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Professional Development and Research Years (Optional)

The IU School of Medicine Department of Surgery is deeply committed to professional development and research in areas of clinical and translational sciences, global health and surgical education. Research allows the team to identify solutions to clinical problems and bring evidence-based approaches to the bedside that benefit patients.

Surgery residents have an opportunity to participate in an optional research fellowship after their second or third clinical year of residency. For those who commit to research within the department, a minimum of two years is required and completion of an advanced degree is highly encouraged. Advanced degrees pursued within Indiana University come at zero cost to the resident. Advanced degrees pursued by our surgery residents at IU School of Medicine include:

Residents who pursue our Global Health Research Fellowship are expected to complete their Master's in Public Health (MPH) through the Richard M. Fairbanks School of Public Health, which is also at no cost to the resident.

Residents who pursue the Surgical Education Research Fellowship are required to complete a Master of Health Professions Education (MHPE) program. Currently, this is not a degree that Indiana University provides, so our research fellows pursue their MPHE online through the University of Illinois-Chicago MPHE program. A stipend of up to $40,000 is provided as well as housing cost for on-site courses. Due to elevated costs with the program being out-of-state, residents who pursue this opportunity do incur a cost of around $10,000. Up to 8 elective courses can be taken at IU School of Medicine, which can decrease the overall cost to the resident.

Professional Development and Resident Research in Surgery

Director of Resident Research, Troy Markel, MD, is available to help answer questions about research fellowship opportunities and assistance in tailoring these experiences to the individual resident’s experience, interests and career ambitions.

Email Dr. Markel

Current Research Opportunities

  • Surgical Education Research Fellowship

    The Surgical Education Research Fellowship in the Department of Surgery was established in 2017 and aims to develop education leaders who will contribute to the advancement of surgical education at IU and nationally through innovation and high impact research output. The fellows work under the mentorship of Dimitrios Stefanidis, MD, PhD and E. Matthew Ritter, MD, MPHE, and are part of a larger education research group that includes surgical educators such as the residency and skills lab directors, research coordinators, research residents, international research fellows, the anesthesia director of education, medical students and other collaborators.

    During the program, fellows expand their knowledge and skills in surgical education and engage in challenging and data-driven education research and teaching activities. Fellows are expected to lead innovative research projects within the Department of Surgery and School of Medicine and produce several high-quality presentations, publications and grant submissions. This two year experience provides fellows with the necessary skills, support and a nurturing environment to empower them to excel in education research and become surgical education leaders. 

  • Surgical Education Numbered Trials with IU SOQIC

    The Surgical Education Numbered Trials research fellowship offers a funded two year on site fellowship focusing on surgical outcomes, health services, health policy, and surgical education through the Indiana University Surgical Outcomes and Quality Improvement Center (IU SOQIC). We are currently seeking applicants for our first research fellow within our department to start in July 2024.

    The overall goal of the research fellowship is to help prepare surgical residents for successful careers post residency in areas of surgical health services and outcomes research.  This pathway will allow for residents to gain firsthand experience in research methodology and practical applications for current and future process improvement needs. The IU SOQIC research fellowship will allow for collaboration with Northwestern University SOQIC as well as team members from The SECOND Trial*. The SECOND Trial is a prospective, pragmatic cluster-randomized trial examining how we can improve the learning environment and well-being of residents led by co-PIs, Drs. Karl Bilimoria at Indiana University and Dr. Yue-Yung Hu at Northwestern University.

    Residents participating in this pathway will also be expected to pursue a Master's Degree in Clinical Science from Indiana University School of Medicine at no cost to the resident.

    • Note: If an applicant already has an advanced/similar level degree, they will not be expected to enroll into an advanced program.

    *The SECOND Trial is made possible by partnerships with the Accreditation Council for Graduate Medical Education (ACGME), American College of Surgeons (ACS), American Board of Surgery (ABS), Association of Program Directors in Surgery (APDS), Association of American Medical Colleges (AAMC), and the Society of Surgical Chairs (SSC). The study is funded by the ACS and the ACGME.

  • Regenstrief Institute General HSR Resident Opportunity with IU SOQIC

    The Regenstrief General HSR Resident Opportunity offers a two-year research fellowship in surgical outcomes, health services, quality improvement, implementation science, health policy, and surgical education research for IUSM surgical residents starting July 2024 in Indianapolis.

    IU SOQIC research fellows will work with a team of faculty mentors of their choosing to conduct research in their specialty interests, and will receive training in informatics, technical skills, and relevant clinical disciplines. Research fellows will participate in Regenstrief early career investigator activities, including the writing group, Faculty Development Lecture Series, HSR and Institute-wide works-in-progress meetings.

    Research fellows will earn a master’s degree that best suits their needs through one of the programs offered at Indiana University, most often a master’s in clinical research that is tailored for surgical resident research fellows interested in health services, outcomes, quality improvement, and implementation science.

    Interested residents should to request an application, or if you have any questions about the program.

  • Global Health Fellowship with Department of Surgery and AMPATH

    Participants in the Masters in Public Health in Global Health program spend the first year completing Master’s in Public Health classwork and the second year at Moi University in Eldoret, Kenya. Due to the course workload, residents in this program are not be required to participate in lab work during the first year. The second year may require six to nine credit hours to be completed online, but residents work with JoAnna Hunter-Squires, M.D. during the second year in pursuit of research in the realm of surgery and global health.

    Participants are eligible to apply for Fulbright Scholar status with this fellowship.

  • Laboratory of Burcin Ekser, MD, PhD, Transplant Surgery

    The Xenotransplantation Research laboratory (Ekser Lab) has a long history at the Department of Surgery, IUSM. The lab has been very productive over the last decade focusing on inter-species immunology, coagulation dysregulation, genetic engineering, and the production of genetically-engineered pigs, having published several seminal papers with the help of students, residents and post-doctoral researchers. As an active transplant and immunology lab, we are engaged in translational projects focused on transplant immunology, creation of desirable genetic combination in porcine cells, which can be used to generate suitable organs for xenotransplant (e.g. Gal-knockout, CMAH gene-knockout, B4GalNT2 gene knockout pigs). We have recently identified for the first time porcine tetraspanins CD37 and CD81 as novel nonGal xenoreactive antigens.

    Most recently, we have also introduced the use of ‘scaffold-free’ 3D-bioprinting of genetically-engineered pig cells, as well as human (normal and/or cancer) cells with the help of 3D-Bioprinting Core of IUPUI. We have so far bioprinted porcine liver models using the 3D-Bioprinter and presented at the Joint IUPUI-Johns Hopkins University 3D-Bioprinting Symposium and at the International Xenotransplantation Association Meeting. On a daily basis, we are engaged in identifying novel xenoantigens using genetic engineering (CRISPR/cas9), immunology, coagulation dysregulation (Chronolog Aggregometer Technology) and 3D-bioprinting of porcine and/or human cells.

  • Laboratory of Al Hassanein, MD, MMSc, Plastic Surgery

    The lab is focuses on two projects (1) lymphedema and (2) breast implant capsular contracture. Lymphedema is a morbid disease most often breast cancer related. There is no cure and it is characterized by chronic, progressive limb enlargement. Capsular contracture is a disease of scar/fibrosis of breast implants characterized clinically by distortion and pain. The goals of the lab are to determine the molecular etiology of lymphedema and the pathogenic basis of capsular contracture. Both projects involve translational research analyzing surgical specimen. The lymphedema study also comprises a rodent tail model. The lab is a collaboration with Dr. Mithun Sinha and Dr. Chandan Sen of the Indiana Center for Regenerative Medicine and Engineering.

  • Laboratory of Savita Khanna, PhD

    Dr. Savita Khanna’s lab has long-standing experience in conducting and leading in vitro and in vivo studies related to mechanisms of tissue injury and interventional rescue. One of the key areas being investigated by Khanna’s laboratory is brain injury, including neurodegeneration and therapeutics. Another major project in her lab focuses on diabetic peripheral neuropathy and modes of rescuing the condition. To address scientific questions related to ongoing projects, the lab is using both in vitro (cell lines and primary cells culture) and in vivo models.

  • Laboratory of Leonidas Koniaris, MD, and Teresa Zimmers, PhD

    Under the direction of Leonidas Koniaris, MD and Teresa Zimmers, PhD, the Cachexia Lab studies mechanisms of tissue growth control and systemic adaptation to acute or chronic organ injury. In practice this has led to a focus on organ injury and regeneration and the pathological perversion of that process—cancer, and the effects of those processes on distant tissues, particularly skeletal muscle and adipose tissue, but also liver, bone and the hematopoietic compartment. We are particularly interested in how growing organs and tumors signal on liver, muscle and adipose tissue to change their metabolism and yield substrates for growth, including amino acids and fatty acids. A regenerating liver or skin burn requires the catabolism of striated muscle and fat—proteolysis and lipolysis, as well as bone loss, in order to fuel the innate immune response and cell proliferation and healing. Some tumors, particularly pancreatic cancer, pervert this adaptive response and lead to a maladaptive and ultimately fatal wasting syndrome. Understanding the cross-talk among the injured organs/tumor and the periphery will allow us to identify targets to manipulate and prevent systemic wasting and debilitation and accelerate recovery after injury and in patients with cancer.

    The laboratory’s research spans cultured cell models to mouse models of human disease to translational studies using prospectively collected human data and specimens. Directed studies interrogating specific pathways are balanced with discovery approaches generated through transcriptomic and proteomic assays. The lab is newly engaged in the identification of small molecules that influence muscle wasting and cachexia, and the production of biologics to inhibit specific protein targets. Pathways of interest include the hedgehog/SMO/GLI, Hippo/YAP, IL-6 family of cytokines, the TGF-beta superfamily and other secreted and circulating growth factors, and lipid modulators of cell growth and wasting.

  • Laboratory of Chandrashekar Kubal, MD

    The mission of the Kubal translational research laboratory is to improve liver transplant outcomes. The laboratory is one aspect of a multidiscipline group of professionals focused on advancing treatments for liver disease. The research within the Kubal laboratory focuses on important complications after liver transplantation, mainly as a result of ischemia reperfusion injury of the liver. Some of the aspects of this phenomenon are being addressed in clinical research with the use of normothermic machine perfusion of human livers as a multicenter clinical trial. However, in the laboratory we are focusing on the remote kidney injury as a result of liver ischemia reperfusion injury.

    Additionally, the liver transplant program has a large database that includes more than 2000 liver transplant patients, which is used extensively for clinical research.
    Dr. Kubal's  clinical trials include immunosuppression related trials.

  • Laboratory of Troy A. Markel, MD, Pediatric Surgery

    The Markel lab has been in existence for the last seven years and primarily focuses on finding novel therapies for the treatment of intestinal ischemia and necrotizing enterocolitis. The primary focus is on stem cell therapy for treatment, and understanding the mechanistic pathways that these cells utilize to bring about end organ protection. Our previous studies have suggested that stem cells can decrease mortality by nearly 60 percent in animal models following intestinal ischemia. In addition, stem cells appear to improve intestinal perfusion, limit mucosal injury, improve tight junction integrity and limit the local inflammatory process. We believe that these cells protect the bowel by releasing key paracrine mediators, such as hydrogen sulfide gas, that work to promote mesenteric vasodilation by interacting with the nitric oxide signaling pathway.

    Additional areas of focus include the differences between adults and children in their response to trauma. There appears to be a loss of childhood protective effects in the adult response to trauma. Our data suggests that this might be due to an impairment of stem cell mobilization from the bone marrow in adults. Current investigations surround the use of animal models to corroborate human data that has already been procured.

  • Laboratory of Michael P. Murphy, MD

    Dr. Murphy's research consortium includes four senior scientists (PhD), two technicians and three study coordinators housed in 1,100 square feet of space in the R3 (Walther Hall) and the Richard Roudebush VAMC. The lab also serves as the 3D Bioprinting Core for the VA Research faculty. Dr. Murphy's expertise is in developing novel therapeutic strategies for cardiovascular disease in the lab and rapidly translating these discoveries into first-in-man investigator-designed clinical trials. The lab collaborates with researchers at Harvard, MIT, and Stanford.

  • Laboratory of Dr. Hari Nakshatri, PhD, General Surgery

    Dr. Nakshatri studies the molecular drivers of therapy resistance in breast cancer. His laboratory was the first to identify the role of the protein complex, NF-kappaB, which controls genes that respond to environmental stress and infection in triple negative breast cancer. He also identified biomarkers that may predict response to anti-estrogen therapy. Utilizing normal breast tissues of women of different ethnic background, his group has discovered genetic ancestry-dependent heterogeneity in the normal breasts, which has important implications on how tumors are characterized for genomic abnormalities. His recently published studies may provide insights into why hormone-responsive breast tumors are more common in women of European ancestry and why triple negative breast cancers are aggressive in women of African ancestry. Additionally, his group is mapping the normal breasts as well as the breasts of BRCA1/2 mutation careers at single cell resolution using single cell sequencing techniques. These efforts may lead to classification of breast cancer based on “cell-of-origin” of tumor. He is using systems biology approaches to understand organ specific breast cancer metastasis and developing patient-derived tumor models that reflect organ-specific metastasis and therapy resistance.

  • Laboratory of Milan Radovich, PhD, General Surgery

    The Radovich laboratory focuses on the use of genomics in translational oncology. In particular, our research concentrates on the use of genomics for precision medicine, clinical trials, genomically-informed drug combinations, circulating biomarkers of cancer detection, companion diagnostics, and novel bioinformatic pipelines for cancer genome analyses. Our lab has long standing-expertise in the research of triple-negative breast cancer, thymic malignancies, and cancer precision medicine. In addition, Dr. Radovich leads the IU Health Precision Genomics Program, a clinical service line that uses cancer genomics to guide therapy for metastatic cancer patients. Research endeavors from this clinical program include: biomarkers of treatment response; understanding germline genetic variation and cancer predisposition; and genomically-directed clinical trials.

  • Laboratory of C. Max Schmidt, MD, PhD

    The Schmidt laboratory performs “bench-to-bedside” or translational research to discover novel biomarkers and targeted treatments for patients with pancreatic neoplasia. Our earlier work involved the use of multiple animal models to investigate the role of inflammatory pathways (i.e. cyclooxygenase-2 (COX-2), transcription factor nuclear factor-κB [NF-κB]) in pancreatic cancer and identify potential therapeutics. More recently, our research has focused on the discovery of biomarkers that can aid the early detection of pancreatic cancer as well as differentiate benign from potentially malignant pancreatic cysts. An invaluable resource available for these biomarker studies is the IU Pancreas Tissue Fluid Bank, established by Dr. Schmidt in 2001. Samples from >1500 patients with pancreatic disease are currently stored in the bank, including plasma/serum, bile, pancreatic cyst/duct fluid, urine and tissue. Additionally, longitudinal samples are being collected from patients “at risk” of pancreatic cancer at the IU Pancreatic Cancer and Cyst Early Detection Center (PCC-EDC,, directed by Dr. Schmidt. Ongoing global analyses include metabolomics/proteomics.

    Residents joining the laboratory have the opportunity to perform clinical outcomes research and translational research projects as outlined below. Residents submit abstracts for oral presentation at regional/national surgical meetings and publish their work in surgical or basic science journals.

  • Laboratory of Dimitrios Stefanidis, MD, PhD

    MIS/ Bariatric Research Fellowship

    This MIS/Bariatric Research Fellowship  in the MIS/ bariatric section of the Department of Surgery at Indiana University School of Medicine aims to provide a comprehensive clinical outcomes research experience in minimally invasive and bariatric surgery to a resident. Along with the research resident, the team includes a PhD psychologist, one data manager, a clinical fellow, a research nurse, an international research fellow, medical students, several MIS/ bariatric surgeons and other ad hoc members. The research resident obtains a Master's in biostatistics to enrich his/her research knowledge and skills, and engages in a number of clinical outcome research and process improvement projects. Their work is presented at a variety of surgical meetings and published in high impact surgical journals. This 2-year experience provides residents with the necessary skills, support and a nurturing environment that empowers them to excel in clinical research and become leaders in MIS bariatric surgery.

  • Laboratory of Nicholas J. Zyromski, MD, Surgical Oncology

    Dr. Zyromski’s laboratory program was established in 2006 and has focused on basic, clinical and translational research related to pancreatic disease since its founding. The current focus of the laboratory is directed toward understanding the natural history of and developing treatments for patients with necrotizing pancreatitis. This focus involves both clinical and translational research. Dr. Zyromski has mentored 19 research residents since 2006.