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Jianlin Shi, MD, PhD

Languages spoken: English

Academic Information

Departments Primary - Internal Medicine , Adjunct - Biomedical Informatics

Divisions: Epidemiology

Education History

Professional Medical West China Medical Center, Sichuan University
 BS, MD
Graduate Training West China Medical Center, Sichuan University
 MS
Residency West China Medical Center, Sichuan University
 Resident
Residency West China Medical Center, Sichuan University
 Chief Resident
Residency West China Medical Center, Sichuan University
 Resident
Graduate Training University of California, Irvine
 MS
Doctoral Training University of Utah
 PhD

Selected Publications

Journal Article

  1. Gan Q, Hu M, Peterson KS, Eyre H, Alba PR, Bowles AE, Stanley JC, DuVall SL, Shi J (2023). A deep learning approach for medication disposition and corresponding attributes extraction. J Biomed Inform, 143, 104391.
  2. Drum B, Shi J, Peterson B, Lamb S, Hurdle JF, Gradick C (2023). Using Natural Language Processing and Machine Learning to Identify Internal Medicine-Pediatrics Residency Values in Applications. Acad Med, 98(11), 1278-1282.
  3. Shi J, Morgan KL, Bradshaw RL, Jung SH, Kohlmann W, Kaphingst KA, Kawamoto K, Fiol GD (2022). Identifying Patients Who Meet Criteria for Genetic Testing of Hereditary Cancers Based on Structured and Unstructured Family Health History Data in the Electronic Health Record: Natural Language Processing Approach. JMIR Med Inform, 10(8), e37842.
  4. Shi J, Hurdle JF, Johnson SA, Ferraro JP, Skarda DE, Finlayson SRG, Samore MH, Bucher BT (2021). Natural language processing for the surveillance of postoperative venous thromboembolism. Surgery, 170(4), 1175-1182.
  5. Johnson SA, Signor EA, Lappe KL, Shi J, Jenkins SL, Wikstrom SW, Kroencke RD, Hallowell D, Jones AE, Witt DM (2021). A comparison of natural language processing to ICD-10 codes for identification and characterization of pulmonary embolism. Thromb Res, 203, 190-195.
  6. Bucher BT, Shi J, Ferraro JP, Skarda DE, Samore MH, Hurdle JF, Gundlapalli AV, Chapman WW, Finlayson SRG (2020). Portable Automated Surveillance of Surgical Site Infections Using Natural Language Processing: Development and Validation. Ann Surg, 272(4), 629-636.
  7. Bian J, Abdelrahman S, Shi J, Del Fiol G (2019). Automatic identification of recent high impact clinical articles in PubMed to support clinical decision making using time-agnostic features. J Biomed Inform, 89, 1-10.
  8. Shi J, Hurdle JF (2018). Trie-based rule processing for clinical NLP: A use-case study of n-trie, making the ConText algorithm more efficient and scalable. J Biomed Inform, 85, 106-113.
  9. Wang L, Bray BE, Shi J, Del Fiol G, Haug PJ (2016). A method for the development of disease-specific reference standards vocabularies from textual biomedical literature resources. Artif Intell Med, 68, 47-57.
  10. Kiser AC, Shi J, Bucher B (2024). An explainable long short-term memory network for surgical site infection identification. Surgery, 176(1), 24-31.
  11. Bradshaw RL, Kawamoto K, Kaphingst KA, Kohlmann WK, Hess R, Flynn MC, Nanjo CJ, Warner PB, Shi J, Morgan K, Kimball K, Ranade-Kharkar P, Ginsburg O, Goodman M, Chambers R, Mann D, Narus SP, Gonzalez J, Loomis S, Chan P, Monahan R, Borsato EP, Shields DE, Martin DK, Kessler CM, Del Fiol (2022). GARDE: a standards-based clinical decision support platform for identifying population health management cohorts. Journal of the American Medical Informatics Association, 29(5), 928-936.
  12. Eyre H, Chapman AB, Peterson KS, Shi J, Alba PR, Jones MM, Box TL, DuVall SL, Patterson O (2022). Launching into clinical space with medspaCy: a new clinical text processing toolkit in Python. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2021, 438-447.
  13. Shi J, Liu S, Pruitt LCC, Luppens CL, Ferraro JP, Gundlapalli AV, Chapman WW, Bucher B (2020). Using Natural Language Processing to improve EHR Structured Data-based Surgical Site Infection Surveillance. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2019, 794-803.
  14. Bucher BT, Shi J, Pettit RJ, Ferraro J, Chapman WW, Gundlapalli (2020). Determination of Marital Status of Patients from Structured and Unstructured Electronic Healthcare Data. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2019, 267-274.