Using PheWAS to Assess Pleiotropy of Genetic Risk Scores for Rheumatoid Arthritis and Coronary Artery Disease in the eMERGE Network. - Robert J. Carroll; Katherine P. Liao; Anne E. Eyler; Lisa Bastarache; Dana C. Crawford; Peggy L. Peissig; Jyotishman Pathak; David Carrell; Abel N. Kho; Rongling Li; Daniel R. Masys; Gail P. Jarvik; et al. (AMIA, 2012)

Portability of an algorithm to identify rheumatoid arthritis in electronic health records. - Robert J. Carroll; William K. Thompson; Anne E. Eyler; Arthur M. Mandelin; Tianxi Cai; Raquel M. Zink; Jennifer A. Pacheco; Chad S. Boomershine; Thomas A. Lasko; Hua Xu 001; Elizabeth W. Karlson; Raúl G. Pérez; et al. (J. Am. Medical Informatics Assoc., 2012)

PheWAS and Genetics Define Subphenotypes in Drug Response. - Robert J. Carroll; Jeremy L. Warner; Anne E. Eyler; Charles Moore; Jayanth Doss; Katherine P. Liao; Robert M. Plenge; Joshua C. Denny (AMIA, 2014)

Demonstrating the Advantages of Applying Data Mining Techniques on Time-Dependent Electronic Medical Records. - Uri Kartoun; Vishesh Kumar; Su-Chun Cheng; Sheng Yu 002; Katherine P. Liao; Elizabeth W. Karlson; Ashwin N. Ananthakrishnan; Zongqi Xia; Vivian S. Gainer; Andrew Cagan; Guergana Savova; Pei J. Chen; et al. (AMIA, 2015)

Toward high-throughput phenotyping: unbiased automated feature extraction and selection from knowledge sources. - Sheng Yu 002; Katherine P. Liao; Stanley Y. Shaw; Vivian S. Gainer; Susanne E. Churchill; Peter Szolovits; Shawn N. Murphy; Isaac S. Kohane; Tianxi Cai (J. Am. Medical Informatics Assoc., 2015)

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 Phenotyping via Denoised Normal Mixture Transformation. - Sheng Yu 002; Yumeng Ma; Jessica L. Gronsbell; Katherine P. Liao; Tianrun A. Cai; Ashwin N. Ananthakrishnan; Vivian S. Gainer; Susanne E. Churchill; Peter Szolovits; Shawn N. Murphy; Isaac S. Kohane; Tianxi Cai (AMIA, 2017)

Surrogate-assisted feature extraction for high-throughput phenotyping. - Sheng Yu 002; Abhishek Chakrabortty; Katherine P. Liao; Tianrun A. Cai; Ashwin N. Ananthakrishnan; Vivian S. Gainer; Susanne E. Churchill; Peter Szolovits; Shawn N. Murphy; Isaac S. Kohane; Tianxi Cai (J. Am. Medical Informatics Assoc., 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)

PheProb: probabilistic phenotyping using diagnosis codes to improve power for genetic association studies. - Jennifer A. Sinnott; Fiona Cai; Sheng Yu 002; Boris P. Hejblum; Chuan Hong; Isaac S. Kohane; Katherine P. Liao (J. Am. Medical Informatics Assoc., 2018)

Enabling phenotypic big data with PheNorm. - Sheng Yu 002; Yumeng Ma; Jessica L. Gronsbell; Tianrun A. Cai; Ashwin N. Ananthakrishnan; Vivian S. Gainer; Susanne E. Churchill; Peter Szolovits; Shawn N. Murphy; Isaac S. Kohane; Katherine P. Liao; Tianxi Cai (J. Am. Medical Informatics Assoc., 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)

Feature extraction for phenotyping from semantic and knowledge resources. - Wenxin Ning; Stephanie Chan 002; Andrew Beam; Ming Yu 003; Alon Geva; Katherine P. Liao; Mary Mullen; Kenneth D. Mandl; Isaac S. Kohane; Tianxi Cai; Sheng Yu 002 (J. Biomed. Informatics, 2019)

Automated grouping of medical codes via multiview banded spectral clustering. - Luwan Zhang; Yichi Zhang; Tianrun A. Cai; Yuri Ahuja; Zeling He; Yuk-Lam Ho; Andrew Beam; Kelly Cho; Robert J. Carroll; Joshua C. Denny; Isaac S. Kohane; Katherine P. Liao; et al. (J. Biomed. Informatics, 2019)

EXTraction of EMR numerical data: an efficient and generalizable tool to EXTEND clinical research. - Tianrun A. Cai; Luwan Zhang; Nicole Yang; Kanako K. Kumamaru; Frank J. Rybicki; Tianxi Cai; Katherine P. Liao (BMC Medical Informatics Decis. Mak., 2019)

ATLAS: an automated association test using probabilistically linked health records with application to genetic studies. - Harrison G. Zhang; Boris P. Hejblum; Griffin M. Weber; Nathan P. Palmer; Susanne E. Churchill; Peter Szolovits; Shawn N. Murphy; Katherine P. Liao; Isaac S. Kohane; Tianxi Cai (J. Am. Medical Informatics Assoc., 2021)

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)

Binary acronym disambiguation in clinical notes from electronic health records with an application in computational phenotyping. - Nicholas B. Link; Sicong Huang 005; Tianrun Cai; Jiehuan Sun; Kumar Dahal; Lauren Costa; Kelly Cho; Katherine P. Liao; Tianxi Cai; Chuan Hong (Int. J. Medical Informatics, 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)

Augmented Transfer Regression Learning with Semi-non-parametric Nuisance Models. - Molei Liu; Yi Zhang; Katherine P. Liao; Tianxi Cai (J. Mach. Learn. Res., 2023)

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)

Semi-supervised calibration of noisy event risk (SCANER) with electronic health records. - Chuan Hong; Liang Liang; Qianyu Yuan; Kelly Cho; Katherine P. Liao; Michael J. Pencina; David C. Christiani; Tianxi Cai (J. Biomed. Informatics, 2023)

Federated One-Shot Ensemble Clustering. - Rui Duan 004; Xin Xiong; Jueyi Liu; Katherine P. Liao; Tianxi Cai (CoRR, 2024)

Unified Representation of Genomic and Biomedical Concepts through Multi-Task, Multi-Source Contrastive Learning. - Hongyi Yuan; Suqi Liu; Kelly Cho; Katherine P. Liao; Alexandre Pereira; Tianxi Cai (CoRR, 2024)

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)

Identifying an Autoinflammatory Syndrome Cohort Using Natural Language Processing with Electronic Medical Record Data. - Maranda Russell; Aleksander Lenert; Katherine P. Liao; Tianrun Cai; Sujin Kim (BIOSTEC (2): HEALTHINF, 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)

Label efficient phenotyping for Long COVID using electronic health records. - Chuan Hong; Jun Wen; Harrison G. Zhang; Vidul Ayakulangara Panickan; Doris Yang; Alicia W. Chen; Xin Xiong; Xuan Wang; Michele Morris; Sara Morini; Rahul Sangar; Andrew Dey; et al. (npj Digit. Medicine, 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)