LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search

The Rainbow Spectrum of RNA Secondary Structures

(2018) Thomas J. X. Li et al.   BULLETIN OF MATHEMATICAL BIOLOGY

Using Genome Sequence to Enable the Design of Medicines and Chemical Probes

(2018) Alicia J. Angelbello et al.   CHEMICAL REVIEWS

mRNAs and lncRNAs intrinsically form secondary structures with short end-to-end distances

(2018) Wan-Jung C. Lai et al.   Nature Communications

Cotranscriptional folding of a riboswitch at nucleotide resolution

(2016) Kyle E Watters et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RNAcentral: a comprehensive database of non-coding RNA sequences

(2016)   NUCLEIC ACIDS RESEARCH

Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures

(2016) Michael F. Sloma et al.   RNA

Cotranscriptional folding of a riboswitch at nucleotide resolution

(2016) Kyle E Watters et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

NONCODE 2016: an informative and valuable data source of long non-coding RNAs

(2015) Yi Zhao et al.   NUCLEIC ACIDS RESEARCH

Discovery of Novel ncRNA Sequences in Multiple Genome Alignments on the Basis of Conserved and Stable Secondary Structures

(2015) Yinghan Fu et al.   PLoS One

Big Data: Astronomical or Genomical?

(2015) Zachary D. Stephens et al.   PLOS BIOLOGY

Faster algorithms for RNA-folding using the Four-Russians method

(2014) Balaji Venkatachalam et al.   Algorithms for Molecular Biology

The separation between the 5′-3′ ends in long RNA molecules is short and nearly constant

(2014) Nehemías Leija-Martínez et al.   NUCLEIC ACIDS RESEARCH

Ensemble-based prediction of RNA secondary structures

(2013) Nima Aghaeepour et al.   BMC BIOINFORMATICS

Global or local? Predicting secondary structure and accessibility in mRNAs

(2012) Sita J. Lange et al.   NUCLEIC ACIDS RESEARCH

Computational analysis of noncoding RNAs

(2012) Stefan Washietl et al.   Wiley Interdisciplinary Reviews-RNA

Reducing the worst case running times of a family of RNA and CFG problems, using Valiant's approach

(2011) Shay Zakov et al.   Algorithms for Molecular Biology

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

Strategies for Recognition of Stem−Loop RNA Structures by Synthetic Ligands: Application to the HIV-1 Frameshift Stimulatory Sequence

(2010) Prakash B. Palde et al.   JOURNAL OF MEDICINAL CHEMISTRY

The ends of a large RNA molecule are necessarily close

(2010) Aron M. Yoffe et al.   NUCLEIC ACIDS RESEARCH

ProbKnot: Fast prediction of RNA secondary structure including pseudoknots

(2010) S. Bellaousov et al.   RNA

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

(2009) Joseph M. Watts et al.   NATURE

The promises and pitfalls of RNA-interference-based therapeutics

(2009) Daniela Castanotto et al.   NATURE

CENTROIDFOLD: a web server for RNA secondary structure prediction

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

Dynamic Combinatorial Selection of Molecules Capable of Inhibiting the (CUG) Repeat RNA−MBNL1 Interaction In Vitro: Discovery of Lead Compounds Targeting Myotonic Dystrophy (DM1)

(2008) Peter C. Gareiss et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The impact of target site accessibility on the design of effective siRNAs

(2008) Hakim Tafer et al.   NATURE BIOTECHNOLOGY