aRNAque: an evolutionary algorithm for inverse pseudoknotted RNA folding inspired by Lévy flights

MoiRNAiFold: a novel tool for complex in silico RNA design

(2021) Gerard Minuesa et al.   NUCLEIC ACIDS RESEARCH

Principles for Predicting RNA Secondary Structure Design Difficulty

(2016) Jeff Anderson-Lee et al.   JOURNAL OF MOLECULAR BIOLOGY

incaRNAfbinv: a web server for the fragment-based design of RNA sequences

(2016) Matan Drory Retwitzer et al.   NUCLEIC ACIDS RESEARCH

antaRNA: ant colony-based RNA sequence design

(2015) Robert Kleinkauf et al.   BIOINFORMATICS

ERD: a fast and reliable tool for RNA design including constraints

(2015) Ali Esmaili-Taheri et al.   BMC BIOINFORMATICS

Evolutionary solution for the RNA design problem

(2014) A. Esmaili-Taheri et al.   BIOINFORMATICS

Construction of RNA nanocages by re-engineering the packaging RNA of Phi29 bacteriophage

(2014) Chenhui Hao et al.   Nature Communications

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

Genetic Screens in Human Cells Using the CRISPR-Cas9 System

(2013) Tim Wang et al.   SCIENCE

Reconstruction of Natural RNA Sequences from RNA Shape, Thermodynamic Stability, Mutational Robustness, and Linguistic Complexity by Evolutionary Computation

(2012) N. Dromi et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

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

Multi-Objective Genetic Algorithm for Pseudoknotted RNA Sequence Design

(2012) Akito Taneda   Frontiers in Genetics

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

Refining transcriptional regulatory networks using network evolutionary models and gene histories

(2010) Xiuwei Zhang 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

Nanoparticle-mediated delivery of siRNA targeting Parp1 extends survival of mice bearing tumors derived from Brca1-deficient ovarian cancer cells

(2010) M. S. Goldberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Auto-validating von Neumann rejection sampling from small phylogenetic tree spaces

(2009) Raazesh Sainudiin et al.   Algorithms for Molecular Biology

PseudoBase++: an extension of PseudoBase for easy searching, formatting and visualization of pseudoknots

(2008) M. Taufer et al.   NUCLEIC ACIDS RESEARCH

Lévy flights and superdiffusion in the context of biological encounters and random searches

(2008) G.M. Viswanathan et al.   Physics of Life Reviews

Higher-Order Cellular Information Processing with Synthetic RNA Devices

(2008) M. N. Win et al.   SCIENCE