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Itai Yanai

Itai Yanai, PhD

Scientific Director, Applied Bioinformatics Laboratories

Professor, Department of Biochemistry and Molecular Pharmacology

cancer, computational biology, developmental genetics, genomics, microbiome, systems biology, single-cell transcriptomics, gene expression atlas construction, genome evolution

Our research revolves around studying dynamic systems including tumorigenesis, host-pathogen interactions, and embryonic development through the lens of global gene expression. Our research accomplishments include providing molecular evidence that embryogenesis is punctuated (rather than gradual) and that ventral enclosure is the nematode phylotypic stage (Dev. Cell 2012). We proposed that endoderm was the first germ layer to evolve (Nature, 2015). Studying species from ten animal phyla we revealed a universal ‘mid-developmental transition’ during embryogenesis (Nature, 2016). We showed that developmental constraints underpin the phylotypic stage in nematodes (Nature Ecology and Evolution, 2017). In 2012, my lab published CEL-Seq, one of the first methods for single-cell RNA-Seq, and one that has been recognized as the most sensitive and robust. We recently published CEL-Seq2, a significant improvement. We also published the first integration of spatial transcriptomics with single-cell technology to create a tumor map (Nature Biotechnology, 2020). As a postdoc, I reported a relationship between gene duplication and alternative splicing (Nature Genetics, 2005) and my lab further revealed that a gene’s length and expression level together control its fate of either accumulating splice variants or multiplying by gene duplication (Genome Research 2014). We revealed a catalog of cancer cell states that recur across tumor types and form specific interactions with the tumor microenvironment (Nature Genetics, 2022). Also, we recently discovered a mechanism – ‘transcriptional scanning’ – to explain the widespread gene expression present in the testis by reducing the germline mutation rate while enabling a select set of genes to diverge faster over evolutionary time-scales (Cell, 2020).



Academic office

@ItaiYanai, 435 East 30th Street

8th Floor, Room 817

New York, NY 10016

Lab Website
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These focus areas and their associated publications are derived from medical subject headings from PubMed.
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Scientific Director, Applied Bioinformatics Laboratories

PhD from Boston University

Pountain, Andrew W; Jiang, Peien; Yao, Tianyou; Homaee, Ehsan; Guan, Yichao; McDonald, Kevin J C; Podkowik, Magdalena; Shopsin, Bo; Torres, Victor J; Golding, Ido; Yanai, Itai

Nature. 2024 Feb; 626(7999):661-669

Cole, Alison G; Hashimshony, Tamar; Du, Zhuo; Yanai, Itai

eLife. 2024 Jan 29; 12:

Pountain, Andrew W.; Jiang, Peien; Yao, Tianyou; Homaee, Ehsan; Guan, Yichao; McDonald, Kevin J.C.; Podkowik, Magdalena; Shopsin, Bo; Torres, Victor J.; Golding, Ido; Yanai, Itai

Nature. 2024 Jan 01; ?-?

Adler, Frederick R; Anderson, Alexander R A; Bhushan, Abhinav; Bogdan, Paul; Bravo-Cordero, Jose Javier; Brock, Amy; Chen, Yun; Cukierman, Edna; DelGiorno, Kathleen E; Denis, Gerald V; Ferrall-Fairbanks, Meghan C; Gartner, Zev Jordan; Germain, Ronald N; Gordon, Deborah M; Hunter, Ginger; Jolly, Mohit Kumar; Karacosta, Loukia Georgiou; Mythreye, Karthikeyan; Katira, Parag; Kulkarni, Rajan P; Kutys, Matthew L; Lander, Arthur D; Laughney, Ashley M; Levine, Herbert; Lou, Emil; Lowenstein, Pedro R; Masters, Kristyn S; Pe'er, Dana; Peyton, Shelly R; Platt, Manu O; Purvis, Jeremy E; Quon, Gerald; Richer, Jennifer K; Riddle, Nicole C; Rodriguez, Analiz; Snyder, Joshua C; Lee Szeto, Gregory; Tomlin, Claire J; Yanai, Itai; Zervantonakis, Ioannis K; Dueck, Hannah

Cell systems. 2023 Apr 19; 14(4):252-257

Avital, Gal; Kuperwaser, Felicia; Pountain, Andrew W; Lacey, Keenan A; Zwack, Erin E; Podkowik, Magdalena; Shopsin, Bo; Torres, Victor J; Yanai, Itai

Cell reports. 2022 10 11; 41(2):111477

Barkley, Dalia; Moncada, Reuben; Pour, Maayan; Liberman, Deborah A; Dryg, Ian; Werba, Gregor; Wang, Wei; Baron, Maayan; Rao, Anjali; Xia, Bo; França, Gustavo S; Weil, Alejandro; Delair, Deborah F; Hajdu, Cristina; Lund, Amanda W; Osman, Iman; Yanai, Itai

Nature genetics. 2022 Aug; 54(8):1192-1201