RPI-Pred: predicting ncRNA-protein interaction using sequence and structural information

SVM-PB-Pred: SVM Based Protein Block Prediction Method Using Sequence Profiles and Secondary Structures

(2014) V. Suresh et al.   PROTEIN AND PEPTIDE LETTERS

Computational prediction of associations between long non-coding RNAs and proteins

(2013) Qiongshi Lu et al.   BMC GENOMICS

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

Structure and function of long noncoding RNAs in epigenetic regulation

(2013) Tim R Mercer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Stimulation of ribosomal frameshifting by RNA G-quadruplex structures

(2013) Chien-Hung Yu et al.   NUCLEIC ACIDS RESEARCH

NPInter v2.0: an updated database of ncRNA interactions

(2013) Jiao Yuan et al.   NUCLEIC ACIDS RESEARCH

Bioinformatic analysis of the protein/DNA interface

(2013) Bohdan Schneider et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

De novo prediction of RNA–protein interactions from sequence information

(2012) Ying Wang et al.   Molecular BioSystems

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Coarse-Grained Prediction of RNA Loop Structures

(2012) Liang Liu et al.   PLoS One

Silencing and Innate Immunity in Plant Defense Against Viral and Non-Viral Pathogens

(2012) Anna Zvereva et al.   Viruses-Basel

Automated and fast building of three-dimensional RNA structures

(2012) Yunjie Zhao et al.   Scientific Reports

Emerging roles of RNA and RNA-binding protein network in cancer cells

(2011) Mee-Young Kim et al.   BMB Reports

Predicting RNA-Protein Interactions Using Only Sequence Information

(2011) Usha K Muppirala et al.   BMC BIOINFORMATICS

Deciphering the role of RNA-binding proteins in the post-transcriptional control of gene expression

(2011) S. Kishore et al.   Briefings in Functional Genomics

PDB-2-PB: a curated online protein block sequence database

(2011) V. Suresh et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY

Physics-Based De Novo Prediction of RNA 3D Structures

(2011) Song Cao et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Predicting protein associations with long noncoding RNAs

(2011) Matteo Bellucci et al.   NATURE METHODS

In silico characterization and prediction of global protein–mRNA interactions in yeast

(2011) Vera Pancaldi et al.   NUCLEIC ACIDS RESEARCH

Diverse roles of host RNA binding proteins in RNA virus replication

(2011) Zhenghe Li et al.   RNA Biology

RNA-RNA and RNA-protein interactions in coronavirus replication and transcription

(2011) Isabel Sola et al.   RNA Biology

RNA–protein interactions in human health and disease

(2011) Ahmad M. Khalil et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Computing the conformational entropy for RNA folds

(2010) Liang Liu et al.   JOURNAL OF CHEMICAL PHYSICS

The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation

(2010) Vidisha Tripathi et al.   MOLECULAR CELL

RBPDB: a database of RNA-binding specificities

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

PRIDB: a protein-RNA interface database

(2010) B. A. Lewis et al.   NUCLEIC ACIDS RESEARCH

The RCSB Protein Data Bank: redesigned web site and web services

(2010) P. W. Rose et al.   NUCLEIC ACIDS RESEARCH

On the significance of an RNA tertiary structure prediction

(2010) C. E. Hajdin et al.   RNA

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

(2009) Debashish Ray et al.   NATURE BIOTECHNOLOGY

RNA processing and its regulation: global insights into biological networks

(2009) Donny D. Licatalosi et al.   NATURE REVIEWS GENETICS

Web 3DNA--a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures

(2009) G. Zheng et al.   NUCLEIC ACIDS RESEARCH

Triplex structures in an RNA pseudoknot enhance mechanical stability and increase efficiency of -1 ribosomal frameshifting

(2009) G. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dissecting the expression dynamics of RNA-binding proteins in posttranscriptional regulatory networks

(2009) N. Mittal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters

(2009) M. A. Jonikas et al.   RNA

Prediction of geometrically feasible three-dimensional structures of pseudoknotted RNA through free energy estimation

(2009) J. Zhang et al.   RNA

RNA Folding: Conformational Statistics, Folding Kinetics, and Ion Electrostatics

(2008) Shi-Jie Chen   Annual Review of Biophysics

The Vienna RNA Websuite

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

Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms

(2008) F. Ding et al.   RNA

Frameshifting RNA pseudoknots: Structure and mechanism

(2008) David P. Giedroc et al.   VIRUS RESEARCH

Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System

(2008) Daniel J Hogan et al.   PLOS BIOLOGY