Preprocessing choices affect RNA velocity results for droplet scRNA-seq data

The emergence and promise of single-cell temporal-omics approaches

(2020) Alex R Lederer et al.   CURRENT OPINION IN BIOTECHNOLOGY

The barcode, UMI, set format and BUStools

(2019) Páll Melsted et al.   BIOINFORMATICS

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

Comprehensive single cell mRNA profiling reveals a detailed roadmap for pancreatic endocrinogenesis

(2019) Aimée Bastidas-Ponce et al.   DEVELOPMENT

Beyond bulk: a review of single cell transcriptomics methodologies and applications

(2019) Ashwinikumar Kulkarni et al.   CURRENT OPINION IN BIOTECHNOLOGY

Single-cell transcriptomic profiling of the aging mouse brain

(2019) Methodios Ximerakis et al.   NATURE NEUROSCIENCE

Cell type-specific transcriptional programs in mouse prefrontal cortex during adolescence and addiction

(2019) Aritra Bhattacherjee et al.   Nature Communications

Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing

(2018) Hannah Hochgerner et al.   NATURE NEUROSCIENCE

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

(2018) Swati Parekh et al.   GigaScience

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data

(2018) Luyi Tian et al.   PLoS Computational Biology

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

The Mammalian Spermatogenesis Single-Cell Transcriptome, from Spermatogonial Stem Cells to Spermatids

(2018) Brian P. Hermann et al.   Cell Reports

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

(2017) Tom Smith et al.   GENOME RESEARCH

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation

(2015) Dimos Gaidatzis et al.   NATURE BIOTECHNOLOGY

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

(2014) Simone Picelli et al.   Nature Protocols

SnapShot-Seq: A Method for Extracting Genome-Wide, In Vivo mRNA Dynamics from a Single Total RNA Sample

(2014) Jesse M. Gray et al.   PLoS One

The promise of single-cell sequencing

(2013) James Eberwine et al.   NATURE METHODS

Method of the Year 2013

(2013)   NATURE METHODS

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Coupled pre-mRNA and mRNA dynamics unveil operational strategies underlying transcriptional responses to stimuli

(2011) A. Zeisel et al.   Molecular Systems Biology

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS