Jump to: Guiding Documents | Book Chapters | Publications | Conference Abstracts | Poster Presentations | Presentations | Podcasts & Media | Public Exhibit | Software & Tools | Tutorials | Workshops

Guiding Documents:

• Tan, S.C. (2026). Guided Self Organizing Team Processes GSOTP.
  • This document outlines our teaming process for those interested in learning more or using it as a model

Publications:

Preprints:

• Lofgren, E.T., Myers, K., & Fefferman, N.H. (2026). When is Enough Enough? A Proposed Termination Point for the Number of Replicates in Computational Simulations.

• Biswas, P., Pedrielli, G., & Candan, K.S. (2026). Causality by Abstraction: Symbolic Rule Learning in Multivariate Timeseries with Large Language Models. CoRR abs/2602.17829.

• Karami, H., Anton, J.R., Jang, G., Candan, K.S., & Chowell, G. (2026). Adaptive COVID-19 Trajectory Forecasting Using Reinforcement-Learning Ensembles. International Journal of Forecasting.

• Ryan, S.J., Lippi, C., & Meredith, J. (2026). Pandemic prediction in the space age: Use of earth observation system (EOS) data. 

• Dadlani, R., McAlister, J.S., Schwarze, A.C., Kawakatsu, M., Iams, S., Eissa, T.L., & Fefferman, N.H. (2026). Planned behavior, perceptual biases, and the dynamics of collective action.

• Lavelle, T.E., Sánchez, C.A., Andrijevic, M., Becker, D.J., Gibb, R., Gonsalves, G.S., O'Donoghue, Z., Pachauri, S., Pereira, L.M., Poisot, T., Ryan, S.J., Seifert, S.N., Whittaker, C., & Carlson, C.J. (2026). Pandemic risk in the Shared Socioeconomic Pathways. 

• ​Bleichrodt, A., Bourouiba, L., Chowell, G., Lofgren, E.T., Michael Reed, J., Ryan, S.J., Fefferman, N.H. (2024). Assembling ensembling: An adventure in approaches across disciplines. arXiv

2026

• Mostafa, F., Sharma, K,. & Khan, H. (2026). Development and validation of dementia diagnosis in adults through machine learning frameworks: a cross-sectional study using clinical and imaging data. BMC Medical Informatics and Decision Making.

• Ashworth, M., Thunström, L., Cherry, T., Fefferman, N.H., Finnoff, D., Newbold, S., & Shogren, J.F. (2026). From hesitation to action: the role of primary care physicians in Covid-19 antiviral uptake. Ethics, Medicine, and Public Health, 34.
• Jang, G., Candan, K.S., & Chowell, G. (2026). A comparative study of simulation-based inference methods for epidemic models with identifiability considerations. PLOS Computational Biology.

• Hasenjager, M.J., Bailey, M.M., & Fefferman, N.H. (2026). Group composition influences diffusion dynamics via impacts on behavioural production. Animal Behaviour, 233(C), 123482. 

• Malinzi, J. & Dubey, P. (2026). Editorial: Integrative mathematical models for disease, volume II. Frontiers in Applied Mathematics and Statistics, 12. 

• Mandal, P., Gorantla, A., Candan, K.S., & Sapino, M.L. (2026). Causal Search for Skylines (CSS): Causally-Informed Selective Data De-Correlation. Proceedings of the ACM on Management of Data, 4(3), 1–27. 

• Anton, J.R., Sapino, M.L., & Candan, K.S. (2026). Gradient Guided Parameter Space Sampling for Knowledge Discovery With Limited Budgets. IEEE Access, 14, 53958–53977.

• Silk, M.J. & Fefferman, N.H. (2026). Multilayer contagions in animal groups. Animal Behaviour, 235(C), 123525. 

• Sisk, A., Silk, M.J., Williams, N.D., & Fefferman, N.H. (2026). A typology of rules for knowledge exchange in higher-order interactions. PLOS Complex Systems, 3(1), e0000080. 

2025

• Bohon, S.A. & Hodges, S. (2025). Digging into Indigenous History. Contexts, 24(3), 34–39. 

• Flory, S.L., Ryan, S.J., Taneja, Y., Munoz, M., Lippi, C., Allan, B. (2025). Impacts of plant invasions on tick-borne disease risk. BioScience, biaf153

• McAlister, J.S., Brunner, J.L., Galvin, D.J., & Fefferman, N.H. (2025). A game theoretic treatment of contagion in trade networks. PLOS Computational Biology, 21(12), e1013845. 

• Fefferman, N.H., Blum, M.J., Bourouiba, L., Gibson, N.L., He, Q., Miller, D.L., Papeș, M., Pasquale, D.K., Verheyen, C., Ryan, S.J. (2025). Identifying outbreak risk factors through case-controls comparisons. Communications Medicine, 5(1). 

• Nuritdinov, F., Woo, J., Schmidt, M.J., Odjourian, N.M., Cristaldo, M., Dougher, M., Antilus-Sainte, R., Heldt, T., Rhee, K., Bourouiba, L., & Gengenbacher, M. (2025). Experimental system enables studies of Mycobacterium tuberculosis during aerogenic transmission. mBio, 16(10).

• Shen, N. & Bourouiba, L. (2025). Assessing bias in susceptible–infected–recovered estimation from aggregated epidemic data. Royal Society Open Science, 12(7). 

2024

• Reed, J.M., Candan, K.S., Miller, D.L., Bromberg, Y., Schreiner, C., Fefferman, N.H., Blum, M.J., He, Q., McAlister, J.S., Szabo-Rogers, H., & Lofgren, E. (2024). An interdisciplinary perspective of the built-environment microbiome. FEMS Microbiology Ecology, 101(1). 

Conference Abstracts:

2026

• Lofgren, E.T. & Fefferman, N.H. (2026). Revisiting Corrupted Blood: Games and Contagion. NordMedia Conference, University of Southern Denmark.
• Mehrotra, S. & Candan, K.S. (2026). Challenges in Sustaining Data Management Research in the GenAI Era. SIGMOD Companion '26: Companion of the International Conference on Management of Data, pp. 546–547. 

2025

• Biswas, P., Pedrielli, G., & Candan, K.S. (2025). PYSIRTEM: An Efficient Modular Simulation Platform for the Analysis of Pandemic Scenarios. 2025 Winter Simulation Conference.
• Kapkı, A., Mandal, P., Gorantla, A., Wan, S., Çoban, E., Sheth, P., Liu, H., & Candan, K.S. (2025). CausalBench: Causal Learning Research Streamlined. ACM KDD '25.

Poster Presentations:

2025

• Azad, F.T., Candan, K.S., & Chowell-Puente, G. (2025). Domain Disentanglement for Epidemic Onset Forecasting: Knowledge Transfer from Data-Rich to Data-Poor Communities. SSRN Electronic Journal.
• Misterka, M. & Bourouiba, L. (2025). Mean-Field Epidemic Models: Effect of Indirect Transmission. Internal MIT Student Poster Presentation.
• Schreiner, C.L., Goodrich-Blair, H., He, Q., Li, S., Miller, D., Sisk, A., Udiani, O., & Fefferman, N.H. (2025). Building exposure risk: a multi-level modeling approach. Ecology and Evolution of Infectious Diseases (EEID) Annual Meeting.
• Sullens, M. (2025). Conceptualizing contagion: modeling complex contagion transmission with differential equations. Conference on Complex Systems, Siena, Italy.
• Schreiner, C.L., Stockmaier, S., & Fefferman, N.H. (2026). An underexplored theory for why culling has unintended consequences in social animals. Ecology and Evolution of Infectious Diseases 2026, Blacksburg, VA.

Presentations:

2026

• Bohon, S.A. & Hodges, S. (2026). Lessons Learned from Process Tracing with a Multidisciplinary Team. Annual Meeting of the Southern Sociological Society, Session 157, Jacksonville, FL.
• Bohon, S.A., Hodges, S., Fefferman, N., Lawrence, S., Ryan, S., Bauer, B., and Brown, M. (2026). Slow Violence, Uncare, and the Nantucket Wampanoag. Presented in Session 70: Racial Politics and Resistance in the Midst of Settler Colonialism at the annual meetings of the Society for the Study of Social Problems, New York, New York.
• Fefferman, N.H. (2026). Self-organization, Infectious Disease, and Social Behavior – An Evolutionary Tale? Presented as a Colloquium talk for the Santa Fe Institute, Santa Fe, New Mexico, USA.
• Bohon, S.A. & Hodges, S. (2026). Lessons Learned from Process Tracing with a Multidisciplinary Team. Annual Meeting of the Southern Sociological Society, Session 157, Jacksonville, FL.
• Bohon, S.A. & Hodges, S. (2026). Slow Violence, Uncare, and the Nantucket Wampanoag. Annual Meeting of the Society for the Study of Social Problems, Session 70, New York, NY.
• Okafor, C.C., Ayodo, C.O., Sham, M., Gass, J.D., & Lenhert, S. (2026). Advancing One Health Surveillance: Lessons from Case-Control Studies of Human Antimicrobial Resistance. International Congress on One Health, Saint-Quay-Portrieux, France.
• Okafor, C.C., Ayodo, C.O., Sham, M., Gass, J.D., & Lenhert, S. (2026). Bridging Clinical Epidemiology and One Health: What U.S. Case-Control Studies Reveal About Human Antimicrobial Resistance. One Health: Antimicrobial Resistance and Emerging Zoonoses, Calgary, Alberta.
• Okafor, C.C., Ayodo, C.O., Sham, M., Gass, J.D., & Lenhert, S. (2026). Where Is One Health in Human AMR Research? A Review of U.S. Case-Control Studies. National Institute of Antimicrobial Resistance Research and Education Conference, Ames, Iowa.

2025

• APPEX Team. (2025). Mathematical modeling training session. North Africa Applied Systems Analysis Centre, IIASA/Institute of National Planning Egypt (virtual).
• Bohon, S.A. & Hodges, S. (2025). Outbreak: Solving a 263-Year-Old Medical Mystery. Southern Demographic Association Annual Meetings, Lexington, KY.
• Candan, K.S. (2025). Keynote: "The Power of 'Why?' in Decision Making in Complex, Dynamic Systems." 12th ACM International Conference on Multimedia Retrieval, Chicago, IL.
• Fefferman, N. (2025). Keynote: Modeling Self-Organizing Networks in Life Sciences and Beyond. 18th Annual Symposium on Biomathematics & Ecology Education and Research, Fairfax, VA.
• Fefferman, N. et al. (2025). APPEX perspectives, research, and Sandbox Simulation Toolkit. Duke University tutorial on "Social Networks and Health."
• Lofgren, E. (2025). Gifts of the Grandfather: Warhammer's Plague Narratives from the Perspective of an Epidemiologist. Warhammer Conference 2025, Heidelberg, Germany.
• McAlister, J. & Fefferman, N. (2025). Replicator Dynamics for Games on Networks. Complex Networks 2025, Binghamton, NY.
• Strand, E. (2025). Invited guest presentation on Team Science and Community Engagement. UT Office of Community Engagement and Outreach Professional Development Seminar Series.
• Strand, E.B. (2025). Team Science: Why and How. Community of Scholars for Resilient Agriculture and Forest Systems, University of Tennessee, Knoxville, TN.
• Sullens, M. & Fefferman, N.H. (2025). Conceptualizing contagion: modeling complex contagion transmission with differential equations. Conference on Complex Systems, Siena, Italy.

Podcast/Media:

• APPEX Researchers (4-Cutting Edge Ensemble Models researchers, 2 project teams). (2025). Podcasts about APPEX research and Pandemic Science. APPEX public media channels.

Public Exhibit:

• Bourouiba, L. et al. (2024). Paradigm Shifts in Science: The History and Science of Epidemics and Germ Theory. MIT Institute for Medical Engineering and Science.

Software/Tools:

• APPEX Team. (2025). Public-facing interactive infectious disease (SEIR) model simulator/dashboard. 
• Whitworth, C., Gorantla, A., Cui, X., Akpa, B., Bromberg, Y., Liu, H., & Candan, K.S. APPEX Metaannotation and Knowledge Synthesis. 

Tutorials:

2026

• Azad, F.T., Kapkiç, A., Mandal, P., Gorantla, A., Wan, S., Sapino, M.L., Liu, H., & Candan, K.S. (2026). Spatio-Causal Modeling and Applications. ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems.

2025

• APPEX Team (Fefferman, N. et al.). (2025). What makes a useful model (virtual tutorial). Open/multi-institutional (35 registrants, 19 universities, 3 continents).
• Candan, K.S. et al. (2025). CausalBench: Causal Learning Research Streamlined (tutorial on causal machine learning and epidemic applications). ACM SIGKDD International Conference on Knowledge Discovery and Data Mining.

Workshops:

2026

• Bourouiba, L. et al. (2026). Fluids & Health: Viral Respiratory Disease Transmission Through the Air. Lorentz Center. 

2025

• Tan, S.C., Gordon, K., Fefferman, N., & Strand, E.B. (2025). Team Science and Community Engagement. Advanced Community Engagement Seminar Series, University of Tennessee, Knoxville, TN.

For all work that results from your APPEX-related effort, please include the following acknowledgement: "This work was supported by NSF grant DBI 2412115 as part of the US NSF Center for Analysis and Prediction of Pandemic Expansion (APPEX)." Similarly, the NSF grant and APPEX Center should be acknowledged in all reports and interviews covering work related to your efforts as part of APPEX.