Understanding the transcriptome through RNA structure

IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming

(2011) Kengo Sato et al.   BIOINFORMATICS

Structural Basis of Cooperative Ligand Binding by the Glycine Riboswitch

(2011) Ethan B. Butler et al.   CHEMISTRY & BIOLOGY

G–quadruplex RNA structure as a signal for neurite mRNA targeting

(2011) Murugan Subramanian et al.   EMBO REPORTS

Solution Structure of the K-Turn and Specifier Loop Domains from the Bacillus subtilis tyrS T-Box Leader RNA

(2011) Jiachen Wang et al.   JOURNAL OF MOLECULAR BIOLOGY

Comparison of Solution and Crystal Structures of PreQ1Riboswitch Reveals Calcium-Induced Changes in Conformation and Dynamics

(2011) Qi Zhang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

RNA Helicase p68 (DDX5) Regulates tau Exon 10 Splicing by Modulating a Stem-Loop Structure at the 5' Splice Site

(2011) A. Kar et al.   MOLECULAR AND CELLULAR BIOLOGY

RNA secondary structure in mutually exclusive splicing

(2011) Yun Yang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Alternate rRNA secondary structures as regulators of translation

(2011) Shu Feng et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RNA structure probing dash seq

(2011) K. M. Weeks   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modeling and automation of sequencing-based characterization of RNA structure

(2011) S. Aviran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)

(2011) J. B. Lucks et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA folding in living cells

(2011) Georgeta Zemora et al.   RNA Biology

An expanded collection and refined consensus model of glmS ribozymes

(2011) P. J. McCown et al.   RNA

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts et al.   GENOME BIOLOGY

Occurrence of a Quadruplex Motif in a Unique Insert within Exon C of the Bovine Estrogen Receptor α Gene (ESR1)

(2010) Kamila Derecka et al.   BIOCHEMISTRY

Dependence of RNA Tertiary Structural Stability on Mg2+Concentration: Interpretation of the Hill Equation and Coefficient

(2010) Desirae Leipply et al.   BIOCHEMISTRY

TheBCL-25′ Untranslated Region Contains an RNA G-Quadruplex-Forming Motif That Modulates Protein Expression

(2010) Ramla Shahid et al.   BIOCHEMISTRY

Fluorescence Competition and Optical Melting Measurements of RNA Three-Way Multibranch Loops Provide a Revised Model for Thermodynamic Parameters

(2010) Biao Liu et al.   BIOCHEMISTRY

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

(2010) Markus Hafner et al.   CELL

Advances in RNA structure analysis by chemical probing

(2010) Kevin M Weeks   CURRENT OPINION IN STRUCTURAL BIOLOGY

Phosphorylation of the PRC2 component Ezh2 is cell cycle-regulated and up-regulates its binding to ncRNA

(2010) S. Kaneko et al.   GENES & DEVELOPMENT

ZBP1 recognition of  -actin zipcode induces RNA looping

(2010) J. A. Chao et al.   GENES & DEVELOPMENT

Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data

(2010) Z. J. Lu et al.   GENOME RESEARCH

Selective Translational Control of the Alzheimer Amyloid Precursor Protein Transcript by Iron Regulatory Protein-1

(2010) Hyun-Hee Cho et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Mutation of the 5′-Untranslated Region Stem-Loop Structure Inhibits α1(I) Collagen Expressionin Vivo

(2010) Christopher J. Parsons et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

SAM Recognition and Conformational Switching Mechanism in the Bacillus subtilis yitJ S Box/SAM-I Riboswitch

(2010) Changrui Lu et al.   JOURNAL OF MOLECULAR BIOLOGY

Involvement of the 3′-untranslated region of the brain-derived neurotrophic factor gene in activity-dependent mRNA stabilization

(2010) Mamoru Fukuchi et al.   JOURNAL OF NEUROCHEMISTRY

Short RNAs Are Transcribed from Repressed Polycomb Target Genes and Interact with Polycomb Repressive Complex-2

(2010) Aditi Kanhere et al.   MOLECULAR CELL

The cspA mRNA Is a Thermosensor that Modulates Translation of the Cold-Shock Protein CspA

(2010) Anna Maria Giuliodori et al.   MOLECULAR CELL

Genome-wide Identification of Polycomb-Associated RNAs by RIP-seq

(2010) Jing Zhao et al.   MOLECULAR CELL

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz et al.   NATURE

A Pumilio-induced RNA structure switch in p27-3′ UTR controls miR-221 and miR-222 accessibility

(2010) Martijn Kedde et al.   NATURE CELL BIOLOGY

FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing

(2010) Jason G Underwood et al.   NATURE METHODS

A′-form RNA helices are required for cytoplasmic mRNA transport in Drosophila

(2010) Simon L Bullock et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A G-quadruplex structure within the 5′-UTR of TRF2 mRNA represses translation in human cells

(2010) Dennis Gomez et al.   NUCLEIC ACIDS RESEARCH

Translation on demand by a simple RNA-based thermosensor

(2010) Jens Kortmann et al.   NUCLEIC ACIDS RESEARCH

Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome

(2010) Daniel P. Riordan et al.   NUCLEIC ACIDS RESEARCH

Identification of a consensus element recognized and cleaved by IRE1α

(2010) Daisuke Oikawa et al.   NUCLEIC ACIDS RESEARCH

Long non-coding RNA ANRIL is required for the PRC2 recruitment to and silencing of p15 INK4B tumor suppressor gene

(2010) Y Kotake et al.   ONCOGENE

G-quadruplex structures in RNA stimulate mitochondrial transcription termination and primer formation

(2010) P. H. Wanrooij et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evaluation of the information content of RNA structure mapping data for secondary structure prediction

(2010) S. Quarrier et al.   RNA

ProbKnot: Fast prediction of RNA secondary structure including pseudoknots

(2010) S. Bellaousov et al.   RNA

Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure

(2010) X. Li et al.   RNA

An Allosteric Self-Splicing Ribozyme Triggered by a Bacterial Second Messenger

(2010) E. R. Lee et al.   SCIENCE

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

(2010) M.-C. Tsai et al.   SCIENCE

Disease-Associated Mutations That Alter the RNA Structural Ensemble

(2010) Matthew Halvorsen et al.   PLoS Genetics

Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes

(2010) Zasha Weinberg et al.   GENOME BIOLOGY

mRNA Localization: Gene Expression in the Spatial Dimension

(2009) Kelsey C. Martin et al.   CELL

Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes

(2009) B. J. Blencowe et al.   GENES & DEVELOPMENT

Bacillus subtilis trpLeader RNA

(2009) Gintaras Deikus et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

An O(n5) Algorithm for MFE Prediction of Kissing Hairpins and 4-Chains in Nucleic Acids

(2009) Ho-Lin Chen et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Architecture and secondary structure of an entire HIV-1 RNA genome

(2009) Joseph M. Watts et al.   NATURE

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

(2009) Debashish Ray et al.   NATURE BIOTECHNOLOGY

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

The protein factors MBNL1 and U2AF65 bind alternative RNA structures to regulate splicing

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

Multiple determinants within iron-responsive elements dictate iron regulatory protein binding and regulatory hierarchy

(2009) J. B. Goforth et al.   RNA

Improved RNA secondary structure prediction by maximizing expected pair accuracy

(2009) Z. J. Lu et al.   RNA

Role of RNA structure in regulating pre-mRNA splicing

(2009) M. Bryan Warf et al.   TRENDS IN BIOCHEMICAL SCIENCES

FlexStem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space

(2008) Xiang Chen et al.   BIOINFORMATICS

Prediction of RNA secondary structure using generalized centroid estimators

(2008) Michiaki Hamada et al.   BIOINFORMATICS

iFoldRNA: three-dimensional RNA structure prediction and folding

(2008) Shantanu Sharma et al.   BIOINFORMATICS

Regulation of ARE transcript 3′ end processing by the yeast Cth2 mRNA decay factor

(2008) Manoël Prouteau et al.   EMBO JOURNAL

The structure of NoRC-associated RNA is crucial for targeting the chromatin remodelling complex NoRC to the nucleolus

(2008) Christine Mayer et al.   EMBO REPORTS

Riboswitch RNAs: using RNA to sense cellular metabolism

(2008) T. M. Henkin   GENES & DEVELOPMENT

A Small Stem Loop Element Directs Internal Initiation of theURE2Internal Ribosome Entry Site inSaccharomyces cerevisiae

(2008) Lucas C. Reineke et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Messenger RNA targeting to endoplasmic reticulum stress signalling sites

(2008) Tomás Aragón et al.   NATURE

The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data

(2008) Marc Parisien et al.   NATURE

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

(2008) Donny D. Licatalosi et al.   NATURE

A stress-responsive RNA switch regulates VEGFA expression

(2008) Partho Sarothi Ray et al.   NATURE

Crystal structures of the SAM-III/SMK riboswitch reveal the SAM-dependent translation inhibition mechanism

(2008) Changrui Lu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structure of the SAM-II riboswitch bound to S-adenosylmethionine

(2008) Sunny D Gilbert et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments

(2008) Stefan E. Seemann et al.   NUCLEIC ACIDS RESEARCH

The Vienna RNA Websuite

(2008) A. R. Gruber et al.   NUCLEIC ACIDS RESEARCH

High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis

(2008) Somdeb Mitra et al.   NUCLEIC ACIDS RESEARCH

GtRNAdb: a database of transfer RNA genes detected in genomic sequence

(2008) P. P. Chan et al.   NUCLEIC ACIDS RESEARCH

Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes

(2008) M. Rabani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accurate SHAPE-directed RNA structure determination

(2008) K. E. Deigan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ShapeFinder: A software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis

(2008) S. M. Vasa et al.   RNA

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE

Polycomb Proteins Targeted by a Short Repeat RNA to the Mouse X Chromosome

(2008) J. Zhao et al.   SCIENCE

High-Throughput SHAPE Analysis Reveals Structures in HIV-1 Genomic RNA Strongly Conserved across Distinct Biological States

(2008) Kevin A Wilkinson et al.   PLOS BIOLOGY

RNA misfolding and the action of chaperones

(2007) Rick Russell   Frontiers in Bioscience-Landmark