Donald C. Comeau

49 papers C 1Misc 3Journal 34Unranked 11
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
2026 J jnl
Med-V1: Small Language Models for Zero-shot and Scalable Biomedical Evidence Attribution.
CoRR
Qiao Jin, Yin Fang, Lauren He, Yifan Yang, Guangzhi Xiong, Zhizheng Wang, Nicholas Wan, Joey Chan, Donald C. Comeau, Robert Leaman, Charalampos S. Floudas, Aidong Zhang, Michael F. Chiang, Yifan Peng, Zhiyong Lu
2024 J jnl
Opportunities and challenges for ChatGPT and large language models in biomedicine and health.
Briefings Bioinform.
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
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
Database resources of the National Center for Biotechnology Information in 2023.
Nucleic Acids Res.
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
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
2023 J jnl
Opportunities and Challenges for ChatGPT and Large Language Models in Biomedicine and Health.
CoRR
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
2022 J jnl
Database resources of the national center for biotechnology information.
Nucleic Acids Res.
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
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 J jnl
Database resources of the National Center for Biotechnology Information.
Nucleic Acids Res.
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
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
Database resources of the National Center for Biotechnology Information.
Nucleic Acids Res.
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
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
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
Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine.
Database J. Biol. Databases Curation
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
2019 J jnl
PMC text mining subset in BioC: about three million full-text articles and growing.
Bioinform.
Donald C. Comeau, Chih-Hsuan Wei, Rezarta Islamaj Dogan, 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 — 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 J jnl
PMC text mining subset in BioC: 2.3 million full text articles and growing.
CoRR
Donald C. Comeau, Chih-Hsuan Wei, Rezarta Islamaj Dogan, 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 — conf
BioCreative VI Precision Medicine Track: creating a training corpus for mining protein-protein interactions affected by mutations.
BioNLP
Rezarta Islamaj Dogan, Andrew Chatr-aryamontri, Sun Kim, Chih-Hsuan Wei, Yifan Peng, Donald C. Comeau, 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 — 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 — 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
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
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
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
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
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
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
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
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
Machine learning with naturally labeled data for identifying abbreviation definitions.
BMC Bioinform.
Lana Yeganova, Donald C. Comeau, W. John Wilbur
2011 — conf
Text Mining Techniques for Leveraging Positively Labeled Data.
BioNLP@ACL
Lana Yeganova, Donald C. Comeau, Won Kim, W. John Wilbur
2010 C conf
Identifying Abbreviation Definitions Machine Learning with Naturally Labeled Data.
ICMLA
Lana Yeganova, Donald C. Comeau, 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
2008 J jnl
Abbreviation definition identification based on automatic precision estimates.
BMC Bioinform.
Sunghwan Sohn, Donald C. Comeau, Won Kim, 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
2006 Misc conf
SemCat: Semantically Categorized Entities for Genomics.
AMIA
Lorraine K. Tanabe, Lynne H. Thom, Wayne Matten, Donald C. Comeau, 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