This page serves as a collection of products created by the NSF COMPASS Center, including papers, software, datasets, and other tools, many of which are intended as resources for the broader research community and the public.
Publications
Kusumegi, Keigo, Yang Wang, and Yian Yin. Specialization of Interdisciplinary Innovators in Science and Technology. Manuscript under review. (2026).
Otieno, Dickson, and Kevine Otieno. Institutional and Partnership Strategies for Community-Engaged Higher Education: Lessons from Virginia Tech and the Africa Centers of Excellence (ACE II). Manuscript under review. (2026).
Brown, Hannah M., and Xiang-Jin Meng. The Evolution of In Vitro Culture Systems for the Study of Hepatitis E Virus Infection. Virology (June, 2026) 110886.
Marr, Linsey C., and Richard L. Corsi. Indoor Air Quality: An Overdue Awakening. Environmental Science & Technology (April 24, 2026).
López-Astacio, Robert A., Brian R. Wasik, Hyunwook Lee, Ian E. H. Voorhees, Wendy S. Weichert, Oluwafemi F. Adu, Laura B. Goodman, Susan L. Hafenstein, Uwe Truyen, and Colin R. Parrish. Distinct Evolutionary Patterns of Endemic and Emerging Parvoviruses and the Origin of a New Pandemic Virus. Proceedings of the National Academy of Sciences of the United States of America 123 no.16 (April 14, 2026) e2515274123.
Memon, Zeeshan, Yiqi Su, Christo Kurisummoottil Thomas, Walid Saad, Liang Zhao, and Naren Ramakrishnan. Toward World Models for Epidemiology. arXiv preprint arXiv:2604.09519 (April 10, 2026).
Antony, Blessy, Amartya Dutta, Sneha Aggarwal, Vasundhara Gatne, Ozan Gokdemir, Samantha L. Grimes, Adam S. Lauring, Brian R Wasik, Anuj Karpatne, and T. M. Murali. VILLA: Versatile Information Retrieval From Scientific Literature Using Large LAnguage Models. arXiv. Accepted for ACM KDD 2026 AI Sciences Track. (March 25, 2026).
Chowdhury, Md, T.M. Murali, Palash Sashittal. A Cophylogenetic Approach for Virus-Host Interaction Prediction. bioRxiv. (February 27, 2026).
Gerdes, Julie, Jon Catherwood-Ginn, Carrie Kroehler, Kathy Hosig, Jessica Jones, T.M. Murali, Paul Skolnik, Lisa M. Lee. Community-Academic Collaboration on the Ethics of Pandemic Research. Emerging Infectious Diseases. Submitted February 22, 2026.
Su, Yiqi, Ray Lee, Jiaming Cui, and Naren Ramakrishnan. How (Not) to Hybridize Neural and Mechanistic Models for Epidemiological Forecasting. arXiv preprint arXiv:2602.06323 (February 6, 2026).
Gerdes, Julie. Infectious Urgency: The Making of an International Public Health Emergency. Columbia, SC: University of South Carolina Press (2026).
Kusumegi, Keigo, X. Yang, P. Ginsparg, M. de Vaan, T. Stuart, and Yian Yin. Scientific Production in the Era of Large Language Models. Science 390, no. 6779 (2025): 1240–1243 (December 18, 2025).
Shanker, Anil. How My Institution Strengthened Research Despite Chronic Underfunding. Nature 648, no. 8094 (December 16, 2025): 500.
Gandhi, Neeti N., and Padmavathy Rajagopalan. Multi-Cellular Human Liver Organoids Enable Complete Maturation of Induced Pluripotent Hepatocyte-like Cells Through Purely Endogenous Signals. bioRxiv (October 10, 2025).
Shelim, Rashed, Shengzhe Xu, Walid Saad, and Naren Ramakrishnan. Is Isotropy a Good Proxy for Generalization in Time Series Forecasting with Transformers? Transactions on Machine Learning Research (October 10, 2025).
Antony, Blessy, Maryam Haghani, Adam Lauring, Anuj Karpatne, and T. M. Murali. HAVEN: Hierarchical Attention for Viral protEin-based host iNference. bioRxiv (June 13, 2025).
U.S. National Science Foundation COMPASS Center. Report on Ethics and Pandemic Science: A National Dialogue. Unpublished report (2025).
Software
NSF COMPASS Center. NSF COMPASS Software. GitHub.
Antony, Blessy, Amartya Dutta, Sneha Aggarwal, Vasundhara Gatne, Ozan Gokdemir, Samantha L. Grimes, Adam S. Lauring, Brian R Wasik, Anuj Karpatne, and T. M. Murali HAVEN Prediction System. GitHub.
NSF COMPASS Center. VILLA. GitHub.
Models
Antony, Blessy, Maryam Haghani, Adam Lauring, Anuj Karpatne, and T. M. Murali. HAVEN Models. May 28, 2025. Zenodo.
Datasets
Self, Nathan, Mira Chaplin, Linsey Marr, and Krista Wigginton. Persist-sciex-data. GitHub. May 28, 2026.
Self, Nathan, Mira Chaplin, Linsey Marr, and Krista Wigginton. Persist-sciex-data. Zenodo, May 28, 2026.
Wasik, Brian. Zoo Flu. Zenodo. April 27, 2026.
Wasik, Brian. Zoo Flu. GitHub. April 27, 2026.
Antony, Blessy, Maryam Haghani, Adam Lauring, Anuj Karpatne, and T. M. Murali. HAVEN Datasets. Zenodo. May 28, 2025.
Presentations
Wasik, B., B. Antony, A. Dutta, S. Aggarwal, K. Sipe, V. Gatne, O. Gökdemir, S. Grimes, A. Lauring, A. Kapartne, and T. M. Murali. “Curating Influenza Zoonotic Mutation Databases by Large Language Models.” ISRV 2026 Options XIII Conference for the Control of Influenza. August 30 – September 2, 2026.
Su, Y., R. Lee, J. Cui, and N. Ramakrishnan. “How (Not) to Hybridize Neural and Mechanistic Models for Epidemiological Forecasting.” Proceedings of the 43rd International Conference on Machine Learning (ICML 2026), Seoul, South Korea, July 2026.
Snodgrass, Rachael, Alexandra Longest, Aaron Prussin II, and Linsey C. Marr. “Infectivity of Non-Enveloped Viruses Depends on Initial Droplet Size.” Presented at the American Association for Aerosol Research Conference, Buffalo, NY, October 13–17, 2025.
Catherwood-Ginn, Jon, Julie Gerdes, and Carolyn Kroehler. “Wellness Begins with ‘We’: Trust in Pandemic Prediction and Prevention.” Presented at the Engagement Scholarship Consortium Conference, Roanoke, VA, October 8–9, 2025.
Nikeghbal, P., I. Akhrymuk, T. Stocker, K. Kehn-Hall, and P. Rajagopalan. “Multicellular 3D Human Liver Organoids As a Platform for Studying Rift Valley Fever Virus Infection.” American Institute of Chemical Engineers Annual Meeting. Submitted April 30, 2026.
Antony, Blessy, Maryam Haghani, Anuj Karpatne, and T. M. Murali. “VirProBERT: A Sequence Language Model for Predicting Viral Hosts.” Presented at the AI for Nucleic Acids Workshop, International Conference on Machine Learning (ICML), April 28, 2025.
Thornton-O’Brien, Leslie, Sarah Gouger, and Hallie Harriman. “My Circus, My Monkeys: Managing with Limited Resources.” Presented at the UPCEA-MEMS Conference on Managing Programs with Limited Resources, Philadelphia, PA, December 4, 2024.
Courses
Lee, Lisa M., Barbara DeCausey, and Iris Jenkins. COMPASS Center Pandemic Ethics Course. 2026.
Theses
Buccilli, Marissa. Ambiguous Evidence: The Rhetorical Work of Interpreting Clinical Knowledge after the Women’s Health Initiative. PhD thesis, Virginia Tech, 2026.
Flor, Rafaela. Repurposing a Kinase Inhibitor for Rift Valley Fever Virus: Combating Hepatic and Neurological Disease Through Antiviral and Immunomodulation Strategies. PhD thesis, Virginia Tech, 2026.
Snodgrass, Rachael. Impact of Initial Droplet Size on the Infectivity of Non-Enveloped Viruses and Their Inactivation by UVC Irradiation. Master’s thesis, Virginia Tech, 2026.
Antony, Blessy. Discovering Viral Hosts, Mutations, and Diseases Using Machine Learning. PhD thesis, Virginia Tech, 2026.
Chaplin, Mira. Mechanistic and Regulatory Insights into Virus Reduction in Water and Wastewater Treatment Through Modeling Approaches. PhD thesis, University of Michigan, 2025.
Patent Applications
Gandhi, N. and P. Rajagopalan. “Maturation of Induced Hepatocyte-Like Cells.” Patent # 63/654,336. Full patent filed in May 2025.
Miscellaneous
Center for Communicating Science at Virginia Tech. “The Book I Recommend”. Virginia Tech. 2026. A community-centered slideshow celebrating the stories behind scientific curiosity. Distributed to seven public libraries across Giles and Montgomery counties in southwest Virginia. Available Upon Request.
Center for Communicating Science at Virginia Tech. “Flip the Fair toolkit.” Virginia Tech. 2026. A step-by-step guide to planning and holding a science outreach event called “Flip the Fair,” a flipped science fair at which graduate students share their research and school children or community members act as judges.
Center for Communicating Science at Virginia Tech. “Personal, direct, spontaneous, responsive, and emotionally vivid: A practical guide to effective science communication.” Virginia Tech. 2026. Six “briefs” describing core elements of effective science communication, accompanied by recommendations for additional reading and exercises for building and practicing skills.