2025

1. Insights to aging prediction with AI based epigenetic clocks

   Levy, Joshua J, Diallo, Alos B, Saldias Montivero, Marietta K, Gabbita, Sameer, Salas, Lucas A, and Christensen, Brock C

   Epigenomics 2025
2. Evaluating Evidence-Based Psychotherapy Utilization Patterns Among Suicide-Risk-Stratified Veterans Diagnosed With Posttraumatic Stress Disorder

   Levis, Maxwell, Dimambro, Monica, Levy, Joshua, Platt, Henry, Fraade, Abby, and Shiner, Brian

   Clinical Psychology & Psychotherapy 2025
3. Chewing-Activated TRPV4/PIEZO1–HIF-1α–Zn Axes in a Rat Periodontal Complex

   Wang, Y, Lee, BH, Yang, Z, Ho, TJ, Ci, H, Jackson, B, Pushon, T, Wang, B, Levy, J, and Ho, SP

   Journal of Dental Research 2025

2024

1. System and method for automation of surgical pathology processes using artificial intelligence

   LeBoeuf, Matthew, Levy, Joshua J, and Vaickus, Louis J

   Journal of Dental Research Jun 2024
2. Integration of a deep learning basal cell carcinoma detection and tumor mapping algorithm into the Mohs micrographic surgery workflow and effects on clinical staffing: A simulated, retrospective study

   Chacko, Rachael, Davis, Matthew J, Levy, Joshua, and LeBoeuf, Matthew

   JAAD international Jun 2024
3. A deep learning algorithm to detect cutaneous squamous cell carcinoma on frozen sections in Mohs micrographic surgery: A retrospective assessment

   Davis, Matthew J, Srinivasan, Gokul, Chacko, Rachael, Chen, Sophie, Suvarna, Anish, Vaickus, Louis J, Torres, Veronica C, Hodge, Sassan, Chen, Eunice Y, Preum, Sarah, and others,

   Experimental Dermatology Jun 2024
4. Spatial Omics Driven Crossmodal Pretraining Applied to Graph-based Deep Learning for Cancer Pathology Analysis

   Azher, Zarif L, Fatemi, Michael, Lu, Yunrui, Srinivasan, Gokul, Diallo, Alos B, Christensen, Brock C, Salas, Lucas A, Kolling IV, Fred W, Perreard, Laurent, Palisoul, Scott M, and others,

   In Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Jun 2024
5. Potential to enhance large scale molecular assessments of skin photoaging through virtual inference of spatial transcriptomics from routine staining

   Srinivasan, Gokul, Davis, Matthew J, LeBoeuf, Matthew R, Fatemi, Michael, Azher, Zarif L, Lu, Yunrui, Diallo, Alos B, Montivero, Marietta K Saldias, Kolling IV, Fred W, Perrard, Laurent, and others,

   In Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Jun 2024
6. Artificial intelligence and deep learning in molecular testing

   Levy, Joshua, and Vaickus, Louis

   In Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Jun 2024
7. Intraoperative margin assessment for basal cell carcinoma with deep learning and histologic tumor mapping to surgical site

   Levy, Joshua J, Davis, Matthew J, Chacko, Rachael S, Davis, Michael J, Fu, Lucy J, Goel, Tarushii, Pamal, Akash, Nafi, Irfan, Angirekula, Abhinav, Suvarna, Anish, and others,

   NPJ Precision Oncology Jun 2024
8. Preparing healthcare leaders of the digital age with an integrative artificial intelligence curriculum: a pilot study

   Park, Soo Hwan, Pinto-Powell, Roshini, Thesen, Thomas, Lindqwister, Alexander, Levy, Joshua, Chacko, Rachael, Gonzalez, Devina, Bridges, Connor, Schwendt, Adam, Byrum, Travis, and others,

   Medical Education Online Jun 2024
9. Integrative Co-Registration of Elemental Imag-ing and Histopathology for Enhanced Spatial Multimodal Analysis of Tissue Sections through TRACE

   Lu, Yunrui, Steiner, Ramsey, Han, Serin, Srivastava, Aruesha, Shaik, Neha, Chan, Matthew, Diallo, Alos, Punshon, Tracy, Jackson, Brian, Kolling IV, Fred, and others,

   bioRxiv Jun 2024
10. Multimodal analysis of metals, spatial transcriptomics, and histological structures in colorectal cancer

    Srivastava, Aruesha, Shaik, Neha, Lu, Yunrui, Chan, Matthew, Diallo, Alos, Han, Serin, Steiner, Ramsey, Punshon, Tracy, Jackson, Brian, Vahdat, Linda, and others,

    Cancer Research Jun 2024
11. A web-based application to co-register elemental imaging with histopathology to enhance the study of metal bioaccumulation within tumors

    Lu, Yunrui, Steiner, Ramsey, Han, Serin, Chan, Matthew, Punshon, Tracy, Jackson, Brian, Vahdat, Linda, Marotti, Jonathan, and Levy, Joshua

    Cancer Research Jun 2024
12. Does ROSE matter? Evaluation of final diagnostic, PD-L1 immunohistochemistry, and molecular testing yields of CT-guided lung biopsies performed before and after the onset of the COVID-19 pandemic

    Jennings, Emma B, Percarpio, Robert B, Tafe, Laura J, Demidenko, Eugene, Levy, Joshua, Gutmann, Edward J, and Marotti, Jonathan D

    Journal of the American Society of Cytopathology Jun 2024
13. Tu1703 MULTI CENTER VALIDATION OF VIDEO-BASED DEEP LEARNING TO INTERPRET ANORECTAL MANOMETRY

    Azher, Zarif, Ginnebaugh, Brian D, Levinthal, David J, Valentin, Nelson, Levy, Joshua J, and Shah, Eric D

    Gastroenterology Jun 2024
14. Machine learning for predicting cognitive deficits using auditory and demographic factors

    Niemczak, Christopher E, Montagnese, Basile, Levy, Joshua, Fellows, Abigail M, Gui, Jiang, Leigh, Samantha M, Magohe, Albert, Massawe, Enica R, and Buckey, Jay C

    Plos one Jun 2024
15. Abstract IA020: AI-powered tool for rapid & reliable bladder cancer screening and surveillance: multicenter validation efforts

    Levy, Joshua, Yao, Keluo, Marotti, Jonathan, Kerr, Darcy, Gutmann, Edward, Harvey, Sam, Sayegh, Yoseph, VandenBussche, Chris, Quick, Michael, Costa, Peter, and others,

    Clinical Cancer Research Jun 2024
16. Abstract B003: Preliminary machine learning integration of DNA methylation-based tumor immune microenvironment deconvolution with histopathological slides for bladder cancer prognostication

    Azher, Zarif L, Zhang, Ze, Christensen, Brock C, Salas, Lucas A, Karagas, Margaret R, Vaickus, Louis J, Fuyura, Hideki, Yao, Keluo, and Levy, Joshua J

    Clinical Cancer Research Jun 2024
17. System and method for rapid and accurate histologic analysis of tumor margins using machine learning

    LeBoeuf, Matthew, Vaickus, Louis J, and Levy, Joshua J

    Clinical Cancer Research May 2024
18. Artificial Intelligence Applications in Cytopathology: Current State of the Art

    Vaickus, Louis J, Kerr, Darcy A, Torres, Jaylou M Velez, and Levy, Joshua

    Surgical Pathology Clinics May 2024
19. Using natural language processing to evaluate temporal patterns in suicide risk variation among high-risk Veterans

    Levis, Maxwell, Levy, Joshua, Dimambro, Monica, Dufort, Vincent, Ludmer, Dana J, Goldberg, Matan, and Shiner, Brian

    Psychiatry research May 2024
20. Effects of per-and polyfluoroalkyl substances on placental features in the New Hampshire Birth Cohort Study

    Romano, Megan Elizabeth, Gallagher, Lisa G, Yim, Gyeyoon, Punshon, Tracy, Bentz, Jessica, Levy, Joshua, Howe, Caitlin G, and Karagas, Margaret R

    In ISEE Conference Abstracts May 2024
21. Characterizing Veteran suicide decedents that were not classified as high-suicide-risk

    Levis, Maxwell, Dimambro, Monica, Levy, Joshua, Dufort, Vincent, Fraade, Abby, Winer, Max, and Shiner, Brian

    Psychological Medicine May 2024
22. Maternal glucose levels and late pregnancy circulating extracellular vesicle and particle miRNAs in the MADRES pregnancy cohort

    Anderson, Elizabeth C, Foley, Helen B, Levy, Joshua J, Romano, Megan E, Gui, Jiang, Bentz, Jessica L, Maldonado, Luis E, Farzan, Shohreh F, Bastain, Theresa M, Marsit, Carmen J, and others,

    Epigenetics May 2024
23. Optimizing Z-Stack Plane Selection within Urothelial Clusters in 3D Urine Cytology via AI to Improve Bladder Cancer Screening and Surveillance: Ongoing Multicenter Study

    Sayegh, Yoseph, Harvey, Samuel, Marotti, Jonathan, Kerr, Darcy, Gutmann, Edward, Yao, Keluo, Liu, Xiaoying, Vaickus, Louis, VandenBussche, Christopher, and Levy, Joshua

    Journal of the American Society of Cytopathology May 2024
24. Using Natural Language Processing to develop risk-tier specific suicide prediction models for Veterans Affairs patients

    Levis, Maxwell, Dimambro, Monica, Levy, Joshua, and Shiner, Brian

    Journal of psychiatric research May 2024
25. An initial game-theoretic assessment of enhanced tissue preparation and imaging protocols for improved deep learning inference of spatial transcriptomics from tissue morphology

    Fatemi, Michael Y, Lu, Yunrui, Diallo, Alos B, Srinivasan, Gokul, Azher, Zarif L, Christensen, Brock C, Salas, Lucas A, Tsongalis, Gregory J, Palisoul, Scott M, Perreard, Laurent, and others,

    Briefings in Bioinformatics May 2024
26. CHARTING THE EVOLUTION AND TRANSFORMATIVE IMPACT OF THE PACIFIC SYMPOSIUM ON BIOCOMPUTING THROUGH A 30-YEAR RETROSPECTIVE ANALYSIS OF COLLABORATIVE NETWORKS AND THEMES USING MODERN COMPUTATIONAL TOOLS

    Zhang, Leah, Garg, Sameeksha, Zhang, Edward, McOsker, Sean, Bobak, Carly, Giffin, Kristine, Christensen, Brock, and Levy, Joshua

    In Biocomputing 2025: Proceedings of the Pacific Symposium May 2024
27. Investigating the Differential Impact of Psychosocial Factors by Patient Characteristics and Demographics on Veteran Suicide Risk Through Machine Learning Extraction of Cross-Modal Interactions

    Levy, Joshua, Dimambro, Monica, Diallo, Alos, Gui, Jiang, Shiner, Brian, and Levis, Maxwell

    In Biocomputing 2025: Proceedings of the Pacific Symposium May 2024
28. Integration of Elemental Imaging and Spatial Transcriptomic Profiling for Proof-of-Concept Metals-Based Pathway Analysis of Colon Tumor Microenvironment

    Srivastava, Aruesha, Shaik, Neha, Lu, Yunrui, Chan, Matthew, Diallo, Alos B, Han, Serin, Punshon, Tracy, Jackson, Brian P, Vahdat, Linda T, Liu, Xiaoying, and others,

    medRxiv May 2024
29. System and method for automation of surgical pathology processes using artificial intelligence

    LeBoeuf, Matthew, Levy, Joshua J, and Vaickus, Louis J

    medRxiv Dec 2024

2023

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

   Digestive Diseases and Sciences Dec 2023
2. Development of an interactive web dashboard to facilitate the reexamination of pathology reports for instances of underbilling of CPT codes

   Greenburg, Jack, Lu, Yunrui, Lu, Shuyang, Kamau, Uhuru, Hamilton, Robert, Pettus, Jason, Preum, Sarah, Vaickus, Louis, and Levy, Joshua

   Journal of Pathology Informatics Dec 2023
3. Identification of spatial proteomic signatures of colon tumor metastasis: a digital spatial profiling approach

   Levy, Joshua J, Zavras, John P, Veziroglu, Eren M, Nasir-Moin, Mustafa, Kolling, Fred W, Christensen, Brock C, Salas, Lucas A, Barney, Rachael E, Palisoul, Scott M, Ren, Bing, and others,

   The American Journal of Pathology Dec 2023
4. Assessment of emerging pretraining strategies in interpretable multimodal deep learning for cancer prognostication

   Azher, Zarif L, Suvarna, Anish, Chen, Ji-Qing, Zhang, Ze, Christensen, Brock C, Salas, Lucas A, Vaickus, Louis J, and Levy, Joshua J

   BioData Mining Dec 2023
5. AI-RADS: Successes and challenges of a novel artificial intelligence curriculum for radiologists across different delivery formats

   Lindqwister, Alexander L, Hassanpour, Saeed, Levy, Joshua, and Sin, Jessica M

   Frontiers in Medical Technology Dec 2023
6. GRANDPA: GeneRAtive network sampling using degree and property augmentation applied to the analysis of partially confidential healthcare networks

   Bobak, Carly A, Zhao, Yifan, Levy, Joshua J, and O’Malley, A James

   Applied Network Science Dec 2023
7. Predictors of gastrostomy tube placement in patients with head and neck cancer undergoing resection and flap-based reconstruction: systematic review and meta-analysis

   Stewart, Talia, Copeland-Halperin, Libby R, Demsas, Falen, Divakar, Prashanthi, Shank, Nina, Blunt, Heather, Levy, Joshua J, Nigriny, John F, and Paydarfar, Joseph A

   Journal of Plastic, Reconstructive & Aesthetic Surgery Dec 2023
8. Functional Reorganization of the Mesial Frontal Premotor Cortex in Patients With Supplementary Motor Area Seizures

   Hong, Jennifer, Quon, Robert J, Song, Yinchen, Xie, Tiankang, Levy, Joshua J, D’Agostino, Erin, Camp, Edward J, Roberts, David W, and Jobst, Barbara C

   Neurosurgery Dec 2023
9. Predictors of Gastrostomy Tube Placement in Head and Neck Cancer Patients at a Rural Tertiary Care Hospital

   Copeland-Halperin, Libby R, Divakar, Prashanthi, Stewart, Talia, Demsas, Falen, Levy, Joshua J, Nigriny, John F, and Paydarfar, Joseph A

   Journal of Reconstructive Microsurgery Open Dec 2023
10. Dynamic suicide topic modelling: Deriving population-specific, psychosocial and time-sensitive suicide risk variables from Electronic Health Record psychotherapy notes

    Levis, Maxwell, Levy, Joshua, Dufort, Vincent, Russ, Carey J, and Shiner, Brian

    Clinical psychology & psychotherapy Dec 2023
11. Large-scale validation study of an improved semiautonomous urine cytology assessment tool: AutoParis-X

    Levy, Joshua J, Chan, Natt, Marotti, Jonathan D, Kerr, Darcy A, Gutmann, Edward J, Glass, Ryan E, Dodge, Caroline P, Suriawinata, Arief A, Christensen, Brock C, Liu, Xiaoying, and others,

    Cancer Cytopathology Dec 2023
12. Examining longitudinal markers of bladder cancer recurrence through a semiautonomous machine learning system for quantifying specimen atypia from urine cytology

    Levy, Joshua J, Chan, Natt, Marotti, Jonathan D, Rodrigues, Nathalie J, Ismail, A Aziz O, Kerr, Darcy A, Gutmann, Edward J, Glass, Ryan E, Dodge, Caroline P, Suriawinata, Arief A, and others,

    Cancer cytopathology Dec 2023
13. Utility of Retrospective Molecular Analysis in Diagnostically Challenging Mesenchymal Neoplasms

    Mindiola Romero, Andres E, Tafe, Laura J, Green, Donald C, Deharvengt, Sophie J, Winnick, Kimberly N, Tsongalis, Gregory J, Baker, Michael L, Linos, Konstantinos, Levy, Joshua J, and Kerr, Darcy A

    International Journal of Surgical Pathology Dec 2023
14. Paired-agent imaging for the rapid and accurate detection of involved margins in Mohs micrographic surgery

    Torres, Veronica, Chacko, Rachel, Hodge, Sassan, Levy, Joshua, Vaickus, Louis, Chen, Eunice, LeBoeuf, Matthew, and Samkoe, Kimberley S

    In Molecular-Guided Surgery: Molecules, Devices, and Applications IX Dec 2023
15. Inferring spatial transcriptomics markers from whole slide images to characterize metastasis-related spatial heterogeneity of colorectal tumors: A pilot study

    Fatemi, Michael, Feng, Eric, Sharma, Cyril, Azher, Zarif, Goel, Tarushii, Ramwala, Ojas, Palisoul, Scott M, Barney, Rachael E, Perreard, Laurent, Kolling, Fred W, and others,

    Journal of Pathology Informatics Dec 2023
16. Alopecia areata and thyroid screening in Down syndrome: Leveraging epic cosmos data set

    Kranyak, Allison, Rork, Jillian, Levy, Joshua, and Burdick, Timothy E

    Journal of the American Academy of Dermatology Dec 2023
17. HiTAIC: hi erarchical tumor artificial intelligence classifier traces tissue of origin and tumor type in primary and metastasized tumors using DNA methylation

    Zhang, Ze, Lu, Yunrui, Vosoughi, Soroush, Levy, Joshua J, Christensen, Brock C, and Salas, Lucas A

    NAR cancer Dec 2023
18. Artificial intelligence: applications in clinical medicine

    Levy, Joshua, Madrigal, Emilio, and Vaickus, Louis

    NAR cancer Dec 2023
19. Paired-agent imaging as a rapid en face margin screening method in Mohs micrographic surgery

    Torres, Veronica C, Hodge, Sassan, Levy, Joshua J, Vaickus, Louis J, Chen, Eunice Y, LeBouef, Matthew, and Samkoe, Kimberley S

    Frontiers in Oncology Dec 2023
20. Leveraging natural language processing to improve electronic health record suicide risk prediction for Veterans Health Administration users

    Levis, Maxwell, Levy, Joshua, Dent, Kallisse R, Dufort, Vincent, Gobbel, Glenn T, Watts, Bradley V, and Shiner, Brian

    The Journal of clinical psychiatry Dec 2023
21. Whole-tissue margin evaluation for Mohs surgery using paired-agent imaging

    Torres, Veronica C, Hodge, Sassan, Chacko, Rachael, Levy, Joshua J, Vaickus, Louis J, Chen, Eunice Y, LeBoeuf, Matthew, and Samkoe, Kimberley S

    In Optical Molecular Probes, Imaging and Drug Delivery Dec 2023
22. DeltaAI: Semi-Autonomous Tissue Grossing Measurements and Recommendations using Neural Radiance Fields for Rapid, Complete Intraoperative Histological Assessment of Tumor Margins

    Suvarna, Anish, Vempati, Ram, Chacko, Rachael, Srinivasan, Gokul, Lu, Yunrui, Hunt, Brady, Torres, Veronica, Samkoe, Kimberly, Davis, Matthew, Fu, Lucy, and others,

    bioRxiv Dec 2023
23. Use of molecular testing results to analyze the overuse of atypia of undetermined significance in thyroid cytology

    Coconubo, Daniel Martinez, Levy, Joshua J, Kerr, Darcy A, Vaickus, Louis J, Vidis, Laura, Glass, Ryan E, Gutmann, Edward J, Marotti, Jonathan D, and Liu, Xiaoying

    Journal of the American Society of Cytopathology Dec 2023
24. Assessing the Impact of Pretraining Domain Relevance on Large Language Models Across Various Pathology Reporting Tasks

    Lu, Yunrui, Srinivasan, Gokul, Preum, Sarah, Pettus, Jason, Davis, Matthew, Greenburg, Jack, Vaickus, Louis, and Levy, Joshua

    medRxiv Dec 2023
25. Dendrite: A Structured, Accessible, and Queryable Pathology Search Database for Streamlined Experiment Planning

    Lu, Yunrui, Hamilton, Robert, Greenberg, Jack, Srinivasan, Gokul, Shah, Parth, Preum, Sarah, Pettus, Jason, Vaickus, Louis, and Levy, Joshua

    medRxiv Dec 2023
26. Feasibility of Inferring Spatial Transcriptomics from Single-Cell Histological Patterns for Studying Colon Cancer Tumor Heterogeneity

    Fatemi, Michael Y, Lu, Yunrui, Sharma, Cyril, Feng, Eric, Azher, Zarif L, Diallo, Alos B, Srinivasan, Gokul, Rosner, Grace M, Pointer, Kelli B, Christensen, Brock C, and others,

    medRxiv Dec 2023
27. The Overlooked Role of Specimen Preparation in Bolstering Deep Learning-Enhanced Spatial Transcriptomics Workflows

    Fatemi, Michael Y, Lu, Yunrui, Diallo, Alos B, Srinivasan, Gokul, Azher, Zarif L, Christensen, Brock C, Salas, Lucas A, Tsongalis, Gregory J, Palisoul, Scott M, Perreard, Laurent, and others,

    medRxiv Dec 2023
28. System and method for rapid and accurate histologic analysis of tumor margins using machine learning

    LeBoeuf, Matthew, Vaickus, Louis J, and Levy, Joshua J

    medRxiv Nov 2023
29. The future of digital cytology and artificial intelligence: an editorial commentary for Digital Cytology part 1 and 2.

    Levy, Joshua, and Yao, Keluo

    Journal of the American Society of Cytopathology Nov 2023
30. Integration of a deep learning basal cell carcinoma detection and tumor mapping algorithm into the Mohs micrographic surgery workflow and effects on clinical staffing: a simulated, retrospective study

    Chacko, Rachael, Davis, Matthew J, Levy, Joshua, and LeBoeuf, Matthew

    medRxiv Nov 2023

2022

1. 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 Nov 2022
2. ArcticAI: a deep learning platform for rapid and accurate histological assessment of intraoperative tumor margins

   Levy, Joshua, Davis, Matthew, Chacko, Rachael, Davis, Michael, Fu, Lucy, Goel, Tarushii, Pamal, Akash, Nafi, Irfan, Angirekula, Abhinav, Christensen, Brock, and others,

   medRxiv Nov 2022
3. Using molecular testing to improve the management of thyroid nodules with indeterminate cytology: an institutional experience with review of molecular alterations

   Glass, Ryan E, Marotti, Jonathan D, Kerr, Darcy A, Levy, Joshua J, Vaickus, Louis J, Gutmann, Edward J, Tafe, Laura J, Motanagh, Samaneh A, Sorensen, Meredith J, Davies, Louise, and others,

   Journal of the American Society of Cytopathology Nov 2022
4. Machine learning approaches for hospital acquired pressure injuries: a retrospective study of electronic medical records

   Levy, Joshua J, Lima, Jorge F, Miller, Megan W, Freed, Gary L, O’Malley, A James, and Emeny, Rebecca T

   Frontiers in Medical Technology Nov 2022
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

   In Proceedings of the 37th ACM/SIGAPP Symposium on Applied Computing Nov 2022
6. Development of biologically interpretable multimodal deep learning model for cancer prognosis prediction

   Azher, Zarif L, Vaickus, Louis J, Salas, Lucas A, Christensen, Brock C, and Levy, Joshua J

   In Proceedings of the 37th ACM/SIGAPP Symposium on Applied Computing Nov 2022
7. Passive order auditing associated with reductions in red blood cell utilization: National blood shortage experience

   Ondrasik, Regina M, Khan, Jenna, Szczepiorkowski, Zbigniew M, Levy, Joshua J, and Dunbar, Nancy M

   Transfusion Nov 2022
8. Large-scale longitudinal comparison of urine cytological classification systems reveals potential early adoption of The Paris System criteria

   Levy, Joshua J, Liu, Xiaoying, Marotti, Jonathan D, Kerr, Darcy A, Gutmann, Edward J, Glass, Ryan E, Dodge, Caroline P, and Vaickus, Louis J

   Journal of the American Society of Cytopathology Nov 2022
9. Magnetic resonance imaging screening after silicone implant breast surgery: patient survey of adherence to US Food and Drug Administration 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 Nov 2022
10. ncovering Additional Predictors of Urothelial Carcinoma from Voided Urothelial Cell Clusters through a Deep Learning-Based Image Preprocessing Technique

    Levy, Joshua J., Liu, Xiaoying, Marotti, Jonathan D., Kerr, Darcy A., Gutmann, Edward J., Glass, Ryan E., Dodge, Caroline P., Suriawinata, Arief A., and Vaickus, Louis J.

    Cancer Cytopathology Nov 2022
11. Rapid tumor margin analysis using paired-agent imaging to guide Mohs micrographic surgery

    Torres, Veronica C, Hodge, Sassan, Chen, Eunice Y, Levy, Joshua, Vaickus, Louis J, LeBoeuf, Matthew, and Samkoe, Kimberley S

    In Molecular-Guided Surgery: Molecules, Devices, and Applications VIII Nov 2022
12. Comparison of symptoms and antibody response following administration of Moderna or Pfizer SARS-CoV-2 vaccines

    Kelliher, Michael T, Levy, Joshua J, Nerenz, Robert D, Poore, Bradley, Johnston, Abigail A, Rogers, Amanda R, Stella, Mary EO, Snow, Sarah E, Cervinski, Mark A, and Hubbard, Jacqueline A

    Archives of Pathology & Laboratory Medicine Nov 2022
13. Leveraging unstructured electronic medical record notes to derive population-specific suicide risk models

    Levis, Maxwell, Levy, Joshua, Dufort, Vincent, Gobbel, Glenn T, Watts, Bradley V, and Shiner, Brian

    Psychiatry research Nov 2022
14. Applications of artificial intelligence in orthopaedic surgery

    Farhadi, Faraz, Barnes, Matthew R, Sugito, Harun R, Sin, Jessica M, Henderson, Eric R, and Levy, Joshua J

    Frontiers in medical technology Nov 2022
15. Inferring Spatially Resolved Transcriptomics Data from Whole Slide Images for the Assessment of Colorectal Tumor Metastasis: A Feasibility Study

    Fatemi, Michael, Feng, Eric, Sharma, Cyril, Azher, Zarif, Goel, Tarushii, Ramwala, Ojas, Palisoul, Scott, Barney, Rachael, Perreard, Laurent, Kolling, Fred, and others,

    bioRxiv Nov 2022
16. Graph neural networks ameliorate potential impacts of imprecise large-scale autonomous immunofluorescence labeling of immune cells on whole slide images

    Reddy, Ramya, Reddy, Ram, Sharma, Cyril, Jackson, Christopher, Palisoul, Scott, Barney, Rachael, Kolling, Fred, Salas, Lucas, Christensen, Brock, Brooks, Gabriel, and others,

    In Geometric Deep Learning in Medical Image Analysis Nov 2022
17. Virtual staining

    Vaickus, Louis, and Levy, Joshua

    In Geometric Deep Learning in Medical Image Analysis Nov 2022
18. Artificial Intelligence, Bioinformatics, and Pathology: Emerging Trends Part IICurrent Applications in Anatomic and Molecular Pathology

    Levy, Joshua, Lu, Yunrui, Montivero, Marietta, Ramwala, Ojas, McFadden, Jason, Miles, Carly, Diamond, Adam Gilbert, Reddy, Ramya, Reddy, Ram, Hudson, Taylor, and others,

    Advances in Molecular Pathology Nov 2022
19. Artificial Intelligence, Bioinformatics, and pathology: Emerging trends part I—An introduction to machine learning technologies

    Levy, Joshua, Lu, Yunrui, Montivero, Marietta, Ramwala, Ojas, McFadden, Jason, Miles, Carly, Diamond, Adam Gilbert, Reddy, Ramya, Reddy, Ram, Hudson, Taylor, and others,

    Advances in Molecular Pathology Nov 2022

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 Jr, Michael J, Suriawinata, Arief, Liu, Xiaoying, Lisovsky, Mikhail, Ren, Bing, Bobak, Carly A, Christensen, Brock C, and Vaickus, Louis J

   Modern Pathology Nov 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 Nov 2021
3. 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 Nov 2021
4. Bridge Category Models: Development of Bayesian Modelling Procedures to Account for Bridge Ordinal Ratings for Disease Staging

   Levy, Joshua, Bobak, Carly, Azizgolshani, Nasim, Andersen Jr, Michael, Suriawinata, Arief, Liu, Xiaoying, Lisovsky, Mikhail, Ren, Bing, Christensen, Brock, Vaickus, Louis, and others,

   biorxiv Nov 2021
5. 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

   biorxiv Nov 2021
6. Improving the Virtual Trichrome Assessment through 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

   biorxiv Nov 2021
7. 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

   In PACIFIC SYMPOSIUM ON BIOCOMPUTING 2022 Nov 2021
8. 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 Nov 2021
9. 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 Nov 2021
10. Emerging Diagnostic and Investigative Technologies: Validation of Deep Learning Technologies for DNA Methylation and Histopathology

    Levy, Joshua J

    Regional Anesthesia & Pain Medicine Nov 2021
11. 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 Nov 2021
12. Artificial intelligence in anatomic pathology

    Levy, Joshua J, and Vaickus, Louis J

    Advances in Molecular Pathology Nov 2021
13. 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 Nov 2021
14. Opportunities and obstacles for deep learning in biology and medicine [update in progress]

    Christensen, Brock C, Gitter, Anthony, Himmelstein, Daniel S, Titus, Alexander J, Levy, Joshua J, Greene, Casey S, and Elton, Daniel C

    Frontiers in public health Nov 2021
15. The Impact of Reflex Molecular Testing on the Management of Indeterminate Thyroid Cytology: A Single Institution Experience

    Glass, Ryan, Motanagh, Samaneh, Levy, Joshua, and Liu, Xiaoying

    Journal of the American Society of Cytopathology Nov 2021
16. Using Human Neural Tissue Methylation to Decipher Epigenetic Characteristics and Cell Type Pathologies in Huntington’s Disease

    Glaser, A, Levy, J, Zhang, Z, and Salas, L

    In MOVEMENT DISORDERS Nov 2021

2020

1. 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, and others,

   Nature Communications Nov 2020
2. 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 Nov 2020
3. Topological feature extraction and visualization of whole slide images using graph neural networks

   Levy, Joshua, Haudenschild, Christian, Barwick, Clark, Christensen, Brock, and Vaickus, Louis

   In BIOCOMPUTING 2021: Proceedings of the Pacific Symposium Nov 2020
4. 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

   bioRxiv Nov 2020
5. 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 Nov 2020
6. 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 Nov 2020
7. Estimating latent positions in social and biological networks using Graph Neural Networks in R with GCN4R

   Levy, Joshua, Bobak, Carly, Christensen, Brock, Vaickus, Louis, and O’Malley, James

   bioRxiv Nov 2020
8. 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 (BIOSTEC 2020) - Volume 3: BIOINFORMATICS Nov 2020
9. 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

   medRxiv Nov 2020
10. MRI Screening after Silicone Implant-Based Breast Surgery: A Survey of Adherence with FDA Recommendations

    Copeland-Halperin, Libby R, Shank, Nina, Wampler, Ariel T, Doughty, Hayden, Rada, Maria L Reategui Via, Levy, Joshua J, and Rosen, Joseph M

    Plastic Surgery 2020 (October 16–19, 2020) Nov 2020
11. Longevity associated geometry identified in satellite images: Sidewalks, driveways and hiking trails

    Levy, Joshua J, Lebeaux, Rebecca M, Hoen, Anne G, Christensen, Brock C, Vaickus, Louis J, and MacKenzie, Todd A

    arXiv preprint arXiv:2003.08750 Nov 2020
12. Investigation of capsule-inspired neural network approaches for dna methylation

    Levy, J, Chen, Youdinghuan, Azizgolshani, Nasim, Petersen, CL, Titus, Alexander J, Moen, Erika L, Vaickus, Louis J, Salas, Lucas A, and Christensen, B

    bioRxiv Nov 2020

2019

1. PathFlowAI: a high-throughput workflow for preprocessing, deep learning and interpretation in digital pathology

   Levy, Joshua J, Salas, Lucas A, Christensen, Brock C, Sriharan, Aravindhan, and Vaickus, Louis J

   In PACIFIC SYMPOSIUM ON BIOCOMPUTING 2020 Nov 2019
2. PolyCRACKER, a robust method for the unsupervised partitioning of polyploid subgenomes by signatures of repetitive DNA evolution

   Gordon, Sean P, Levy, Joshua J, and Vogel, John P

   BMC genomics Nov 2019
3. PyMethylProcess—convenient high-throughput preprocessing workflow for DNA methylation data

   Levy, Joshua J, Titus, Alexander J, Salas, Lucas A, and Christensen, Brock C

   Bioinformatics Nov 2019
4. MethylNet: A Modular Deep Learning Approach to Methylation Prediction

   Levy, Joshua J, Titus, Alexander J, Petersen, Curtis L, Chen, Youdinghuan, Salas, Lucas A, and Christensen, Brock C

   bioRxiv Nov 2019
5. PyMethylProcess-highly parallelized preprocessing for DNA methylation array data

   Levy, Joshua J, Titus, Alexander J, Salas, Lucas A, and Christensen, Brock C

   bioRxiv Nov 2019

2018