Single-cell RNA counting at allele and isoform resolution using Smart-seq3

Benchmarking single-cell RNA-sequencing protocols for cell atlas projects

(2020) Elisabetta Mereu et al.   NATURE BIOTECHNOLOGY

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Tn5Prime, a Tn5 based 5′ capture method for single cell RNA-seq

(2018) Charles Cole et al.   NUCLEIC ACIDS RESEARCH

Sensitive and powerful single-cell RNA sequencing using mcSCRB-seq

(2018) Johannes W. Bagnoli et al.   Nature Communications

zUMIs - A fast and flexible pipeline to process RNA sequencing data with UMIs

(2018) Swati Parekh et al.   GigaScience

Genomic encoding of transcriptional burst kinetics

(2018) Anton J. M. Larsson et al.   NATURE

Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells

(2018) Ishaan Gupta et al.   NATURE BIOTECHNOLOGY

Comparative Analysis of Single-Cell RNA Sequencing Methods

(2017) Christoph Ziegenhain et al.   MOLECULAR CELL

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells

(2017) Ashley Byrne et al.   Nature Communications

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Compounds that enhance the tailing activity of Moloney murine leukemia virus reverse transcriptase

(2017) Yoshiyuki Ohtsubo et al.   Scientific Reports

Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA–seq

(2016) Björn Reinius et al.   NATURE GENETICS

RNA G-quadruplexes are globally unfolded in eukaryotic cells and depleted in bacteria

(2016) J. U. Guo et al.   SCIENCE

RNA mis-splicing in disease

(2015) Marina M. Scotti et al.   NATURE REVIEWS GENETICS

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells

(2014) Q. Deng et al.   SCIENCE

Control of alternative splicing in immune responses: many regulators, many predictions, much still to learn

(2013) Nicole M. Martinez et al.   IMMUNOLOGICAL REVIEWS

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

Entering the era of single-cell transcriptomics in biology and medicine

(2013) Rickard Sandberg   NATURE METHODS

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Mouse genomic variation and its effect on phenotypes and gene regulation

(2011) Thomas M. Keane et al.   NATURE

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE