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: Group Leaders, 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

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David Bean | David received his BA in Biochemistry and Visual Arts from Bowdoin College in 2013. He joined the Allen Lab in early 2014 where he studies the early evolution and diversity of viral infection in both acutely infected patients and in the BLT mouse model.  Outside of the lab, David can be found working on his paintings or playing soccer with friends in the Boston area.

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.

Vinita Joshi | Vinita
is a graduate student in the Virology Ph.D program at Harvard Medical School. She received her B.Tech in biotechnology from India and her Master’s degree in Biotechnology from the University of Pennsylvania. She worked with Dr. Michael Farzan, initially at the New England Primate Research Center before moving to Scripps, Florida. Her work on HIV during this time drove her to apply for the Virology program at Harvard, where she rotated in and subsequently joined the Allen lab for her Ph.D thesis. She is currently interested in studying the evolution of HIV and the host immune system in patients that develop broadly neutralizing antibodies.

Ruchi Newman | Ruchi Newman is a Research Specialist in the Allen lab.  She received her Ph.D. in Molecular Microbiology from Tufts Medical School and completed postdoctoral training in immunology at the Burnham Institute and in virology at Harvard Medical School/New England Primate Research Center.  Prior to joining the Ragon Institute, Ruchi was a Research Scientist in the Viral Genomics group within the Genome Sequencing and Analysis Program at the Broad Institute.  Her work at the Broad focused on using next generation sequencing techniques and computational analysis tools to study host-pathogen interaction in an effort to understand how these encounters impact evolution of both the viral pathogens and host immune response.  Ruchi’s current work continues to use genomics to study viral evolution and neutralizing antibody response in HIV-infected patients.

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Melissa Pack | Mel joined the Allen lab in fall of 2014, after completing her B.S. in Neuroscience at Brandeis University. Her work at the Ragon focuses on how antibodies drive HIV envelope mutation, and vice versa. Recent projects include studying the envelope region by single genome analysis, and generating pseudovirus to study antibody neutralization longitudinally. Outside of lab she enjoys knitting, crossword puzzles, and aquariums.

Damien Tully | Damien 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. He obtained his PhD in Genetics from Trinity College Dublin, Ireland and crossed the globe to complete a postdoctoral fellowship at the Nebraska Center for Virology where he studied HIV-1 evolution in the context of Mother-to-Child-transmission.  His current research focuses on investigating at a genetic and molecular level the nature of the virus that establishes infection following HIV-1 sexual transmission. Other interests lie in studying HCV transmission and early viral evolution. Damien is a recipient of a 2013 amfAR, The foundation for AIDS Research, Mathilde Krim Fellowship award in Basic Biomedical Research. Outside the lab Damien enjoys going on adventures with his wife and dog and is a 2nd degree black belt in art of Kenpo Karate.

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.