Complete RNA inverse folding: computational design of functional hammerhead ribozymes

A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution

(2013) Vladimir Reinharz et al.   BIOINFORMATICS

RNAiFold: a web server for RNA inverse folding and molecular design

(2013) Juan Antonio Garcia-Martin et al.   NUCLEIC ACIDS RESEARCH

Thermozymes

(2013) Athanasios Saragliadis et al.   RNA Biology

Engineered Allosteric Ribozymes That Sense the Bacterial Second Messenger Cyclic Diguanosyl 5′-Monophosphate

(2012) Hongzhou Gu et al.   ANALYTICAL CHEMISTRY

Frnakenstein: multiple target inverse RNA folding

(2012) Rune B Lyngsø et al.   BMC BIOINFORMATICS

Synthetic Biology: Bits and pieces come to life

(2012) James Collins   NATURE

Direct and specific chemical control of eukaryotic translation with a synthetic RNA–protein interaction

(2012) Stephen J. Goldfless et al.   NUCLEIC ACIDS RESEARCH

De novo design of a synthetic riboswitch that regulates transcription termination

(2012) M. Wachsmuth et al.   NUCLEIC ACIDS RESEARCH

Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches

(2012) Evan Senter et al.   PLoS One

RNAiFOLD: A CONSTRAINT PROGRAMMING ALGORITHM FOR RNA INVERSE FOLDING AND MOLECULAR DESIGN

(2012) JUAN ANTONIO GARCIA-MARTIN et al.   Journal of Bioinformatics and Computational Biology

ViennaRNA Package 2.0

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

R2R - software to speed the depiction of aesthetic consensus RNA secondary structures

(2011) Zasha Weinberg et al.   BMC BIOINFORMATICS

Design and self-assembly of siRNA-functionalized RNA nanoparticles for use in automated nanomedicine

(2011) Kirill A Afonin et al.   Nature Protocols

Engineering a Direct and Inducible Protein−RNA Interaction To Regulate RNA Biology

(2010) Brian J. Belmont et al.   ACS Chemical Biology

Inverse folding of RNA pseudoknot structures

(2010) James ZM Gao et al.   Algorithms for Molecular Biology

Nucleic acid sequence design via efficient ensemble defect optimization

(2010) Joseph N. Zadeh et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Reprogramming bacteria to seek and destroy an herbicide

(2010) Joy Sinha et al.   Nature Chemical Biology

Rfam: Wikipedia, clans and the "decimal" release

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

Topology Links RNA Secondary Structure with Global Conformation, Dynamics, and Adaptation

(2010) M. H. Bailor et al.   SCIENCE

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

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

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

Improved Aptazyme Design and In Vivo Screening Enable Riboswitching in Bacteria

(2008) Markus Wieland et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Generation of synthetic RNA-based thermosensors

(2008) Torsten Waldminghaus et al.   BIOLOGICAL CHEMISTRY

Computational strategies for the automated design of RNA nanoscale structures from building blocks using NanoTiler

(2008) Eckart Bindewald et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Programming biomolecular self-assembly pathways

(2008) Peng Yin et al.   NATURE

The Vienna RNA Websuite

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

Hammerhead redux: Does the new structure fit the old biochemical data?

(2008) J. A. Nelson et al.   RNA