Single-cell Analysis

Pathogenic bacteria can reside in a mammalian host for a life-long period and chronic carriers form a reservoir leading to recurrent infections. Despite the importance of chronic infections for public health, how a subset of pathogens escape the host’s immune surveillance and how the host contains the spread of bacteria are still poorly understood. Scientists within the Single-Cell Analysis group develop and use single-cell transcriptomics and computational approaches to decipher the microenvironments of individual pathogens and ultimately their functional consequences on infection outcome.


Selected Publications

Cochain C*, Vafadarnejad E*, Arampatzi P, Pelisek J, Winkels H, Ley K, Wolf D, Saliba AE*, Zernecke A*
Single-cell RNA-seq reveals the transcriptional landscape and heterogeneity of aortic macrophages in murine atherosclerosis
Circulation Res 2018, DOI: 10.1161/CIRCRESAHA.117.312509

Saliba AE, C Santos S, Vogel J
New RNA-seq approaches for the study of bacterial pathogens
Curr Opin Microbiol 2017, 35:78-87

Saliba AE, Li L, Westermann AJ, Appenzeller S, Stapels DA, Schulte LN, Helaine S, Vogel J
Single-cell RNA-seq ties macrophage polarization to growth rate of intracellular Salmonella
Nature Microbiol 2016, 2:16206

Saliba AE, Vonkova I, Deghou S, Ceschia S, Tischer C, Kugler KG, Bork P, Ellenberg J, Gavin AC
A protocol for the systematic and quantitative measurement of protein-lipid interactions using the liposome-microarray-based assay
Nature Protoc 2016, 11(6): 1021-1038

Vonkova I*, Saliba AE*, Deghou S, Anand K, Ceschia S, Doerks T, Galih A, Kugler KG, Maeda K, Rybin V, van Noort V, Ellenberg J, Bork P, Gavin AC
Lipid Cooperativity as a General Membrane-Recruitment Principle for PH Domains
Cell Rep 2015, 12(9): 1519-1530

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