeled Data. BioNLP@ACL (2011)
Lana Yeganova, Donald C. Comeau, W. John Wilbur
Machine learning with naturally labeled data for identifying abbreviation definitions. BMC Bioinform. 12 (S-3) (2011)
Lana Yeganova, Won Kim, Donald C. Comeau, W. John Wilbur
Comparison of Two Methods for Finding Biomedical Categories in Medline. ICMLA (2) (2011)
Lana Yeganova, Donald C. Comeau, W. John Wilbur
Identifying Abbreviation Definitions Machine Learning with Naturally Labeled Data. ICMLA (2010)
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) (2009)
Sunghwan Sohn, Won Kim, Donald C. Comeau, W. John Wilbur
Assignment. J. Am. Medical Informatics Assoc. 15 (4) (2008)
Sunghwan Sohn, Donald C. Comeau, Won Kim, W. John Wilbur
Abbreviation definition identification based on automatic precision estimates. BMC Bioinform. 9 (2008)
Lorraine K. Tanabe, Lynne H. Thom, Wayne Matten, Donald C. Comeau, W. John Wilbur
SemCat: Semantically Categorized Entities for Genomics. AMIA (2006)
Donald C. Comeau, W. John Wilbur
Non-word identification or spell checking without a dictionary. J. Assoc. Inf. Sci. Technol. 55 (2) (2004)