High Throughput Modularized NLP System for Clinical Text. - Serguei V. S. Pakhomov; James D. Buntrock; Patrick H. Duffy (ACL, 2005)

Domain-specific language models and lexicons for tagging. - Anni Coden; Sergey V. Pakhomov; Rie Kubota Ando; Patrick H. Duffy; Christopher G. Chute (J. Biomed. Informatics, 2005)

Technical Brief: Mayo Clinic NLP System for Patient Smoking Status Identification. - Guergana K. Savova; Philip V. Ogren; Patrick H. Duffy; James D. Buntrock; Christopher G. Chute (J. Am. Medical Informatics Assoc., 2008)

TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data. - Yan W. Asmann; Sumit Middha; Asif Hossain; Saurabh Baheti; Ying Li; High-Seng Chai; Zhifu Sun; Patrick H. Duffy; Ahmed A. Hadad; Asha A. Nair; Xiaoyu Liu; Yuji Zhang 001; et al. (Bioinform., 2012)

The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation. - Jean-Pierre A. Kocher; Daniel J. Quest; Patrick H. Duffy; Michael A. Meiners; Raymond M. Moore; David N. Rider; Asif Hossain; Steven N. Hart; Valentin Dinu (Bioinform., 2014)

VCF-Miner: GUI-based application for mining variants and annotations stored in VCF files. - Steven N. Hart; Patrick H. Duffy; Daniel J. Quest; Asif Hossain; Michael A. Meiners; Jean-Pierre A. Kocher (Briefings Bioinform., 2016)