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

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

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

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

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

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

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

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

LATTE: Label-efficient Incident Phenotyping from Longitudinal Electronic Health Records. - Wen, Jun; Hou, Jue; Bonzel, Clara-Lea; Zhao, Yihan; Castro, Victor M.; Gainer, Vivian S.; Weisenfeld, Dana; Cai, Tianrun; Ho, Yuk-Lam; Panickan, Vidul Ayakulangara; Costa, Lauren; Hong, Chuan; et al. (CoRR, 2023)

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

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

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

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

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

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

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

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

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. - Coffey, Christopher S.; Hebert, Patricia R.; Ritchie, Marylyn D.; Krumholz, Harlan M.; Gaziano, J. Michael; Ridker, Paul M.; Brown, Nancy J.; Vaughan, Douglas E.; Moore, Jason H. (BMC Bioinform., 2004)