Education:
B.A. Dartmouth College (2015)
Ph.D. Stony Brook University (2023)
Current Position:
8th Year MSTP
4th Year Medical Student
Advisor:
Vincent Yang
Joel Saltz (Co-Mentor)
Graduate Program:
Biomedical Informatics
Research Interest:
My interests are in utilizing computational histopathological approaches for the characterization of colitis mouse models with a focus on the interplay between local tissue cues and immune cell interactions. Histology captures a visual snapshot of the cascade of events that have occurred to that point in time, yet histological phenotypes remain underutilized in colitis mouse model characterizations. I hope to assess whether histological phenotypes can be defined and aggregated across multiple, well-controlled colitis mouse models to generate a more comprehensive murine representation of clinical IBD histology than from single models.
Publications:
Kobayashi S., Sullivan, S., Bialkowska A.B., Saltz J.H., Yang V.W. (2023). Computational immunohistochemical mapping adds immune context to histological phenotypes in mouse models of colitis. Scientific Reports. doi: 10.1038/s41598-023-41574-8.
Gupta R., Kaczmarzyk J., Kobayashi S., Kurc T., Saltz J.H. (2023). Artificial Intelligence for Science: A Deep Learning Revolution. Chapter 19. AI and Pathology: Steering Treatment and Predicting Outcomes; p. 337-353. doi: 10.1142/13123. (Book Chapter).
Kobayashi S., Shieh J., Ruiz de Sabando A., Kim J., Liu Y., Zee S.Y., Prasanna P., Bialkowska A.B., Saltz J.H., Yang V.W. (2022). Deep learning-based approach for the characterization and quantification of histopathology in mouse models of colitis. PLoS One. doi: 10.1371/journal.pone.0268954.
Fassler J., Torre-Healy L.A., Gupta R., Hamilton A.M., Kobayashi S., et al. (2022). Spatial Characterization of Tumor-Infiltrating Lymphocytes and Breast Cancer Progression. Cancers. doi: 10.3390/cancers14092148.
Shieh J., Chu T.H., Liu Y., Kim J., Ruiz de Sabando A., Kobayashi S., Zee S.Y., Sheridan B.S., Bialkowska A.B., Yang V.W. (2022). KLF5 protects the intestinal epithelium against Th17 immune response in a murine colitis model. JCI Insight. doi: 10.1172/jci.insight.153488.
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.
