An application of conditional logistic regression and multifactor dimensionality reduction for detecting gene-gene Interactions on risk of myocardial infarction: The importance of model validation. - Christopher S. Coffey; Patricia R. Hebert; Marylyn D. Ritchie; Harlan M. Krumholz; J. Michael Gaziano; Paul M. Ridker; Nancy J. Brown; Douglas E. Vaughan; Jason H. Moore (BMC Bioinform., 2004)

Improving EHR Chart Review Efficiency via Semantic Similarity Assessment. - Tianrun A. Cai; Andrew Beam; Stephanie Chan 002; Jacqueline Honerlaw; Yichi Zhang; David R. Gagnon; Kelly Cho; J. Michael Gaziano; Katherine P. Liao; Tianxi Cai (AMIA, 2017)

High-Throughput Multimodal Automated Phenotyping (MAP) Incorporating Natural Language Processing with Application to PheWAS. - Katherine P. Liao; Jiehuan Sun; Tianrun A. Cai; Nicholas B. Link; Chuan Hong; Jie Huang 030; Jennifer E. Huffman; Jessica L. Gronsbell; Lauren Costa; Victor M. Castro; Vivian S. Gainer; Shawn N. Murphy; et al. (AMIA, 2018)

Yield and bias in defining a cohort study baseline from electronic health record data. - Jason Vassy; Yuk-Lam Ho; Jacqueline Honerlaw; Kelly Cho; J. Michael Gaziano; Peter W. F. Wilson; David R. Gagnon (J. Biomed. Informatics, 2018)

High-throughput multimodal automated phenotyping (MAP) with application to PheWAS. - Katherine P. Liao; Jiehuan Sun; Tianrun A. Cai; Nicholas B. Link; Chuan Hong; Jie Huang 030; Jennifer E. Huffman; Jessica L. Gronsbell; Yichi Zhang; Yuk-Lam Ho; Victor M. Castro; Vivian S. Gainer; et al. (J. Am. Medical Informatics Assoc., 2019)

Clinical knowledge extraction via sparse embedding regression (KESER) with multi-center large scale electronic health record data. - Chuan Hong; Everett Neil Rush; Molei Liu; Doudou Zhou; Jiehuan Sun; Aaron Sonabend W.; Victor M. Castro; Petra Schubert; Vidul Ayakulangara Panickan; Tianrun Cai; Lauren Costa; Zeling He; et al. (npj Digit. Medicine, 2021)

Knowledge-Driven Online Multimodal Automated Phenotyping System. - Molei Liu; Sara Morini; Xin Xiong; Chuan Hong; Clara-Lea Bonzel; Vidul Ayakulangara Panickan; Everett Neil Rush; Yuk-Lam Ho; Kelly Cho; J. Michael Gaziano; Katherine P. Liao; Tianxi Cai; et al. (AMIA, 2022)

Scalable relevance ranking algorithm via semantic similarity assessment improves efficiency of medical chart review. - Tianrun Cai; Zeling He; Chuan Hong; Yichi Zhang; Yuk-Lam Ho; Jacqueline Honerlaw; Alon Geva; Vidul Ayakulangara Panickan; Amanda King; David R. Gagnon; J. Michael Gaziano; Kelly Cho; et al. (J. Biomed. Informatics, 2022)

Multiview Incomplete Knowledge Graph Integration with application to cross-institutional EHR data harmonization. - Doudou Zhou; Ziming Gan; Xu Shi; Alina Patwari; Everett Neil Rush; Clara-Lea Bonzel; Vidul Ayakulangara Panickan; Chuan Hong; Yuk-Lam Ho; Tianrun Cai; Lauren Costa; Xiaoou Li; et al. (J. Biomed. Informatics, 2022)

Multimodal representation learning for predicting molecule-disease relations. - Jun Wen; Xiang Zhang 012; Everett Neil Rush; Vidul Ayakulangara Panickan; Xingyu Li; Tianrun Cai; Doudou Zhou; Yuk-Lam Ho; Lauren Costa; Edmon Begoli; Chuan Hong; J. Michael Gaziano; et al. (Bioinform., 2023)

Framework of the Centralized Interactive Phenomics Resource (CIPHER) standard for electronic health data-based phenomics knowledgebase. - Jacqueline Honerlaw; Yuk-Lam Ho; Francesca Fontin; Jeffrey Gosian; Monika Maripuri; Michael Murray; Rahul Sangar; Ashley Galloway; Andrew J. Zimolzak; Stacey B. Whitbourne; Juan P. Casas; Rachel B. Ramoni; et al. (J. Am. Medical Informatics Assoc., 2023)

Centralized Interactive Phenomics Resource: an integrated online phenomics knowledgebase for health data users. - Jacqueline Honerlaw; Yuk-Lam Ho; Francesca Fontin; Michael Murray; Ashley Galloway; David Heise; Keith Connatser; Laura Davies; Jeffrey Gosian; Monika Maripuri; John Russo 001; Rahul Sangar; et al. (J. Am. Medical Informatics Assoc., 2024)

LATTE: Label-efficient incident phenotyping from longitudinal electronic health records. - Jun Wen; Jue Hou; Clara-Lea Bonzel; Yihan Zhao; Victor M. Castro; Vivian S. Gainer; Dana Weisenfeld; Tianrun Cai; Yuk-Lam Ho; Vidul Ayakulangara Panickan; Lauren Costa; Chuan Hong; et al. (Patterns, 2024)

Effectiveness of electronic medical record-based strategies for death and hospital admission endpoint capture in pragmatic clinical trials. - Maryam Rahafrooz; Danne C. Elbers; Jay R. Gopal; Junling Ren; Nathan H. Chan; Cenk Yildirim; Akshay S. Desai; Abigail A. Santos; Karen Murray; Thomas Havighurst; Jacob A. Udell; Michael E. Farkouh; et al. (J. Am. Medical Informatics Assoc., 2025)

ARCH: Large-scale knowledge graph via aggregated narrative codified health records analysis. - Ziming Gan; Doudou Zhou; Everett Neil Rush; Vidul Ayakulangara Panickan; Yuk-Lam Ho; George Ostrouchov; Zhiwei Xu; Shuting Shen; Xin Xiong; Kimberly F. Greco; Chuan Hong; Clara-Lea Bonzel; et al. (J. Biomed. Informatics, 2025)

DOME: Directional medical embedding vectors from Electronic Health Records. - Jun Wen; Hao Xue 005; Everett Neil Rush; Vidul Ayakulangara Panickan; Tianrun Cai; Doudou Zhou; Yuk-Lam Ho; Lauren Costa; Edmon Begoli; Chuan Hong; J. Michael Gaziano; Kelly Cho; et al. (J. Biomed. Informatics, 2025)

Representation Learning to Advance Multi-institutional Studies with Electronic Health Record Data. - Doudou Zhou; Han Tong; Linshanshan Wang; Suqi Liu; Xin Xiong; Ziming Gan; Romain Griffier; Boris P. Hejblum; Yun-Chung Liu; Chuan Hong; Clara-Lea Bonzel; Tianrun Cai; et al. (CoRR, 2025)