UMass Disease Modeling Lab

Disease Modeling Lab, PI: Chaitra Gopalappa

PRE-PRINT (In journal review)

• Sharma, D., Shah, A., Gopalappa, C., A Multi-Agent Reinforcement Learning Framework for Evaluating the U.S. Ending the HIV Epidemic Plan, https://arxiv.org/abs/2311.00855

• Gopalappa, C. and Khoshegbhal, A. Mechanistic modeling of social conditions into disease predictions for public health intervention-analyses: application to HIV, (In journal review) Preprint, 2023, https://doi.org/10.1101/2023.03.01.23286591

PUBLICATIONS

1. 2024 France, A.M., Panneer, N., Farnham, P.G., Oster, A.M., Viguerie, A., and Gopalappa, C. “Extent and composition of molecular HIV sexual transmission clusters in a nationally representative simulation model indicate intervention opportunities,” JAIDS, InPrint, 2024

2. 2023 Zhao, X., Gopalappa, C., Joint modeling HIV and HPV using a new hybrid agent-based network and compartmental simulation technique, PLoS ONE 18(11): e0288141. https://doi.org/10.1371/journal.pone.0288141; doi:https://doi.org/10.1101/2022.12.25.22283941

3. 2023 Khatami S.N., Gopalappa C. Deep reinforcement learning framework for controlling infectious disease outbreaks in the context of multi-jurisdictions. Mathematical Biosciences and Engineering, 2023, Volume 20, Issue 8: 14306-14326. doi: 10.3934/mbe.2023640

4. 2023 Koenig, L., Khurana, N., Hafiz, Md I., Gopalappa, C., Farnham, P., Closing the gaps in the continuum of depression care for persons with HIV: modeling the impact on viral suppression in the United States, AIDS, 2023 Jun 1;37(7):1147-1156, doi: 10.1097/QAD.0000000000003536

5. 2023 Gopalappa, C., Balasubramanian, H., and Haas, P.J., A new mixed agent-based network and compartmental simulation framework for joint modeling of related infectious diseases- application to sexually transmitted infections,Infectious Disease Modelling, Volume 8, Issue 1, 2023, Pages 84-100, ISSN 2468-0427, https://doi.org/10.1016/j.idm.2022.12.003.

6. 2022 Tatapudi, H. and Gopalappa, C., Evaluating the sensitivity of jurisdictional-heterogeneity and jurisdictional-mixing in national-level HIV prevention analyses: Context of the U.S. Ending the HIV Epidemic goal, BMC Medical Research Methodology, 22(1):304.doi: 10.1186/s12874-022-01756-w

7. 2021 Khatami, N., and Gopalappa, C., A reinforcement learning model to inform optimal decision paths for HIV elimination, Mathematical Biosciences and Engineering, Volume 18, Issue 6: 7666-7684, 2021. doi: 10.3934/mbe.2021380
   ** _Finalist for student best paper poster competition, SMDM

8. 2021 Zhao, X., Tatapudi, H., Corey, G., Gopalappa, C., Threshold analyses on combinations of testing, population size, and vaccine coverage for COVID-19 control in a university setting, PLoSOne, 2021 https://doi.org/10.1371/journal.pone.0255864

9. 2021 Eden, M., Castonguay, R., Munkbat, B., Balasubramanian, H., Gopalappa, C., Agent-based evolving network modeling: a new simulation method for modeling low prevalence infectious diseases, Health Care Management Science, 24, 623–639 (2021). https://doi.org/10.1007/s10729-021-09558-0
   ** _Finalist best paper award, INFORMS, Operations Research track

10. 2021 Singh, S., France, A. M., Chen, Y-H, Farnham, P. G., Oster, A. M., Gopalappa, C., Progression and Transmission of HIV (PATH4.0): A new agent-based evolving network simulation for modeling HIV transmission clusters; Mathematical Biosciences and Engineering, 18 (3), 2021, doi: 10.3934/mbe.2021109
    ** Best paper award, Institute for Industrial and Systems Engineers (IISE), Simulation and Modeling track, 2021 ** Work in collaboration with the Centers for Disease Control and Prevention

11. 2020 Shifali Bansal, BS, Vijeta Deshpande, MS, Xinmeng Zhao, BS, Jeremy A. Lauer, PhD, Filip Meheus, PhD, André Ilbawi, MD, Chaitra Gopalappa1, PhD, Analysis of mammography screening schedules under varying resource constraints for planning breast cancer control programs in low- and middle- income countries: a mathematical study, Medical Decision Making, Vol. 40(3), 2020 PDF LINK
    ** Work in collaboration with the World Health Organization (WHO) and Institute for Research on Cancer (IARC)

12. 2018 Ambinintsoa H. Ralaidovy, Chaitra Gopalappa, André Ilbawi, Carel Pretorius and Jeremy A. Lauer, Cost-effective interventions for breast cancer, cervical cancer, and colorectal cancer: new results from WHO-CHOICE, Cost Effectiveness and Resource Allocation, 18 (38), 2018 LINK LINK
    ** Work in collaboration with the World Health Organization (WHO)

13. 2018 Gopalappa, C., Guo, J., Meckoni, P., Munkhbat, B., Pretorius, C., Lauer, J., Ilbawi, A., Bertram, M., A two-step Markov processes approach for parameterization of cancer state-transition models for low- and middle- income countries, Medical Decision Making, Vol. 38(4) 520–530, 2018, PDF technical-suppl LINK
    _** Work in collaboration with the World Health Organization (WHO) and Avenir Health
    ** Informed: World Health Organization, Cancer Interventions Technical Briefing For The Updated (2017) Appendix 3 Of The Global Action Plan For The Prevention And Control Of Noncommunicable Diseases 2013-2020, LINK
    ** Informed: World Health Organization, Best buys and other recommended interventions for the prevention and control of noncommunicable diseases, Updated (2017) appendix 3 of the global action plan for the prevention and control of noncommunicable diseases 2013-2020, LINK_

14. 2017 Gopalappa, C., Farnham, P.G., Chen, Y-H., and Sansom, S.L. Combinations of interventions to achieve a national HIV incidence reduction goal: insights from an agent-based model. AIDS, November 28, 2017 - Volume 31 - Issue 18 - p 2533 to 2539 LINK
    **Work in collaboration with the Centers for Disease Control and Prevention

15. 2017 Gopalappa, C., Farnham, P.G., Chen, Y-H., and Sansom, S.L. Progression and Transmission of HIV/AIDS (PATH 2.0): A New Agent-Based Model to Estimate HIV Transmissions in the United States, Med Decis Making 2017 Feb;37(2):224-233. doi: 10.1177/0272989X16668509 LINK
    ** Work in collaboration with the Centers for Disease Control and Prevention ** Cited in CDC’s Vital Signs “Dailey AF, Hoots BE, Hall HI, et al. Vital Signs: Human Immunodeficiency Virus Testing and Diagnosis Delays — United States. MMWR Morb Mortal Wkly Rep 2017;66:1300–1306. DOI: http://dx.doi.org/10.15585/mmwr.mm6647e1”

16. 2015 Eaton, J., Bacaër, N., Bershteyn, A., Cambiano, V., Cori, A., Dorrington, R.E., Fraser, C., Gopalappa, C., Hontelez, J.A.C., Johnson, L.F., Klein, D.J., Phillips, A.N., Pretorius, C., Stover, J., Rehle, T.M., Hallett, T.B., Assessment of epidemic projections using recent HIV survey data in South Africa: a validation analysis of ten mathematical models of HIV epidemiology in the antiretroviral therapy era, The Lancet Global Health, Vol 3, e598, October 2015; DOI: http://dx.doi.org/10.1016/S2214-109X(15)00080-7; LINK

17. 2014 Stover, J., Andreev, K., Slaymaker, E., Gopalappa, C., Sabin, K., Velasquez, C., Nakiyingi-Miiro, J., Crampin, A., Lutalo, T., Herbst, K., Gregson, S., and Urassa, M., Updates to the Spectrum model to estimate key HIV indicators for adults and children, AIDS 2014, 28 (Suppl 4):S427–S434 PDF

18. 2014 Gopalappa, C., Stover, J., Shaffer, N., and Mahy, M., The Costs and Benefits of Option B+ for the Prevention of Mother-to-Child Transmission of HIV, AIDS, 28 Suppl. 1:S5-14, 2014 LINK
    ** Cited in Guideline on when to start antiretroviral therapy and on pre-exposure prophylaxis for HIV, The World Health Organization, September 2015, http://apps.who.int/iris/bitstream/10665/186275/1/9789241509565_eng.pdf

19. 2014 Stover, J., Hallett, T., Wu, Z., Warren, M., Gopalappa, C., Pretorius, C., Ghys, P.D., Montaner, J., Schwartländer, B.; New Prevention Technology Study Group, How can we go to Zero? The Potential Contribution of Biomedical Prevention and the Investment Framework towards an Effective Response to HIV, PLoS One, 9(11):e111956, 2014 PDF

20. 2014 Stover, J., Gopalappa, C., Mahy, M., Doherty, M.C., Easterbrook, P.J., Weiler, G., and Ghys, P.D., The impact and cost of the 2013 WHO recommendations on eligibility for antiretroviral therapy, AIDS, 28 Suppl. 2:S225-30, 2014 PDF
    ** Cited in Guideline on when to start antiretroviral therapy and on pre-exposure prophylaxis for HIV, The World Health Organization, September 2015, http://apps.who.int/iris/bitstream/10665/186275/1/9789241509565_eng.pdf

21. 2014 Pretorius, C., Menzies, N.A., Chindelevitch, L., Cohen, T., Cori, A., Eaton, J. A., Fraser, C., Gopalappa, C., Hallett, T. B., Salomon, J. A., Stover, J., White, R. G., Dodd, P. J., The potential effects of changing HIV treatment policy on TB outcomes in South Africa: results from three TB-HIV transmission models, AIDS, 28 Suppl 1:S25-34, 2014

22. 2014 Eaton, J., Menzies, N., Stover, J., Cambiano, V., Chindelevitch, L., Cori, A., Hontelez, J. A. C., Humair, S., Kerr C. C., Klein, D J., Mishra, S., Mitchell, K. M., Nichols, B.E., Vickerman, V., Bakker, R., Barnighausen, T., Bershteyn, A., Bloom, D.E., Boily, M-C, Chang, S.T., Cohen, T., Dodd, P.J., Fraser, C., Gopalappa, C., Lundgren, J., Martin, N.K., Mikkelsen, E., Mountain, E., Pham, Q.D., Pickles, M., Phillips, A., Platt, L., Pretorius, C., Prudden, H.J., Salomon, J.A., van de Vijver, D.A.M.C., de Vlas, S. J., Wagner, B. G., White, R.G., Wilson, D.P., Zhang, L., Blandford, J., Meyer-Rath, G., Remme, M., Revill, P., Sangrujee, N., Terris-Prestholt, F., Doherty, M., Shaffer, N., Easterbrook, P.J., Hirnschall, G., Hallett, T.B., How should HIV programmes respond to evidence for the benefits of earlier treatment initiation? A combined analysis of twelve mathematical models, Lancet Global Health, 2(1):e23, 2014

23. 2013 Gopalappa, C., Huang, Y., Melanie, T., Kwame, O., and Gift, T., Cost-effectiveness of screening men in Maricopa County jails for chlamydia and gonorrhea to avert infections in women, STD, 40 (10):776-783, 2013 MODEL

24. 2013 Farnham, P., Gopalappa, C., Sansom, S., Updates of lifetime costs of care and quality-of-life estimates for HIV-infected persons in the United States: late versus early diagnosis and entry into care, JAIDS, 64(2):183-189, 2013. MODEL
    **Cited in the National HIV AIDS Strategy for the United States: Update to 2020, The White House, July 2015 https://www.aids.gov/federal-resources/national-hiv-aids-strategy/nhas-update.pdf
    ** Cited in the CDC FY 2017 Congressional Justification for Budget Request, Justification of Estimates to the Appropriations Committees, 2016,https://www.cdc.gov/budget/documents/fy2017/fy-2017-cdc-congressional-justification.pdf

25. 2013 Farnham, P.G., Holtgrave, D. R., Gopalappa, C., Angela B. Hutchinson, Stephanie L. Sansom, Lifetime Costs and QALYs Saved from HIV Prevention in the Test and Treat Era, Letter to the Editor, JAIDS, 64(2):e15-e18, 2013

26. 2013 Gopalappa, C., Stover, J., and Pretorius, C., HIV prevalence patterns by age: Exploring differences among 19 countries, DHS Analytical Studies, No. 40. Calverton, Maryland, USA: ICF International, 2013.
    ** Cited in Guidelines for conducting HIV surveillance among pregnant women attending antenatal clinics based on routine programme data, World Health Organization, August 2015 http://apps.who.int/iris/bitstream/10665/197864/1/9789241509725_eng.pdf (last accessed: Dec 2015)

27. 2012 Gopalappa, C., Farnham, P., Hutchinson, A., and Sansom, S., Cost-effectiveness of the National HIV/AIDS Strategy (NHAS) goal of increasing the proportion linking to care at diagnosis, JAIDS, 61 (1):99-105, 2012.

28. 2011 Gopalappa, C., Cremaschi, S., Das, T., Orcun, S., Applied Probability Models for Estimating Progression Rates between Colorectal Cancer Stages, Health Care Management Science 14(1), March 2011: Pg 1-21 pdf
    **Institute of Industrial Engineers (IIE) Pritsker Doctoral Dissertation Award

29. 2009 Gopalappa, C., Das, T., Enkemann, S., and Eschrich, S., Removal of Hybridization and Scanning Noise from Microarrays, IEEE Transactions on Nanobioscience, 8(3), 2009