Separating the signal from the noise in scRNA-Seq data (new paper!)

tl;dr - We've developed a smoothing algorithm that makes the analysis of high-throughput single-cell RNA-Seq a lot easier. The algorithm effectively removes technical noise while largely preserving biological heterogeneity. You can read the paper on bioRxiv and find reference implementations in Python/R/Matlab on github. In the YanaiLab, we love single-cell RNA-Seq data, and we're proud... Continue Reading →

Computational biologists: moving to the driver’s seat

Computational biologists: moving to the driver's seat Itai Yanai and Eva Chmielnicki Genome Biology201718:223   Published: 23 November 2017 Abstract The recent shift of computational biologists from bioinformatics service providers to leaders of cutting-edge programs highlights the accompanying cultural and conceptual changes that should be implemented by funding bodies and academic institutions.


Genome Biol. 2017 Oct 27;18(1):200. doi: 10.1186/s13059-017-1340-x. scDual-Seq: mapping the gene regulatory program of Salmonella infection by host and pathogen single-cell RNA-sequencing. Avital G1,2, Avraham R3,4, Fan A3, Hashimshony T2, Hung DT3,5,6, Yanai I7. The interaction between a pathogen and a host is a highly dynamic process in which both agents activate complex programs. Here, we introduce a single-cell RNA-sequencing method,... Continue Reading →

Development and evolution through the lens of global gene regulation

Trends in Genetics has published this review on the Yanai lab's contributions to evo-devo. Evolution and development are two inherently intertwined processes. As the embryo develops it does so in ways that both reflect past constraints and bias the future evolution of the species. While research exploiting this insight typically studies individual genes, transcriptomic analyses have sparked... Continue Reading →


Several years ago, we presented the BLIND method which is able to determine the temporal order of transcriptomes in large datasets, thus allowing for the massive collection of samples, to be ordered at the analysis stage: Anavy L, Levin M, Khair S, Nakanishi N, Valverde SF, Degnan BM, and Yanai I. BLIND ordering of large-scale... Continue Reading →

Developmental constraints

Zalts H and Yanai I. Developmental constraints shape the evolution of the nematode mid-developmental transition. Nature Ecology and Evolution 2017 doi:10.1038/s41559-017-0113 News & Views by Ronald E. Ellis Since the works of Ernst Haeckel and Karl Ernst von Baer in the 19th century, it has been recognized that a stage in mid-embryogenesis is remarkably conserved... Continue Reading →

Rob Knight Seminar

  We are pleased to welcome Rob Knight for a seminar on Tuesday, September 13, 2016 for the inaugural lecture of microbiome seminar series. Rob Knight Professor, Departments of Pediatrics and Computer Science & Engineering University of California at San Diego “Spatial and temporal patterning of the human microbiome" 1:00pm – 2:00pm Refreshments at 12:30 Skirball... Continue Reading →

NYU’s new Institute!

The Institute for Computational Medicine NYU School of Medicine’s Institute for Computational Medicine applies computational biology to medical challenges, tackling systems that are vast, complex, and dynamic. Our focus is on the fields of cancer biology, host-pathogen interactions, adaptive immune systems, and genetic diseases. We recognize opportunities in these disciplines require expertise in big-data analyses,... Continue Reading →

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