A max-margin training of RNA secondary structure prediction integrated with the thermodynamic model

Evolutionary conservation of long non-coding RNAs; sequence, structure, function

(2013) Per Johnsson et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

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

(2013) Elena Rivas   RNA Biology

DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition

(2012) Kengo Sato et al.   BIOINFORMATICS

ViennaRNA Package 2.0

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

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

(2011) Kengo Sato et al.   BIOINFORMATICS

Rich Parameterization Improves RNA Structure Prediction

(2011) Shay Zakov et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more

(2011) E. Rivas et al.   RNA

RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming

(2010) Yuki Kato et al.   BIOINFORMATICS

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

Rfam: Wikipedia, clans and the "decimal" release

(2010) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH

Computational approaches for RNA energy parameter estimation

(2010) M. Andronescu et al.   RNA

A NON-PARAMETRIC BAYESIAN APPROACH FOR PREDICTING RNA SECONDARY STRUCTURES

(2010) KENGO SATO et al.   Journal of Bioinformatics and Computational Biology

Genome-wide searching with base-pairing kernel functions for noncoding RNAs: computational and expression analysis of snoRNA families in Caenorhabditis elegans

(2009) K. Morita et al.   NUCLEIC ACIDS RESEARCH

CENTROIDFOLD: a web server for RNA secondary structure prediction

(2009) K. Sato et al.   NUCLEIC ACIDS RESEARCH

NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure

(2009) Douglas H. Turner et al.   NUCLEIC ACIDS RESEARCH

Improved RNA secondary structure prediction by maximizing expected pair accuracy

(2009) Z. J. Lu et al.   RNA

Prediction of RNA secondary structure using generalized centroid estimators

(2008) Michiaki Hamada et al.   BIOINFORMATICS

Directed acyclic graph kernels for structural RNA analysis

(2008) Kengo Sato et al.   BMC BIOINFORMATICS

Centroid estimation in discrete high-dimensional spaces with applications in biology

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