RNA structure through multidimensional chemical mapping

Automated band annotation for RNA structure probing experiments with numerous capillary electrophoresis profiles

(2015) Seungmyung Lee et al.   BIOINFORMATICS

iFoldRNA v2: folding RNA with constraints: Fig. 1.

(2015) Andrey Krokhotin et al.   BIOINFORMATICS

Structural Snapshots of Actively Translating Human Ribosomes

(2015) Elmar Behrmann et al.   CELL

Metal Ion-Mediated Nucleobase Recognition by the ZTP Riboswitch

(2015) Jeremiah J. Trausch et al.   CHEMISTRY & BIOLOGY

The architecture of the spliceosomal U4/U6.U5 tri-snRNP

(2015) Thi Hoang Duong Nguyen et al.   NATURE

Structural imprints in vivo decode RNA regulatory mechanisms

(2015) Robert C. Spitale et al.   NATURE

High-throughput determination of RNA structure by proximity ligation

(2015) Vijay Ramani et al.   NATURE BIOTECHNOLOGY

Crystal structure of the Varkud satellite ribozyme

(2015) Nikolai B Suslov et al.   Nature Chemical Biology

Integrative, dynamic structural biology at atomic resolution—it's about time

(2015) Henry van den Bedem et al.   NATURE METHODS

Primerize: automated primer assembly for transcribing non-coding RNA domains

(2015) Siqi Tian et al.   NUCLEIC ACIDS RESEARCH

SHAPE Selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data

(2015) Line Dahl Poulsen et al.   RNA

RNA-PuzzlesRound II: assessment of RNA structure prediction programs applied to three large RNA structures

(2015) Zhichao Miao et al.   RNA

Structural basis of pre-mRNA splicing

(2015) Jing Hang et al.   SCIENCE

The RNA structurome: transcriptome-wide structure probing with next-generation sequencing

(2015) Chun Kit Kwok et al.   TRENDS IN BIOCHEMICAL SCIENCES

Rich RNA Structure Landscapes Revealed by Mutate-and-Map Analysis

(2015) Pablo Cordero et al.   PLoS Computational Biology

Computational Analysis of Conserved RNA Secondary Structure in Transcriptomes and Genomes

(2014) Sean R. Eddy   Annual Review of Biophysics

Bayesian Energy Landscape Tilting: Towards Concordant Models of Molecular Ensembles

(2014) Kyle A. Beauchamp et al.   BIOPHYSICAL JOURNAL

Landscape and variation of RNA secondary structure across the human transcriptome

(2014) Yue Wan et al.   NATURE

Structural insights into recognition of c-di-AMP by the ydaO riboswitch

(2014) Ang Gao et al.   Nature Chemical Biology

c-di-AMP binds the ydaO riboswitch in two pseudo-symmetry–related pockets

(2014) Aiming Ren et al.   Nature Chemical Biology

RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP)

(2014) Nathan A Siegfried et al.   NATURE METHODS

Mapping the miRNA interactome by cross-linking ligation and sequencing of hybrids (CLASH)

(2014) Aleksandra Helwak et al.   Nature Protocols

Massive parallel-sequencing-based hydroxyl radical probing of RNA accessibility

(2014) Lukasz Jan Kielpinski et al.   NUCLEIC ACIDS RESEARCH

Structural basis for diversity in the SAM clan of riboswitches

(2014) J. J. Trausch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Speciation of a group I intron into a lariat capping ribozyme

(2014) M. Meyer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-molecule correlated chemical probing of RNA

(2014) P. J. Homan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA design rules from a massive open laboratory

(2014) Jeehyung Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA secondary structure modeling at consistent high accuracy using differential SHAPE

(2014) G. M. Rice et al.   RNA

High-throughput mutate-map-rescue evaluates SHAPE-directed RNA structure and uncovers excited states

(2014) Siqi Tian et al.   RNA

Mod-seq: high-throughput sequencing for chemical probing of RNA structure

(2014) J. Talkish et al.   RNA

Structure of the Yeast Mitochondrial Large Ribosomal Subunit

(2014) A. Amunts et al.   SCIENCE

Seq and CLIP through the miRNA world

(2014) Nitish Mittal et al.   GENOME BIOLOGY

Principles for Understanding the Accuracy of SHAPE-Directed RNA Structure Modeling

(2013) Christopher W. Leonard et al.   BIOCHEMISTRY

GPU-based acceleration of an RNA tertiary structure prediction algorithm

(2013) Yongkweon Jeon et al.   COMPUTERS IN BIOLOGY AND MEDICINE

RNA structure analysis of human spliceosomes reveals a compact 3D arrangement of snRNAs at the catalytic core

(2013) Maria Anokhina et al.   EMBO JOURNAL

Three-state mechanism couples ligand and temperature sensing in riboswitches

(2013) Anke Reining et al.   NATURE

Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions

(2013) Zsuzsanna Sükösd et al.   NUCLEIC ACIDS RESEARCH

Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots

(2013) C. E. Hajdin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Thermostable group II intron reverse transcriptase fusion proteins and their use in cDNA synthesis and next-generation RNA sequencing

(2013) S. Mohr et al.   RNA

Comparison of SIV and HIV-1 Genomic RNA Structures Reveals Impact of Sequence Evolution on Conserved and Non-Conserved Structural Motifs

(2013) Elizabeth Pollom et al.   PLoS Pathogens

Quantitative Dimethyl Sulfate Mapping for Automated RNA Secondary Structure Inference

(2012) Pablo Cordero et al.   BIOCHEMISTRY

An RNA Mapping DataBase for curating RNA structure mapping experiments

(2012) Pablo Cordero et al.   BIOINFORMATICS

On the Use of Experimental Observations to Bias Simulated Ensembles

(2012) Jed W. Pitera et al.   Journal of Chemical Theory and Computation

Determining RNA three-dimensional structures using low-resolution data

(2012) Marc Parisien et al.   JOURNAL OF STRUCTURAL BIOLOGY

Genome-wide Measurement of RNA Folding Energies

(2012) Yue Wan et al.   MOLECULAR CELL

Emerging roles of non-coding RNAs in brain evolution, development, plasticity and disease

(2012) Irfan A. Qureshi et al.   NATURE REVIEWS NEUROSCIENCE

Structural insights into ligand binding and gene expression control by an adenosylcobalamin riboswitch

(2012) Alla Peselis et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction

(2012) Stefan Washietl et al.   NUCLEIC ACIDS RESEARCH

Understanding the Errors of SHAPE-Directed RNA Structure Modeling

(2011) Wipapat Kladwang et al.   BIOCHEMISTRY

HiTRACE: high-throughput robust analysis for capillary electrophoresis

(2011) Sungroh Yoon et al.   BIOINFORMATICS

Structural Basis of Cooperative Ligand Binding by the Glycine Riboswitch

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

Automated RNA tertiary structure prediction from secondary structure and low-resolution restraints

(2011) Matthew G. Seetin et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble

(2011) Andrew C Stelzer et al.   Nature Chemical Biology

A two-dimensional mutate-and-map strategy for non-coding RNA structure

(2011) Wipapat Kladwang et al.   Nature Chemistry

Characterizing RNA dynamics at atomic resolution using solution-state NMR spectroscopy

(2011) Jameson R Bothe et al.   NATURE METHODS

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

A mutate-and-map strategy accurately infers the base pairs of a 35-nucleotide model RNA

(2011) W. Kladwang et al.   RNA

A Mutate-and-Map Strategy for Inferring Base Pairs in Structured Nucleic Acids: Proof of Concept on a DNA/RNA Helix

(2010) Wipapat Kladwang et al.   BIOCHEMISTRY

Advances in RNA structure analysis by chemical probing

(2010) Kevin M Weeks   CURRENT OPINION IN STRUCTURAL BIOLOGY

Discrete Structure of an RNA Folding Intermediate Revealed by Cryo-electron Microscopy

(2010) Nathan J. Baird et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz et al.   NATURE

Rosetta in CAPRI rounds 13-19

(2010) Sarel J. Fleishman et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Riboswitch function: Flipping the switch or tuning the dimmer?

(2010) Nathan J. Baird et al.   RNA Biology

Dissecting electrostatic screening, specific ion binding, and ligand binding in an energetic model for glycine riboswitch folding

(2010) J. Lipfert et al.   RNA

A balance between circular and linear forms of the dengue virus genome is crucial for viral replication

(2010) S. M. Villordo et al.   RNA

Protein Sectors: Evolutionary Units of Three-Dimensional Structure

(2009) Najeeb Halabi et al.   CELL

Toward a structural understanding of IRES RNA function

(2009) Megan E Filbin et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

(2009) Joseph M. Watts et al.   NATURE

Macromolecular Modeling with Rosetta

(2008) Rhiju Das et al.   Annual Review of Biochemistry

Molecular modelling of the GIR1 branching ribozyme gives new insight into evolution of structurally related ribozymes

(2008) Bertrand Beckert et al.   EMBO JOURNAL

A Three-Dimensional Model of a Group II Intron RNA and Its Interaction with the Intron-Encoded Reverse Transcriptase

(2008) Lixin Dai et al.   MOLECULAR CELL

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

(2008) Somdeb Mitra et al.   NUCLEIC ACIDS RESEARCH

Structural inference of native and partially folded RNA by high-throughput contact mapping

(2008) R. Das 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

Riboswitches in Eubacteria Sense the Second Messenger Cyclic Di-GMP

(2008) N. Sudarsan et al.   SCIENCE

The Eukaryotic Genome as an RNA Machine

(2008) P. P. Amaral et al.   SCIENCE