Itai Yanai, PhD

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Professor of Biochemistry and Molecular Pharmacology
Ph.D., 2002, Boston University

Yanai Lab Website
Tumor evolution, host-pathogen interactions, developmental pathways, single-cell genomics
Single-cell RNA-Seq, evolutionary and developmental biology, gene regulatory pathways, computational biology, genome evolution

Contact Information

 Contact Information
New York University School of Medicine
Alexandria Life Sciences Building, 510
430 East 29th Street. New York, NY 10016
Tel.: (646) 501-4603
Lab: (646) 501-4633
Lab Website:

Single-cell gene expression analyses of embryonic development, cancer evolution, and bacterial infection

Single-cell gene expression analyses of embryonic development, cancer evolution, and bacterial infection.

Our research occurs at the interface of gene expression, development, and evolution. We are experimental embryologists, molecular biologists, and computational biologists, and together we explore how developmental pathways evolve at the molecular level. We carry out intricate embryological experiments at the level of individual cells and apply computational approaches to explore the resulting data. Our approach is systematic, as well as comparative, and aimed at studying gene pathways across diverse animal species in order to understand the regulatory genomic architecture. At NYU’s School of Medicine, we are the founding lab of the Institute for Computational Medicine (ICM), whose goal is to harness computational approaches for fundamental and medically-relevant discoveries.

Our lab has been fascinated by the constraints imposed by evolution on animal embryogenesis and what it can teach us about development. Using systematic gene expression analyses, we provided evidence that developmental milestones punctuate gene expression and proposed that ventral enclosure is the nematode phylotypic stage. We identified the time and germ-layer of expression of all genes throughout C. elegans embryogenesis, and used this information to infer the evolutionary history of the endoderm germ layer. Studying ten phyla at the transcriptome level, we also revealed a universal ‘mid-developmental transition’ during the embryogenesis of each species, which we believe has implications for the study of animal body plans. Our lab developed CEL-Seq, a method for single-cell RNA-Seq that is highly multiplexed and uses linear amplification by in vitro transcription. CEL-Seq has become among the most applied methods that drive the single-cell biology revolution. We have shown that our latest CEL-Seq2 protocol is the most sensitive and reproducible method available for singe-cell transcriptomics. We are adapting this method to capture small RNAs and intracellular bacterial pathogens, and have rendered it high-throughput for studying thousands of cells.

Selected Publications: 

·       Levin M, Anavy L, Cole AG, Winter E, Mostov N, Khair S, Senderovich N, Kovalev E, Silver DH, Feder M, Fernandez-Valverde SL, Nakanishi N, Simmons D, Simakov O, Larsson T, Liu SY, Jerafi-Vider A, Yaniv K, Ryan JF, Martindale MQ, Rink JC, Arendt D, Degnan SM, Degnan BM, Hashimshony T, and Yanai I. The mid-developmental transition and the evolution of animal body plans. Nature. 2016. 531:637-41.

·       Hashimshony T, Senderovich N, Avital G, Klochendler A, de Leeuw Y, Anavy L, Gennert D, Li S, Livak KJ, Rozenblatt-Rosen O, Dor Y, Regev A, and Yanai I. CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq. Genome Biology. 2016 17(1):77.

·       Hashimshony T, Feder M, Levin M, Hall BK, and Yanai I. Spatiotemporal transcriptomics reveals the evolutionary history of the endoderm germ layer. Nature. 2015 519:219-22.

·       Levin M, Hashimshony T, Wagner F, and Yanai I. Developmental milestones punctuate gene expression in the Caenorhabditis embryo. Developmental Cell 2012 22:1101-8.

·       Kopelman, N, Lancet D, and Yanai I. Alternative splicing and gene duplication are inversely related evolutionary mechanisms. Nature Genetics 2005 37:588-589.