4.5 Review

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

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

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

Joseph V. Geisberg et al.

Article Medicine, Research & Experimental

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

Henrike Maatz et al.

JOURNAL OF CLINICAL INVESTIGATION (2014)

Article Biochemistry & Molecular Biology

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

Ishaan Gupta et al.

MOLECULAR SYSTEMS BIOLOGY (2014)

Article Biochemistry & Molecular Biology

STarMir: a web server for prediction of microRNA binding sites

William Rennie et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biochemistry & Molecular Biology

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

Inbal Paz et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Multidisciplinary Sciences

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

Tao Wang et al.

PLOS ONE (2014)

Review Cell Biology

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

Andreas R. Gruber et al.

WILEY INTERDISCIPLINARY REVIEWS-RNA (2014)

Review Cell Biology

Finding the target sites of RNA-binding proteins

Xiao Li et al.

WILEY INTERDISCIPLINARY REVIEWS-RNA (2014)

Article Biotechnology & Applied Microbiology

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

Matthew B. Friedersdorf et al.

GENOME BIOLOGY (2014)

Article Biotechnology & Applied Microbiology

dCLIP: a computational approach for comparative CLIP-seq analyses

Tao Wang et al.

GENOME BIOLOGY (2014)

Article Biotechnology & Applied Microbiology

GraphProt: modeling binding preferences of RNA-binding proteins

Daniel Maticzka et al.

GENOME BIOLOGY (2014)

Article Biotechnology & Applied Microbiology

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

Steve Hoffmann et al.

GENOME BIOLOGY (2014)

Article Biotechnology & Applied Microbiology

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

Beibei Chen et al.

GENOME BIOLOGY (2014)

Review Biochemistry & Molecular Biology

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

Christoph Schweingruber et al.

BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS (2013)

Article Biochemical Research Methods

RIP-chip enrichment analysis

Florian Erhard et al.

BIOINFORMATICS (2013)

Article Biochemical Research Methods

STAR: ultrafast universal RNA-seq aligner

Alexander Dobin et al.

BIOINFORMATICS (2013)

Article Biochemical Research Methods

SplicingCompass: differential splicing detection using RNA-Seq data

Moritz Aschoff et al.

BIOINFORMATICS (2013)

Article Biochemical Research Methods

mRNAStab-a web application for mRNA stability analysis

Andrei Alic et al.

BIOINFORMATICS (2013)

Article Biochemical Research Methods

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

Alper Kucukural et al.

BIOINFORMATICS (2013)

Article Biotechnology & Applied Microbiology

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

Jeroen Crappe et al.

BMC GENOMICS (2013)

Article Biochemical Research Methods

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

Marie-Agnes Dillies et al.

BRIEFINGS IN BIOINFORMATICS (2013)

Article Biochemistry & Molecular Biology

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

Yuanchao Xue et al.

Article Cell Biology

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

Alisa A. Mueller et al.

CURRENT OPINION IN CELL BIOLOGY (2013)

Review Biochemistry & Molecular Biology

Advances in the Techniques for the Prediction of microRNA Targets

Hao Zheng et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2013)

Article Multidisciplinary Sciences

A compendium of RNA-binding motifs for decoding gene regulation

Debashish Ray et al.

NATURE (2013)

Article Biotechnology & Applied Microbiology

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

Cole Trapnell et al.

NATURE BIOTECHNOLOGY (2013)

Article Biochemical Research Methods

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

Mainul Hoque et al.

NATURE METHODS (2013)

Article Biochemical Research Methods

QuaNCAT: quantitating proteome dynamics in primary cells

Andrew J. M. Howden et al.

NATURE METHODS (2013)

Review Genetics & Heredity

Alternative cleavage and polyadenylation: extent, regulation and function

Ran Elkon et al.

NATURE REVIEWS GENETICS (2013)

Article Biochemistry & Molecular Biology

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

Yin Hu et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Biochemistry & Molecular Biology

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

Chaolin Zhang et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Biochemistry & Molecular Biology

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

Yue Li et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Multidisciplinary Sciences

Structural features of Argonaute-GW182 protein interactions

Janina Pfaff et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Review Genetics & Heredity

Gene Expression Regulation by Upstream Open Reading Frames and Human Disease

Cristina Barbosa et al.

PLOS GENETICS (2013)

Review Cell Biology

Computational biology of RNA interactions

Christoph Dieterich et al.

WILEY INTERDISCIPLINARY REVIEWS-RNA (2013)

Review Cell Biology

Translation regulation gets its 'omics' moment

Scott Kuersten et al.

WILEY INTERDISCIPLINARY REVIEWS-RNA (2013)

Article Biotechnology & Applied Microbiology

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

Fabricio Loayza-Puch et al.

GENOME BIOLOGY (2013)

Article Biochemical Research Methods

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

Bjoern Schwalb et al.

BIOINFORMATICS (2012)

Article Biochemical Research Methods

Site identification in high-throughput RNA-protein interaction data

Philip J. Uren et al.

BIOINFORMATICS (2012)

Review Biochemical Research Methods

Tools for mapping high-throughput sequencing data

Nuno A. Fonseca et al.

BIOINFORMATICS (2012)

Article Biochemistry & Molecular Biology

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

Alfredo Castello et al.

Article Biochemistry & Molecular Biology

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

Claudia Fritsch et al.

GENOME RESEARCH (2012)

Article Biochemistry & Molecular Biology

A quantitative atlas of polyadenylation in five mammals

Adnan Derti et al.

GENOME RESEARCH (2012)

Article Biochemistry & Molecular Biology

Detecting differential usage of exons from RNA-seq data

Simon Anders et al.

GENOME RESEARCH (2012)

Article Biochemistry & Molecular Biology

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

David W. Reid et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2012)

Article Biochemistry & Molecular Biology

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

Gabriel B. Loeb et al.

MOLECULAR CELL (2012)

Article Biochemistry & Molecular Biology

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

Alexander G. Baltz et al.

MOLECULAR CELL (2012)

Article Multidisciplinary Sciences

The translational landscape of mTOR signalling steers cancer initiation and metastasis

Andrew C. Hsieh et al.

NATURE (2012)

Article Multidisciplinary Sciences

FMRP targets distinct mRNA sequence elements to regulate protein expression

Manuel Ascano et al.

NATURE (2012)

Review Genetics & Heredity

Regulation of cytoplasmic mRNA decay

Daniel R. Schoenberg et al.

NATURE REVIEWS GENETICS (2012)

Review Cell Biology

NMD: a multifaceted response to premature translational termination

Stephanie Kervestin et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2012)

Article Biochemistry & Molecular Biology

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

Thanasis Vergoulis et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biochemistry & Molecular Biology

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

Gerd Anders et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biochemistry & Molecular Biology

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

Maria Kalyna et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biochemistry & Molecular Biology

An in-depth map of polyadenylation sites in cancer

Yuefeng Lin et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biochemistry & Molecular Biology

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

Marion Scheibe et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biochemistry & Molecular Biology

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

Shihao Shen et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Multidisciplinary Sciences

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

Antonio Lembo et al.

PLOS ONE (2012)

Article Multidisciplinary Sciences

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

Sooncheol Lee et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Multidisciplinary Sciences

Decoding Human Cytomegalovirus

Noam Stern-Ginossar et al.

SCIENCE (2012)

Article Biochemistry & Molecular Biology

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

Svetlana Lebedeva et al.

MOLECULAR CELL (2011)

Article Multidisciplinary Sciences

Global quantification of mammalian gene expression control

Bjoern Schwanhaeusser et al.

NATURE (2011)

Article Biotechnology & Applied Microbiology

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

Razvan Nutiu et al.

NATURE BIOTECHNOLOGY (2011)

Article Biotechnology & Applied Microbiology

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

Chaolin Zhang et al.

NATURE BIOTECHNOLOGY (2011)

Review Biochemical Research Methods

Computational methods for transcriptome annotation and quantification using RNA-seq

Manuel Garber et al.

NATURE METHODS (2011)

Article Neurosciences

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

James R. Tollervey et al.

NATURE NEUROSCIENCE (2011)

Review Genetics & Heredity

RNA sequencing: advances, challenges and opportunities

Fatih Ozsolak et al.

NATURE REVIEWS GENETICS (2011)

Review Genetics & Heredity

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

Eric Huntzinger et al.

NATURE REVIEWS GENETICS (2011)

Review Genetics & Heredity

Non-coding RNAs in human disease

Manel Esteller

NATURE REVIEWS GENETICS (2011)

Article Biochemistry & Molecular Biology

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

Andreas R. Gruber et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Biochemistry & Molecular Biology

RBPDB: a database of RNA-binding specificities

Kate B. Cook et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Biochemistry & Molecular Biology

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

Mohsen Khorshid et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Biochemistry & Molecular Biology

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

Jian-Hua Yang et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Biochemistry & Molecular Biology

miRBase: integrating microRNA annotation and deep-sequencing data

Ana Kozomara et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Biotechnology & Applied Microbiology

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

David L. Corcoran et al.

GENOME BIOLOGY (2011)

Article Genetics & Heredity

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

Songbo Huang et al.

Frontiers in Genetics (2011)

Article Biochemical Research Methods

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

Mark D. Robinson et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

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

Thomas D. Wu et al.

BIOINFORMATICS (2010)

Article Oncology

Clinical significance of pAKT and CD44v6 overexpression with breast cancer

Pei Yu et al.

JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY (2010)

Article Biochemistry & Molecular Biology

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

Christine Vogel et al.

MOLECULAR SYSTEMS BIOLOGY (2010)

Article Multidisciplinary Sciences

Mammalian microRNAs predominantly act to decrease target mRNA levels

Huili Guo et al.

NATURE (2010)

Article Biochemical Research Methods

Analysis and design of RNA sequencing experiments for identifying isoform regulation

Yarden Katz et al.

NATURE METHODS (2010)

Review Cell Biology

The mechanism of eukaryotic translation initiation and principles of its regulation

Richard J. Jackson et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2010)

Article Biochemistry & Molecular Biology

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

Hongqing Du et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2010)

Article Biochemistry & Molecular Biology

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

Julian Koenig et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2010)

Article Biochemistry & Molecular Biology

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

Miriam Llorian et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2010)

Article Biochemistry & Molecular Biology

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

Kin Fai Au et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Biochemistry & Molecular Biology

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

Kai Wang et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Multidisciplinary Sciences

ExprTarget: An Integrative Approach to Predicting Human MicroRNA Targets

Eric R. Gamazon et al.

PLOS ONE (2010)

Review Biology

Transcription and post-transcriptional regulation of spermatogenesis

Anilkumar Bettegowda et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2010)

Article Biochemistry & Molecular Biology

iCLIP Predicts the Dual Splicing Effects of TIA-RNA Interactions

Zhen Wang et al.

PLOS BIOLOGY (2010)

Article Biochemical Research Methods

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

Hilal Kazan et al.

PLOS COMPUTATIONAL BIOLOGY (2010)

Article Biotechnology & Applied Microbiology

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

Adam Ameur et al.

GENOME BIOLOGY (2010)

Review Biotechnology & Applied Microbiology

From RNA-seq reads to differential expression results

Alicia Oshlack et al.

GENOME BIOLOGY (2010)

Article Biotechnology & Applied Microbiology

Differential expression analysis for sequence count data

Simon Anders et al.

GENOME BIOLOGY (2010)

Review Microbiology

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

Heather M. Hood et al.

ANNUAL REVIEW OF MICROBIOLOGY (2009)

Article Biochemical Research Methods

TopHat: discovering splice junctions with RNA-Seq

Cole Trapnell et al.

BIOINFORMATICS (2009)

Article Biochemistry & Molecular Biology

Coordinated posttranscriptional mRNA population dynamics during T-cell activation

Neelanjan Mukherjee et al.

MOLECULAR SYSTEMS BIOLOGY (2009)

Article Biotechnology & Applied Microbiology

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

Debashish Ray et al.

NATURE BIOTECHNOLOGY (2009)

Review Genetics & Heredity

RNA-Seq: a revolutionary tool for transcriptomics

Zhong Wang et al.

NATURE REVIEWS GENETICS (2009)

Article Biochemistry & Molecular Biology

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

Gene W. Yeo et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2009)

Article Multidisciplinary Sciences

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

Sander Granneman et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Multidisciplinary Sciences

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

Sarah E. Calvo et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Multidisciplinary Sciences

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

Nicholas T. Ingolia et al.

SCIENCE (2009)

Article Biochemistry & Molecular Biology

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

David G. Hendrickson et al.

PLOS BIOLOGY (2009)

Article Biochemical Research Methods

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

Steve Hoffmann et al.

PLOS COMPUTATIONAL BIOLOGY (2009)

Article Biotechnology & Applied Microbiology

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

Martin Akerman et al.

GENOME BIOLOGY (2009)

Article Biotechnology & Applied Microbiology

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

Ben Langmead et al.

GENOME BIOLOGY (2009)

Article Biochemistry & Molecular Biology

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

Joseph P. Doyle et al.

Review Biochemistry & Molecular Biology

RNA-binding proteins and post-transcriptional gene regulation

Tina Glisovic et al.

FEBS LETTERS (2008)

Article Multidisciplinary Sciences

Alternative isoform regulation in human tissue transcriptomes

Eric T. Wang et al.

NATURE (2008)

Article Multidisciplinary Sciences

The impact of microRNAs on protein output

Daehyun Baek et al.

NATURE (2008)

Article Multidisciplinary Sciences

Widespread changes in protein synthesis induced by microRNAs

Matthias Selbach et al.

NATURE (2008)

Article Multidisciplinary Sciences

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

Donny D. Licatalosi et al.

NATURE (2008)

Article Biochemical Research Methods

Mapping and quantifying mammalian transcriptomes by RNA-Seq

Ali Mortazavi et al.

NATURE METHODS (2008)

Article Biochemistry & Molecular Biology

New modes of translational control in development, behavior, and disease

Nahum Sonenberg et al.

MOLECULAR CELL (2007)

Article Genetics & Heredity

The role of site accessibility in microRNA target recognition

Michael Kertesz et al.

NATURE GENETICS (2007)

Article Biochemistry & Molecular Biology

MicroRNA targeting specificity in mammals: Determinants beyond seed pairing

Andrew Grimson et al.

MOLECULAR CELL (2007)

Article Critical Care Medicine

Electromagnetic navigation diagnostic bronchoscopy in peripheral lung lesions

Ralf Eberhardt et al.

CHEST (2007)

Article Biochemical Research Methods

A survey of DNA motif finding algorithms

Modan K. Das et al.

BMC BIOINFORMATICS (2007)

Article Biochemistry & Molecular Biology

PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes

Ju Youn Lee et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Biotechnology & Applied Microbiology

Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array

Paul J. Gardina et al.

BMC GENOMICS (2006)

Article Biochemistry & Molecular Biology

Using RNA secondary structures to guide sequence motif finding towards single-stranded regions

Michael Hiller et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Biochemical Research Methods

Prediction of mRNA polyadenylation sites by support vector machine

Yiming Cheng et al.

BIOINFORMATICS (2006)

Article Biochemistry & Molecular Biology

Mammalian CELF/Bruno-like RNA-binding proteins:: molecular characteristics and biological functions

Carine Barreau et al.

BIOCHIMIE (2006)

Article Biochemical Research Methods

CMfinder - a covariance model based RNA motif finding algorithm

ZZ Yao et al.

BIOINFORMATICS (2006)

Article Biochemistry & Molecular Biology

ARED 3.0: the large and diverse AU-rich transcriptome

Tala Bakheet et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Biochemistry & Molecular Biology

Alternative splicing: A new drug target of the post-genome era

M Hagiwara

BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS (2005)

Article Biochemistry & Molecular Biology

Human RISC couples microRNA biogenesis and posttranscriptional gene silencing

RI Gregory et al.

Article Biochemical Research Methods

PACdb:: PolyA cleavage site and 3′-UTR database

JM Brockman et al.

BIOINFORMATICS (2005)

Article Multidisciplinary Sciences

TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing

TP Chendrimada et al.

NATURE (2005)

Article Genetics & Heredity

Combinatorial microRNA target predictions

A Krek et al.

NATURE GENETICS (2005)

Article Multidisciplinary Sciences

Identifying tissue-selective transcription factor bindings sites in vertebrate promoters

AD Smith et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Biochemistry & Molecular Biology

Limitations and potentials of current motif discovery algorithms

JJ Hu et al.

NUCLEIC ACIDS RESEARCH (2005)

Review Biochemistry & Molecular Biology

MicroRNAs: Genomics, biogenesis, mechanism, and function

DP Bartel

Article Multidisciplinary Sciences

Crystal structure of argonaute and its implications for RISC slicer activity

JJ Song et al.

SCIENCE (2004)

Article Biochemistry & Molecular Biology

Transcriptional control in the segmentation gene network of Drosophila

MD Schroeder et al.

PLOS BIOLOGY (2004)

Article Biochemistry & Molecular Biology

RNA-binding proteins to assess gene expression states of co-cultivated cells in response to tumor cells

Luiz O. F. Penalva et al.

MOLECULAR CANCER (2004)

Article Multidisciplinary Sciences

CLIP identifies Nova-regulated RNA networks in the brain

J Ule et al.

SCIENCE (2003)

Review Genetics & Heredity

The power of the 3′ UTR:: Translational control and development

S Kuersten et al.

NATURE REVIEWS GENETICS (2003)

Article Multidisciplinary Sciences

Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae

Y Arava et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)

Article Biochemistry & Molecular Biology

Discovery of RNA structural elements using evolutionary computation

GB Fogel et al.

NUCLEIC ACIDS RESEARCH (2002)

Article Biochemistry & Molecular Biology

Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP

HD Zhang et al.

EMBO JOURNAL (2002)

Article Biochemistry & Molecular Biology

Ribonuclease activity and RNA binding of recombinant human Dicer

P Provost et al.

EMBO JOURNAL (2002)

Article Multidisciplinary Sciences

Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans

PJ Roy et al.

NATURE (2002)

Article Multidisciplinary Sciences

Precision and functional specificity in mRNA decay

YL Wang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)

Article Biochemistry & Molecular Biology

Dynalign: An algorithm for finding the secondary structure common to two RNA sequences

DH Mathews et al.

JOURNAL OF MOLECULAR BIOLOGY (2002)

Article Genetics & Heredity

Alternative splicing and genome complexity

D Brett et al.

NATURE GENETICS (2002)

Article Multidisciplinary Sciences

Argonaute2, a link between genetic and biochemical analyses of RNAi

SM Hammond et al.

SCIENCE (2001)

Article Biochemistry & Molecular Biology

Recent advances in RNA-protein recognition

JM Pérez-Cañadillas et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2001)

Article Multidisciplinary Sciences

Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays

SA Tenenbaum et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2000)

Review Biochemistry & Molecular Biology

Upstream open reading frames as regulators of mRNA translation

DR Morris et al.

MOLECULAR AND CELLULAR BIOLOGY (2000)

Article Biochemistry & Molecular Biology

Patterns of variant polyadenylation signal usage in human genes

E Beaudoing et al.

GENOME RESEARCH (2000)

Article Biochemical Research Methods

DNA binding sites: representation and discovery

GD Stormo

BIOINFORMATICS (2000)