Genome-scale characterization of RNA tertiary structures and their functional impact by RNA solvent accessibility prediction

Contact Statistics Highlight Distinct Organizing Principles of Proteins and RNA

(2016) Lei Liu et al.   BIOPHYSICAL JOURNAL

From static to dynamic: the need for structural ensembles and a predictive model of RNA folding and function

(2015) Daniel Herschlag et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Structural imprints in vivo decode RNA regulatory mechanisms

(2015) Robert C. Spitale et al.   NATURE

Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction

(2015) Eleonora De Leonardis et al.   NUCLEIC ACIDS RESEARCH

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

Improving prediction of secondary structure, local backbone angles and solvent accessible surface area of proteins by iterative deep learning

(2015) Rhys Heffernan et al.   Scientific Reports

The impact of RNA structure on coding sequence evolution in both bacteria and eukaryotes

(2014) Wanjun Gu et al.   BMC EVOLUTIONARY BIOLOGY

Landscape and variation of RNA secondary structure across the human transcriptome

(2014) Yue Wan et al.   NATURE

Insights into RNA structure and function from genome-wide studies

(2014) Stefanie A. Mortimer et al.   NATURE REVIEWS GENETICS

CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction

(2014) T. Puton et al.   NUCLEIC ACIDS RESEARCH

The RCSB Protein Data Bank: views of structural biology for basic and applied research and education

(2014) Peter W. Rose et al.   NUCLEIC ACIDS RESEARCH

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

(2013) Silvi Rouskin et al.   NATURE

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

The four ingredients of single-sequence RNA secondary structure prediction. A unifying perspective

(2013) Elena Rivas   RNA Biology

Inactive or moderately active human promoters are enriched for inter-individual epialleles

(2013) Carolina Gemma et al.   GENOME BIOLOGY

Regulation of eukaryotic gene expression by the untranslated gene regions and other non-coding elements

(2012) Lucy W. Barrett et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

1000 Genomes-based imputation identifies novel and refined associations for the Wellcome Trust Case Control Consortium phase 1 Data

(2012) Jie Huang et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Functional complexity and regulation through RNA dynamics

(2012) Elizabeth A. Dethoff et al.   NATURE

Sensitive measurement of single-nucleotide polymorphism-induced changes of RNA conformation: application to disease studies

(2012) Raheleh Salari et al.   NUCLEIC ACIDS RESEARCH

Predicting the effects of frameshifting indels

(2012) Jing Hu et al.   GENOME BIOLOGY

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates

(2011) Y. Yang et al.   BIOINFORMATICS

Understanding the transcriptome through RNA structure

(2011) Yue Wan et al.   NATURE REVIEWS GENETICS

Taming free energy landscapes with RNA chaperones

(2011) Sarah A. Woodson   RNA Biology

The functional spectrum of low-frequency coding variation

(2011) Gabor T Marth et al.   GENOME BIOLOGY

Probing Mechanism and Transition State of RNA Refolding

(2010) Boris Fürtig et al.   ACS Chemical Biology

Quantifying the relationship between sequence and three-dimensional structure conservation in RNA

(2010) Emidio Capriotti et al.   BMC BIOINFORMATICS

The RNA structurome: high-throughput probing

(2010) Eric Westhof et al.   NATURE METHODS

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Disease-Associated Mutations That Alter the RNA Structural Ensemble

(2010) Matthew Halvorsen et al.   PLoS Genetics

The Centrality of RNA

(2009) Phillip A. Sharp   CELL

Prediction of protein functional residues from sequence by probability density estimation

(2008) J. D. Fischer et al.   BIOINFORMATICS

Strategies for measuring evolutionary conservation of RNA secondary structures

(2008) Andreas R Gruber et al.   BMC BIOINFORMATICS