Research Training (Years 2-3)

Basic, translational, clinical, and epidemiologic research

Research training occupies the majority of the second and third years of fellowship. Fellows are supported in identifying a mentor and may select from a broad range of research opportunities in basic, translational, clinical, epidemiologic, education, or outcomes research within Infectious Diseases (ID), the Weill Department of Medicine, other departments within the Medical College (e.g. Department of Microbiology and Immunology, Department of Population Health Sciences) or at affiliated institutions (Rockefeller University, Memorial Sloan-Kettering Cancer Center, Cornell University (Ithaca), and Hospital for Special Surgery). Faculty mentorship from within these institutions allows a wide range of research opportunities.

Our division has an NIH-sponsored T32 training grant to support developing physician-scientists during fellows' research years (AI007613; Gulick, 1999-2025). The objective is to train physician-scientists in biomedical research, with an emphasis on the pathogenesis of infectious diseases. Weill Cornell also has an NIH-funded Clinical and Translational Science Center (CTSC; TR00457; Imperato, 2007-2027) with state-of-the-art facilities for conducting translational and clinical research. The ID Division facilities include over 12,000 square feet of research and administrative space. There are 10 research laboratories (7,500 sq. ft.) in the medical college and the Belfer Research Building equipped for basic and translational molecular, microbiological, and immunologic studies. Current annual funding for sponsored research and training in the ID Division in 2022-2023 exceeded $37.5 million.

Several departmental and medical school-wide programs are available to support fellows interested in research careers with the transition to junior faculty. These opportunities include the Weill Department of Medicine’s Fund for the Future, the JumpStart Research Career Development Program and CTSC’s KL2 Career Development Awards.

The following pathways are intended to serve as a guide for the 2nd/3rd years and are meant to be flexible and adaptable to match individual fellows' interests.

Research pathways in years 2/3

Basic science/lab research

Example fellow publications
  • Saito K, Mishra S, Warrier T, Cicchetti N, Mi J, Weber E, Jiang X, Roberts J, Gouzy A, Kaplan E, Brown CD, Gold B, Nathan C. “Oxidative damage and delayed replication allow viable Mycobacterium tuberculosis to go undetected” Sci Transl Med 2021 Nov 24;13(621).
  • Vorkas CK, Wipperman MW, Li K, Bean J, Adamow M, Wong P, Jean Juste MA, Aubé J, Bucci V, Fitzgerald DW, Glickman MS. Mucosal-associated invariant and  gd T cells respond to initial Mycobacterium tuberculosis infection. JCI Insight. 2018 Oct 4;3(19). pii: 121899. doi: 10.1172/jci.insight.121899
  • Saito K, Warrier T, Somersan-Karakaya S, Kaminski K, Mi J, Jiang X, Park S, Shigyo K, Gold B, Roberts J, Weber E, Jacobs WR, Nathan C. Rifamycin action on RNA polymerase in antibiotic tolerant Mycobacterium tuberculosis results in differentially detectable populations. Proceedings of the National Academy of Sciences 2017; 114:E4832-E4840
  • Isa F, Collins S, Lee MH, et al. Mass Spectrometric Identification of Urinary Biomarkers of Pulmonary Tuberculosis. EBioMedicine 2018;31:157-65

Clinical/translational research

Example fellow publications
  • McLean J, Stoeckle K, Huang S, Berardi J, Gray B, Glesby MJ, Zucker J. “Tecovirimat Treatment of People With HIV During the 2022 Mpox Outbreak : A Retrospective Cohort Study” Ann Intern Med 2023 May;176(5):642-648.
  • Magleby R, Westblade LF, Trzebucki A, Simon MS, Rajan M, Park J, Goyal P, Safford MM, Satlin MJ. Impact of SARS-CoV-2 Viral Load on Risk of Intubation and Mortality Among Hospitalized Patients With Coronavirus Disease 2019. Clin Infect Dis. 2020 Jun 30 [Epub ahead of print].
  • Johnston CD, Ifeagwu KC, Siegler EL, Derry H, Burchett CO, Rice MC, Gupta SK, Choi ME, Glesby MJ. Elevated cardiac risk score by ASCVD calculation is associated with albuminuria in older people living with HIV. AIDS. 2020 Feb 5;. doi: 10.1097/QAD.0000000000002492. [Epub ahead of print]
  • Kapadia SN, Johnston CD, Marks KM, Schackman BR, Martin EG. Strategies for Improving Hepatitis C Treatment Access in the United States: State Officials Address High Drug Prices, Stigma, and Building Treatment Capacity. J Public Health Manag Prac. 2019 May/Jun;25(3):245-52

Healthcare epidemiology/antimicrobial stewardship

  • For interested fellows, there is opportunity to receive intensive training in this exciting field. Fellows are invited to actively participate in departmental activities, initiatives, and meetings to gain practical experience in all aspects of healthcare epidemiology, such as healthcare-associated infection surveillance, reporting, outbreak investigation, antimicrobial stewardship, and hospital policy development and implementation. The IP&C Department is integrated across all NYP campuses, allowing fellows to gain experience in coordinating an IP&C program and an antimicrobial stewardship program (ASP) across a large healthcare system.
  • Observational studies can be carried out utilizing infection control surveillance data, clinical microbiology data, and a robust hospital-based clinical database, which can be queried electronically. There is potential for collaborative projects, including observational as well as individual and cluster randomized trials, with Columbia University Medical Center and other NYP hospitals.
  • Potential mentors include: David CalfeeMatthew SimonHarjot Singh.
  • Major research areas:
    • Epidemiology of healthcare associated infections and/or multi-drug resistant infection.
    • Epidemiology and management of multi-drug resistant infections.
    • Environmental cleaning/disinfection.
    • Antimicrobial stewardship.
    • Rapid molecular diagnostics and diagnostic stewardship.
  • Potential supplementary education: General Preventive Medicine Residency and/or Master’s in Clinical and Translational Investigation.
Example fellow publications
  • Trzebucki AM, Westblade LF, Loo, Mazur S, Jenkins SG, Calfee DP, Satlin MJ, Simon MS “Real-world implementation and impact of a rapid carbapenemase detection test in an area endemic for carbapenem-resistant Enterobacterales.” Infect Control Hosp Epidemiol. 2021 Feb 15;1-4.
  • Kondo M, Simon MS, Westblade LF, Jenkins SG, Babady EN, Loo AS, Calfee DP on behalf of the SHEA Research Network. “Implementation of Infectious Diseases Rapid Molecular Diagnostic Tests and Antimicrobial Stewardship Program Involvement in Acute Care Hospitals.” Infect Control Hosp Epidemiol. 2021 May;42(5):609-11.
  • Wang TZ, White KN, Scarr JV, Simon MS, Calfee DP. “Preparing Your Healthcare Facility for the New Fungus Among Us: An Infection Preventionist's Guide to Candida Auris.” 2020 Jul;48(7):825-827
  • Wang TZ, Simon MS, Westblade LF, Saiman L, Furuya, EY, Calfee DP. “Quantitative Characterization of High-Touch Surfaces in Emergency Departments and Hemodialysis Facilities.” Infect Control Hosp Epidemiol. 2021 Apr;42(4):474-76.

Global health

  • The goal of the Weill Cornell Center for Global Health (CGH) [MSS1] is to improve health care in low and middle income countries through the conduct of research, clinical service, and training. The three priority research areas are infectious diseases, women’s health, and cardiovascular diseases.
  • The Division of Infectious Diseases collaborates closely with the CGH, with multiple faculty members shared between the two groups, including full-time faculty who are based at or travel frequently to programs in Brazil, Haiti, India, Tanzania, or Uganda.
  • The CGH has 16 core faculty members who conduct NIH-funded research and have a track record of advancing the careers of postdoctoral fellows. Six of the Center’s junior faculty currently have NIH K career development awards.
  • Postdoctoral fellows interested in conducting mentored research in global health are encouraged to reach out to the Center’s faculty to learn more about their research.
  • Major research areas and potential mentors may include:
  • Potential supplementary education: Master’s in Clinical Epidemiology and Health Services Research with Global Health Track[MSS2] , 
Example fellow publications
  • Pham K, Mtalitinya GS, Aristide C, Airewele EA, Nyakaru DK, McMahon P, Mulaki GM, Corstjens PLAM, J de Dood C, van Dam GJ, Changalucha JM, Mazigo HD, Lee MH, Jaka H, Downs JA. “Effects of Schistosoma mansoni and praziquantel treatment on the lower gastrointestinal mucosa: A cohort study in Tanzania.” Acta Trop. 2023 Feb;23.
  • Pham K, Mertelsmann A, Mages K, Kingery JR, Mazigo HD, Jaka H, Kalokola F, Changalucha JM, Kapiga S, Peck RN, Downs JA. “Effects of helminths and anthelmintic treatment on cardiometabolic diseases and risk factors: A systematic review” PLoS Negl Trop Dis. 2023 Feb 24.
  • Batavia AS, Severe P, Lee MH, Apollon A, Zhu YS, Dupnik KM, McNairy ML, Pape JW, Fitzgerald DW, Peck RN. Blood pressure and mortality in a prospective cohort of HIV-infected adults in Port-au-Prince, Haiti. J Hypertens 2018;36:1533-1539.
  • Dupnik KM, Bair TB, Maia AO, Amorim FM, Costa MR, Keesen TSL, Valverde JG, Queiroz MAP, Medeiros LL, de Lucena NL, Wilson ME, Nobre ML, Johnson WD, and Jeronimo SMB. Transcriptional changes that characterize the immune reactions of leprosy. J Infect Dis. 2015;211:1658-76.
  • Mathad JS, Bhosale R, Sangar V, Mave V, Gupte N, Kanade S, Nangude A, Chopade K, Suryavanshi N, Deshpande P, Kulkarni V, Glesby MJ, Fitzgerald D, Bharadwaj R, Sambarey P, Gupta A. Pregnancy differentially impacts performance of latent tuberculosis diagnostics in a high-burden setting. PLoS One 2014; 9:e92308.

Medical education

  • Fellows interested in medical education may gain expertise as clinician-educators through a new Department of Medicine certificate program in Medical Education.
  • The goal of the program is to provide trainees with structured training on fundamental aspects of medical education.
  • Collaborations between the Department of Medicine and the ID division allow numerous opportunities for curriculum innovation and the development of ID-specific clinical teaching skills.
  • Examples include case-based small group and large group didactic sessions for 1st and 2nd year medical students during their ID/microbiology course, clinical teaching with 3rd/4th year medical students, internal medicine and ophthalmology housestaff during rotations on the ID consult service and curriculum development, evidence-based medicine and clinical reasoning educational opportunities for medical students, physician assistants, internal medicine and other specialty housestaff.
  • Medical Education certificate program requirements include:
    • Completion of Foundations of Medical Education elective and/or Stanford clinical teaching program.
    • Educational portfolio consisting of mixture of small/large group teaching sessions and observed feedback sessions.
    • Scholarly project presented at regional/national conference or published in peer reviewed literature.
  • Potential mentors may include individuals within Infectious Diseases as well as the Division of General Internal Medicine.
Example fellow publications
  • Gottesdiener LS, Stoeckle K, Loo A, Mazur, S, Gudi K, Marks K, Simon MS. “A Required Infectious Diseases Rotation Improves Antimicrobial Stewardship Knowledge for Internal Medicine Interns.” IDWeek 2021 poster abstract.
  • Chida N, Brown C, Mathad J, Carpenter K, Nelson G, Schechter MC, Giles N, Rebolledo PA, Ray S, Fabre V, Cantillo DS, Longworth S, Amorosa V, Petrauskis C, Boulanger C, Cain N, Gupta A, McKenzie-White J, Bollinger R, Melia MT. Internal Medicine Residents' Knowledge and Practice of Pulmonary Tuberculosis Diagnosis. Open Forum Infect Dis. 2018 Jun 27; 5(7)
  • Chida N, Brown C, Mathad J, Carpenter K, Nelson G, Schechter MC, Rebolledo PA, Fabre V, Cantillo DS, Longworth S, Amorosa V, Petrauskis C, Boulanger C, Cain N, Gupta A, McKenzie-White J, Bollinger R, Melia M. Developing an Assessment Framework for Essential Internal Medicine Subspecialty Topics. J Grad Med Educ. 2018 Jun; 10(3):331-335

Public Health (Joint ID/EIS Fellowship)

We are thrilled to participate in the new Infectious Disease (ID)/Epidemic Intelligence Service (EIS) joint fellowship in partnership with the Infectious Diseases Society of America (IDSA) and the Centers for Disease Control and Prevention (CDC). The ID/EIS program provides an exciting new opportunity for combining training in infectious diseases and public health. New York City’s unique environment offers unparalleled exposure to emerging infectious disease and public health threats. Joint fellows will first complete two years of ID fellowship at NewYork-Presbyterian-Weill Cornell Medical Center, followed by two year of EIS fellowship at either the CDC’s headquarters in Atlanta, Georgia, or a state or local health department. Our Division’s strong connections with New York City Department of Health and Mental Hygiene and the New York State Department of Health offers ID fellows an opportunity to form critical public health connections before starting their EIS assignment. More detailed information is available on the IDSA ID/EIS program website.    

Transplant Oncology ID Program

  • Fellows interested in a career in Transplant Oncology ID will be able to gain expertise in the field during their fellowship. Fellows will rotate both on our solid organ transplant and bone marrow transplant service. Interested fellows will participate in multidisciplinary rounds with our transplant and oncology colleagues, perform pre-transplant evaluations, manage infections in the post-transplant period, and develop research projects with mentors in the field.
  • Potential mentors include:  Catherine Small, Michael SatlinPriya Kodiyanplakkal.
  • Major research areas:
    • Invasive fungal infections.
    • Multi-drug resistant bacterial infections.
    • Viral infections.
    • HIV and transplantation.
    • COVID-19 in immunocompromised hosts.
Example fellow publications
  • Isa FSaito K, Huang YT, Schuetz A, Babady NE, Salvatore S, Pessin M, vanBesien K, Perales MA, Giralt S, Sepkowitz K, Papanicolaou GA, Soave R, Kamboj M. Implementation of Molecular Surveillance After a Cluster of Fatal Toxoplasmosis at 2 Neighboring Transplant Centers. Clin Infect Dis 2016;63:565-8.
  • Jacobs SE, Lamson DM, Soave R, Huertas B, Shore TB, Ritchie EK, Zappetti D, Satlin MJ, Leonard JP, Van Besien K, Schuetz AN, Jenkins SG, St. George K, Walsh TJ. Clinical and molecular epidemiology of human rhinovirus infections in patients with hematology malignancy. J Clin Virol 2015;71:51-58.
  • McCarthy M, Rosengart A, Schuetz AN, Kontoyiannis DP, Walsh TJ. Mold infections of the central nervous system. N Engl J Med 2014; 371:150-60.

Infectious Diseases

Roy M. Gulick, M.D., Chief

Avi Bueno, Administrator
Tel: (212) 746-4914
Fax: (212) 746-8675

Infectious Diseases Fellowship Program

Matthew S. Simon, M.D., Program Director
Rosy Priya L. Kodiyanplakkal, M.D, Associate Program Director
Ole Vielemeyer, M.D., Associate Program Director

Lizzette Checo, Program Coordinator
1300 York Avenue, A-421
New York, NY 10065
Tel: (212) 746-7602
Fax: (212) 746-8675