Shawn N. Murphy
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View article: Cloud vs. On-Premise Large Language Models for Urgent Patient- Portal Message Screening: A Comparative Evaluation
Cloud vs. On-Premise Large Language Models for Urgent Patient- Portal Message Screening: A Comparative Evaluation Open
Importance Patient portal messaging has become a core feature of outpatient care, particularly in neurology. In epilepsy care, timely triage of urgent symptoms — such as breakthrough seizures or adverse medication effects — and efficient e…
View article: Sexual selection’s role in the persistence of polymorphism in an aposematic signal
Sexual selection’s role in the persistence of polymorphism in an aposematic signal Open
The persistence of polymorphisms in aposematic species remains one of the most interesting paradoxes in evolutionary biology because aposematism theory suggests that polymorphisms should be unstable over time. We offer an explanation for t…
View article: Artificial intelligence in clinical data analysis: A review of large language models, foundation models, digital twins, and allergy applications
Artificial intelligence in clinical data analysis: A review of large language models, foundation models, digital twins, and allergy applications Open
Recent advances in computing technology and the development of data utilization environments have rapidly accelerated the application of artificial intelligence in clinical research and healthcare. This review provides a comprehensive over…
View article: Effectiveness and safety of rivaroxaban vs warfarin in patients with pulmonary embolism and right ventricular dysfunction: a retrospective cohort study
Effectiveness and safety of rivaroxaban vs warfarin in patients with pulmonary embolism and right ventricular dysfunction: a retrospective cohort study Open
Rivaroxaban was associated with lower risk of recurrent VTE compared with warfarin, without a significant difference in risk of major bleeding.
View article: A Comprehensive Evaluation of LLM Phenotyping Using Retrieval-Augmented Generation (RAG): Insights for RAG Optimization
A Comprehensive Evaluation of LLM Phenotyping Using Retrieval-Augmented Generation (RAG): Insights for RAG Optimization Open
Objective ICD codes are commonly used to filter patient cohorts but may not accurately reflect disease presence. Furthermore, many health problems are recorded in unstructured clinical notes, complicating cohort discovery from EHR data. Ex…
View article: Personalized and Precision Oncology (PPO) via Cancer Pathologyrelated Modeling and IT-Assisted Clinical Practice to Prevent, to Treat and to Get Cured Cancer and Its Complications: A Role of Precision Cancer Pathology in the Era of PPO
Personalized and Precision Oncology (PPO) via Cancer Pathologyrelated Modeling and IT-Assisted Clinical Practice to Prevent, to Treat and to Get Cured Cancer and Its Complications: A Role of Precision Cancer Pathology in the Era of PPO Open
A new systems approach to diseased states and wellness result in a new branch in the healthcare services, namely, Personalized and Precision Medicine (PPM). To achieve the implementation of PPM concept, it is necessary to create a fundamen…
View article: Real-world effectiveness of immunoglobulin replacement for hypogammaglobulinemia and infections in multiple myeloma
Real-world effectiveness of immunoglobulin replacement for hypogammaglobulinemia and infections in multiple myeloma Open
This study assessed the real-world effectiveness of immunoglobulin replacement therapy (IgRT) for treatment of hypogammaglobulinemia and infections in patients with multiple myeloma (MM). A retrospective study was conducted on adult patien…
View article: Current Limitations of Electronic Health Record Systems in Supporting Pragmatic Clinical Trials: Insights from the eMERGE Consortium
Current Limitations of Electronic Health Record Systems in Supporting Pragmatic Clinical Trials: Insights from the eMERGE Consortium Open
Pragmatic clinical trials (PCTs) evaluate interventions in real-world settings, often using electronic health records (EHRs) for efficient data collection. We report on the challenges in performing EHR analysis of health-care provider orde…
View article: Temporal Learning with Dynamic Range (TLDR) for Modeling Recurrent Exposure and Treatment Outcomes
Temporal Learning with Dynamic Range (TLDR) for Modeling Recurrent Exposure and Treatment Outcomes Open
Background The temporal sequence of clinical events is crucial in outcomes research, yet standard machine learning (ML) approaches often overlook this aspect in electronic health records (EHRs), limiting predictive accuracy. Methods We int…
View article: Real-World Assessment of All-Cause Hospital Readmissions among Pulmonary Embolism Patients Treated With Rivaroxaban Versus Apixaban
Real-World Assessment of All-Cause Hospital Readmissions among Pulmonary Embolism Patients Treated With Rivaroxaban Versus Apixaban Open
Background Although hospital readmission after pulmonary embolism (PE) is common, there is limited evidence on the comparative risk of readmission between rivaroxaban and apixaban. This study compared the real-world risk of all-cause hospi…
View article: An Agentic AI Workflow for Detecting Cognitive Concerns in Real-world Data
An Agentic AI Workflow for Detecting Cognitive Concerns in Real-world Data Open
Early identification of cognitive concerns is critical but often hindered by subtle symptom presentation. This study developed and validated a fully automated, multi-agent AI workflow using LLaMA 3 8B to identify cognitive concerns in 3,33…
View article: Author Correction: Establishing responsible use of AI guidelines: a comprehensive case study for healthcare institutions
Author Correction: Establishing responsible use of AI guidelines: a comprehensive case study for healthcare institutions Open
View article: Environment scan of generative AI infrastructure for clinical and translational science
Environment scan of generative AI infrastructure for clinical and translational science Open
View article: The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment
The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment Open
OBJECTIVE: Coronavirus disease 2019 (COVID-19) poses societal challenges that require expeditious data and knowledge sharing. Though organizational clinical data are abundant, these are largely inaccessible to outside researchers. Statisti…
View article: Understanding Data Differences across the ENACT Federated Research Network
Understanding Data Differences across the ENACT Federated Research Network Open
Objective Federated research networks, like Evolve to Next-Gen Accrual of patients to Clinical Trials (ENACT), aim to facilitate medical research by exchanging electronic health record (EHR) data. However, poor data quality can hinder this…
View article: Ethnic and racial differences in children and young people with respiratory and neurological post-acute sequelae of SARS-CoV-2: an electronic health record-based cohort study from the RECOVER Initiative
Ethnic and racial differences in children and young people with respiratory and neurological post-acute sequelae of SARS-CoV-2: an electronic health record-based cohort study from the RECOVER Initiative Open
National Institutes of Health.
View article: Human Health, Environmental Comfort and Well-Being. Part 2. Ecological Comfort as a New and Strategic Factor in the Protection of Modern Human Health
Human Health, Environmental Comfort and Well-Being. Part 2. Ecological Comfort as a New and Strategic Factor in the Protection of Modern Human Health Open
Since the dawn of humanity, human beings have inherently sought a state of security, trying to make their existence as comfortable as possible. Accordingly, among the many factors affecting human health, comfort and well-being, the quality…
View article: Estimation of prevalence of autoimmune diseases in the United States using electronic health record data
Estimation of prevalence of autoimmune diseases in the United States using electronic health record data Open
BACKGROUNDPrevious epidemiologic studies of autoimmune diseases in the US have included a limited number of diseases or used metaanalyses that rely on different data collection methods and analyses for each disease.METHODSTo estimate the p…
View article: Establishing responsible use of AI guidelines: a comprehensive case study for healthcare institutions
Establishing responsible use of AI guidelines: a comprehensive case study for healthcare institutions Open
View article: A standards-based application for improving platelet transfusion workflow
A standards-based application for improving platelet transfusion workflow Open
View article: Precision phenotyping for curating research cohorts of patients with unexplained post-acute sequelae of COVID-19
Precision phenotyping for curating research cohorts of patients with unexplained post-acute sequelae of COVID-19 Open
This research was funded by the US National Institute of Allergy and Infectious Diseases (NIAID).
View article: Prevalent Metformin Use in Adults With Diabetes and the Incidence of Long COVID: An EHR-Based Cohort Study From the RECOVER Program
Prevalent Metformin Use in Adults With Diabetes and the Incidence of Long COVID: An EHR-Based Cohort Study From the RECOVER Program Open
Studies show metformin use before and during SARS-CoV-2 infection reduces severe COVID-19 and postacute sequelae of SARS-CoV-2 (PASC) in adults. Our objective was to describe the incidence of PASC and possible associations with prevalent m…
View article: Environment Scan of Generative AI Infrastructure for Clinical and Translational Science
Environment Scan of Generative AI Infrastructure for Clinical and Translational Science Open
This study reports a comprehensive environmental scan of the generative AI (GenAI) infrastructure in the national network for clinical and translational science across 36 institutions supported by the Clinical and Translational Science Awa…
View article: Prevalent Metformin Use in Adults with Diabetes and the Incidence of Long Covid: An EHR-based Cohort Study from the RECOVER Program
Prevalent Metformin Use in Adults with Diabetes and the Incidence of Long Covid: An EHR-based Cohort Study from the RECOVER Program Open
Objective: Studies show metformin use before and during SARS-CoV-2 infection reduces severe COVID-19 and post-acute sequelae of SARS-CoV-2 (PASC) in adults. Our objective was to describe the incidence of PASC and possible associations with…
View article: Towards cross-application model-agnostic federated cohort discovery
Towards cross-application model-agnostic federated cohort discovery Open
Objectives To demonstrate that 2 popular cohort discovery tools, Leaf and the Shared Health Research Information Network (SHRINE), are readily interoperable. Specifically, we adapted Leaf to interoperate and function as a node in a federat…
View article: Personalized and Precision Medicine (Ppm) Through the View of Biomarker-Driven Applications to Support Their Global Impact in the Upgraded Healthcare-Related Services
Personalized and Precision Medicine (Ppm) Through the View of Biomarker-Driven Applications to Support Their Global Impact in the Upgraded Healthcare-Related Services Open
Personalized and precision medicine (PPM) relies on specific biomarkers to guide clinical decisions, distinguishing between predictive and prognostic biomarkers. Biomarkers are crucial in diagnosis, risk assessment, treatment guidance, and…
View article: Creation of a Limb Loss and Preservation Registry for Improving the Quality of Patient Care in the United States
Creation of a Limb Loss and Preservation Registry for Improving the Quality of Patient Care in the United States Open
The LLPR creates opportunities to apply large-data analytical methodologies to provides caregivers, researchers, manufacturers, payers, and policy makers the tools needed to improve the quality of clinical care, quantify patient-centric ou…
View article: IgG testing, immunoglobulin replacement therapy, and infection outcomes in patients with CLL or NHL: real-world evidence
IgG testing, immunoglobulin replacement therapy, and infection outcomes in patients with CLL or NHL: real-world evidence Open
Patients with chronic lymphocytic leukemia (CLL) and non-Hodgkin lymphoma (NHL) can develop hypogammaglobulinemia, a form of secondary immune deficiency (SID), from the disease and treatments. Patients with hypogammaglobulinemia with recur…
View article: Author Correction: The frequency of pathogenic variation in the All of Us cohort reveals ancestry-driven disparities
Author Correction: The frequency of pathogenic variation in the All of Us cohort reveals ancestry-driven disparities Open