2025

1. Integrative co-registration of elemental imaging and histopathology for enhanced spatial multimodal analysis of tissue sections through TRACE

   Lu, Yunrui, Han, Serin, Srivastava, Aruesha, Shaik, Neha, Chan, Matthew, Diallo, Alos, Kumar, Naina, Paruchuri, Nishita, Deosthali, Hrishikesh, Ravikumar, Vismay, and others,

   Bioinformatics Advances 2025
2. 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
3. Mapping Three-Dimensional Tumor Heterogeneity through Deep Learning Inference of Spatial Transcriptomics from Routine Histopathology: A Proof-of-Concept Comparative Study

   Azher, Zarif, Srinivasan, Gokul, Yao, Keluo, Le, Minh-Khang, Lau, Ken, Kaur, Harsimran, Kolling, Fred, Vaickus, Louis, Lu, Xiaoying, and Levy, Joshua

   In Machine Learning for Health (ML4H) 2025
4. 1386 Evaluating the Effectiveness of Large-Scale Spatial Transcriptomics Inference from Histology to Facilitate Spatial Molecular Epidemiological Studies for Colon Cancer Progression

   Srinivasan, Gokul, Le, Minh-Khang, Azher, Zarif, Diallo, Alos, Liu, Xiaoying, Vaickus, Louis, Yao, Keluo, and Levy, Joshua

   Laboratory Investigation 2025
5. 629 Landscaping the Tumor Microenvironment Using Statistical Concepts and Deep Learning in Colon Adenocarcinoma

   Le, Minh-Khang, Srinivasan, Gokul, Azher, Zarif, Diallo, Alos, Liu, Xiaoying, Yao, Keluo, Vaickus, Louis, and Levy, Joshua

   Laboratory Investigation 2025
6. 1339 Preliminary 3D Investigation of Colorectal Cancer Heterogeneity Enabled by Spatial Transcriptomics Inferred from Routine Histopathology Using Deep Learning

   Azher, Zarif, Le, Minh-Khang, Srinivasan, Gokul, Diallo, Alos, Liu, Xiaoying, Vaickus, Louis, Yao, Keluo, and Levy, Joshua

   Laboratory Investigation 2025
7. Preliminary feasibility of co-registering tissue autofluorescence with 3D spatial transcriptomics for multimodal analysis of destructively profiled colorectal tumor sections

   Azher, Zarif, Srinivasan, Gokul, Le, Minh-Khang, Diallo, Alos, Kaur, Harsimran, Kolling, Fred, Perreard, Laurent, Palisoul, Scott, Yao, Keluo, Lau, Ken S, and others,

   Cancer Research 2025
8. Spatial transcriptomics-informed latent diffusion models generate histopathological images reflective of tumor microenvironment

   Srinivasan, Gokul, Le, Minh-Khang, Azher, Zarif, Kaur, Harsimran, Kolling, Fred, Yao, Keluo, Lau, Ken S, Liu, Xiaoying, Vaickus, Louis J, and Levy, Joshua J

   Cancer Research 2025
9. Characterization of the tumor microenvironment’s histologic landscape through histology-based deep learning spatial transcriptomic cell-type deconvolution of colon tumors

   Le, Minh-Khang, Srinivasan, Gokul, Kolling, Fred, Yao, Keluo, Diallo, Alos, Azher, Zarif, Vaickus, Louis J, Liu, Xiaoying, and Levy, Joshua

   Cancer Research 2025
10. Histology-Based Virtual RNA Inference Identifies Pathways Associated with Metastasis Risk in Colorectal Cancer

    Srinivasan, Gokul, Le, Minh-Khang, Azher, Zarif, Liu, Xiaoying, Vaickus, Louis, Kaur, Harsimran, Kolling IV, Fred, Palisoul, Scott, Perreard, Laurent, Lau, Ken S, and others,

    medRxiv 2025
11. Association of Deep Learning-Derived Histologic Features of Placental Chorionic Villi with Maternal and Infant Characteristics in the New Hampshire Birth Cohort Study

    Anderson, Elizabeth C, Srinivasan, Gokul, Howe, Caitlin G, Zhang, Edward, Jeon, Catherine, Paruchuri, Gnan Suchir Gupta, Zhang, Leah, Hwang, Lindsay, Sengar, Aditya, Reddy, Neha, and others,

    medRxiv 2025

2024

1. 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 2024
2. 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 2024
3. 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 2024
4. 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 2024
5. 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 2024
6. 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 2024
7. 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 2024
8. 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 2024
9. 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 2024
10. 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, Han, Serin, Punshon, Tracy, Jackson, Brian, Vahdat, Linda, Liu, Xiaoying, and others,

    medRxiv 2024
11. 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

    In CLINICAL CANCER RESEARCH 2024

2023

1. 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 2023
2. 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 2023
3. 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 2023
4. 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 2023
5. 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 2023
6. 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 2023
7. 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 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 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 2022
3. 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 2022
4. 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 2022
5. 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 2022
6. 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 2022
7. 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 2022