Phenome-Based Analysis as a Means for Discovering Context-Dependent Clinical Reference Ranges. - Jeremy L. Warner; Gil Alterovitz (AMIA, 2012)

Towards an Annotation Schema for Cancer Trajectory State Detection. - Jeremy L. Warner; Peter Anick; Kenneth Roach; Nianwen Xue; Robin M. Joyce; Charles Safran; Pengyu Hong (AMIA, 2012)

Constructing a Novel Cancer Ontology. - Michael C. Gao; Jeremy L. Warner; Peter C. Yang; Gil Alterovitz (AMIA, 2013)

Sharing of Genomic Information: Perspectives from Stakeholders. - Jeremy L. Warner; Gil Alterovitz; Joshua C. Denny; Robert Fassett; Kevin S. Hughes (AMIA, 2013)

Phenometric analysis of electronic health records: a new approach to visualization of high dimensional biomedical information. - Jeremy L. Warner; Quan Ding; David A. Kreda; Zi'ou Zheng; Keshav Gupta; Joshua C. Denny; Gil Alterovitz (AMIA, 2013)

Analytic Approaches to Phenotypic Complexity. - Jeremy L. Warner; Joshua C. Denny; David A. Kreda; Gil Alterovitz (MedInfo, 2013)

Automated Synthesis and Visualization of a Chemotherapy Treatment Regimen Network. - Jeremy L. Warner; Peter C. Yang; Gil Alterovitz (MedInfo, 2013)

Brief communication: External phenome analysis enables a rational federated query strategy to detect changing rates of treatment-related complications associated with multiple myeloma. - Jeremy L. Warner; Gil Alterovitz; Kelly Bodio; Robin M. Joyce (J. Am. Medical Informatics Assoc., 2013)

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)

Identifying Metastases from Pathology Reports in Lung Cancer Patients. - Ergin Soysal; Jeremy L. Warner; Joshua C. Denny; Hua Xu 001 (AMIA, 2014)

Evaluation of Diagnosis Codes, Clinical Notes, and Medications on Identifying Subjects with a Specific Disease Phenotype. - Wei-Qi Wei; Pedro L. Teixeira; Huan Mo; Robert M. Cronin; Jeremy L. Warner; Joshua C. Denny (AMIA, 2014)

Mining electronic health record data to detect drug-repurposing signals for cancers. - Hua Xu 001; Qingxia Chen; Jeremy L. Warner; Han Xue; Min Jiang 007; Anushi Shah; Melinda Aldrich; Qi Dai; Joshua C. Denny (AMIA, 2014)

Visualizing High Dimensional Clinical and Tumor Genotyping Data. - Matthew J. Rioth; Jeremy L. Warner (AMIA, 2015)

SMART on FHIR Genomics: facilitating standardized clinico-genomic apps. - Gil Alterovitz; Jeremy L. Warner; Peijin Zhang; Yishen Chen; Mollie Ullman-Cullere; David A. Kreda; Isaac S. Kohane (J. Am. Medical Informatics Assoc., 2015)

Seeing the forest through the trees: uncovering phenomic complexity through interactive network visualization. - Jeremy L. Warner; Joshua C. Denny; David A. Kreda; Gil Alterovitz (J. Am. Medical Informatics Assoc., 2015)

Development, implementation, and initial evaluation of a foundational open interoperability standard for oncology treatment planning and summarization. - Jeremy L. Warner; Suzanne E. Maddux; Kevin S. Hughes; John C. Krauss; Peter Paul Yu; Lawrence N. Shulman; Deborah K. Mayer; Mike Hogarth; Mark Shafarman; Allison Stover Fiscalini; Laura Esserman; Liora Alschuler; et al. (J. Am. Medical Informatics Assoc., 2015)

Validating drug repurposing signals using electronic health records: a case study of metformin associated with reduced cancer mortality. - Hua Xu 001; Melinda C. Aldrich; Qingxia Chen; Hongfang Liu; Neeraja B. Peterson; Qi Dai; Mia A. Levy; Anushi Shah; Han Xue; Xiaoyang Ruan; Min Jiang 007; Ying Li; et al. (J. Am. Medical Informatics Assoc., 2015)

Workshop on Visual Analytics in Healthcare. - Jesus Caban; Adam Perer; Uba Backonja; Jeremy L. Warner; Shira Fischer (AMIA, 2016)

Pragmatic precision oncology: the secondary uses of clinical tumor molecular profiling. - Matthew J. Rioth; Ramya Thota; David B. Staggs; Douglas B. Johnson; Jeremy L. Warner (J. Am. Medical Informatics Assoc., 2016)

SMART precision cancer medicine: a FHIR-based app to provide genomic information at the point of care. - Jeremy L. Warner; Matthew J. Rioth; Kenneth D. Mandl; Joshua C. Mandel; David A. Kreda; Isaac S. Kohane; Daniel Carbone; Ross Oreto; Lucy Wang; Shilin Zhu; Heming Yao; Gil Alterovitz (J. Am. Medical Informatics Assoc., 2016)

CUSTOM-SEQ: a prototype for oncology rapid learning in a comprehensive EHR environment. - Jeremy L. Warner; Lucy Wang; William Pao; Jeffrey A. Sosman; Ravi V. Atreya; Pam Carney; Mia A. Levy (J. Am. Medical Informatics Assoc., 2016)

Combining billing codes, clinical notes, and medications from electronic health records provides superior phenotyping performance. - Wei-Qi Wei; Pedro L. Teixeira; Huan Mo; Robert M. Cronin; Jeremy L. Warner; Joshua C. Denny (J. Am. Medical Informatics Assoc., 2016)

Classification of hospital acquired complications using temporal clinical information from a large electronic health record. - Jeremy L. Warner; Peijin Zhang; Jenny Liu; Gil Alterovitz (J. Biomed. Informatics, 2016)

Identification of Patient Subgroups in Metastatic Breast Cancer Patients Based on Somatic Copy Number Alterations: A Bipartite Network Analysis. - Suresh K. Bhavnani; Archana Ayyaswami; Tianlong Chen 004; Jeremy L. Warner (AMIA, 2017)

Identifying Metastases related Information from Pathology Reports of Lung Cancer Patients. - Ergin Soysal; Jeremy L. Warner; Joshua C. Denny; Hua Xu 001 (CRI, 2017)

The Power of the Patient Voice: Learning Indicators of Treatment Adherence From An Online Breast Cancer Forum. - Zhijun Yin; Bradley A. Malin; Jeremy L. Warner; Pei-Yun Sabrina Hsueh; Ching-Hua Chen (ICWSM, 2017)

Using network graphs to visualize changing documentation styles in an oncology practice before and after opennotes implementation. - Sandeep Kumar Jain; Maryam Rahimian; Robin M. Joyce; Jessica A. Zerillo; Jeremy L. Warner (VAHC, 2017)

connecTPL: A Tool for Connecting Drugs and Publications to their Clinical Trials. - Krysten Harvey; Andrew M. Malty; Samuel M. Rubinstein; Jeremy L. Warner (AMIA, 2018)

Exploring Mutational Heterogeneity in the GENIE Tumor Database Using Visual Analytics. - Jeremy L. Warner; Samuel M. Rubinstein; Julie Wu; Emmanuel A. Santillana; Suresh K. Bhavnani (AMIA, 2018)

Computable Longitudinal Patient Trajectories. - Jeremy L. Warner; Guergana Savova; Noemie Elhadad; Lisa Bastarache; David Gotz (AMIA, 2018)

Learning When Communications Between Healthcare Providers Indicate Hormonal Therapy Medication Discontinuation. - Zhijun Yin; Jeremy L. Warner; Bradley A. Malin (AMIA, 2018)

The therapy is making me sick: how online portal communications between breast cancer patients and physicians indicate medication discontinuation. - Zhijun Yin; Morgan Harrell; Jeremy L. Warner; Qingxia Chen; Daniel Fabbri; Bradley A. Malin (J. Am. Medical Informatics Assoc., 2018)

Continuum of Interoperability in Oncology EHR Implementations. - Elmer V. Bernstam; Jeremy L. Warner; John C. Krauss; Edward P. Ambinder; Wendy S. Rubinstein; George Komatsoulis; Robert S. Miller; James L. Chen (AMIA, 2019)

Flipping Clinical Documentation on its Head. - Yaa A. Kumah-Crystal; Liz Salmi; Chethan Sarabu; Jeffery Smith; Jeremy L. Warner (AMIA, 2019)

HemOnc.org: Evaluation of Information Models for Cancer Therapy Representation. - Zachary H. Moldwin; Harry Hochheiser; Jeremy L. Warner (AMIA, 2019)

Patient Messaging Content Associated with Initiating Hormonal Therapy after a Breast Cancer Diagnosis. - Zhijun Yin; Jeremy L. Warner; Qingxia Chen; Bradley A. Malin (AMIA, 2019)

Developing Customizable Cancer Information Extraction Modules for Pathology Reports Using CLAMP. - Ergin Soysal; Jeremy L. Warner; Jingqi Wang; Min Jiang 007; Krysten Harvey; Sandeep Kumar Jain; Xiao Dong; Hsing-yi Song; Harish Siddhanamatha; Liwei Wang 010; Qi Dai; Qingxia Chen; et al. (MedInfo, 2019)

HemOnc: A new standard vocabulary for chemotherapy regimen representation in the OMOP common data model. - Jeremy L. Warner; Dmitry Dymshyts; Christian G. Reich; Michael J. Gurley; Harry Hochheiser; Zachary H. Moldwin; Rimma Belenkaya; Andrew E. Williams; Peter C. Yang (J. Biomed. Informatics, 2019)

Extracting Relations between Radiotherapy Treatment Details. - Danielle S. Bitterman; Timothy Miller 002; David Harris 004; Chen Lin 002; Sean Finan; Jeremy L. Warner; Raymond H. Mak; Guergana Savova (ClinicalNLP@EMNLP, 2020)

Recommendations for patient similarity classes: results of the AMIA 2019 workshop on defining patient similarity. - Nathan D. Seligson; Jeremy L. Warner; William S. Dalton; David Martin; Robert S. Miller; Debra Patt; Kenneth L. Kehl; Matvey B. Palchuk; Gil Alterovitz; Laura K. Wiley; Ming Huang 006; Feichen Shen; et al. (J. Am. Medical Informatics Assoc., 2020)

A retrospective approach to evaluating potential adverse outcomes associated with delay of procedures for cardiovascular and cancer-related diagnoses in the context of COVID-19. - Neil S. Zheng; Jeremy L. Warner; Travis J. Osterman; Quinn Stanton Wells; Xiao-Ou Shu; Stephen A. Deppen; Seth J. Karp; Shon Dwyer; QiPing Feng; Nancy J. Cox; Josh F. Peterson; C. Michael Stein; et al. (J. Biomed. Informatics, 2021)

DeepPhe: Natural Language Processing Tools for Cancer Research and Surveillance. - Harry Hochheiser; Sean Finan; Zhou Yuan; John D. Levander; Eric B. Durbin; Isaac Hands; Ramakanth Kavuluru; Jeremy L. Warner; Guergana Savova (AMIA, 2022)

Evaluation of mCODE Coverage in EHR: a Scoping Review of Cancer Natural Language Processing. - Liwei Wang 010; Sunyang Fu; Andrew Wen; Xiaoyang Ruan; Huan He; Sijia Liu 002; Sungrim Moon; Michelle Mai; Irbaz Bin Riaz; Nan Wang; Ping Yang; Hua Xu 001; et al. (ICHI, 2022)

Quantitating and assessing interoperability between electronic health records. - Elmer V. Bernstam; Jeremy L. Warner; John C. Krauss; Edward P. Ambinder; Wendy S. Rubinstein; George Komatsoulis; Robert S. Miller; James L. Chen (J. Am. Medical Informatics Assoc., 2022)

Introducing a Comprehensive Score of Systemic Anticancer Treatment Relevance. - Travis Zack; Jeremy L. Warner (MedInfo, 2023)

Natural language processing to automatically extract the presence and severity of esophagitis in notes of patients undergoing radiotherapy. - Shan Chen 004; Marco Guevara; Nicolas Ramirez; Arpi Murray; Jeremy L. Warner; Hugo J. W. L. Aerts; Timothy A. Miller; Guergana K. Savova; Raymond H. Mak; Danielle S. Bitterman (CoRR, 2023)

Next-generation phenotyping: introducing phecodeX for enhanced discovery research in medical phenomics. - Megan M. Shuey; William W. Stead; Ida Aka; April L. Barnado; Lisa Bastarache; Elly Brokamp; Meredith Campbell; Robert J. Carroll; Jeffrey A. Goldstein; Adam Lewis; Beth A. Malow; Jonathan D. Mosley; et al. (Bioinform., 2023)

Using Large Language Model for Efficient Extraction of Treatment Discontinuation Information - A Study of Online Breast Cancer Community Posts. - Qingyuan Song; Jessie Yang; Ndidiamaka Obi; Congning Ni; Jeremy L. Warner; Qingxia Chen; Lijun Song; S. Trent Rosenbloom; Bradley A. Malin; Zhijun Yin (AIME (2), 2025)

Collaborative large language models for automated data extraction in living systematic reviews. - Muhammad Ali Khan; Umair Ayub; Syed Arsalan Ahmed Naqvi; Kaneez Zahra Rubab Khakwani; Zaryab bin Riaz Sipra; Ammad Raina; Sihan Zhou; Huan He; Amir Saeidi; Bashar Hasan; Robert Bryan Rumble; Danielle S. Bitterman; et al. (J. Am. Medical Informatics Assoc., 2025)

MedBrowseComp: Benchmarking Medical Deep Research and Computer Use. - Shan Chen 004; Pedro Moreira; Yuxin Xiao; Sam Schmidgall; Jeremy L. Warner; Hugo J. W. L. Aerts; Thomas Hartvigsen; Jack Gallifant; Danielle S. Bitterman (CoRR, 2025)