FACULTY MEMBER

Shyam PRABHAKAR

Senior Group Leader, Computational and Systems Biology
Associate Director, Integrated Genomics

RESEARCH

Gene-Regulatory Mechanisms of Human Diseases

The majority of genetic mutations responsible for common diseases reside within gene-regulatory sequences such as enhancers, promoters and insulators. In addition, transcriptional and epigenetic dysregulation are known to drive tumorigenesis, tumor progression and drug resistance. Thus, gene regulation lies at the heart of many disease mechanisms.

The Prabhakar Lab uses a combination of high-throughput omics assays (wet-lab) and data analytics (dry-lab) to study gene-regulatory mechanisms of human diseases. In particular, we use single-cell RNA-seq, cohort-scale histone ChIP-seq and other NGS approaches to study autism, psychiatric drug response, lung and colon cancer, autoimmune disorders and host response to infection. We also develop cutting-edge algorithms and pipelines for deriving biological insights from large datasets.

Major achievements include the first single-cell transcriptomic analysis of colorectal tumors (Li, Courtois et al., Nat Genet, in press), the first study of histone acetylation changes in autism spectrum disorder (Sun, Poschmann et al., Cell 2016), the first large-scale study of disease-causing genetic variants that affect histone acetylation (del Rosario, Poschmann et al., Nat Methods 2015) and the first unified signal-processing method for peak detection in whole-genome profiling data (Kumar et al., Nat Biotechnol 2013). We have also uncovered fundamental properties of transcription factor binding to genomic DNA (Jankowski et al., Genome Res 2013) and demonstrated that H2BK20ac is a distinctive signature of enhancers and cell-type-specific promoters (Kumar, Rayan, Muratani et al., Genome Res 2016). Earlier work explored the contribution of gene regulatory elements to human origins (Prabhakar, Noonan et al., Science 2006; Prabhakar et al., Science 2008).

Jobs:
Ph.D. and Postdoctoral positions available, starting immediately

- Wet-lab: single-cell analysis of lung cancer and colorectal cancer, biomarkers, precision oncology
- Wet-lab: epigenomics of psychiatric and immune-related diseases
- Dry-lab: algorithms for NGS data analysis (single cell omics, chromatin profiling)


KEY ACHIEVEMENTS

  • 2008 First prize: poster competition at HUGO 13th Human Genome Meeting

    2001 American Physical Society Award for Outstanding Doctoral Thesis Research in Beam Physics

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