Chief, Viral Genomics Section and Systems Serology Core

U.S. Military HIV Research Program (MHRP)

Dr. Morgane Rolland received her Ph.D. from the University of Bordeaux, France in 2003. She completed a post-doctoral fellowship with Professor James I. Mullins in the Microbiology department of the University of Washington in Seattle between 2004 and 2010.

Dr. Rolland is interested in better understanding the infectious disease dynamics of emerging human viral pathogens, in particular HIV-1, and translating this knowledge to develop vaccines. The Rolland Lab generates and analyzes molecular sequence data to infer evolutionary and population dynamic processes, while also integrating structural bioinformatics to the analysis of pathogen sequences. Our studies aim to characterize the interplay between evolutionary dynamics and the host immune pressure in the context of natural infection or following vaccination.

The Rolland Lab has pioneered sieve analyses methods, aiding understanding of the genetic consequences of vaccine-induced immune responses in breakthrough infections, thereby providing insights on potential mechanisms of vaccine protection or on risks for future vaccine resistance.

The fact that vaccine efficacy was seen in the absence of high titers of neutralizing antibodies in the context of HIV-1 or Dengue vaccination led us to develop a systems serology platform allowing us to profile Fc-antibody functions. With this approach, the lab integrates data from different immunological assays generated by us, or our collaborators, using machine learning methods to provide a systems-level understanding of antibody functions.

Dr. Rolland’s group includes scientists with expertise in molecular biology, evolutionary biology, population genetics, structural bioinformatics, immunology, mathematical modeling and statistics.

Professor, Director – Health Statistics and Geography Lab

Department of Public Health, Center of Biomedical and Health Research in Data Sciences (CHORDS)

Health Statistics and Geography Lab, UMass, Lowell

Core Member, Institute for Medical Engineering and Science (IMES), MIT
Associate Professor of Chemistry
Extramural Member, The Koch Institute for Integrative Cancer Research, MIT
Member, Ragon Institute of MGH, MIT, and Harvard
Institute Member, Broad Institute of MIT and Harvard
Assistant in Immunology, Massachusetts General Hospital
Instructor, Health Sciences and Technology, Harvard Medical School

Alex K. Shalek, PhD, (pronouns: he/him/his) received his bachelor’s degree summa cum laude from Columbia University and his Ph.D. from Harvard University in chemical physics under the guidance of Hongkun Park, and performed postdoctoral training under Hongkun Park and Aviv Regev (Broad/MIT). His lab’s research is directed towards the development and application of new approaches to elucidate cellular and molecular features that inform tissue-level function and dysfunction across the spectrum of human health and disease. Dr. Shalek and his work have received numerous honors including a NIH New Innovator Award, a Beckman Young Investigator Award, a Searle Scholar Award, a Pew-Stewart Scholar Award, the Avant-Garde (DP1 Pioneer) Award from the National Institute for Drug Abuse (NIDA), and an Alfred P. Sloan Research Fellowship in Chemistry, as well as the 2019-2020 Harold E. Edgerton Faculty Achievement Award at MIT and the 2020 HMS Young Mentor Award.

Chief, Laboratory of Integrative Multiomics
US Military HIV Research Program (MHRP)

Dr. Rasmi Thomas obtained her Ph.D. in Biotechnology from the Rajiv Gandhi Center for Biotechnology at the University of Kerala, India. She completed her postdoctoral training with Dr. Mary Carrington from the National Cancer Institute, NIH in Frederick, MD.

Dr. Thomas oversees the Laboratory of Integrative Multiomics with the U.S. Military HIV Research Program at the Walter Reed Army Institute of Research. The Laboratory of Integrative Multiomics utilizes cutting-edge next-generation sequencing (NGS) technologies to identify variation in genes involved in host-pathogen interaction. We support studies related to disease acquisition, pathogenesis, response to vaccination or treatment outcomes.

In order to advance MHRP’s mission to develop an effective vaccine and eradicate HIV, we employ laboratory and bioinformatic methods to characterize host genetic, transcriptomic, epigenetic and microbiome variation using unbiased genome-wide sequencing approaches. Previous studies using gene chips have been limited, as they only screen a targeted number of variations and are inherently biased towards particular populations. Our lab uses unbiased NGS technologies to study diverse populations across Asia, Africa, Europe and the Americas, screening genetic variations and identifying their functional basis. NGS methods for genotyping immune response genes that have previously been implicated in HIV-1 disease pathogenesis, such as the Human Leukocyte Antigen (HLA), have been developed in the laboratory and support ongoing clinical and research activities. RNA-Sequencing (RNA-Seq) technology is being used for whole transcriptome expression profiling to elucidate mRNA gene expression and to analyze non-coding RNA.

Relevant to MHRP’s mission to develop an effective prophylactic vaccine, we recently showed that a vaccine-induced gene signature correlates with protection in both non-human primate and human trials. We are at the forefront of developing these RNA-Seq technologies for analysis of transcriptomes of single cells and detection of transcripts from intracellular pathogens. Integrating proteomics with other ‘omics’ datasets to shed light on mechanisms is another important focus of the group. Microbiome sequencing of gut and genital tract mucosa of HIV-1 infected patients by NGS is also being performed to support activities in other sections at MHRP. By using a range of innovative multifaceted strategies this group continues to make discoveries that can be applied to the central mission of MHRP to fight HIV.