Metabolic labeling of RNA using multiple ribonucleoside analogs enables the simultaneous evaluation of RNA synthesis and degradation rates

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

Tuning of mRNA stability through altering 3′-UTR sequences generates distinct output expression in a synthetic circuit driven by p53 oscillations

(2019) Woo Seuk Koh et al.   Scientific Reports

SLAM-ITseq: sequencing cell type-specific transcriptomes without cell sorting

(2018) Wayo Matsushima et al.   DEVELOPMENT

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

(2018) Jeremy A Schofield et al.   NATURE METHODS

RNA dynamics revealed by metabolic RNA labeling and biochemical nucleoside conversions

(2018) Marisa A P Baptista et al.   NATURE METHODS

QuantSeq 3′ mRNA sequencing for RNA quantification

(2018) Pamela Moll et al.   NATURE METHODS

Expanding the Nucleoside Recoding Toolkit: Revealing RNA Population Dynamics with 6-Thioguanosine

(2018) Lea Kiefer et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Gaining insight into transcriptome‐wide RNA population dynamics through the chemistry of 4‐thiouridine

(2018) Erin E. Duffy et al.   Wiley Interdisciplinary Reviews-RNA

Thiol-linked alkylation of RNA to assess expression dynamics

(2017) Veronika A Herzog et al.   NATURE METHODS

Determinants of RNA metabolism in the Schizosaccharomyces pombe genome

(2016) P. Eser et al.   Molecular Systems Biology

An integrative transcriptomics approach identifies miR-503 as a candidate master regulator of the estrogen response in MCF-7 breast cancer cells

(2016) Jeanette Baran-Gale et al.   RNA

TT-seq maps the human transient transcriptome

(2016) Björn Schwalb et al.   SCIENCE

INSPEcT: a computational tool to infer mRNA synthesis, processing and degradation dynamics from RNA- and 4sU-seq time course experiments

(2015) Stefano de Pretis et al.   BIOINFORMATICS

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

(2015) Sho Maekawa et al.   BMC GENOMICS

Next-generation analysis of gene expression regulation – comparing the roles of synthesis and degradation

(2015) Joel McManus et al.   Molecular BioSystems

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

(2014) Michal Rabani et al.   CELL

Posttranscriptional regulation of gene networks by GU-rich elements and CELF proteins

(2014) Irina A. Vlasova et al.   RNA Biology

What do you mean by transcription rate?

(2013) José E. Pérez-Ortín et al.   BIOESSAYS

BRIC-seq: A genome-wide approach for determining RNA stability in mammalian cells

(2013) Naoto Imamachi et al.   METHODS

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

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

A complex ‘mRNA degradation code’ controls gene expression during animal development

(2012) Claudio R. Alonso   TRENDS IN GENETICS

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

(2011) Michal Rabani et al.   NATURE BIOTECHNOLOGY

AREsite: a database for the comprehensive investigation of AU-rich elements

(2010) A. R. Gruber et al.   NUCLEIC ACIDS RESEARCH

bioDBnet: the biological database network

(2009) Uma Mudunuri et al.   BIOINFORMATICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Conserved GU-Rich Elements Mediate mRNA Decay by Binding to CUG-Binding Protein 1

(2008) Irina A. Vlasova et al.   MOLECULAR CELL

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH