Publications

2026

1. Teaching agentic AI to learn expert reasoning for rare disease diagnosis

   Minh-Ha Nguyen, Erica Gray, Bryce A Schuler, Kevin W Byram, Chih-Ting Yang, Fan Ma, Hua Xu, Wu-Chen Su, Chao Yan, Wei-Qi Wei, Adam Wright, Lisa Bastarache, Josh Peterson, Lingyao Li, Siyuan Ma, Undiagnosed Diseases Network, Rizwan Hamid, Thomas A Cassini, and Cathy Shyr

   arXiv preprint arXiv:2606.16149, 2026

   DOI
2. Diagnostic accuracy of large language models for rare diseases: a systematic review and meta-analysis

   Minh-Ha Nguyen, Chih-Ting Yang, Thomas A Cassini, Fan Ma, Rizwan Hamid, Lisa Bastarache, Josh F Peterson, Hua Xu, Lingyao Li, Siyuan Ma, and Cathy Shyr

   npj Digital Medicine, 2026

   DOI
3. An EHR-based framework for modeling growth curves and constructing growth centile charts for genetic disorders

   Cathy Shyr, Rory J Tinker, Rebekah F Brown, Adam Wright, Josh F Peterson, John A III Phillips, S Trent Rosenbloom, and Lisa Bastarache

   npj Genomic Medicine, 2026

   DOI
4. A safety-oriented hypothetico-deductive framework for AI-assisted differential diagnosis

   Fan Ma, Mauro Giuffrè, Donald Wright, Kent McCann, Mark Iscoe, Lingfei Qian, Mingyang Jiang, Chi Wing Ng, Na Hong, Huan He, Cathy Shyr, Qingyu Chen, Lee Schwamm, Lucila Ohno-Machado, and Hua Xu

   arXiv preprint arXiv:2607.08038, 2026

   DOI
5. Adverse Childhood Experiences and Growth Outcomes in Childhood: A Longitudinal EHR-Based Study

   Samuel A Palmer, Cathy Shyr, Theodore Morley, John Shelley, Lide Han, Jill Simmons, Cosmin Bejan, Colin Walsh, and Douglas M Ruderfer

   medRxiv, 2026

   DOI
6. Generative artificial intelligence implementation in REDCap

   Cathy Shyr, Robert Taylor, Vaishali Jagtap, Alex C Cheng, and Paul A Harris

   JAMIA Open, 2026

   DOI
7. LLM-as-a-Judge in Healthcare: A Scoping Analysis of Applications, Methods, and Human Alignment

   Lingyao Li, Deyi Li, Chen Chen, Renkai Ma, Runlong Yu, Mingquan Lin, Rui Yin, Lizhou Fan, Cathy Shyr, Siyuan Ma, Mei Liu, and Steven Bethard

   arXiv preprint arXiv:2605.25273, 2026
8. Practical Healthcare Statistics with Examples in Python and R: A Guide for the Uninitiated

   Cathy Shyr

   Biometrics, 2026

   Book review

   DOI
9. Sex-Based Disparities in Fabry Disease Cause Challenges in Newborn Screening

   Yutaka Furuta, Neena S Agrawal, Natalie N Owen, Lisa A Bastarache, Cathy Shyr, Hanabi U Geiger, Elvira Ponce, Chelsea J Lauderdale, Camille R Carter, Karee A Morgan, Rizwan Hamid, John A Phillips, and Rory J Tinker

   Public Health Genomics, 2026

   DOI
10. GEN-KnowRD: Reframing AI for Rare Disease Recognition

    Chao Yan, Wu-Chen Su, Yi Xin, Monika E Grabowska, Vern E Kerchberger, Victor A Borza, Jinlian Wang, Liwei Wang, Rui Li, Jacob Lynn, Alyson L Dickson, Cathy Shyr, QiPing Feng, Charles M Stein, Kai Wang, Peter J Embí, Bradley A Malin, Hongfang Liu, and Wei-Qi Wei

    medRxiv, 2026
11. An artificial intelligence framework for end-to-end rare disease phenotyping from clinical notes using large language models

    Cathy Shyr, Yan Hu, Rory J Tinker, Thomas A Cassini, Kevin W Byram, Rizwan Hamid, Daniel V Fabbri, Adam Wright, Josh F Peterson, Lisa Bastarache, and Hua Xu

    arXiv preprint arXiv:2602.20324, 2026
12. Information extraction from clinical notes: are we ready to switch to large language models?

    Yan Hu, Xu Zuo, Yujia Zhou, Xueqing Peng, Jimin Huang, Vipina K Keloth, Vincent J Zhang, Ruey-Ling Weng, Cathy Shyr, Qingyu Chen, Xiaoqian Jiang, Kirk E Roberts, and Hua Xu

    Journal of the American Medical Informatics Association, 2026

    DOI
13. Evaluating pregnancy and neonatal outcomes in mothers with genetic disease using electronic health care records

    Rory J Tinker, Lucas D Richter, Yutaka Furuta, Cathy Shyr, Sherwin M Shirazi, Jennifer Sucre, Luke A Gatta, John A III Phillips, Josh F Peterson, and Lisa Bastarache

    Genetics in Medicine, 2026

    DOI

2025

1. Multi-study R-learner for estimating heterogeneous treatment effects across studies using statistical machine learning

   Cathy Shyr, Boyu Ren, Prasad Patil, and Giovanni Parmigiani

   Biostatistics, 2025
2. Opportunities, barriers, and remedies for implementing REDCap integration with electronic health records via Fast Healthcare Interoperability Resources (FHIR)

   Alex C Cheng, Cathy Shyr, Adam Lewis, Francesco Delacqua, Teresa Bosler, Mary K Banasiewicz, Robert Taylor, Christopher J Lindsell, and Paul A Harris

   JAMIA open, 2025
3. All of Us Research Program year in review: 2024

   Tara Dutka, Erika J Faust, C Scott Gallagher, Travis Hyams, Elyse Kozlowski, Erica Landis, Minnkyong Lee, Grace F Liou, Tamara R Litwin, Christopher Lunt, Sana H Mian, Anjene Musick, Nguyen Park, Theresa Patten, Janeth Sanchez, Sheri D Schully, Cathy Shyr, and Geoffrey S Ginsburg

   The American Journal of Human Genetics, 2025
4. Large Language Models for Rare Disease Diagnosis at the Undiagnosed Diseases Network

   Cathy Shyr, Thomas A Cassini, Rory J Tinker, Kevin W Byram, Peter J Embí, Lisa Bastarache, Josh F Peterson, Hua Xu, Rizwan Hamid, and Undiagnosed Diseases Network

   JAMA Network Open, 2025
5. Accuracy of Large Language Models in Generating Rare Disease Differential Diagnosis Using Key Clinical Features

   Cathy Shyr, Rory J Tinker, Paul A Harris, Alex C Cheng, Kevin W Byram, Lisa Bastarache, Josh F Peterson, Rizwan Hamid, Hua Xu, and Thomas A Cassini

   In MEDINFO 2025—Healthcare Smart\times Medicine Deep, 2025
6. A statistical framework for evaluating the repeatability and reproducibility of large language models

   Cathy Shyr, Boyu Ren, Chih-Yuan Hsu, Rory J Tinker, Thomas A Cassini, Rizwan Hamid, Adam Wright, Lisa Bastarache, Josh F Peterson, Bradley A Malin, and Hua Xu

   medRxiv, 2025

   DOI
7. Expert advice from ResearchMatch volunteers: Recruitment Innovation Center use cases and innovation

   Maeve Tischbein, Sarah K Cook, Cathy Shyr, Katelyn Benhoff, Amna Baig, Kaysi Quarles, Leslie R Boone, Loretta M Byrne, Mariela Rodriguez, Terri Edwards, Consuelo H Wilkins, and Paul A Harris

   Journal of Clinical and Translational Science, 2025
8. Reply to Layne et al.’s Letter to the Editor

   Cathy Shyr and Paul A Harris

   Journal of the American Medical Informatics Association, 2025
9. O27: Leveraging electronic health records to characterize growth patterns and curves in individuals with genetic disease

   Cathy Shyr, Rory Tinker, John Phillips, and Lisa Bastarache

   Genetics in Medicine Open, 2025
10. Sex-Specific Diagnostic Inequality in Fabry Disease: Lessons Learned from Analysis of Newborn Screening and Cascade Testing in Tennessee from 2017 to 2024

    Yutaka Furuta, Neena S Agrawal, Natalie N Owen, Lisa A Bastarache, Cathy Shyr, Hanabi U Geiger, Shayna Jackson, Chelsea J Lauderdale, Camille R Carter, Karee A Morgan, Rizwan Hamid, John A Phillips, and Rory J Tinker

    Available at SSRN 5337995, 2025

2024

1. Identifying and extracting rare diseases and their phenotypes with large language models

   Cathy Shyr, Yan Hu, Lisa Bastarache, Alex Cheng, Rizwan Hamid, Paul Harris, and Hua Xu

   Journal of healthcare informatics research, 2024
2. Impact of financial compensation on enrollment and participation in a remote, mobile-app based research study

   Shelby Meier, Alex Cheng, Maeve Tischbein, Cathy Shyr, Rebecca N Jerome, Terri L Edwards, Mary Stroud, Consuelo H Wilkins, and Paul A Harris

   Journal of Clinical and Translational Science, 2024
3. Illuminating the landscape of high-level clinical trial opportunities in the All of Us Research Program

   Cathy Shyr, Lina Sulieman, and Paul A Harris

   Journal of the American Medical Informatics Association, 2024
4. A phase I study of ATR inhibitor BAY1895344 (elimusertib) plus topotecan (ETCTN 10402): Results of dose escalation.

   Shannon Stockton, Cathy Shyr, Michael Cecchini, Raid Aljumaily, Thorvardur Ragnar Halfdanarson, Mohamad B Sonbol, Jennifer Whisenant, S Percy Ivy, Patricia LoRusso, Satya Das, Steven David Gore, Jordan Berlin, Jan Hendrik Beumer, and Thatcher Ross Heumann

   2024
5. A phase I study of irinotecan combined with BAY1895344 (ATR inhibitor) in advanced solid tumors: Results of ETCTN 10402 dose escalation.

   Thatcher Ross Heumann, Shannon Stockton, Michael Cecchini, Raid Aljumaily, Cathy Shyr, Jennifer Whisenant, Jason S Starr, Farshid Dayyani, Joaquina Celebre Baranda, Nikolaos Trikalinos, S Percy Ivy, Patricia LoRusso, Satya Das, Steven Gore, Jan Hendrik Beumer, and Jordan Berlin

   2024
6. Leveraging artificial intelligence to summarize abstracts in lay language for increasing research accessibility and transparency

   Cathy Shyr, Randall W Grout, Nan Kennedy, Yasemin Akdas, Maeve Tischbein, Joshua Milford, Jason Tan, Kaysi Quarles, Terri L Edwards, Laurie L Novak, Jules White, Consuelo H Wilkins, and Paul A Harris

   Journal of the American Medical Informatics Association, 2024
7. Empowering the biomedical research community: Innovative SAS deployment on the All of Us Researcher Workbench

   Izabelle Humes, Cathy Shyr, Moira Dillon, Zhongjie Liu, Jennifer Peterson, Chris St Jeor, Jacqueline Malkes, Hiral Master, Brandy Mapes, Romuladus Azuine, Nakia Mack, Bassent Abdelbary, Joyonna Gamble-George, Emily Goldmann, Stephanie Cook, Fatemeh Choupani, Rubin Baskir, Sydney McMaster, Chris Lunt, Karriem Watson, Minnkyong Lee, Sophie Schwartz, Ruchi Munshi, David Glazer, Eric Banks, Anthony Philippakis, Melissa Basford, Dan Roden, and Paul A Harris

   Journal of the American Medical Informatics Association, 2024

2023

1. Multi-study r-learner for heterogeneous treatment effect estimation

   Cathy Shyr, Boyu Ren, Prasad Patil, and Giovanni Parmigiani

   arXiv preprint arXiv:2306.01086, 2023
2. Multi-Study R-Learner for Estimating Heterogeneous Treatment Effects Across Studies Using Statistical Machine Learning

   Cathy Shyr, Boyu Ren, Prasad Patil, and Giovanni Parmigiani

   arXiv preprint arXiv:2306.01086, 2023

2022

1. Penetrance of male breast cancer susceptibility genes: a systematic review

   Reem S Chamseddine, Cathy Wang, Kanhua Yin, Jin Wang, Preeti Singh, Jingan Zhou, Mark E Robson, Danielle Braun, and Kevin S Hughes

   Breast Cancer Research and Treatment, 2022
2. Multi-Study Boosting: Theoretical Considerations for Merging vs. Ensembling

   Cathy Shyr, Pragya Sur, Giovanni Parmigiani, and Prasad Patil

   arXiv preprint arXiv:2207.04588, 2022
3. Evaluation of Lynch syndrome risk models in a multicenter diverse population.

   Jenny Lu, Stephen Knapp, Gubidxa Gutierrez Seymour, Cathy Wang, Theodore Huang, Jane Liang, Kai Yang, Danielle Castillo, Josef Herzog, Giovanni Parmigiani, Stephen B Gruber, Danielle Braun, and Gregory Idos

   2022
4. Statistical and Machine Learning Methods for Multi-Study Prediction and Causal Inference

   Cathy Wang

   Harvard University, 2022
5. A validation of models for prediction of pathogenic variants in mismatch repair genes

   Cathy Shyr, Amanda L Blackford, Theodore Huang, Jianfeng Ke, Nofal Ouardaoui, Lorenzo Trippa, Sapna Syngal, Chinedu Ukaegbu, Hajime Uno, Khedoudja Nafa, Zsofia K Stadler, Kenneth Offit, Christopher I Amos, Patrick M Lynch, Sining Chen, Francis M Giardiello, Daniel D Buchanan, John L Hopper, Mark A Jenkins, Melissa C Southey, Aung Ko Win, Jane C Figueiredo, Danielle Braun, and Giovanni Parmigiani

   Genetics in Medicine, 2022

2021

1. Quantitative assessment of learning behaviors for oncology providers

   Marie Wood, Thomas J George, Rami Manochakian, Maura Polansky, Allyson Baer, Anne Grupe, Yu Shyr, Cathy Wang, and Leora Horn

   Journal of Cancer Education, 2021
2. Establishing and evaluating an ASCO learning cohort: A longitudinal project assessing the learning needs and behaviors of oncology professionals

   Rami Manochakian, Thomas J George, Marie Wood, Maura Polansky, Allyson Baer, Anne Grupe, Yu Shyr, Cathy Wang, and Leora Horn

   Journal of Cancer Education, 2021

2020

1. A flexible nonlinear mixed effects model for HIV viral load rebound after treatment interruption

   Rui Wang, Ante Bing, Cathy Wang, Yuchen Hu, Ronald J Bosch, and Victor DeGruttola

   Statistics in medicine, 2020
2. Penetrance of colorectal cancer among mismatch repair gene mutation carriers: a meta-analysis

   Cathy Wang, Yan Wang, Kevin S Hughes, Giovanni Parmigiani, and Danielle Braun

   JNCI Cancer Spectrum, 2020
3. Quantitative analysis of oncology professional learning preferences

   Thomas J George, Rami Manochakian, Marie Wood, Maura Polansky, Allyson Baer, Anne Grupe, Yu Shyr, Cathy Wang, Jennifer Williams, and Leora Horn

   JCO Oncology Practice, 2020

2019

1. Validation of a semiautomated natural language processing–based procedure for meta-analysis of cancer susceptibility gene penetrance

   Zhengyi Deng, Kanhua Yin, Yujia Bao, Victor Diego Armengol, Cathy Wang, Ankur Tiwari, Regina Barzilay, Giovanni Parmigiani, Danielle Braun, and Kevin S Hughes

   JCO clinical cancer informatics, 2019
2. Using machine learning and natural language processing to review and classify the medical literature on cancer susceptibility genes

   Yujia Bao, Zhengyi Deng, Yan Wang, Heeyoon Kim, Victor Diego Armengol, Francisco Acevedo, Nofal Ouardaoui, Cathy Wang, Giovanni Parmigiani, Regina Barzilay, Danielle Braun, and Kevin S Hughes

   JCO Clinical Cancer Informatics, 2019

2015

1. The Alzheimer’s Disease Neuroimaging Initiative phase 2: Increasing the length, breadth, and depth of our understanding

   Laurel A Beckett, Michael C Donohue, Cathy Wang, Paul Aisen, Danielle J Harvey, Naomi Saito, and Alzheimer’s Disease Neuroimaging Initiative

   Alzheimer’s & Dementia, 2015