Single-cell RNA cap and tail sequencing (scRCAT-seq) reveals subtype-specific isoforms differing in transcript demarcation

C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution

(2019) Tsukasa Kouno et al.   Nature Communications

Template-switching artifacts resemble alternative polyadenylation

(2019) Zsolt Balázs et al.   BMC GENOMICS

Single-Cell RNA Sequencing of hESC-Derived 3D Retinal Organoids Reveals Novel Genes Regulating RPC Commitment in Early Human Retinogenesis

(2019) Xiying Mao et al.   Stem Cell Reports

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

SEASTAR: systematic evaluation of alternative transcription start sites in RNA

(2018) Zhiyi Qin et al.   NUCLEIC ACIDS RESEARCH

Cell Cycle Regulation by Alternative Polyadenylation of CCND1

(2018) Qiong Wang et al.   Scientific Reports

Understanding dynamic tissue organization by studying the human body one cell at a time: the human cell atlas (HCA) project

(2018) Michela Noseda et al.   CARDIOVASCULAR RESEARCH

Extensive Structural Differences of Closely Related 3′ mRNA Isoforms: Links to Pab1 Binding and mRNA Stability

(2018) Zarmik Moqtaderi et al.   MOLECULAR CELL

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

(2018) Ishaan Gupta et al.   NATURE BIOTECHNOLOGY

Update of the FANTOM web resource: expansion to provide additional transcriptome atlases

(2018) Marina Lizio et al.   NUCLEIC ACIDS RESEARCH

Mechanistic Differences in Transcription Initiation at TATA-Less and TATA-Containing Promoters

(2017) Rafal Donczew et al.   MOLECULAR AND CELLULAR BIOLOGY

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues

(2017) Alejandro Reyes et al.   NUCLEIC ACIDS RESEARCH

PolyA_DB 3 catalogs cleavage and polyadenylation sites identified by deep sequencing in multiple genomes

(2017) Ruijia Wang et al.   NUCLEIC ACIDS RESEARCH

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

Alternative Polyadenylation: Methods, Findings, and Impacts

(2017) Wei Chen et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

STRT-seq-2i: dual-index 5ʹ single cell and nucleus RNA-seq on an addressable microwell array

(2017) Hannah Hochgerner et al.   Scientific Reports

Revealing the vectors of cellular identity with single-cell genomics

(2016) Allon Wagner et al.   NATURE BIOTECHNOLOGY

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

Single-cell polyadenylation site mapping reveals 3' isoform choice variability

(2015) L. Velten et al.   Molecular Systems Biology

CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses

(2015) Vanja Haberle et al.   NUCLEIC ACIDS RESEARCH

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

(2015) A. Zeisel et al.   SCIENCE

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Deep learning of the tissue-regulated splicing code

(2014) Michael K. K. Leung et al.   BIOINFORMATICS

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

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

(2014) Simone Picelli et al.   Nature Protocols

Quantitative single-cell RNA-seq with unique molecular identifiers

(2013) Saiful Islam et al.   NATURE METHODS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Transcriptome sequencing of single cells with Smart-Seq

(2012) Jillian J Goetz et al.   NATURE BIOTECHNOLOGY

Suppression of artifacts and barcode bias in high-throughput transcriptome analyses utilizing template switching

(2012) Dave T. P. Tang et al.   NUCLEIC ACIDS RESEARCH

Mechanisms and Consequences of Alternative Polyadenylation

(2011) Dafne Campigli Di Giammartino et al.   MOLECULAR CELL

Coupling genetics and post-genomic approaches to decipher the cellular splicing code at a systems-wide level: Figure 1

(2010) Yilei Liu et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Deciphering the splicing code

(2010) Yoseph Barash et al.   NATURE

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2008) Qun Pan et al.   NATURE GENETICS