Native molecule sequencing by nano-ID reveals synthesis and stability of RNA isoforms

Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns

(2020) Alison D. Tang et al.   Nature Communications

A large-scale binding and functional map of human RNA-binding proteins

(2020) Eric L. Van Nostrand et al.   NATURE

Deep-learning augmented RNA-seq analysis of transcript splicing

(2019) Zijun Zhang et al.   NATURE METHODS

Long-read sequencing reveals the complex splicing profile of the psychiatric risk gene CACNA1C in human brain

(2019) Michael B. Clark et al.   MOLECULAR PSYCHIATRY

Nanopore native RNA sequencing of a human poly(A) transcriptome

(2019) Rachael E. Workman et al.   NATURE METHODS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

TimeLapse-seq: adding a temporal dimension to RNA sequencing through nucleoside recoding

(2018) Jeremy A Schofield et al.   NATURE METHODS

Highly parallel direct RNA sequencing on an array of nanopores

(2018) Daniel R Garalde et al.   NATURE METHODS

The CCR4-NOT deadenylase complex controls Atg7-dependent cell death and heart function

(2018) Tomokazu Yamaguchi et al.   Science Signaling

Alternative polyadenylation in the regulation and dysregulation of gene expression

(2018) Rachael Emily Turner et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

The CCR4-NOT deadenylase complex controls Atg7-dependent cell death and heart function

(2018) Tomokazu Yamaguchi et al.   Science Signaling

Correction of diverse muscular dystrophy mutations in human engineered heart muscle by single-site genome editing

(2018) Chengzu Long et al.   Science Advances

Detection of splice isoforms and rare intermediates using multiplexed primer extension sequencing

(2018) Hansen Xu et al.   NATURE METHODS

An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms

(2017) Javier Tapial et al.   GENOME RESEARCH

DNA sequencing at 40: past, present and future

(2017) Jay Shendure et al.   NATURE

Thiol-linked alkylation of RNA to assess expression dynamics

(2017) Veronika A Herzog et al.   NATURE METHODS

Transcriptional response to stress is pre-wired by promoter and enhancer architecture

(2017) Anniina Vihervaara et al.   Nature Communications

Use of conditioned media is critical for studies of regulation in response to rapid heat shock

(2016) Dig B. Mahat et al.   CELL STRESS & CHAPERONES

Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters

(2016) Yun Chen et al.   NATURE GENETICS

TT-seq maps the human transient transcriptome

(2016) Björn Schwalb et al.   SCIENCE

RNA splicing is a primary link between genetic variation and disease

(2016) Yang I. Li et al.   SCIENCE

Fast and sensitive mapping of nanopore sequencing reads with GraphMap

(2016) Ivan Sović et al.   Nature Communications

Comprehensive transcriptome analysis using synthetic long-read sequencing reveals molecular co-association of distant splicing events

(2015) Hagen Tilgner et al.   NATURE BIOTECHNOLOGY

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

(2014) S. Anders et al.   BIOINFORMATICS

TAIL-seq: Genome-wide Determination of Poly(A) Tail Length and 3′ End Modifications

(2014) Hyeshik Chang et al.   MOLECULAR CELL

Poly(A)-tail profiling reveals an embryonic switch in translational control

(2014) Alexander O. Subtelny et al.   NATURE

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers

(2014) Leighton J Core et al.   NATURE GENETICS

Ribosome Profiling Reveals Pervasive Translation Outside of Annotated Protein-Coding Genes

(2014) Nicholas T. Ingolia et al.   Cell Reports

Extensive transcriptional heterogeneity revealed by isoform profiling

(2013) Vicent Pelechano et al.   NATURE

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

(2013) Silvi Rouskin et al.   NATURE

Assessment of transcript reconstruction methods for RNA-seq

(2013) Tamara Steijger et al.   NATURE METHODS

Transcriptional response to stress in the dynamic chromatin environment of cycling and mitotic cells

(2013) Anniina Vihervaara et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA sequencing of cancer reveals novel splicing alterations

(2013) Jeyanthy Eswaran et al.   Scientific Reports

Analysis of interferon-beta mRNA stability control after poly(I:C) stimulation using RNA metabolic labeling by ethynyluridine

(2012) Kaito Abe et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast

(2011) C. Miller et al.   Molecular Systems Biology

Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells

(2011) Michal Rabani et al.   NATURE BIOTECHNOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The Many Pathways of RNA Degradation

(2009) Jonathan Houseley et al.   CELL

Exploring RNA transcription and turnover in vivo by using click chemistry

(2008) C. Y. Jao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay

(2008) L. Dolken et al.   RNA