Soma Kobayashi

Image:Soma new


B.A. Dartmouth College (2015)

Current Position:

5th Year MSTP

3rd Year Grad Student


Primary Mentor: Dr. Vincent Yang

Co-Mentor: Dr. Joel Saltz

Graduate Program:

Biomedical Informatics

Research Interest:

My major interest is in immunology, and my previous work focused on the context of cancer. During my gap years, I had the chance to assist on a study that aimed to characterize both the immune response and the specific tumor-driven changes to the immune compartment that occurred in the lesions of early stage (Stage I/II) human lung adenocarcinoma patients. From here, I developed a desire to study local tissue cues of the tumor microenvironment and the intercellular interactions that occur within this niche.

Now in my PhD years, I will be moving away from cancer research and focus instead on IBD. However, my goal is still to continue looking into the interplay that can occur between local tissue cues and immune cell interactions. Instead of the tumor microenvironment, I will be shifting my focus to the intestinal mucosal niche that is shaped by the acute flares and chronic inflammation present in IBD. In combination with cellular and molecular biology techniques, I plan to utilize programmatic spatial analysis of histological specimens to further understand and dissect the inflammatory response in these conditions.


Kobayashi S., Saltz JH, Yang VW. (2021). State of machine and deep learning in histopathological applications in digestive diseases. World Journal of Gastroenterology. doi: 10.3748/wjg.v27.i20.2545. (Review)

Shieh J., Kobayashi S., Yang VW. (2020). Aberrant differentiation of intestinal stem cells due to inflammation-induced mitochondrial dysfunction predicts postoperative recurrence of Crohn’s disease. Digestive Medicine Research. doi: 10.21037/dmr-2020-15. (Editorial)

Casanova-Acebes M., Menéndez-Gutiérrez MP., Porcuna J., Álvarez-Errico D., Lavin L., García A., Kobayashi S., Le Berichel J., Núñez V., Were F., Jiménez-Carretero D., Sánchez-Cabo F, Merad M., Ricote M. (2019). RXRs are required for neonatal expansion and maintenance of the serosal macrophage pool and contribute to ovarian cancer progression. Nature Communications. 11(1):1655.

Rahman A.H., Lavin Y., Kobayashi S., Leader A., and Merad M. (2017) High-dimensional single cell mapping of cerium distribution in the lung immune microenvironment of an active smoker. Cytometry Part B: Clinical Cytometry. doi: 10.1002/cyto.b.21545

Lavin Y., Kobayashi S., Leader A., Amir E.D., Elefant N, Bigenwald C., Remark R., Sweeney R., Becker C.D., Levine J.H., Meinhof K., Chow A., Kim-Schulze S., Wolf A., Medaglia C., Li H., Rytlewski J.A., Emerson R.O., Solovyov A., Greenbaum B.D., Sanders C., Vignali M., Beasley M.B., Flores R., Gnjatic S., Pe’er D., Rahman A., Amit I., Merad M. (2017) Innate Immune Landscape in Early Lung Adenocarcinoma by Paired Single-Cell Analyses. Cell. doi: 10.1016/j.cell.2017.04.014.