Explanipedia

Increasing Value in the Veterans Affairs Healthcare System (VA) with Precision Health: A Continuing Landmark Collaboration with the Department of Energy Open

Amy C. Justice, Benjamin H. McMahon, Daniel Jacobson, Kelly Cho, Anuj J. Kapadia , et al. · 2025

Objective By personalizing healthcare to an individual’s specific requirements, precision health promises to maximize benefit and minimize harm, thereby maximizing value. We describe here, how in Phase 2 of the Million Veteran Program–Comp…

A Complex Presentation of Anorexia Nervosa and Takotsubo Cardiomyopathy in a Patient of East Asian Descent Open

William Rienas, Jingxiong Pu, Benjamin H. McMahon, Vivek Parameswara Sarma, Rachel Silverman , et al. · 2025

Quantification of heterogeneity in human CD8+ T cell responses to vaccine antigens: an HLA-guided perspective Open

Duane C. Harris, Apoorv Shanker, Makaela M. Montoya, Trent R. Llewellyn, Anna R. Matuszak , et al. · 2024

Vaccines have historically played a pivotal role in controlling epidemics. Effective vaccines for viruses causing significant human disease, e.g. , Ebola, Lassa fever, or Crimean Congo hemorrhagic fever virus, would be invaluable to public…

Effectiveness and safety of immune checkpoint inhibitors in Black patients versus White patients in a US national health system: a retrospective cohort study Open

Sean R. Miller, Ralph Jiang, Matthew J. Schipper, Lars Fritsche, Garth W. Strohbehn , et al. · 2024

A landmark federal interagency collaboration to promote data science in health care: Million Veteran Program-Computational Health Analytics for Medical Precision to Improve Outcomes Now Open

Amy C. Justice, Benjamin H. McMahon, Ravi Madduri, Silvia Crivelli, Scott M. Damrauer , et al. · 2024

Objectives In 2016, the Department of Veterans Affairs (VA) and the Department of Energy (DOE) established an Interagency Agreement (IAA), the Million Veteran Program-Computational Health Analytics for Medical Precision to Improve Outcomes…

Molecular dynamics simulation of phosphorylation-induced conformational transitions in the mycobacterium tuberculosis response regulator PrrA Open

Guo Chen, Benjamin H. McMahon, Chang - Shung Tung · 2024

Phosphorylation-activated modulation of response regulators (RR) is predominantly used by bacteria as a strategy in regulating their two-component signaling (TCS) systems, the underlying molecular mechanisms are however far from fully unde…

High dimensional predictions of suicide risk in 4.2 million US Veterans using ensemble transfer learning Open

Sayera Dhaubhadel, Kumkum Ganguly, Ruy M. Ribeiro, Judith D. Cohn, James M. Hyman , et al. · 2024

We present an ensemble transfer learning method to predict suicide from Veterans Affairs (VA) electronic medical records (EMR). A diverse set of base models was trained to predict a binary outcome constructed from reported suicide, suicide…

GWAS Meta-Analysis of Suicide Attempt: Identification of 12 Genome-Wide Significant Loci and Implication of Genetic Risks for Specific Health Factors Open

Anna R. Docherty, Niamh Mullins, Allison E. Ashley‐Koch, Xuejun Qin, Jonathan R. I. Coleman , et al. · 2023

This multi-ancestry analysis of suicide attempt identified several loci contributing to risk and establishes significant shared genetic covariation with clinical phenotypes. These findings provide insight into genetic factors associated wi…

Deep sequential neural network models improve stratification of suicide attempt risk among US veterans Open

Carianne Martinez, Drew Levin, Jessica Jones, Patrick D. Finley, Benjamin H. McMahon , et al. · 2023

Objective To apply deep neural networks (DNNs) to longitudinal EHR data in order to predict suicide attempt risk among veterans. Local explainability techniques were used to provide explanations for each prediction with the goal of ultimat…

High dimensional predictions of suicide risk in 4.2 million US Veterans using ensemble transfer learning Open

Sayera Dhaubhadel, Kumkum Ganguly, Ruy M. Ribeiro, Judith D. Cohn, James M. Hyman , et al. · 2023

We present an ensemble transfer learning model to predict suicide from Veterans Affairs (VA) electronic medical records (EMR). A diverseset of base models was trained to predict a binary outcome constructed from reported suicide, suicide a…

Entire Expressed Peripheral Blood Transcriptome in Pediatric Severe Malarial Anemia Open

Samuel B. Anyona, Qiuying Cheng, Yan Guo, Evans Raballah, Ivy Hurwitz , et al. · 2023

This study on severe malarial anemia (SMA: Hb < 6.0 g/dL), a leading global cause of childhood morbidity and mortality, analyzed the entire expressed transcriptome in whole blood from children with non-SMA (Hb ≥ 6.0 g/dL, n = 41) and SMA (…

Cardiovascular Disease Risk Assessment Using Traditional Risk Factors and Polygenic Risk Scores in the Million Veteran Program Open

Jason L. Vassy, Daniel Posner, Yuk‐Lam Ho, David Gagnon, Ashley Galloway , et al. · 2023

Importance Primary prevention of atherosclerotic cardiovascular disease (ASCVD) relies on risk stratification. Genome-wide polygenic risk scores (PRSs) are proposed to improve ASCVD risk estimation. Objective To determine whether genome-wi…

Evidence of Novel Susceptibility Variants for Prostate Cancer and a Multiancestry Polygenic Risk Score Associated with Aggressive Disease in Men of African Ancestry Open

Fei Chen, Ravi Madduri, Alex A Rodriguez, Burcu F. Darst, Alisha Chou , et al. · 2023

Evidence of Novel Susceptibility Variants for Prostate Cancer and a Multiancestry Polygenic Risk Score Associated with Aggressive Disease in Men of African Ancestry Open

Fangfang Chen, Ravi Madduri, A.A. Rodriguez, B.F. Darst, Alisha Chou , et al. · 2023

Human NCR3 gene variants rs2736191 and rs11575837 influence susceptibility to the longitudinal development of pediatric severe malarial anemia Open

Clinton Onyango, Qiuying Cheng, Elly O. Munde, Evans Raballah, Samuel B. Anyona , et al. · 2022

Background Plasmodium falciparum malaria is a leading cause of pediatric morbidity and mortality in holoendemic transmission areas. Severe malarial anemia [SMA, hemoglobin (Hb) < 5.0g/dL] is the most common clinical manifestation of severe…

Identification of Novel, Replicable Genetic Risk Loci for Suicidal Thoughts and Behaviors Among US Military Veterans Open

Nathan A. Kimbrel, Allison E. Ashley‐Koch, Xuejun Qin, Jennifer H. Lindquist, Melanie E. Garrett , et al. · 2022

Importance Suicide is a leading cause of death; however, the molecular genetic basis of suicidal thoughts and behaviors (SITB) remains unknown. Objective To identify novel, replicable genomic risk loci for SITB. Design, Setting, and Partic…

MACE prediction using high-dimensional machine learning and mechanistic interpretation: A longitudinal cohort study in US veterans Open

Sayera Dhaubhadel, Beauty Kolade, Ruy M. Ribeiro, Kumkum Ganguly, Nicolas Hengartner , et al. · 2022

High dimensional predictive models of Major Adverse Cardiac Events (MACE), which includes heart attack (AMI), stroke, and death caused by cardiovascular disease (CVD), were built using four longitudinal cohorts of Veterans Administration (…

In with the old, in with the new: machine learning for time to event biomedical research Open

Ioana Danciu, Greeshma Agasthya, Janet P. Tate, Mayanka Chandra-Shekar, Ian Goethert , et al. · 2022

The predictive modeling literature for biomedical applications is dominated by biostatistical methods for survival analysis, and more recently some out of the box machine learning approaches. In this article, we show a presentation of a ma…

Genome-wide association study meta-analysis of suicide attempt identifies twelve genome-wide significant loci and implicates genetic risks for specific health factors Open

Anna R. Docherty, Niamh Mullins, Allison E. Ashley‐Koch, Xuejun Qin, Jonathan R. I. Coleman , et al. · 2022

Objective Suicidal behavior is heritable and a major cause of death worldwide. Two large-scale genome-wide association studies (GWAS) recently discovered and cross-validated genome-wide significant (GWS) loci for suicide attempt (SA). The …

Continuous-time probabilistic models for longitudinal electronic health records Open

Alan D. Kaplan, Uttara Tipnis, Jean C. Beckham, Nathan A. Kimbrel, David W. Oslin , et al. · 2022

Using Explainable-AI to Find Geospatial Environmental and Sociodemographic Predictors of Suicide Attempts Open

Mirko Pavicic, Angelica M. Walker, Kyle A. Sullivan, John Lagergren, Ashley Cliff , et al. · 2022

Despite a global decrease in suicide rates in recent years, death by suicide has increased in the United States. It is therefore imperative to identify the risk factors associated with suicide attempts in order to combat this growing epide…

Digging deeper into GWAS signal using GRIN implicates additional genes contributing to suicidal behavior Open

Kyle A. Sullivan, Matthew Lane, Mikaela Cashman, J Izaak Miller, Mirko Pavicic , et al. · 2022

Genome-wide association studies (GWAS) identify genetic variants underlying complex traits but are limited by stringent genome-wide significance thresholds. Here we dramatically relax GWAS stringency by orders of magnitude and apply GRIN (…

A genome-wide association study of suicide attempts in the million veterans program identifies evidence of pan-ancestry and ancestry-specific risk loci Open

Nathan A. Kimbrel, Allison E. Ashley‐Koch, Xuejun Qin, Jennifer H. Lindquist, Melanie E. Garrett , et al. · 2022

BASELINE METABOLIC PROFILING AND RISK OF DEATH FROM COVID-19 Open

Glen H. Murata, Allison Murata, Heather Campbell, Brent Wagner, Benjamin H. McMahon , et al. · 2022

Objective To derive a predicted probability of death (PDeathLabs) based upon complete value sets for 11 clinical measurements (CM) obtained on patients prior to their diagnosis of coronavirus disease (COVID-19). PDeathLabs is intended for …

A NOVEL METHOD FOR HANDLING PRE-EXISTING CONDITIONS IN PREDICTION MODELS FOR COVID-19 DEATH Open

Glen H. Murata, Allison Murata, Heather Campbell, Benjamin H. McMahon, Jenny T. Mao · 2022

Objective To derive a predicted probability of death (PDeathDx) based upon complete sets of ICD-10 codes assigned to patients prior to their diagnosis of COVID-19. PDeathDx is intended for use as a summary metric for pre-existing condition…

SUSTAINED BENEFICIAL EFFECTS OF VACCINATION ON THE CASE FATALITY RATE FOR COVID-19 INFECTIONS Open

Glen H. Murata, Allison Murata, Douglas J. Perkins, Heather Campbell, Jenny T. Mao , et al. · 2022

Objective To evaluate the benefits of vaccination on the case fatality rate (CFR) for COVID-19 infections. Design Multivariate modeling of data from electronic medical records Setting 130 medical centers of the United States Department of …

Continuous-Time Probabilistic Models for Longitudinal Electronic Health Records Open

Alan D. Kaplan, Uttara Tipnis, Jean C. Beckham, Nathan A. Kimbrel, David W. Oslin , et al. · 2022

Analysis of longitudinal Electronic Health Record (EHR) data is an important goal for precision medicine. Difficulty in applying Machine Learning (ML) methods, either predictive or unsupervised, stems in part from the heterogeneity and irr…

Integrative structural studies of the SARS-CoV-2 spike protein during the fusion process (2022) Open

Jacob C. Miner, Paul W. Fenimore, Will Fischer, Benjamin H. McMahon, Karissa Y. Sanbonmatsu , et al. · 2022

A novel method for handling pre-existing conditions in multivariate prediction model development for COVID-19 death in the Department of Veterans Affairs Open

Heather Campbell, Allison Murata, Jenny T. Mao, Benjamin H. McMahon, Glen H. Murata · 2022

Many mathematical models have been proposed to predict death following the Coronavirus Disease 2019 (COVID-19); all started with comorbidity subsets for this still-little understood disease. Thus, we derived a novel predicted probability o…

Staged progression epidemic models for the transmission of invasive nontyphoidal <i>Salmonella</i> (iNTS) with treatment Open

Zhuolin Qu, Benjamin H. McMahon, Douglas J. Perkins, James M. Hyman · 2021

We develop and analyze a stage-progression compartmental model to study the emerging invasive nontyphoidal Salmonella (iNTS) epidemic in sub-Saharan Africa. iNTS bloodstream infections are often fatal, and the diverse and non-specific clin…

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