We develop computational methods for design and analysis of high-throughput functional genomic assays and perturbations, with a focus on multi-modal single-cell, spatial and genome editing technologies. We apply these methods to study regulatory genomics of cell function and cell-cell interactions in vivo, with a focus on immunology and cancer.

Examples of our past and ongoing work are presented below.

CD8 T cells form the central component of the adaptive immune system and are essential in defense against viral and bacterial infections and in tumor immunity. Better molecular characterization of CD8 T cells in different contexts is fundamentally important and can lead to improved clinical results in cancer immunotherapies, infectious diseases, autoimmunity. We performed an extensive genomic, single-cell, and transcription factor analysis of CD8 T cell functional and dysfunctional states. We now continue studying regulatory mechanisms and cell-cell interactions governing CD8 T cell activation and functional commitment across immune challenges in mouse and human using single-cell and spatial multi-omics. We are also expanding these approaches to other immune cell types.

Regulatory T (Treg) cells are critical for tolerance to self-antigens and preventing autoimmunity. Their differentiation and function are controlled by transcription factor Foxp3, but mechanistic understanding of Foxp3 role remains elusive. Using functional genomic analysis, we explored Foxp3 function and its interaction with a highly expressed closely related factor Foxp1. We are now studying the role of Foxp3 and other factors in chromatin organization and gene expression regulation in functionally heterogeneous Treg cells across tissues.

Programmable genome editing using CRISPR has tremendously advanced life sciences. To facilitate the use of this technology, especially in the noncoding genome and for batch screens, we developed GuideScan, a fully customizable CRISPR guide RNA (gRNA) design tool. We recently developed GuideScan2 with substantially expanded and new functionality for memory-efficient, parallelizable construction of high-specificity gRNA databases and user-friendly gRNA design in custom genomes. We now continue working on tools for design and analysis of CRISPR-based genome perturbations and their combinations with single-cell functional genomic assays.

Cross-linking immunoprecipitation followed by sequencing (CLIP-seq) is a family of methods for profiling sites of protein binding to RNA. In particular, CLIP has been used to identify targets of microRNAs, small non-coding RNA molecules that bind to a protein Ago2 and thus regulate gene expression post-transcriptionally. We developed a new algorithm CLIPanalyze for analysis of such data and used it for comprehensive analysis of microRNA targets in vivo in mouse embryonic stem cells, developing embryos, adult tissues and multiple cancer models. We now continue development and application of methods for studies of post-transcriptional regulation.

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