Online Patient Center: Expanding Patient Portals by Integrating Patient-Generated Data Directly into a Primary Care Provider's EHR Workflow. - Jon-David Ethington; Jianlin Shi; Scott D. Nelson (AMIA, 2014)

POETenceph - Automatic identification of clinical notes indicating encephalopathy using a realist ontology. - Kristina Doing-Harris; Charlene R. Weir; Sean Igo; Jianlin Shi; YiJun Shao; John F. Hurdle (AMIA, 2015)

UtahPOET: Disorder Mention Identification and Context Slot Filling with Cognitive Inspiration. - Kristina Doing-Harris; Sean Igo; Jianlin Shi; John F. Hurdle (SemEval@NAACL-HLT, 2015)

RuSH: a Rule-based Segmentation Tool Using Hashing for Extremely Accurate Sentence Segmentation of Clinical Text. - Jianlin Shi; Danielle L. Mowery; Kristina M. Doing-Harris; John F. Hurdle (AMIA, 2016)

PrecMed: A collaborative environment for precision medicine research and practice. - Jianlin Shi; Lance Pflieger (AMIA, 2016)

A method for the development of disease-specific reference standards vocabularies from textual biomedical literature resources. - Liqin Wang; Bruce E. Bray; Jianlin Shi; Guilherme Del Fiol; Peter J. Haug (Artif. Intell. Medicine, 2016)

Extracting Intrauterine Device Usage from Clinical Texts Using Natural Language Processing. - Jianlin Shi; Danielle L. Mowery; Mingyuan Zhang; Jessica Sanders; Wendy W. Chapman; Lori Gawron (ICHI, 2017)

Trie-based rule processing for clinical NLP: A use-case study of n-trie, making the ConText algorithm more efficient and scalable. - Jianlin Shi; John F. Hurdle (J. Biomed. Informatics, 2018)

Determination of Marital Status of Patients from Structured and Unstructured Electronic Healthcare Data. - Brian T. Bucher; Jianlin Shi; Robert J. Pettit; Jeffrey P. Ferraro; Wendy W. Chapman; Adi V. Gundlapalli (AMIA, 2019)

Extracting Disease Onset from Family History Comments in the Electronic Health Record using Fast Healthcare Interoperability Resources. - Jianlin Shi; Kensaku Kawamoto; Wendy Kohlmann; Danielle L. Mowery; Richard L. Bradshaw; Subhadeep Deep; Wendy W. Chapman; Guilherme Del Fiol (AMIA, 2019)

Using Natural Language Processing to improve EHR Structured Data-based Surgical Site Infection Surveillance. - Jianlin Shi; Siru Liu; Liese C. Pruitt; Carolyn Luppens; Jeffrey P. Ferraro; Adi V. Gundlapalli; Wendy W. Chapman; Brian T. Bucher (AMIA, 2019)

FastContext: an efficient and scalable implementation of the ConText algorithm. - Jianlin Shi; John F. Hurdle (CoRR, 2019)

A generic rule-based system for clinical trial patient selection. - Jianlin Shi; Kevin Graves; John F. Hurdle (CoRR, 2019)

Automatic identification of recent high impact clinical articles in PubMed to support clinical decision making using time-agnostic features. - Jiantao Bian; Samir E. AbdelRahman; Jianlin Shi; Guilherme Del Fiol (J. Biomed. Informatics, 2019)

Removing barriers to clinical text processing with MedSpaCy. - Hannah Eyre; Olga V. Patterson; Jianlin Shi; Kelly S. Peterson; Alec B. Chapman; Patrick R. Alba; Scott L. DuVall (AMIA, 2020)

Launching into clinical space with medspaCy: a new clinical text processing toolkit in Python. - Hannah Eyre; Alec B. Chapman; Kelly S. Peterson; Jianlin Shi; Patrick R. Alba; Makoto M. Jones; Tamara L. Box; Scott L. DuVall; Olga V. Patterson (AMIA, 2021)

GARDE: a standards-based clinical decision support platform for identifying population health management cohorts. - Richard L. Bradshaw; Kensaku Kawamoto; Kimberly A. Kaphingst; Wendy Kohlmann; Rachel Hess; Michael C. Flynn; Claude J. Nanjo; Phillip B. Warner; Jianlin Shi; Keaton L. Morgan; Kadyn Kimball; Pallavi Ranade-Kharkar; et al. (J. Am. Medical Informatics Assoc., 2022)

A deep learning approach for medication disposition and corresponding attributes extraction. - Qiwei Gan; Mengke Hu; Kelly S. Peterson; Hannah Eyre; Patrick R. Alba; Annie E. Bowles; Johnathan C. Stanley; Scott L. DuVall; Jianlin Shi (J. Biomed. Informatics, 2023)

Representing and utilizing clinical textual data for real world studies: An OHDSI approach. - Vipina Kuttichi Keloth; Juan M. Banda; Michael J. Gurley; Paul M. Heider; Georgina Kennedy; Hongfang Liu; Feifan Liu; Timothy Miller 002; Karthik Natarajan; Olga V. Patterson; Yifan Peng 002; Kalpana Raja; et al. (J. Biomed. Informatics, 2023)

Accelerating Clinical NLP at Scale with a Hybrid Framework with Reduced GPU Demands: A Case Study in Dementia Identification. - Jianlin Shi; Qiwei Gan; Elizabeth Hanchrow; Annie E. Bowles; Johnathan C. Stanley; Adam Bress; Jordana B. Cohen; Patrick R. Alba (CoRR, 2025)

Initial Investigation of LLM-Assisted Development of Rule-Based Clinical NLP System. - Jianlin Shi; Brian T. Bucher (CoRR, 2025)