Alison L Hill / Viral dynamics research


I am an independent Research Associate at the Program for Evolutionary Dynamics at Harvard. I study how infectious diseases spread, evolve, and respond to treatment using mathematical and computational methods. My work on HIV/AIDS is funded by the NIH Early Independence Award program and Harvard's Center for AIDS Research.

Office @ the Program for Evolutionary Dynamics
1 Brattle Sq, Room 638
Cambridge MA, 02138 [map]

Email: alhill at fas dot harvard dot edu

Find me: Google Scholar, ResearchGate, Twitter, LinkedIn

Photo by Lan Li



2007 - 2013 : PhD, Biophysics Program, Harvard University and Medical Engineering and Medical Physics (MEMP) Program, Harvard-MIT Division of Health Sciences and Technolgy (HST). Thesis advisor: Martin Nowak

2003-2007 : BS, Physics. Queen's University, Canada. Thesis advisor: Robert Gooding



I use mathematical models to understand how infectious diseases spread within and between individuals, cause disease, and continually evolve in response to our immune systems and medical interventions. This field is often called viral dynamics. Most of my research focuses on HIV, the virus that causes AIDS. Questions I'm interested in include: How can we optimize antiretroviral therapy and prevent the emergence of drug resistance ? What are the dynamics of the latently infected cells that allow HIV to persist even with potent drugs? How can we cure HIV infection? What are the mechanisms of HIV pathogenesis? How does the immune system try, and fail, to control HIV?

I am also generally interested in factors that influence the evolution of viruses and other parasites, the emergence of drug resistant infections, and the cross-species transmission of novel viruses.

Models and mechanisms for understanding viral dynamics are increasingly finding applications outside traditional virology. They can be used to study the dynamics of behaviors, to help predict and interevene in their spread. Previous projects I've worked on have applied infectious disease models to social contagion.

In the past I've used mathematical models to understand how our body maintains iron homeostasis and how cyanobacteria - the first multi-cellular organism - create a precise pattern of differentiated cells. I also spent a few years studying MRI and researching techniques to use nanoparticles to image specific molecular targets.



Google Scholar | ResearchGate | ORCID

  1. Hill AL , Rosenbloom DIS, Siliciano JD, Siliciano RF (2016). Insufficient evidence for rare activation of latent HIV in the absence of reservoir-reducing interventions. PLoS Pathogens (In press) .

  2. Hill AL, Rosenbloom DIS, Goldstein E, Hanhauser E, Kuritzkes DR, Siliciano RF, Henrich TJ (2016) Real-time predictions of reservoir size and rebound time during antiretroviral therapy interruption trials for HIV. PLOS Pathogens, 12(4):e1005535. doi:10.1371/journal.ppat.1005535. ( BioRxiv, PubMed )

  3. Moreno-Gámez S*, Hill AL*, Rosenbloom DIR, Petrov D, Nowak MA, Pennings P (2015). Imperfect drug penetration leads to spatial monotherapy and rapid evolution of multi-drug resistance. PNAS, 112(22):E2874-E2883. doi:10.1073/pnas.1424184112. (BioRxiv, PubMed)

  4. Rosenbloom DIS, Elliott O, Hill AL, Henrich TJ, Siliciano JM, Siliciano RF (2015). Designing and interpreting limiting dilution assays: general principles and applications to the latent reservoir for HIV-1. Open Forum InfectiousDiseases, 2(4):ofv123. doi:10.1093/ofid/ofv123. (BioRxiv, PubMed )

  5. Laird GM, Bullen CK, Rosenbloom DIS, Martin AR, Hill AL, Durand CM, Siliciano JD, Siliciano RF (2015). Ex vivo analysis identifies effective HIV-1 latency–reversing drug combinations. Journal of Clinical Investigation. doi:10.1172/JCI80142 (PubMed)

  6. Leventhal GE*, Hill AL*, Nowak MA, Bonhoeffer S (2015). Evolution and emergence of infectious diseases in theoretical and real world networks. Nature Communications, 6 (6101); doi:10.1038/ncomms7101 (PubMed)

  7. Hill AL*, Rosenbloom DIS*, Fu F, Nowak MA, Siliciano RF (2014). Predicting the outcomes of treatments to eradicate the latent reservoir for HIV-1. PNAS, 111 (37), 13475-13480. (Arxiv, PubMed)
    - Covered by Nature Medicine News, International AIDS Society, PNAS Commentary
  8. Whitney JB, Hill AL, Sanisetty S, Penaloza-MacMaster P, Shetty M, Parenteau L, Cabral C, Shields J, Blackmore S, Smith JY, Brinkman AL, Peter LE, Mathew SI, Smith KM, Borducchi EN, Rosenbloom DIS, Lewis MG, Hattersley J, Li B, Hesselgesser J, Geleziunas R, Robb ML, Kim JH, Michael NL, Barouch DH (2014). Rapid establishment of the viral reservoir prior to systemic viremia following mucosal SIV infection of rhesus monkeys. Nature. Published online Jul 20 (PubMed)
    - Covered by Los Angeles Times, International AIDS Society, Ragon Institute News
  9. Henrich TJ, Hanhauser E, Marty MF, Sirignano MN, Keating S, Lee T-H, Robles YP, Li JZ, Heisey A, Hill AL, Busch MP, Armand P, Soiffer RJ, Altfeld M, Kuritzkes DR (2014). Antiretroviral-free HIV-1 remission and viral rebound following allogeneic stem-cell transplantation: implications for HIV-1 cure research. Annals of Internal Medicine, 161(5):319-327 (PubMed)
    - Covered by New York Times, Nature News
  10. Humplik J, Hill AL, Nowak MA (2014). Evolution of infectious diseases in finite populations.  Journal of Theoretical Biology, 360 (149-162) (PDF, PubMed)

  11. Rosenbloom DIS*, Hill AL*, Rabi SA*, Siliciano RF, Nowak MA (2012). Antiretroviral dynamics determines HIV evolution and predicts therapy outcome. Nature Medicine, 18 (9) , 1378-1385. (PubMed)
  12. - Covered by Harvard Gazette, Johns Hopkins Medicine News, Positively Aware
  13. Hill AL, Rosenbloom DIS, Nowak MA (2012). Evolutionary dynamics of HIV at multiple spatial and temporal scales. J Mol Med, 90 (5), 543-561. (PubMed)
    - Part of a special issue on Evolutionary Medicine
  14. Thankachan P, Kalasurmath S, Hill AL, Thomas T, Bhat K, Kurpad AV (2012) A mathematical model for the hemoglobin response to iron intake, based on iron absorption measurements from habitually consumed Indian meals. Eur J Clin Nutr, 66 (4), 481-487. (PubMed)

  15. Hill AL, Rand DG, Nowak MA, Christakis NC (2010) Infectious disease modeling of social contagion in networks. PLoS Computational Biology, 6 (11). (PubMed)
  16. - Covered by Harvard Gazette, Boston Globe
  17. Hill AL*, Rand DG*, Nowak MA, Christakis NC (2010) Emotions as infectious diseases in a large social network: the SISa model. Proc Roy Soc B, 277 (1701). (PubMed)
  18. - Covered by Wired Science
  19. Aptekar JW, Cassidy MC, Johnson AC, Barton RA, Lee M, Ogier AC, Vo C, Anahtar MN, Ren Y, Bhatia SN, Ramanathan C, Cory DG, Hill AL, Mair RW, Rosen MS, Walsworth RL and Marcus CM (2009) Silicon nanoparticles as hyperpolarized magnetic resonance imaging agents. ACS Nano, 3 (12), 4003- 4008. (PDF, PubMed)

  20. Allard JF, Hill AL, Rutenburg AD (2007) Heterocyst pattern without patterning proteins in cyanobacterial filaments. Developmental Biology, 312 427-434. (PDF, PubMed)

[* Joint first authorship]


Viral dynamics team


Morgan Craig
Postdoctoral Fellow

Jeff Gerold
Graduate Student, Biomedical Informatics & Genomics

Julia Neagu
Graduate Student, Physics

Chris Bruno
Research Assistant
Applied Mathematics, Harvard College '16


Shirley Mo
Research Assistant, Senior Thesis Student
Applied Mathematics, Harvard College '16
Current: Harvard Medical School Class of 2020

Lily Hu
Research Assistant
Mathematics, Harvard College '16
Current: Fulbright Spain, Graduate Student in Applied Mathematics, Harvard

Mark Freeman
Senior Thesis Student
Applied Mathematics, Harvard College '16

Ellen Rice
Senior Thesis Student
Mathematics, Harvard College '12
Current: University of Washington St Louis Medical School Class of 2019


If you are a Harvard or MIT undergraduate or graduate student looking to do a research project, senior thesis, or rotation at the Program for Evolutionary Dynamics (co-supervised with Martin Nowak), feel free to contact me at the address above.



HIV modelers: Daniel Rosenbloom, Ali Rabi, Feng Fu
HIV experimentalists: Bob Siliciano,Tim Henrich, James Whitney, Dan Barouch
Infectious disease epidemiology: Jan Humplik, Gabriel Leventhal, Sebastian Bonhoeffer
Drug resistance: Pleuni Pennings, Stefany Moreno
Social contagion: David Rand, Nicholas Christakis
Iron homeostasis: Anura Kurpad, Prashanth Thankachan
Magnetic resonance imaging: Maja Cassidy, Ron Walsworth, Chris Bowen, Steven Beyea
Bacterial pattern formation: Andrew Rutenberg, Jun Allard



Early Independence Award from the NIH covered by the Harvard Gazette (Oct 2014)

Popular science piece "Why There's No HIV Cure Yet" published by PBS NOVA (Aug 2014)

Grand Challenges Explorations Grant from the Gates Foundation covered by the Harvard Crimson (Nov 2011)


Other Activities

Science Club for Girls (Outreach group) - Summer Program Mentor/Facilitator
Neuwrite Boston (Science writing group) - Member
Physical Sciences 2 (Mechanics, Elasticity, Fluids, Diffusion) - Teaching Assistant
Math 153 (Mathematical Biology - Evolutionary Dynamics) - Teaching Assistant
Math 243 (Evolutionary Dynamics) - Teaching Assistant
Harvard Biomathematics Seminar - Co-organizer
Mount Auburn Hospital - Introduction to Clinical Medicine - clerkship for PhD students
Dudley House (the graduate student center) - social coordinator
Harvard GSAS Science Policy Group - executive member
Harvard GSAS Canadian Club - Governor General