Our research interest is the development of computational genomic tools for the study of human diseases and cellular development. We focus on integrative analyses of genomic and epigenomic data generated by high-throughput sequencing to address specific questions related to disease progression, treatment response, stem cell differentiation and neurological processes. Our research is performed by two closely interacting groups. The Applied Bioinformatics Core performes project-based specialized analysis with various research groups that span a wide range of scientific topics. The group has extensive expertise in analyzing data from diverse types of genomic assays and building customized pipelines. Visit our website for more details about the core and sample publications. Our independent research projects that are led by students and post-docs in the group are broadly grouped in two major categories: cancer genomics and stem cell biology.
Cancer Genomics
In this work we are studying mechanisms of initiation and development of GI malignancies. In collaboration with physicians and researchers at WCM and MSKCC we are engaged in several projects studying the impact of microbial content and host immune response on gastric cancer, characterization of the immune microenvironment of GI tumors and sarcoma tumorigenesis, which are outlined below:- The role of microbiome in gastric tumors. In collaboration with Manish Shah we are studying the gastric microbial composition
in patients with active H.pylori infection and gastric tumors and correlating those with immune states.
- The Immune microenvironment of esophageal tumors and its role in treatment response. In another collaboration with Manish Shah
we are using single-cell approaches to profile the tumor immune microenvironment (TIME)
in esophageal cancer patients undergoing checkpoint inhibition therapy and correlating with treatment response.
- The Initiation and development of Undifferentiated Pleomorphic Sarcoma (UPS). In collaboration with
Tuomas Tammela we are studying tumorigenesis of UPS tumors. In this project we are using
a novel mouse model of UPS, PDX models, and advance single-cell approaches to investigate the cell of origin and tumorigenesis of UPS.
Stem Cell Biology
In this branch of our work we are collaborating with the group of Lorenz Studer (MSKCC) to study neurodegenerative diseases using stem cells models. In these projects we are studying the differentiation processes of pluripotent stem cells to mature dopamine neurons and the effects of aging on neurodegenerative diseases.- Modeling late onset neurodegenerative diseases using iPSC and induced aging phenotype. Using detailed genomic and epigenomic profiling of
aged and rejuvenated cells (by iPS reprogramming) we aim to identify aging markers that contribute to neurodegeneration.
- Development of new differentiation approaches of stem cell derived Dopamine neurons towards regenerative therapy. This project
addresses key challenges for therapeutic application
of regenerative medicine by improving the differentiation of dopamine subtypes and increasing the efficacy of in vivo engraftment of neurons.
- New characterization of näive-to-prime pluripotent state. In a recent study
we identified a new, stable näive-to-prime intermediate pluripotent state
that is characterized by lipid biosynthesis, which resembles in vivo pre-implantation epiblast.