This repo is a collection of papers and notes from the Pachter Lab reading group.
So far this is a non-exhaustive list of some single cell RNA-Seq (scRNA-Seq) papers. The papers in bold are papers that I am slightly partial to covering. The papers include analytical methods, protocols, reviews, and applications.
- Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells
- Computational and analytical challenges in single-cell transcriptomics
- The Technology and Biology of Single-Cell RNA Sequencing
- Bayesian approach to single-cell differential expression analysis
- The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
- Entering the era of single-cell transcriptomics in biology and medicine
- From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing
- Full-length RNA-seq from single cells using Smart-seq2
- Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types
- The promise of single-cell sequencing
- Quantitative assessment of single-cell RNA-sequencing methods
- Reconstruction of the Mouse Otocyst and Early Neuroblast Lineage at Single-Cell Resolution
- Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq
- Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma
- Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells
- Single-cell RNA-seq reveals dynamic paracrine control of cellular variation
- Single-Cell RNA Sequencing Reveals T Helper Cells Synthesizing Steroids De Novo to Contribute to Immune Homeostasis
- Quantitative single-cell RNA-seq with unique molecular identifiers
- Accounting for technical noise in single-cell RNA-seq experiments
- Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data
- Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing
- RNA-sequencing from single nuclei
- Single-Cell Analysis Reveals that Expression of Nanog Is Biallelic and Equally Variable as that of Other Pluripotency Factors in Mouse ESCs
- Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells
- Single-cell sequencing-based technologies will revolutionize whole-organism science
- Smart-seq2 for sensitive full-length transcriptome profiling in single cells
- Two methods for full-length RNA sequencing for low quantities of cells and single cells
- Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity
- CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification
- Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells