Research

Understanding disease through evolutionary biology and single-cells.

The Yanai Lab is located in NYU’s School of Medicine in the New Science Building.

Our current main interests are:

  1. Single-cell RNA-Seq. Our lab developed CEL-Seq, a popular method for single-cell RNA-Seq that is highly-multiplexed and uses linear amplification by in vitro transcription. We have shown that our latest CEL-Seq2 protocol is the most sensitive method for singe-cell transcriptomics. We have also adapted this method to capture intracellular bacterial pathogens and have rendered it high-throughput for studying thousands of cells.
  2. Cancer gene expression programs: We are studying the hallmarks of cancer using single-cell RNA-Seq by analyzing different tumor types as evolving developmental systems as well as drug resistance in cancer cell lines.
  3. Host-pathogen interactions and microbiomes: We recently developed a single-cell RNA-Seq method called scDual-Seq that can study host and pathogen transcriptomes at the level of individual cells. We are using scDual-Seq to study infection across diverse pathogens. We also search for general principles driving microbiome differences between disease and healthy populations.
  4. Spatial gene expression atlas construction: We recently developed an approach that integrates spatial transcriptomics and single-cell RNA-Seq. We are using this approach now to study cancer and pathogen infection.
  5. Genome evolution: Studying gene expression during spermatogenesis, led us to propose that ‘transcriptional scanning’ in the testes reduces the germline mutation rate while enabling a select set of genes to diverge faster over evolutionary time-scales.
  6. Computational methods: We have recently developed a computational approach to denoise single-cell RNA-Seq data.