Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data

Transcription Dynamics Regulate Poly(A) Tails and Expression of the RNA Degradation Machinery to Balance mRNA Levels

(2020) Boris Slobodin et al.   MOLECULAR CELL

Global donor and acceptor splicing site kinetics in human cells

(2019) Leonhard Wachutka et al.   eLife

Translation affects mRNA stability in a codon-dependent manner in human cells

(2019) Qiushuang Wu et al.   eLife

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Determining mRNA half-lives on a transcriptome-wide scale

(2018) Andrew Lugowski et al.   METHODS

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

(2018) Jeremy A Schofield et al.   NATURE METHODS

Evaluation of two main RNA-seq approaches for gene quantification in clinical RNA sequencing: polyA+ selection versus rRNA depletion

(2018) Shanrong Zhao et al.   Scientific Reports

Chromatin run-on and sequencing maps the transcriptional regulatory landscape of glioblastoma multiforme

(2018) Tinyi Chu et al.   NATURE GENETICS

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

Impact of Methods on the Measurement of mRNA Turnover

(2017) Takeo Wada et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Thiol-linked alkylation of RNA to assess expression dynamics

(2017) Veronika A Herzog et al.   NATURE METHODS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Oxidative stress rapidly stabilizes promoter-proximal paused Pol II across the human genome

(2017) Kyle A. Nilson et al.   NUCLEIC ACIDS RESEARCH

The Encyclopedia of DNA elements (ENCODE): data portal update

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

Inference of RNA decay rate from transcriptional profiling highlights the regulatory programs of Alzheimer’s disease

(2017) Rached Alkallas et al.   Nature Communications

CDK9-dependent RNA polymerase II pausing controls transcription initiation

(2017) Saskia Gressel et al.   eLife

Multiplexed gene control reveals rapid mRNA turnover

(2017) Antoine Baudrimont et al.   Science Advances

Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs

(2016) Marta Melé et al.   GENOME RESEARCH

Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq)

(2016) Dig Bijay Mahat et al.   Nature Protocols

Integrative classification of human coding and noncoding genes through RNA metabolism profiles

(2016) Neelanjan Mukherjee et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

TT-seq maps the human transient transcriptome

(2016) Björn Schwalb et al.   SCIENCE

Integrative classification of human coding and noncoding genes through RNA metabolism profiles

(2016) Neelanjan Mukherjee et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Elucidating MicroRNA Regulatory Networks Using Transcriptional, Post-transcriptional, and Histone Modification Measurements

(2016) Sara J.C. Gosline et al.   Cell Reports

Analysis of RNA decay factor mediated RNA stability contributions on RNA abundance

(2015) Sho Maekawa et al.   BMC GENOMICS

Recursive splicing in long vertebrate genes

(2015) Christopher R. Sibley et al.   NATURE

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

(2015) Dimos Gaidatzis et al.   NATURE BIOTECHNOLOGY

Identification of active transcriptional regulatory elements from GRO-seq data

(2015) Charles G Danko et al.   NATURE METHODS

Roles of miR-182 in sensory organ development and cancer

(2015) Qing Wei et al.   Thoracic Cancer

Predicting effective microRNA target sites in mammalian mRNAs

(2015) Vikram Agarwal et al.   eLife

MatchIt: Nonparametric Preprocessing for Parametric Causal Inference

(2015) Daniel E. Ho et al.   Journal of Statistical Software

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

(2014) S. Anders et al.   BIOINFORMATICS

genomation: a toolkit to summarize, annotate and visualize genomic intervals

(2014) A. Akalin et al.   BIOINFORMATICS

High-Resolution Sequencing and Modeling Identifies Distinct Dynamic RNA Regulatory Strategies

(2014) Michal Rabani et al.   CELL

Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications

(2014) A. Veloso et al.   GENOME RESEARCH

Coupling mRNA Synthesis and Decay

(2014) K. A. Braun et al.   MOLECULAR AND CELLULAR BIOLOGY

A shared architecture for promoters and enhancers

(2014) Shira Weingarten-Gabbay et al.   NATURE GENETICS

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

(2014) Leighton J Core et al.   NATURE GENETICS

Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons

(2014) Iris Jonkers et al.   eLife

Gene Expression Is Circular: Factors for mRNA Degradation Also Foster mRNA Synthesis

(2013) Gal Haimovich et al.   CELL

3' UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts

(2013) N. Spies et al.   GENOME RESEARCH

Signaling Pathways Differentially Affect RNA Polymerase II Initiation, Pausing, and Elongation Rate in Cells

(2013) Charles G. Danko et al.   MOLECULAR CELL

Promoter directionality is controlled by U1 snRNP and polyadenylation signals

(2013) Albert E. Almada et al.   NATURE

Polyadenylation site–induced decay of upstream transcripts enforces promoter directionality

(2013) Evgenia Ntini et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

(2013) H. Kwak et al.   SCIENCE

Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs

(2012) H. Tilgner et al.   GENOME RESEARCH

Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution

(2012) L. Windhager et al.   GENOME RESEARCH

Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals

(2012) H. Tani et al.   GENOME RESEARCH

Genome-wide analysis of long noncoding RNA stability

(2012) M. B. Clark et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples

(2012) Günter P. Wagner et al.   THEORY IN BIOSCIENCES

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

Promoter Elements Regulate Cytoplasmic mRNA Decay

(2011) Almog Bregman et al.   CELL

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

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

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

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

(2011) Michal Rabani et al.   NATURE BIOTECHNOLOGY

Transcriptome Kinetics Is Governed by a Genome-Wide Coupling of mRNA Production and Degradation: A Role for RNA Pol II

(2011) Ophir Shalem et al.   PLoS Genetics

Regulation of Alternative Splicing by Histone Modifications

(2010) R. F. Luco et al.   SCIENCE

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

The stability of mRNA influences the temporal order of the induction of genes encoding inflammatory molecules

(2009) Shengli Hao et al.   NATURE IMMUNOLOGY

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

GC level and expression of human coding sequences

(2008) Stilianos Arhondakis et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Database for mRNA Half-Life of 19 977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse Embryonic Stem Cells

(2008) L. V. Sharova et al.   DNA RESEARCH

Transcription in the nucleus and mRNA decay in the cytoplasm are coupled processes

(2008) V. Goler-Baron et al.   GENES & DEVELOPMENT

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

(2008) L. Dolken et al.   RNA