publications by categories in reversed chronological order.


  1. Mixed Effects Machine Learning Models for Colon Cancer Metastasis Prediction using Spatially Localized Immuno-Oncology Markers
    Levy, Joshua J., Bobak, Carly A., Nasir-Moin, Mustafa, Veziroglu, Eren M., Palisoul, Scott M., Barney, Rachael E., Salas, Lucas A., Christensen, Brock C., Tsongalis, Gregory J., and Vaickus, Louis J.
    Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2022
  2. Comparison of machine-learning algorithms for the prediction of current procedural terminology (CPT) codes from pathology reports
    Levy, Joshua, Vattikonda, Nishitha, Haudenschild, Christian, Christensen, Brock, and Vaickus, Louis
    Journal of Pathology Informatics 2022


  1. Video-Based Deep Learning to Detect Dyssynergic Defecation with 3D High-Definition Anorectal Manometry
    Levy, Joshua J., Navas, Christopher M., Chandra, Joan A., Christensen, Brock C., Vaickus, Louis J., Curley, Michael, Chey, William D., Baker, Jason R., and Shah, Eric D.
    bioRxiv Dec 2021
  2. DNA 5-hydroxymethylcytosine in pediatric central nervous system tumors may impact tumor classification and is a positive prognostic marker
    Azizgolshani, Nasim, Petersen, Curtis L., Chen, Youdinghuan, Levy, Joshua J., Salas, Lucas A., Perreard, Laurent, Nguyen, Lananh N., and Christensen, Brock C.
    Clinical Epigenetics Sep 2021
  3. Journey across epidemiology’s third variables: an anesthesiologist’s guide for successfully navigating confounding, mediation, and effect modification
    Levy, Joshua, Lebeaux, Rebecca, Christensen, Brock, Tosteson, Tor, and Bryan, Yvon
    Regional Anesthesia & Pain Medicine May 2021
  4. Using Satellite Images and Deep Learning to Identify Associations Between County-Level Mortality and Residential Neighborhood Features Proximal to Schools: A Cross-Sectional Study
    Levy, Joshua J., Lebeaux, Rebecca M., Hoen, Anne G., Christensen, Brock C., Vaickus, Louis J., and MacKenzie, Todd A.
    Frontiers in Public Health May 2021
  5. Configuring a federated network of real-world patient health data for multimodal deep learning prediction of health outcomes.
    Haudenschild, Christian, Vaickus, Louis, and Levy, Joshua
    Nov 2021
  6. Development of Biologically Interpretable Multimodal Deep Learning Model for Cancer Prognosis Prediction
    Azher, Zarif L, Vaickus, Louis J, Salas, Lucas A, Christensen, Brock, and Levy, Joshua
    Nov 2021
  7. Improving the Virtual Trichrome Assessment through Bridge Category Models
    Levy, Joshua, Bobak, Carly A, Azizgolshani, Nasim, Liu, Xiaoying, Ren, Bing, Lisovsky, Mikhail, Suriawinata, Arief A, Christensen, Brock, O’Malley, James, and Vaickus, Louis J
    Nov 2021
  8. Estimating the Inter- and Intra-Rater Reliability for NASH Fibrosis Staging in the Presence of Bridge Ordinal Ratings with Hierarchical Bridge Category Models
    Levy, Joshua, Bobak, Carly, Azizgolshani, Nasim, Liu, Xiaoying, Ren, Bing, Lisovsky, Mikhail, Suriawinata, Arief, Christensen, Brock, O’Malley, James, and Vaickus, Louis
    Oct 2021
  9. MethylSPWNet and MethylCapsNet: Biologically Motivated Organization of DNAm Neural Networks, Inspired by Capsule Networks
    Levy, Joshua J., Chen, Youdinghuan, Azizgolshani, Nasim, Petersen, Curtis L., Titus, Alexander J., Moen, Erika L., Vaickus, Louis J., Salas, Lucas A., and Christensen, Brock C.
    npj Systems Biology and Applications Aug 2021
  10. Bridge Category Models: Development of Bayesian Modelling Procedures to Account for Bridge Ordinal Ratings for Disease Staging
    Levy, Joshua, Bobak, Carly A, Azizgolshani, Nasim, Andersen, Michael J, Suriawinata, Arief, Liu, Xiaoying, Lisovsky, Mikhail, Ren, Bing, Christensen, Brock, Vaickus, Louis, and O’Malley, James
    Aug 2021
  11. Atypia of undetermined significance in thyroid cytology: Nuclear atypia and architectural atypia are associated with different molecular alterations and risks of malignancy
    Glass, Ryan E., Levy, Joshua J., Motanagh, Samaneh A., Vaickus, Louis J., and Liu, Xiaoying
    Cancer Cytopathology Aug 2021
  12. MRI Screening after Silicone Implant Breast Surgery: Patient Survey of Adherence to FDA Recommendations
    Copeland-Halperin, Libby R., Wampler, Ariel T., Doughty, Hayden, Shank, Nina, Levy, Joshua J., Rada, Maria L. Reategui Via, and Rosen, Joseph M.
    Plastic and Reconstructive Surgery Aug 2021
  13. Evaluating the mediating effects of perceived vulnerability to disease in the relation between disgust and contamination-based OCD
    Brady, Robert E., Badour, Christal L., Arega, Enat A., Levy, Joshua J., and Adams, Thomas G.
    Journal of Anxiety Disorders Apr 2021
  14. Topological Feature Extraction and Visualization of Whole Slide Images using Graph Neural Networks.
    Levy, Joshua, Haudenschild, Christian, Barwick, Clark, Christensen, Brock, and Vaickus, Louis
    Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Apr 2021
  15. Emerging Diagnostic and Investigative Technologies: Validation of Deep Learning Technologies for Dna Methylation and Histopathology
    Levy, Joshua
    Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Apr 2021
  16. Artificial Intelligence in Anatomic Pathology
    Levy, Joshua J., and Vaickus, Louis J.
    Advances in Molecular Pathology Nov 2021


  1. A large-scale internal validation study of unsupervised virtual trichrome staining technologies on nonalcoholic steatohepatitis liver biopsies
    Levy, Joshua J., Azizgolshani, Nasim, Andersen, Michael J., Suriawinata, Arief, Liu, Xiaoying, Lisovsky, Mikhail, Ren, Bing, Bobak, Carly A., Christensen, Brock C., and Vaickus, Louis J.
    Modern Pathology Dec 2020
  2. Don’t dismiss logistic regression: the case for sensible extraction of interactions in the era of machine learning
    Levy, Joshua J., and O’Malley, A. James
    BMC Medical Research Methodology Jun 2020
  3. Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors
    Gordon, Sean P., Contreras-Moreira, Bruno, Levy, Joshua J., Djamei, Armin, Czedik-Eysenberg, Angelika, Tartaglio, Virginia S., Session, Adam, Martin, Joel, Cartwright, Amy, Katz, Andrew, Singan, Vasanth R., Goltsman, Eugene, Barry, Kerrie, Dinh-Thi, Vinh Ha, Chalhoub, Boulos, Diaz-Perez, Antonio, Sancho, Ruben, Lusinska, Joanna, Wolny, Elzbieta, Nibau, Candida, Doonan, John H., Mur, Luis A. J., Plott, Chris, Jenkins, Jerry, Hazen, Samuel P., Lee, Scott J., Shu, Shengqiang, Goodstein, David, Rokhsar, Daniel, Schmutz, Jeremy, Hasterok, Robert, Catalan, Pilar, and Vogel, John P.
    Nature Communications Jul 2020
  4. MethylNet: an automated and modular deep learning approach for DNA methylation analysis
    Levy, Joshua J., Titus, Alexander J., Petersen, Curtis L., Chen, Youdinghuan, Salas, Lucas A., and Christensen, Brock C.
    BMC Bioinformatics Mar 2020
  5. Estimating latent positions in social and biological networks using Graph Neural Networks in R with GCN4R
    Levy, Joshua, Bobak, Carly A, Christensen, Brock, Vaickus, Louis J, and O’Malley, A. James
    Nov 2020
  6. Does the timing of postoperative showering impact infection rates? A systematic review and meta-analysis
    Copeland-Halperin, Libby R., Rada, Maria L. Reategui Via, Levy, Joshua, Shank, Nina, Funderburk, Christopher D., and Shin, Joseph H.
    Journal of Plastic, Reconstructive & Aesthetic Surgery Jul 2020
  7. Investigating the potential for machine learning prediction of patient outcomes: a retrospective study of hospital acquired pressure injuries
    Levy, Joshua J., Lima, Jorge F., Miller, Megan W., Freed, Gary L., O’Malley, A. James, and Emeny, Rebecca T.
    Apr 2020
  8. PathFlow-MixMatch for Whole Slide Image Registration: An Investigation of a Segment-Based Scalable Image Registration Method
    Levy, Joshua J, Jackson, Christopher R, Haudenschild, Christian C, Christensen, Brock C, and Vaickus, Louis J
    Mar 2020
  9. PathFlowAI: A High-Throughput Workflow for Preprocessing, Deep Learning and Interpretation in Digital Pathology
    Levy, Joshua, Salas, Lucas A, Christensen, Brock C, Sriharan, Aravindhan, and Vaickus, Louis J
    Pacific Symposium on Biocomputing Mar 2020
  10. Preliminary Evaluation of the Utility of Deep Generative Histopathology Image Translation at a Mid-sized NCI Cancer Center
    Levy, Joshua, Jackson, Christopher, Sriharan, Aravindhan, Christensen, Brock, and Vaickus, Louis
    In Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies Mar 2020


  1. PyMethylProcess—convenient high-throughput preprocessing workflow for DNA methylation data
    Levy, Joshua J, Titus, Alexander J, Salas, Lucas A, and Christensen, Brock C
    Bioinformatics Aug 2019
  2. PolyCRACKER, a robust method for the unsupervised partitioning of polyploid subgenomes by signatures of repetitive DNA evolution.
    Levy, Joshua, Gordon, Sean, and Vogel, John
    BMC genomics Aug 2019