Single-cell messenger RNA sequencing reveals rare intestinal cell types

By Dominic Grün, A. Lyubimova, L. Kester, K. Wiebrands, O. Basak, Nobuo Sasaki, Hans Clevers, Alexander van Oudenaarden. Nature, 2015

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SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation (2016, methodology): “This enables several analyses such as the identification of cell types [2, 3], especially of rare cells [4, 5], and the estimation of cellular lineages [6, 7].”
Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq. (2016, neutral): “…2014), including in cells of the brain, gut, liver, pancreas, bone marrow, as well as immune cell types in various tissues and disease states (Gru¨n et al., 2015; Gury-BenAri et al., 2016; Jaitin et al., 2014; Junker and van Oudenaarden, 2014; La Manno et al., 2016; Paul et al., 2015;…”
COMPREHENSIVE CLASSIFICATION OF RETINAL BIPOLAR NEURONS BY SINGLE-CELL TRANSCRIPTOMICS (2016, neutral): “Because of its long running time (due to the gap statistic calculations), RaceID could only be run on the 5,000-cell dataset (2123 genes selected), and took 4 days to complete on an Intel(R) Xeon(R) CPU, 2.67GHz, 100 GB of memory.”
Long-Term Expansion of Functional Mouse and Human Hepatocytes as 3D Organoids. (2018, positive): “Hepatocytes in liver lobules differentially express zonation markers along the pericentral (PC)-to-periportal vein (PP) axis (Halpern et al., 2017; Burke et al., 2009; Gru¨n et al., 2015).”