ASU at TREC 2006 Genomics Track. - Luis Tari; Graciela Gonzalez 001; Robert Leaman; Shawn Nikkila; Ryan Wendt; Chitta Baral (TREC, 2006)

Passage Relevancy Through Semantic Relatedness. - Luis Tari; Phan Huy Tu; Barry Lumpkin; Robert Leaman; Graciela Gonzalez 001; Chitta Baral (TREC, 2007)

Inter-species normalization of gene mentions with GNAT. - Jörg Hakenberg; Conrad Plake; Robert Leaman; Michael Schroeder 001; Graciela Gonzalez 001 (ECCB, 2008)

BANNER: An Executable Survey of Advances in Biomedical Named Entity Recognition. - Robert Leaman; Graciela Gonzalez 001 (Pacific Symposium on Biocomputing, 2008)

Towards Internet-Age Pharmacovigilance: Extracting Adverse Drug Reactions from User Posts in Health-Related Social Networks. - Robert Leaman; Laura Wojtulewicz; Ryan Sullivan; Annie Skariah; Jian Yang 026; Graciela Gonzalez 001 (BioNLP@ACL, 2010)

A Distributional Semantics Approach to Simultaneous Recognition of Multiple Classes of Named Entities. - Siddhartha Jonnalagadda; Robert Leaman; Trevor Cohen; Graciela Gonzalez 001 (CICLing, 2010)

Efficient Extraction of Protein-Protein Interactions from Full-Text Articles. - Jörg Hakenberg; Robert Leaman; Nguyen Ha Vo; Siddhartha Jonnalagadda; Ryan Sullivan; Christopher Miller; Luis Tari; Chitta Baral; Graciela Gonzalez 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2010)

The DIEGO Lab Graph Based Gene Normalization System. - Ryan Sullivan; Robert Leaman; Graciela Gonzalez 001 (ICMLA (2), 2011)

The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. - 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; et al. (BMC Bioinform., 2011)

Enhancing phylogeography by improving geographical information from GenBank. - Matthew Scotch; Indra Neil Sarkar; Changjiang Mei; Robert Leaman; Kei-Hoi Cheung; Pierina Ortiz; Ashutosh Singraur; Graciela Gonzalez 001 (J. Biomed. Informatics, 2011)

A SNPshot of PubMed to associate genetic variants with drugs, diseases, and adverse reactions. - Jörg Hakenberg; Dmitry Voronov; Nguyen Ha Vo; Shanshan Liang; Saadat Anwar; Barry Lumpkin; Robert Leaman; Luis Tari; Chitta Baral (J. Biomed. Informatics, 2012)

NCBI Disease Corpus: A Valuable Resource for Disease Name Recognition and Normalization. - Rezarta Islamaj Dogan; Robert Leaman; Zhiyong Lu (AMIA, 2013)

DNorm: A New Method and Online Tool for Disease Name Normalization. - Robert Leaman; Rezarta Islamaj Dogan; Chih-Hsuan Wei; Zhiyong Lu (AMIA, 2013)

NCBI at 2013 ShARe/CLEF eHealth Shared Task: Disorder Normalization in Clinical Notes with Dnorm. - Robert Leaman; Ritu Khare; Zhiyong Lu (CLEF (Working Notes), 2013)

Session introduction. - Graciela Gonzalez 001; Kevin Bretonnel Cohen; Casey S. Greene; Udo Hahn; Maricel G. Kann; Robert Leaman; Nigam Shah; Jieping Ye (Pacific Symposium on Biocomputing, 2013)

DNorm: disease name normalization with pairwise learning to rank. - Robert Leaman; Rezarta Islamaj Dogan; Zhiyong Lu (Bioinform., 2013)

Disease named entity recognition and normalization with DNorm. - Robert Leaman; Zhiyong Lu (BCB, 2014)

SimConcept: a hybrid approach for simplifying composite named entities in biomedicine. - Chih-Hsuan Wei; Robert Leaman; Zhiyong Lu (BCB, 2014)

Automated Disease Normalization with Low Rank Approximations. - Robert Leaman; Zhiyong Lu (BioNLP@ACL, 2014)

Session introduction. - Graciela Gonzalez 001; Kevin Bretonnel Cohen; Robert Leaman; Casey S. Greene; Nigam Shah; Maricel G. Kann; Jieping Ye (Pacific Symposium on Biocomputing, 2014)

tmBioC: improving interoperability of text-mining tools with BioC. - Ritu Khare; Chih-Hsuan Wei; Yuqing Mao; Robert Leaman; Zhiyong Lu (Database J. Biol. Databases Curation, 2014)

NCBI disease corpus: A resource for disease name recognition and concept normalization. - Rezarta Islamaj Dogan; Robert Leaman; Zhiyong Lu (J. Biomed. Informatics, 2014)

Session Introduction. - Robert Leaman; Benjamin M. Good; Andrew I. Su; Zhiyong Lu (Pacific Symposium on Biocomputing, 2015)

Challenges in clinical natural language processing for automated disorder normalization. - Robert Leaman; Ritu Khare; Zhiyong Lu (J. Biomed. Informatics, 2015)

The CHEMDNER corpus of chemicals and drugs and its annotation principles. - Martin Krallinger; Obdulia Rabal; Florian Leitner; Miguel Vazquez; David Salgado; Zhiyong Lu; Robert Leaman; Yanan Lu; Donghong Ji; Daniel M. Lowe; Roger A. Sayle; Riza Theresa Batista-Navarro; et al. (J. Cheminformatics, 2015)

tmChem: a high performance approach for chemical named entity recognition and normalization. - Robert Leaman; Chih-Hsuan Wei; Zhiyong Lu (J. Cheminformatics, 2015)

SimConcept: A Hybrid Approach for Simplifying Composite Named Entities in Biomedical Text. - Chih-Hsuan Wei; Robert Leaman; Zhiyong Lu (IEEE J. Biomed. Health Informatics, 2015)

Large-scale Semantic Indexing with Biomedical Ontologies. - Chih-Hsuan Wei; Robert Leaman; Zhiyong Lu (ICBO/BioCreative, 2016)

Crowdsourcing in biomedicine: challenges and opportunities. - Ritu Khare; Benjamin M. Good; Robert Leaman; Andrew I. Su; Zhiyong Lu (Briefings Bioinform., 2016)

Mining chemical patents with an ensemble of open systems. - Robert Leaman; Chih-Hsuan Wei; Cherry Zou; Zhiyong Lu (Database J. Biol. Databases Curation, 2016)

BioCreative V CDR task corpus: a resource for chemical disease relation extraction. - Jiao Li 001; Yueping Sun; Robin J. Johnson; Daniela Sciaky; Chih-Hsuan Wei; Robert Leaman; Allan Peter Davis; Carolyn J. Mattingly; Thomas C. Wiegers; Zhiyong Lu (Database J. Biol. Databases Curation, 2016)

Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges. - Ayush Singhal; Robert Leaman; Natalie L. Catlett; Thomas Lemberger 001; Johanna R. McEntyre; Shawn W. Polson; Ioannis Xenarios; Cecilia N. Arighi; Zhiyong Lu (Database J. Biol. Databases Curation, 2016)

Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task. - Chih-Hsuan Wei; Yifan Peng 002; Robert Leaman; Allan Peter Davis; Carolyn J. Mattingly; Jiao Li 001; Thomas C. Wiegers; Zhiyong Lu (Database J. Biol. Databases Curation, 2016)

TaggerOne: joint named entity recognition and normalization with semi-Markov Models. - Robert Leaman; Zhiyong Lu (Bioinform., 2016)

Beyond accuracy: creating interoperable and scalable text-mining web services. - Chih-Hsuan Wei; Robert Leaman; Zhiyong Lu (Bioinform., 2016)

ezTag: tagging biomedical concepts via interactive learning. - Dongseop Kwon; Sun Kim; Chih-Hsuan Wei; Robert Leaman; Zhiyong Lu (Nucleic Acids Res., 2018)

A Text-Mining System for Concept Annotation in Biomedical Full Text Articles. - Chih-Hsuan Wei; Alexis Allot; Robert Leaman; Zhiyong Lu (BCB, 2019)

Biomedical Mention Disambiguation using a Deep Learning Approach. - Chih-Hsuan Wei; Kyubum Lee; Robert Leaman; Zhiyong Lu (BCB, 2019)

Text Mining and Machine Learning for Precision Medicine. - Graciela Gonzalez 001; Zhiyong Lu; Robert Leaman; Davy Weissenbacher; Mary Regina Boland; Yong Chen 016; Jingcheng Du; Juliane Fluck; Casey S. Greene; John H. Holmes; Aditya Kashyap; Rikke Linnemann Nielsen; et al. (PSB, 2019)

PubTator central: automated concept annotation for biomedical full text articles. - Chih-Hsuan Wei; Alexis Allot; Robert Leaman; Zhiyong Lu (Nucleic Acids Res., 2019)

A Comprehensive Dictionary and Term Variation Analysis for COVID-19 and SARS-CoV-2. - Robert Leaman; Zhiyong Lu (NLP4COVID@EMNLP, 2020)

Navigating the landscape of COVID-19 research through literature analysis: A bird's eye view. - Lana Yeganova; Rezarta Islamaj Dogan; Qingyu Chen 001; Robert Leaman; Alexis Allot; Chih-Hsuan Wei; Donald C. Comeau; Won Kim 003; Yifan Peng 002; W. John Wilbur; Zhiyong Lu (CoRR, 2020)

Artificial Intelligence (AI) in Action: Addressing the COVID-19 Pandemic with Natural Language Processing (NLP). - Qingyu Chen 001; Robert Leaman; Alexis Allot; Ling Luo 001; Chih-Hsuan Wei; Shankai Yan; Zhiyong Lu (CoRR, 2020)

NLM-Chem, a Gold-Standard Corpus for Chemical Entity Recognition in PubMed Full Text Literature. - Rezarta Islamaj; Robert Leaman; David Cissel; Cathleen Coss; Carol Fisher; Rob Guzman; Preeti Gokal Kochar; Dorothy Trinh; Deborah Whitman; Keiko Sekiya; Zhiyong Lu (AMIA, 2021)

Long Covid: A Comprehensive Collection of Articles Regarding Long-Haul Symptoms in COVID-19 Survivors. - Robert Leaman; Qingyu Chen 001; Alexis Allot; Zhiyong Lu (AMIA, 2021)

Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations. - Qingyu Chen 001; Alexis Allot; Robert Leaman; Rezarta Islamaj; Jingcheng Du; Li Fang; Wang Kai; Shuo Xu 001; Yuefu Zhang; Parsa Bagherzadeh; Sabine Bergler; Aakash Bhatnagar; et al. (Database J. Biol. Databases Curation, 2022)

NLM-Chem-BC7: manually annotated full-text resources for chemical entity annotation and indexing in biomedical articles. - Rezarta Islamaj; Robert Leaman; David Cissel; Cathleen Coss; Joseph Denicola; Carol Fisher; Rob Guzman; Preeti Gokal Kochar; Nicholas Miliaras; Zoe Punske; Keiko Sekiya; Dorothy Trinh; et al. (Database J. Biol. Databases Curation, 2022)

Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations. - Qingyu Chen 001; Alexis Allot; Robert Leaman; Rezarta Islamaj Dogan; Jingcheng Du; Li Fang; Wang Kai; Shuo Xu 001; Yuefu Zhang; Parsa Bagherzadeh; Sabine Bergler; Aakash Bhatnagar; et al. (CoRR, 2022)

Comprehensive identification of Long Covid articles with human-in-the-loop machine learning. - Robert Leaman; Rezarta Islamaj Dogan; Alexis Allot; Qingyu Chen 001; W. John Wilbur; Zhiyong Lu (CoRR, 2022)

Chemical identification and indexing in full-text articles: an overview of the NLM-Chem track at BioCreative VII. - Robert Leaman; Rezarta Islamaj; Virginia Adams; Mohammed Alliheedi; João Rafael Almeida; Rui Antunes 002; Robert Bevan; Yung-Chun Chang; Arslan Erdengasileng; Matthew Hodgskiss; Ryuki Ida; Hyunjae Kim; et al. (Database J. Biol. Databases Curation, 2023)

PubMed and Beyond: Recent Advances and Best Practices in Biomedical Literature Search. - Qiao Jin 001; Robert Leaman; Zhiyong Lu (CoRR, 2023)

LitCovid in 2022: an information resource for the COVID-19 literature. - Qingyu Chen 001; Alexis Allot; Robert Leaman; Chih-Hsuan Wei; Elaheh Aghaarabi; John J. Guerrerio; Lilly Xu; Zhiyong Lu (Nucleic Acids Res., 2023)

Comprehensively identifying Long Covid articles with human-in-the-loop machine learning. - Robert Leaman; Rezarta Islamaj; Alexis Allot; Qingyu Chen 001; W. John Wilbur; Zhiyong Lu (Patterns, 2023)

AIONER: all-in-one scheme-based biomedical named entity recognition using deep learning. - Ling Luo 001; Chih-Hsuan Wei; Po-Ting Lai; Robert Leaman; Qingyu Chen 001; Zhiyong Lu (Bioinform., 2023)

PubTator 3.0: an AI-powered Literature Resource for Unlocking Biomedical Knowledge. - Chih-Hsuan Wei; Alexis Allot; Po-Ting Lai; Robert Leaman; Shubo Tian; Ling Luo 001; Qiao Jin 001; Zhizheng Wang; Qingyu Chen 001; Zhiyong Lu (CoRR, 2024)

EnzChemRED, a rich enzyme chemistry relation extraction dataset. - Po-Ting Lai; Elisabeth Coudert; Lucila Aimo; Kristian B. Axelsen; Lionel Breuza; Edouard De Castro; Marc Feuermann; Anne Morgat; Lucille Pourcel; Ivo Pedruzzi; Sylvain Poux; Nicole Redaschi; et al. (CoRR, 2024)

Demystifying Large Language Models for Medicine: A Primer. - Qiao Jin 001; Nicholas Wan; Robert Leaman; Shubo Tian; Zhizheng Wang; Yifan Yang 006; Zifeng Wang 008; Guangzhi Xiong; Po-Ting Lai; Qingqing Zhu; Benjamin Hou; Maame Sarfo-Gyamfi; et al. (CoRR, 2024)

Ensuring Safety and Trust: Analyzing the Risks of Large Language Models in Medicine. - Yifan Yang 006; Qiao Jin 001; Robert Leaman; Xiaoyu Liu 003; Guangzhi Xiong; Maame Sarfo-Gyamfi; Changlin Gong; Santiago Ferrière-Steinert; W. John Wilbur; Xiaojun Li; Jiaxin Yuan; Bang An 001; et al. (CoRR, 2024)

Archive of PubTator 3.0 source code and trained models. - Chih-Hsuan Wei; Alexis Allot; Po-Ting Lai; Robert Leaman; Shubo Tian; Ling Luo 001; Qiao Jin 001; Zhizheng Wang; Qingyu Chen 001; Zhiyong Lu (Zenodo, 2024)

EnzChemRED, a rich enzyme chemistry relation extraction dataset. - Po-Ting Lai; Elisabeth Coudert; Lucila Aimo; Kristian B. Axelsen; Lionel Breuza; Edouard De Castro; Marc Feuermann; Anne Morgat; Lucille Pourcel; Ivo Pedruzzi; Sylvain Poux; Nicole Redaschi; et al. (Zenodo, 2024)

Enhancing Biomedical Relation Extraction with Directionality. - Po-Ting Lai; Chih-Hsuan Wei; Shubo Tian; Robert Leaman; Zhiyong Lu (CoRR, 2025)

Knowledge-guided Contextual Gene Set Analysis Using Large Language Models. - Zhizheng Wang; Chi-Ping Day; Chih-Hsuan Wei; Qiao Jin 001; Robert Leaman; Yifan Yang 006; Shubo Tian; Aodong Qiu; Yin Fang; Qingqing Zhu; Xinghua Lu 001; Zhiyong Lu (CoRR, 2025)