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

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

Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing

(2015) Takayuki Nojima et al.   CELL

Control of Transcript Variability in Single Mammalian Cells

(2015) Nico Battich et al.   CELL

Long noncoding RNADANCRincreases stemness features of hepatocellular carcinoma by derepression ofCTNNB1

(2015) Sheng-xian Yuan et al.   HEPATOLOGY

Human Long Noncoding RNAs Are Substantially Less Folded than Messenger RNAs

(2015) Jian-Rong Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry

(2015) Erin E. Duffy et al.   MOLECULAR CELL

Human Promoters Are Intrinsically Directional

(2015) Sascha H.C. Duttke et al.   MOLECULAR CELL

A method for calculating probabilities of fitness consequences for point mutations across the human genome

(2015) Brad Gulko et al.   NATURE GENETICS

The landscape of long noncoding RNAs in the human transcriptome

(2015) Matthew K Iyer et al.   NATURE GENETICS

Detecting actively translated open reading frames in ribosome profiling data

(2015) Lorenzo Calviello et al.   NATURE METHODS

Comparing the performance of biomedical clustering methods

(2015) Christian Wiwie et al.   NATURE METHODS

Unexpected selection to retain high GC content and splicing enhancers within exons of multiexonic lncRNA loci

(2015) Wilfried Haerty et al.   RNA

The Landscape of long noncoding RNA classification

(2015) Georges St. Laurent et al.   TRENDS IN GENETICS

Nuclear Retention of mRNA in Mammalian Tissues

(2015) Keren Bahar Halpern et al.   Cell Reports

Canonical Poly(A) Polymerase Activity Promotes the Decay of a Wide Variety of Mammalian Nuclear RNAs

(2015) Stefan M. Bresson et al.   PLoS Genetics

Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution

(2015) Moran N Cabili et al.   GENOME BIOLOGY

qgraph: Network Visualizations of Relationships in Psychometric Data

(2015) Sacha Epskamp et al.   Journal of Statistical Software

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

(2014) A. Akalin et al.   BIOINFORMATICS

Influence of RNA extraction methods and library selection schemes on RNA-seq data

(2014) Marc Sultan et al.   BMC GENOMICS

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

(2014) Michal Rabani et al.   CELL

Long Noncoding RNA MALAT1 Regulates Endothelial Cell Function and Vessel Growth

(2014) Katharina M. Michalik et al.   CIRCULATION RESEARCH

Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate

(2014) Nova Fong et al.   GENES & DEVELOPMENT

Purifying Selection on Splice-Related Motifs, Not Expression Level nor RNA Folding, Explains Nearly All Constraint on Human lincRNAs

(2014) Andreas Schüler et al.   MOLECULAR BIOLOGY AND EVOLUTION

MOV10 Is a 5′ to 3′ RNA Helicase Contributing to UPF1 mRNA Target Degradation by Translocation along 3′ UTRs

(2014) Lea H. Gregersen et al.   MOLECULAR CELL

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

The evolution of lncRNA repertoires and expression patterns in tetrapods

(2014) Anamaria Necsulea et al.   NATURE

A census of human RNA-binding proteins

(2014) Stefanie Gerstberger et al.   NATURE REVIEWS GENETICS

lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs

(2014) Xiu Cheng Quek et al.   NUCLEIC ACIDS RESEARCH

Nuclear stability and transcriptional directionality separate functionally distinct RNA species

(2014) Robin Andersson et al.   Nature Communications

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

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

Considerations when investigating lncRNA function in vivo

(2014) Andrew R Bassett et al.   eLife

Extensive localization of long noncoding RNAs to the cytosol and mono- and polyribosomal complexes

(2014) Sebastiaan van Heesch et al.   GENOME BIOLOGY

Divergent Transcription: A Driving Force for New Gene Origination?

(2013) Xuebing Wu et al.   CELL

lincRNAs: Genomics, Evolution, and Mechanisms

(2013) Igor Ulitsky et al.   CELL

Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins

(2013) Mitchell Guttman et al.   CELL

Effects of Coexisting Pneumonia and End-stage Renal Disease on Pleural Fluid Analysis in Patients With Hydrostatic Pleural Effusion

(2013) Peter Doelken et al.   CHEST

Frac-seq reveals isoform-specific recruitment to polyribosomes

(2013) T. Sterne-Weiler et al.   GENOME RESEARCH

Comparative analysis of RNA sequencing methods for degraded or low-input samples

(2013) Xian Adiconis et al.   NATURE METHODS

Multiple knockout mouse models reveal lincRNAs are required for life and brain development

(2013) Martin Sauvageau et al.   eLife

Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing

(2013) Shivendra Kishore et al.   GENOME BIOLOGY

Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs

(2013) Ana C Marques et al.   GENOME BIOLOGY

Genome Regulation by Long Noncoding RNAs

(2012) John L. Rinn et al.   Annual Review of Biochemistry

Intron-centric estimation of alternative splicing from RNA-seq data

(2012) D. D. Pervouchine et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Suppression of progenitor differentiation requires the long noncoding RNA ANCR

(2012) M. Kretz et al.   GENES & DEVELOPMENT

The RNA polymerase II CTD coordinates transcription and RNA processing

(2012) J.-P. Hsin et al.   GENES & DEVELOPMENT

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

Long noncoding RNAs are rarely translated in two human cell lines

(2012) B. Banfai 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

Discovery of hundreds of mirtrons in mouse and human small RNA data

(2012) E. Ladewig 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

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Genome-Wide Assessment of AU-Rich Elements by the AREScore Algorithm

(2012) Milan Spasic et al.   PLoS Genetics

Rapid Turnover of Long Noncoding RNAs and the Evolution of Gene Expression

(2012) Claudia Kutter et al.   PLoS Genetics

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

Integrative Regulatory Mapping Indicates that the RNA-Binding Protein HuR Couples Pre-mRNA Processing and mRNA Stability

(2011) Neelanjan Mukherjee et al.   MOLECULAR CELL

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

(2011) Michal Rabani et al.   NATURE BIOTECHNOLOGY

When one is better than two: RNA with dual functions

(2010) Damien Ulveling et al.   BIOCHIMIE

A flexible R package for nonnegative matrix factorization

(2010) Renaud Gaujoux et al.   BMC BIOINFORMATICS

The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation

(2010) Vidisha Tripathi et al.   MOLECULAR CELL

Chromosomal Redistribution of Male-Biased Genes in Mammalian Evolution with Two Bursts of Gene Gain on the X Chromosome

(2010) Yong E. Zhang et al.   PLOS BIOLOGY

Genome-Wide Association between Branch Point Properties and Alternative Splicing

(2010) André Corvelo et al.   PLoS Computational Biology

A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster

(2009) X. Zhang et al.   BLOOD

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

SROOGLE: webserver for integrative, user-friendly visualization of splicing signals

(2009) S. Schwartz et al.   NUCLEIC ACIDS RESEARCH

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

(2009) Ahmad M. Khalil et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY