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 assays 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.
Applied Bioinformatics Core (ABC)
ABC performs project-based specialized analysis with various research groups that span a wide range of scientific topics. Our group has extensive expertise in analyzing data from diverse types of genomic assays and building customized pipelines. Examples of several recent projects include:- In collaboration with the Schietinger lab at MSKCC and the Philip lab at Vanderbilt we contributed to several studies investigating autoreactive CD8 T cells in Type I diabetes mouse models and dysfunctional CD8 T cells in tumor microenvironment.
- Our group has extensive expertise in the analysis of single cell modalities such as scRNA-seq, scATAC-seq T/B-cell receptors, sc methylation, CITE-seq, as well as spatial transcriptomics platforms (Xenium, Visium, CosMX, COMET and more). We have a track-record of highly successful and productive research projects in immunology, stem cell biology, cardiology and cancer biology.
- In close collaboration with Brad Jones' group we are studying the mechanism of HIV resistance to immune response and HIV latency models.
Research Group
Our independent research projects, that are led by students and post-docs in the group, are centered on the development and application of statistical and machine learning approaches towards new biomedical discoveries. Our algorithmic work addresses specific analytical challenges that are common in our projects. One such example is deep learning framework for cross-species comparison of single cell data. Our collaborative projects are broadly grouped in two major biomedical categories: cancer genomics and stem cell biology.Cancer Genomics
In this work we are studying mechanisms of initiation and development of malignancies as well as immunotherapy approaches. In collaboration with physicians and researchers at WCM and MSKCC we are engaged in several projects studying the immune microenvironment of GI tumors and sarcoma tumorigenesis, examples include:- In collaboration with Manish Shah we are using single-cell and spatial profiling approaches to profile the tumor immune microenvironment (TIME) in several GI tumors undergoing checkpoint inhibition therapy and correlating with treatment response.
- 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 advanced 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 cell models. In these projects we are studying the differentiation processes of pluripotent stem cells to mature dopamine neurons and the effects of cellular aging on neurodegenerative diseases.- Modeling late onset neurodegenerative diseases using iPSC and induced aging phenotype. Using detailed genomic and epigenomic profiling of aged fibroblasts and neurons 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.
- Integration of single cell data towards cellular atlas of fetal and adult midbrain.