Single Cell

“Network Inference with Granger Causality Ensembles on Single-Cell Transcriptomic Data” by Atul Deshpande, Li-Fang Chu, Ron Stewart, Anthony Gitter. https://doi.org/10.1101/534834 I selected this article for review for four reasons: I work with single-cell RNA-Sequencing (scRNA-seq) data quite a bit. I was curious to learn more about methods related to infer gene regulatory networks using single-cell data. I was curious to learn how the authors were benchmarking their results from the network reconstruction algorithm. »

Update: This paper has now been published at Nature Biotech “Panoramic stitching of heterogeneous single-cell transcriptomic data” by Brian L Hie, Bryan Bryson, Bonnie Berger. https://doi.org/10.1101/371179 I selected this article for review for three reasons: I work with single-cell RNA-Sequencing (scRNA-seq) data quite a bit. Methods that can integrate two or more scRNA-seq data sets (across experiments, conditions, treatments, etc) are in high demand and are actively being worked on by many groups. »

Update: This paper has now been published at Nature Communications. “Single cell RNA-seq denoising using a deep count autoencoder” by Gokcen Eraslan, Lukas M. Simon (both first-authors contributed equally), Maria Mircea, Nikola S. Mueller, Fabian J. Theis. https://doi.org/10.1101/300681 I selected this article for review for two reasons: I work with single-cell RNA-Sequencing (scRNA-seq) data quite a bit and I have a general interest in methods that remove technical sources of variation from it. »

Update: This paper has now been published in BMC Biology. “Comprehensive catalog of dendritically localized mRNA isoforms from sub-cellular sequencing of single mouse neurons” Sarah A. Middleton, James Eberwine and Junhyong Kim https://doi.org/10.1101/278648 I selected this article for review for the following reasons: In neurons, RNA localization is a fundamental way to control protein expression. To my knowledge this is the first attempt to map dendritically localized RNAs at single cell resolution The findings reported are very intriguing, in particular the potential role of SINE elements in localization of RNA to dendrites. »

This paper has now been published at PLOS Computational Biology. “Active degradation of a regulator controls coordination of downstream genes” by Nicholas A. Rossi, Thierry Mora, Aleksandra M. Walczak, and Mary J. Dunlop https://doi.org/10.1101/272120 In this article, Rossi and colleagues observed how noise develops in the expression of genes downstream of stress response activator gene MarA by manipulating MarA degradation and expression levels and then measuring variability in downstream gene expression in single cells. »