Todd Allen, PhD

Lab Info:

Principal Investigator: Todd Allen, PhD

Lab Staff: 4 post-doctoral fellows, 5 research technicians, 1 lab manager

Office/Location: 400TS 764

Phone: (857) 268-7002


Category: Members

The Allen laboratory is primarily investigating the impact that viral sequence diversity has on immune control in the setting of HIV-1 infection. Cellular CD8+ T cell responses (CTL) represent a critical arm of the immune response in the control of HIV-1 infections. The ability of HIV to rapidly evolve and escape from these responses within a host, combined with the enormous sequence diversity of HIV strains worldwide, is one of the largest hurdles facing an AIDS vaccine. Unfortunately, we still lack a thorough understanding of the impact that viral escape from these responses has on immune control.


The laboratory employs full length viral genome sequencing of HIV in acute and chronic HIV infected subjects to identify the extent to which HIV is capable of evading host immune responses over the course of infection, and the degree to which such forces are shaping HIV sequence evolution on the global level. Extensions of this work are now characterizing the boundaries by which HIV sequence evolution is restricted by protein structure and function by investigating whether particular mutations are capable of compromising the replicative fitness of HIV and thus contributing to immune control. Similarly, my lab is exploring issues of viral escape and replication in the setting of hepatitis C virus (HCV), another highly variable virus whose infections are also endemic in the human population. These studies are designed to aid in the development of effective vaccines against HIV and HCV though a better understanding of the routes by which these pathogens compromise host immune defenses and evolve on the global level. Finally, in collaboration with the Chulalongkorn Medical Research Center in Bangkok, Thailand we are characterizing immune responses and viral sequence evolution in a population where highly unique strains of HIV are circulating.

Important Contributions

  • Characterizing the role of immune pressures in shaping the sequence diversity of HIV.
  • Identifying the role of HIV superinfection in loss of immune control and disease progression.
  • Characterizing the role of sequence constraints on reversion of transmitted mutations in HIV.
  • Development of a flow-based reporter system to measure replication of primary HIV strains.

Present Areas of Investigation

  • Determining the impact of CTL escape mutations on immune control following acute HIV infection.
  • Defining the extent of HLA-class I associated (CTL escape) sequence polymorphisms across the HIV and HCV proteomes.
  • Examining the role of viral replication capacity on immune control of HIV.
  • Current News:
  • Immune Responses Select for Mutations that Significantly Impair
  • Hepatitis C Virus Replication


Laboratory Members

 Molly-Amero2 Molly Amero | MAMERO@mgh.harvard.eduProject Manager
 Resized-Batorsky Rebecca Batorsky |
Rebecca Batorsky is a Research Fellow at the Ragon Institute working of intra-patient viral evolution with a focus on the genetic determinants of transmission. She got her Ph.D. in Physics at Tufts University in 2012 where she applied mathematical modeling to study the interaction between HIV and the immune system. She joined the Allen lab  in the Fall of 2012. When she is not surrounded by computer monitors with inverted color schemes she enjoys running, cycling, and playing guitar.
 Resized-Boutwell Christian Boutwell | cboutwell@partners.orgChristian is a Senior Research Scientist at the Ragon Institute investigating the mechanisms and dynamics of HIV immune escape in an effort to inform the design of effective HIV vaccine immunogens. He received his BS and MS degrees in Biological Sciences from Stanford University where he studied evolutionary biology. After work experiences in the snow sciences, the Human Genome Project, and herpesvirus molecular biology, Christian earned his PhD from the Committee on Virology at Harvard Medical School for his studies of HIV immune adaptation. Outside of the Allen Lab, Christian relaxes by raising his 3 children.
 Resized-Dudek Tim Dudek | tdudek@partners.orgI received my Ph.D. from Harvard University in the program for Biological Sciences in Public Health working on herpes virus vaccines and vaccine vectors in the laboratory of Dr. David M. Knipe. My interest in virology and vaccines led me to join Dr. Todd Allen’s team here at the Ragon Institute to focus on the characterization of the humanized BLT mouse model. Using this small animal model to study human-specific immune responses we hope to gain a better understand the dominance hierarchies of T cell responses allowing for the design of HIV vaccine antigens that will elicit cellular immune responses focused on viral epitopes that are known to be refractory to escape. Such a vaccine should allow for long-term suppression of HIV and potentially even clearance.
 Resized-Karpel Marshall Karpel | mkarpel@partners.orgMarshall received his B.S in Biological Chemistry in 2008 from Bates College, where he designed escape-resistant RNAi against catalytic portions of the HIV genome as his undergraduate thesis. He moved to Boston later that year to develop and test a novel therapeutic for Ebola virus infections with Dr. Ian Michelow and Dr. Emmet Schmidt, before moving to MIT, where he spent two years in the lab of Dr. Robert Langer, redesigning the enzymatic interfaces of therapeutic nanoparticles. He joined the Allen Lab in the summer of 2013, where he has been adapting our ultra-deep sequencing technology to study the changing antibody repertoire in our HIV-infected humanized mice.
Resized-Maldini Colby Maldini | cmaldini@partners.orgColby joined the Allen Lab in the summer of 2012 after receiving a BS in biological chemistry from Bates College. His work at the Ragon Institute primarily focuses on further establishing BLT mice as an effective model for studying HIV. Outside of the lab, he is an avid New England sports fan and enjoys exploring Boston and the surrounding areas.
 Resized-Ogilvie Colin Ogilvie | cogilvie@partners.orgColin is a research technician in the Allen lab who studies the early evolution and diversity of HIV in acutely infected subjects. He is a recent graduate from Bowdoin College, where he got his BA in Biochemistry and Mathematics. In the lab he can be found at the bench setting up PCRs, at his computer analyzing sequencing data, or in the tissue culture room growing cells and harvesting virus. Outside of lab Colin enjoys running and getting to know new places in Cambridge, Somerville, and Boston.
 Resized-Tully Damien Tully | Tully.Damien@mgh.harvard.eduDamien is a Research Fellow at the Ragon Institute where his research is centered on elucidating the viral-host interactions responsible for HIV-1 transmission and pathogenesis. In particular he is interested in the application of innovative sequencing technology and algorithms to understand viral transmission and early viral diversification. He is now extending this work to study acute HCV infection and viral evolution pre and post liver transplantation. Damien obtained his PhD in Genetics from Trinity College Dublin and before moving to Boston completed a postdoctoral fellowship at the Nebraska Center for Virology where he studied HIV-1 in the context of Mother-to-Child-Transmission. He is a recent recipient of the amFARMathildeKrim Fellowship in Basic Biomedical Research.
 Resized-Power  Karen Power | kapower@partners.orgKaren received her B.S. from Cornell University and her Master’s Degree from Boston University. She joined the Allen Lab in 2006 as a technologist and is now the Senior Laboratory Manager of the Allen Lab, Departmental Safety Coordinator for the Ragon Institute, and Associate Director of the Virology Core. Interests include safety, sequencing and skydiving. A native New Yorker, she will always love the Yankees, but has converted to the New England Patriots for the sake of her marriage.
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