Research Mentors

Trainees interested in pursuing a career in research investigation have a wide variety of opportunities ranging from HIV clinical research including behavioral and epidemiologic studies to bench work focusing on host-responses and innate immunity. To make the transition to the research years, fellows will work with a faculty advisor during their first year of fellowship. This advisor will be chosen based on a fellows' particular area of interest, and will work with a fellow to identify a specific research. Once identified, fellows will work with this designated mentor throughout the remainder of their training. This mentor will supervise a fellow's development into an independent investigator which includes the development and implementation of research projects, publications, and grant submissions that will be used to obtain funding for project support and salary support in the non-ACGME years.

Dan Barouch, MD, PhD, FIDSA

Dr. Barouch is the Director of the Center for Virology and Vaccine Research at BIDMC. His research focuses on studying the immunology and virology of HIV-1 infection and developing novel vaccine strategies. Dr. Barouch's team has demonstrated that humoral and cellular immune responses elicited by adenovirus and poxvirus vectors can partially protect against acquisition of infection and can control viral replication following pathogenic virus challenges in rhesus monkeys. They have also developed a series of alternative serotype and chimeric adenovirus vector-based vaccines that are designed to circumvent the high titers of neutralizing antibodies to the common adenovirus serotype 5 (Ad5) vector in the developing world. They have constructed a variety of novel vaccine vectors, explored their immunogenicity and protective efficacy in preclinical studies, and advanced optimal vaccine candidates into clinical trials. Four phase 1 clinical trials with these novel HIV-1 vaccine vectors are currently in progress in the United States and sub-Saharan Africa. Dr. Barouch's group is a key part of the Bill and Melinda Gates Foundation Collaborative for AIDS Vaccine Discovery (CAVD), the NIH Center for HIV/AIDS Vaccine Immunology (CHAVI), and the Ragon Institute of MGH, MIT and Harvard. Read more

Raphael Dolin, MD

Dr. Dolin has a major interest in the development and evaluation of HIV vaccines. As part of the NIH sponsored Harvard HIV Vaccine Trials Unit, studies of candidate HIV vaccines are carried out in normal volunteers for safety and immunogenicity. Recent vaccines which have been studied include DNA vaccines which code for HIV-1 envelope genes, and genes for gag, pol, and nef proteins. Studies of candidate vaccines based on adenovirus vectors are also underway. Laboratory investigation of immune responses also has been undertaken, including studies of both humoral and cell-mediated immune responses. The latter employ techniques to measure T-cell responses by ELISPOT, intracellular cytokine staining, and tetramer assays. Establishment of highly sensitive, specific neutralization antibody assays is a particular interest of the group.

Dr. Dolin and colleagues are also interested in the development of safe and more tolerable smallpox vaccines, as part of the NIH sponsored Translational Immunology Center. Clinical studies of vaccinia and Modified Vaccinia Ankara (MVA) vaccines in human volunteers are being undertaken along with measurement of humoral and cell mediated immune responses in vaccines. The goal of the studies is to develop a new generation of genetically modified and defined vaccines for biodefense uses. Read more

Kenneth Mayer, MD, FIDSA

Dr. Mayer has been conducting bio-behavioral studies of HIV prevention in high-risk populations in the US at Fenway Health, and in several international studies overseas, particularly India. He has led studies of HIV chemoprophylaxis (PEP, PrEP, and topical microbicides), vaccines, as well as social and structural interventions. He is the New England site Principal Investigator for the NIH's HIV Prevention Trials Network (HPTN) and Microbicides Trials Network (MTN) consortia; and co-PI of the Harvard HIV Vaccine Trials Unit. He was one of the national chairs of HPTN 061, a study focused on developing HIV prevention interventions for Black men who have sex with men, and is Protocol Co-Chair of HPTN 069, which is evaluating Maraviroc for use as PrEP. He is also funded by NIMH to work with behavioral scientists to develop adherence interventions for PrEP users.

Dr. Mayer is also involved with several natural history studies of HIV, including the CFAR Network of Clinical Integrated Systems (CNICS), which follows more than 30,000 HIV-infected patients in care at 8 US centers. He is also leading an effort to train other community health centers to use their electronic health records to conduct clinical research. His recent papers have appeared in the Annals of Internal Medicine, Lancet, New England Journal of Medicine, AIDS, Journal of AIDS, Clinical Infectious Diseases, and other journals. He continues to work with several centers in India, and is part of the Executive Committee of the HPTN, working on developing combination HIV prevention interventions. Read more

Christopher Rowley, MD, MPH

Dr. Rowley is an Assistant Professor of Medicine at Harvard Medical School and a member of the Essex Laboratory at the Harvard School of Public Health. His primary laboratory research interests are related to HIV drug resistance in southern Africa. He was the principal investigator of an NIH-funded study to monitor for transmitted HIV drug resistance in Botswana and has worked to develop techniques allowing for low cost alternatives for resistance testing. He also has been engaged in research within the Infectious Diseases Division related to infectious complications of opioid use disorder and serves as the Director of Opioid Use Disorder Education for the Department of Medicine at Beth Israel Deaconess Medical Center.Read more

Roger Shapiro, MD, MPH

Dr. Shapiro is an Associate Professor in Medicine at Harvard Medical School and the Harvard TH Chan School of Public Health. His primary research interests are in the prevention of mother-to-child HIV transmission (PMTCT) and the reduction of morbidity and mortality among infants born to HIV-infected women. Since 1999, Dr. Shapiro has studied infant outcomes and PMTCT strategies in several large NIH-funded clinical trials in Botswana. He was a co-investigator of the Mashi Study, which evaluated several PMTCT interventions among 1200 mother-infant pairs; the principal investigator of the Mma Bana Study, which compared 3 different antiretroviral combinations during pregnancy, delivery, and breastfeeding among 730 mothers-infant pairs; co-principal investigator of the Mpepu Study, which evaluated strategies for reduce infant mortality among over 3,000 HIV-exposed uninfected infants; and principal investigator for several studies of adverse birth outcomes. He is currently the principal investigator for NIH-funded studies that perform nationwide surveillance studies to evaluate the mechanisms by which antiretrovirals impact adverse birth outcomes; an ongoing clinical trial of early antiretroviral treatment to improve clinical outcomes in HIV-infected infants; and novel use of broadly neutralizing monoclonal antibodies as alternate treatment for early-treated, low-reservoir children. Dr. Shapiro works closely with the Botswana PMTCT Program, and is a member of the PMTCT Advisory Panel for the World Health Organization. Dr. Shapiro helps to mentor Infectious Disease fellows, residents, and students who are interested in research projects related to international HIV, and established a clinical teaching and training program at the Scottish Livingstone Hospital in Molepolole, Botswana, to support residents, fellows and junior faculty starting careers in international HIV.Read more.

Peter Weller, MD, FIDSA

Dr. Weller has many active areas of basic laboratory research centered around understanding basic mechanisms of leukocyte functioning in forms of inflammation. The two principal areas of investigation are:

  1. The immunobiology of eosinophilic leukocytes
  2. The intracellular regulation and compartmentalization of inducible mediators of inflammation in neutrophils and other leukocytes.

Studies of human eosinophils are aimed at defining mechanisms whereby eosinophils may collaboratively interact with other cellular elements of the immune system. These studies include investigations of the mechanisms whereby eosinophils may function as antigen-presenting cells in governing T-lymphocyte dependent immune responses, and include investigations of the in vivo migration and function of eosinophils and of the regulated expression of cell surface proteins involved in collaborative interactions between eosinophils and other cell types.

Additional studies are focused on defining the molecular mechanisms governing the synthesis, granule storage and release mechanisms of eosinophil derived cytokines. The roles of eosinophils in wound healing and fibrosis and the activities of chemokines and cytokines released by eosinophils that contribute to tissue remodeling are being studied. The second area of research involves the molecular and cellular biologic bases of inducible responses of leukocytes participating in host defense and other forms of inflammation. These are centered on a unique intracellular compartment, termed the lipid body, whose formation is rapidly inducible in leukocytes. The intracellular signaling mechanisms responsible for lipid body induction and especially the roles of lipid bodies as distinct sites of cytokine and eicosanoid mediator formation are being studied.

In addition to investigating previously undefined pathways of leukocyte responses to inflammation, these studies also offer the potential to identify novel anti-inflammatory therapeutic targets. Our research indicates that lipid bodies in leukocytes have roles as sites of regulated formation of eicosanoids and as distinct extranuclear sites of translation. The biology of these structures is intimately related to the roles of leukocytes in acute inflammation. Read more

Sharon Wright, MD, MPH, FIDSA

Dr. Wright is the Director of the Division of Infection Control/Hospital Epidemiology in the Department of Health Care Quality and the Director of Infection Control Research. She studies the risk factors, outcomes and costs of healthcare-associated infections. Dr. Wright's work also focuses on staff education and quality improvement in infection prevention, specifically related to prevention of surgical site infections and device-associated infections. A more detailed description of the research activities related to Healthcare Epidemiology can be found here. Read more

Other Investigator-Initiated Research

Carolyn Alonso, MD - Dr. Carolyn Alonso serves as the Director of the Transplant and Immunocompromised Host Program at Beth Israel Deaconess Medical Center. Her research focuses on the epidemiology and outcomes of C. difficile infection among immunosuppressed patients. Dr. Alonso has several open clinical trials in C. difficile research as well as an investigator-initiated grant to study C. difficile immune response within transplant and immunocompromised patients. Additional areas of active research investigation include clinical trials evaluating invasive fungal infections as well as a trial investigating patients treated with systemic mold-active triazole medications. (read more)
Adolf W. Karchmer, MD, FIDSA - Antibiotic chemotherapy, endocarditis, infections of foreign bodies, infections in diabetics and immunocompromised patients (read more)
Douglas Krakower, MD - Provider attitudes towards HIV prevention strategies (read more)
Nira Pollock, MD, PhD - Microbiology, molecular diagnostics, Mycobacterium tuberculosis (read more)
Chen Sabrina Tan, MD - Viral central nervous system infection in immunosuppressed patients (read more)

Mentorship Outside of BIDMC

BBIDMC fellows have the opportunity to work with primary mentors outside the BIDMC at one of the Harvard affiliated hospitals. Our fellows have a track record of working with mentors from Massachusetts General Hospital, Children's Hospital Boston, Brigham and Women's Hospital and The Ragon Institute. Fellows interested in working with mentors outside of BIDMC will continue to meet regularly with a BIDMC advisor throughout their fellowship training.

The Infectious Diseases Fellowship Training Program at Beth Israel Deaconess Medical Center (BIDMC), Harvard Medical School is a fully ACGME-accredited program that offers comprehensive Infectious Diseases clinical training and education and many different research opportunities. Trainees joining our fellowship program will participate in the primary and consultative care for a diverse population of patients at BIDMC.


Peter F. Weller, MD, Division Chief
Wendy Stead, MD, Fellowship Program Director
Christopher F. Rowley, MD, Associate Program Director

The following represents a snapshot of BIDMC's characteristics important to an infectious diseases fellow:

  • 649 licensed beds, including 440 medical/surgical beds, 77 critical care, and 60 OB/GYN
  • Level 1 Trauma Center, roof-top heliport, ED services 54,000 patients/year
  • Cancer Center, Transplant Programs (Bone Marrow Transplant and Solid Organ Transplants), Cardiovascular InstituteSpine Center
  • Care for more than 1500 HIV+ patients in the region
  • Close collaboration with Joslin Diabetes CenterBoston Children's Hospital
  • Ranks fourth among independent hospitals in US for NIH research grant funding
  • Center for Life Science (CLS), a state-of-the-art biomedical research facility which opened its doors in 2008 and is the largest research facility in the Longwood medical area
  • Expanding network of hospital and community practice affiliates including The Fenway Community Health Center, a national leader in advancing health care in the LGBT community

Clinical Activities

Activities within the Division of Infectious Diseases at BIDMC pertinent to fellowship training include:

  • Two active inpatient consultation services - each service includes two ID fellows and an attending ID faculty member. One consultative team is primarily focused on immunocompromised patients while the second consultative service provides general ID consults and is primarily responsible for patients in the intensive care units.

Infectious Diseases outpatient clinics:

  • Fellow continuity clinic - fellows with their faculty mentor provide longitudinal care for their HIV patients, see new ID consults in the outpatient setting, and follow patients for post-discharge care.
  • Travel Clinic - a vibrant clinic primarily staffed by a nurse practitioner that provides fellows with opportunities to learn travel medicine.
  • Outpatient Parenteral Antibiotic Therapy (OPAT) - a clinic with dedicated physician oversight, nursing and administrative staff that facilitate the follow-up of inpatients discharged on parenteral antibiotic regimens.
  • Urgent Care Clinic - fellows participate in the walk-in evaluation and care of patients with infectious diseases issues.

Fellowship Funding

For the two years of ACGME-accredited ID fellowship training, full salary support is provided for both years by BIDMC.

Shared Harvard-Wide Activities

The BIDMC ID fellowship program collaboratively interacts with the other Harvard Medical School-affiliated ID fellowship programs at Boston Children's Hospital and at Brigham and Women's Hospital/Massachusetts General Hospital. Common efforts amongst the ID programs include a weekly conference that, in the early months, is focused on didactic educational offerings by senior faculty from the several programs and is followed thereafter by fellow-presented case conferences. The BIDMC ID program also shares a weekly immunocompromised focused conference with Children's HospitalBrigham and Women's Hospital and the Dana-Farber Cancer Center. We also participate in Harvard Medical School-wide Centers for AIDS Research (CFAR) conferences.

BIDMC Infectious Diseases Conferences

The BIDMC Infectious Diseases program has a weekly conference schedule that includes: a case conference (with a focus on teaching and involvement by faculty from ID, the clinical microbiology program, antibiotic pharmacy PharmDs and other case-specific disciplines), a journal club/research in progress conference, a dedicated fellow-focused educational conference and a multidisciplinary HIV conference with the primary care division and microbiology plate rounds.

Fellowship Program and Options

YEAR ONE:The first year of ID fellowship is focused primarily on the inpatient ID consult experience where fellows encounter diverse general ID-related problems on the medical and surgical services, as well as work with immunocompromised hosts (bone marrow and solid organ transplant), and patients on the OB-GYN service. In addition, fellows will rotate through the outpatient Urgent Care ID Clinic at BIDMC, the Clinical Microbiology Laboratory and Boston Children's Hospital (for inpatient pediatric ID). Throughout the first two years of training, all fellows spend one-half day per week seeing patients with their assigned preceptor in their continuity clinic.

YEAR TWO:In year two, fellows continue to have their required outpatient continuity clinics and have limited inpatient ID consultation coverage. Fellows have a variety of choices with two and three (or more) year training options. Two year tracks provide focused training in specific areas such as transplant ID, hepatitis, microbiology, medical education and infection control. For those interested in a more focused research experience, there are options in clinical HIV-related research, basic science and translational research and Hospital Epidemiology. Fellows choosing to pursue a career in clinical or translational research will be able to apply for different educational opportunities such as the program in Clinical Effectiveness summer course at the Harvard T. H. Chan School of Public Health and the Master's Program in Clinical and Translational Investigation through the Harvard Catalyst Program.

To make the transition to second year, fellows will work with the fellowship program directors to assist him/her with identifying the best track and mentor for his/her career development. Once identified, fellows will work with this designated mentor throughout the remainder of their training. For those in the two year tracks, this mentor will help devise a training plan that incorporates the clinical and scholarly activities. For those interested in the research tracks, this mentor will supervise their development into an independent investigator, which includes the development and implementation of research projects, publications, and grant submissions that will be used to obtain funding for project support and salary support in the non-ACGME years.