Computational challenges, tools, and resources for analyzing co- and post-transcriptional events in high throughput

Global Analysis of mRNA Isoform Half-Lives Reveals Stabilizing and Destabilizing Elements in Yeast

(2014) Joseph V. Geisberg et al.   CELL

CD44v6 Is a Marker of Constitutive and Reprogrammed Cancer Stem Cells Driving Colon Cancer Metastasis

(2014) Matilde Todaro et al.   Cell Stem Cell

RNA-binding protein RBM20 represses splicing to orchestrate cardiac pre-mRNA processing

(2014) Henrike Maatz et al.   JOURNAL OF CLINICAL INVESTIGATION

Alternative polyadenylation diversifies post-transcriptional regulation by selective RNA-protein interactions

(2014) I. Gupta et al.   Molecular Systems Biology

Comprehensive analysis of RNA-protein interactions by high-throughput sequencing–RNA affinity profiling

(2014) Jacob M Tome et al.   NATURE METHODS

Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis

(2014) Michael J Moore et al.   Nature Protocols

STarMir: a web server for prediction of microRNA binding sites

(2014) William Rennie et al.   NUCLEIC ACIDS RESEARCH

RBPmap: a web server for mapping binding sites of RNA-binding proteins

(2014) Inbal Paz et al.   NUCLEIC ACIDS RESEARCH

Genomic Analyses Reveal Broad Impact of miR-137 on Genes Associated with Malignant Transformation and Neuronal Differentiation in Glioblastoma Cells

(2014) Saleh Tamim et al.   PLoS One

A Model-Based Approach to Identify Binding Sites in CLIP-Seq Data

(2014) Tao Wang et al.   PLoS One

Advancing the functional utility of PAR-CLIP by quantifying background binding to mRNAs and lncRNAs

(2014) Matthew B Friedersdorf et al.   GENOME BIOLOGY

dCLIP: a computational approach for comparative CLIP-seq analyses

(2014) Tao Wang et al.   GENOME BIOLOGY

GraphProt: modeling binding preferences of RNA-binding proteins

(2014) Daniel Maticzka et al.   GENOME BIOLOGY

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

(2014) Steve Hoffmann et al.   GENOME BIOLOGY

PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis

(2014) Beibei Chen et al.   GENOME BIOLOGY

PAR-CLIP data indicate that Nrd1-Nab3-dependent transcription termination regulates expression of hundreds of protein coding genes in yeast

(2014) Shaun Webb et al.   GENOME BIOLOGY

Nonsense-mediated mRNA decay — Mechanisms of substrate mRNA recognition and degradation in mammalian cells

(2013) Christoph Schweingruber et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

SplicingCompass: differential splicing detection using RNA-Seq data

(2013) Moritz Aschoff et al.   BIOINFORMATICS

mRNAStab—a web application for mRNA stability analysis

(2013) Andrei Alic et al.   BIOINFORMATICS

ASPeak: an abundance sensitive peak detection algorithm for RIP-Seq

(2013) A. Kucukural et al.   BIOINFORMATICS

Correlation of CD44v6 expression with ovarian cancer progression and recurrence

(2013) Jun Shi et al.   BMC CANCER

Combining in silico prediction and ribosome profiling in a genome-wide search for novel putatively coding sORFs

(2013) Jeroen Crappé et al.   BMC GENOMICS

Direct Conversion of Fibroblasts to Neurons by Reprogramming PTB-Regulated MicroRNA Circuits

(2013) Yuanchao Xue et al.   CELL

Direct Competition between hnRNP C and U2AF65 Protects the Transcriptome from the Exonization of Alu Elements

(2013) Kathi Zarnack et al.   CELL

All's well that ends well: alternative polyadenylation and its implications for stem cell biology

(2013) Alisa A Mueller et al.   CURRENT OPINION IN CELL BIOLOGY

Ribosome profiling reveals resemblance between long non-coding RNAs and 5′ leaders of coding RNAs

(2013) Guo-Liang Chew et al.   DEVELOPMENT

Quantitative proteomic analysis reveals concurrent RNA-protein interactions and identifies new RNA-binding proteins in Saccharomyces cerevisiae

(2013) D. M. Klass et al.   GENOME RESEARCH

Advances in the Techniques for the Prediction of microRNA Targets

(2013) Hao Zheng et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

QuaNCAT: quantitating proteome dynamics in primary cells

(2013) Andrew J M Howden et al.   NATURE METHODS

Alternative cleavage and polyadenylation: extent, regulation and function

(2013) Ran Elkon et al.   NATURE REVIEWS GENETICS

Prediction of clustered RNA-binding protein motif sites in the mammalian genome

(2013) Chaolin Zhang et al.   NUCLEIC ACIDS RESEARCH

RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments

(2013) Yue Li et al.   NUCLEIC ACIDS RESEARCH

Structural features of Argonaute-GW182 protein interactions

(2013) J. Pfaff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

FUS regulates genes coding for RNA-binding proteins in neurons by binding to their highly conserved introns

(2013) T. Nakaya et al.   RNA

Gene Expression Regulation by Upstream Open Reading Frames and Human Disease

(2013) Cristina Barbosa et al.   PLoS Genetics

Means to an end: mechanisms of alternative polyadenylation of messenger RNA precursors

(2013) Andreas R. Gruber et al.   Wiley Interdisciplinary Reviews-RNA

Finding the target sites of RNA-binding proteins

(2013) Xiao Li et al.   Wiley Interdisciplinary Reviews-RNA

Translation regulation gets its ‘omics’ moment

(2013) Scott Kuersten et al.   Wiley Interdisciplinary Reviews-RNA

p53 induces transcriptional and translational programs to suppress cell proliferation and growth

(2013) Fabricio Loayza-Puch et al.   GENOME BIOLOGY

The RNA-Binding Protein Musashi1 Affects Medulloblastoma Growth via a Network of Cancer-Related Genes and Is an Indicator of Poor Prognosis

(2012) Dat T. Vo et al.   AMERICAN JOURNAL OF PATHOLOGY

Measurement of genome-wide RNA synthesis and decay rates with Dynamic Transcriptome Analysis (DTA)

(2012) B. Schwalb et al.   BIOINFORMATICS

RIP-chip enrichment analysis

(2012) Florian Erhard et al.   BIOINFORMATICS

Site identification in high-throughput RNA–protein interaction data

(2012) Philip J. Uren et al.   BIOINFORMATICS

Tools for mapping high-throughput sequencing data

(2012) Nuno A. Fonseca et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

(2012) M.-A. Dillies et al.   BRIEFINGS IN BIOINFORMATICS

Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins

(2012) Alfredo Castello et al.   CELL

Identifying differentially spliced genes from two groups of RNA-seq samples

(2012) Weichen Wang et al.   GENE

Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting

(2012) C. Fritsch et al.   GENOME RESEARCH

A quantitative atlas of polyadenylation in five mammals

(2012) Adnan Derti et al.   GENOME RESEARCH

Detecting differential usage of exons from RNA-seq data

(2012) S. Anders et al.   GENOME RESEARCH

Transcriptome-wide miR-155 Binding Map Reveals Widespread Noncanonical MicroRNA Targeting

(2012) Gabriel B. Loeb et al.   MOLECULAR CELL

The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts

(2012) Alexander G. Baltz et al.   MOLECULAR CELL

Systematic discovery of structural elements governing stability of mammalian messenger RNAs

(2012) Hani Goodarzi et al.   NATURE

The translational landscape of mTOR signalling steers cancer initiation and metastasis

(2012) Andrew C. Hsieh et al.   NATURE

FMRP targets distinct mRNA sequence elements to regulate protein expression

(2012) Manuel Ascano et al.   NATURE

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Analysis of alternative cleavage and polyadenylation by 3′ region extraction and deep sequencing

(2012) Mainul Hoque et al.   NATURE METHODS

Regulation of cytoplasmic mRNA decay

(2012) Daniel R. Schoenberg et al.   NATURE REVIEWS GENETICS

NMD: a multifaceted response to premature translational termination

(2012) Stephanie Kervestin et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Analysis of C. elegans intestinal gene expression and polyadenylation by fluorescence-activated nuclei sorting and 3′-end-seq

(2012) Simon Haenni et al.   NUCLEIC ACIDS RESEARCH

DiffSplice: the genome-wide detection of differential splicing events with RNA-seq

(2012) Yin Hu et al.   NUCLEIC ACIDS RESEARCH

An in-depth map of polyadenylation sites in cancer

(2012) Yuefeng Lin et al.   NUCLEIC ACIDS RESEARCH

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae

(2012) Intawat Nookaew et al.   NUCLEIC ACIDS RESEARCH

Quantitative mass spectrometry and PAR-CLIP to identify RNA-protein interactions

(2012) Marion Scheibe et al.   NUCLEIC ACIDS RESEARCH

MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data

(2012) Shihao Shen et al.   NUCLEIC ACIDS RESEARCH

Shortening of 3′UTRs Correlates with Poor Prognosis in Breast and Lung Cancer

(2012) Antonio Lembo et al.   PLoS One

Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution

(2012) S. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ribosome Profiling Shows That miR-430 Reduces Translation Before Causing mRNA Decay in Zebrafish

(2012) A. A. Bazzini et al.   SCIENCE

Decoding Human Cytomegalovirus

(2012) N. Stern-Ginossar et al.   SCIENCE

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

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

Global Patterns of Tissue-Specific Alternative Polyadenylation in Drosophila

(2012) Peter Smibert et al.   Cell Reports

Computational biology of RNA interactions

(2012) Christoph Dieterich et al.   Wiley Interdisciplinary Reviews-RNA

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

Primary Role for Endoplasmic Reticulum-bound Ribosomes in Cellular Translation Identified by Ribosome Profiling

(2011) David W. Reid et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Genomic Analyses of the RNA-binding Protein Hu Antigen R (HuR) Identify a Complex Network of Target Genes and Novel Characteristics of Its Binding Sites

(2011) Philip J. Uren et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Lipopolysaccharide Signaling without a Nucleus: Kinase Cascades Stimulate Platelet Shedding of Proinflammatory IL-1 -Rich Microparticles

(2011) G. T. Brown et al.   JOURNAL OF IMMUNOLOGY

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

(2011) Neelanjan Mukherjee et al.   MOLECULAR CELL

Transcriptome-wide Analysis of Regulatory Interactions of the RNA-Binding Protein HuR

(2011) Svetlana Lebedeva et al.   MOLECULAR CELL

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument

(2011) Razvan Nutiu et al.   NATURE BIOTECHNOLOGY

Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data

(2011) Chaolin Zhang et al.   NATURE BIOTECHNOLOGY

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

Characterizing the RNA targets and position-dependent splicing regulation by TDP-43

(2011) James R Tollervey et al.   NATURE NEUROSCIENCE

Gene silencing by microRNAs: contributions of translational repression and mRNA decay

(2011) Eric Huntzinger et al.   NATURE REVIEWS GENETICS

Non-coding RNAs in human disease

(2011) Manel Esteller   NATURE REVIEWS GENETICS

TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support

(2011) T. Vergoulis et al.   NUCLEIC ACIDS RESEARCH

doRiNA: a database of RNA interactions in post-transcriptional regulation

(2011) Gerd Anders et al.   NUCLEIC ACIDS RESEARCH

Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis

(2011) Maria Kalyna et al.   NUCLEIC ACIDS RESEARCH

From RNA-seq reads to differential expression results

(2011) Alicia Oshlack et al.   GENOME BIOLOGY

PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data

(2011) David L Corcoran et al.   GENOME BIOLOGY

SOAPsplice: Genome-Wide ab initio Detection of Splice Junctions from RNA-Seq Data

(2011) Songbo Huang et al.   Frontiers in Genetics

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

Comprehensive Polyadenylation Site Maps in Yeast and Human Reveal Pervasive Alternative Polyadenylation

(2010) Fatih Ozsolak et al.   CELL

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

Clinical significance of pAKT and CD44v6 overexpression with breast cancer

(2010) Pei Yu et al.   JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY

Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line

(2010) Christine Vogel et al.   Molecular Systems Biology

Mammalian microRNAs predominantly act to decrease target mRNA levels

(2010) Huili Guo et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

The mechanism of eukaryotic translation initiation and principles of its regulation

(2010) Richard J. Jackson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Aberrant alternative splicing and extracellular matrix gene expression in mouse models of myotonic dystrophy

(2010) Hongqing Du et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution

(2010) Julian König et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB

(2010) Miriam Llorian et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Detection of splice junctions from paired-end RNA-seq data by SpliceMap

(2010) K. F. Au et al.   NUCLEIC ACIDS RESEARCH

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

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

RBPDB: a database of RNA-binding specificities

(2010) K. B. Cook et al.   NUCLEIC ACIDS RESEARCH

CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins

(2010) M. Khorshid et al.   NUCLEIC ACIDS RESEARCH

starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data

(2010) Jian-Hua Yang et al.   NUCLEIC ACIDS RESEARCH

miRBase: integrating microRNA annotation and deep-sequencing data

(2010) A. Kozomara et al.   NUCLEIC ACIDS RESEARCH

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

Transcription and post-transcriptional regulation of spermatogenesis

(2010) A. Bettegowda et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

ExprTarget: An Integrative Approach to Predicting Human MicroRNA Targets

(2010) Eric R. Gamazon et al.   PLoS One

A comprehensive in silico expression analysis of RNA binding proteins in normal and tumor tissue; identification of potential players in tumor formation

(2010) Pedro A. F. Galante et al.   RNA Biology

iCLIP Predicts the Dual Splicing Effects of TIA-RNA Interactions

(2010) Zhen Wang et al.   PLOS BIOLOGY

RNAcontext: A New Method for Learning the Sequence and Structure Binding Preferences of RNA-Binding Proteins

(2010) Hilal Kazan et al.   PLoS Computational Biology

Global and unbiased detection of splice junctions from RNA-seq data

(2010) Adam Ameur et al.   GENOME BIOLOGY

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Evolutionary Roles of Upstream Open Reading Frames in Mediating Gene Regulation in Fungi

(2009) Heather M. Hood et al.   Annual Review of Microbiology

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

The mRNA-Destabilizing Protein Tristetraprolin Is Suppressed in Many Cancers, Altering Tumorigenic Phenotypes and Patient Prognosis

(2009) S. E. Brennan et al.   CANCER RESEARCH

Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells

(2009) Christine Mayr et al.   CELL

Genome-wide Analysis of PTB-RNA Interactions Reveals a Strategy Used by the General Splicing Repressor to Modulate Exon Inclusion or Skipping

(2009) Yuanchao Xue et al.   MOLECULAR CELL

Coordinated posttranscriptional mRNA population dynamics during T-cell activation

(2009) Neelanjan Mukherjee et al.   Molecular Systems Biology

Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins

(2009) Debashish Ray et al.   NATURE BIOTECHNOLOGY

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

(2009) Qun Pan et al.   NATURE GENETICS

An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells

(2009) Gene W Yeo et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs

(2009) S. Granneman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans

(2009) S. E. Calvo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

Concordant Regulation of Translation and mRNA Abundance for Hundreds of Targets of a Human microRNA

(2009) David G. Hendrickson et al.   PLOS BIOLOGY

Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures

(2009) Steve Hoffmann et al.   PLoS Computational Biology

A computational approach for genome-wide mapping of splicing factor binding sites

(2009) Martin Akerman et al.   GENOME BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Application of a Translational Profiling Approach for the Comparative Analysis of CNS Cell Types

(2008) Joseph P. Doyle et al.   CELL

RNA-binding proteins and post-transcriptional gene regulation

(2008) Tina Glisovic et al.   FEBS LETTERS

Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2

(2008) C. Zhang et al.   GENES & DEVELOPMENT

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

The impact of microRNAs on protein output

(2008) Daehyun Baek et al.   NATURE

Widespread changes in protein synthesis induced by microRNAs

(2008) Matthias Selbach et al.   NATURE

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

(2008) Donny D. Licatalosi et al.   NATURE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

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

(2008) L. Dolken et al.   RNA

Proliferating Cells Express mRNAs with Shortened 3' Untranslated Regions and Fewer MicroRNA Target Sites

(2008) R. Sandberg et al.   SCIENCE