Cooperative gene regulation by microRNA pairs and their identification using a computational workflow

Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding

(2013) Aleksandra Helwak et al.   CELL

Tertiary structure-based analysis of microRNA-target interactions

(2013) H. H. Gan et al.   RNA

The Structure of Human Argonaute-2 in Complex with miR-20a

(2012) Elad Elkayam et al.   CELL

Computational analysis of target hub gene repression regulated by multiple and cooperative miRNAs

(2012) Xin Lai et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

Automated 3D structure composition for large RNAs

(2012) Mariusz Popenda et al.   NUCLEIC ACIDS RESEARCH

Molecular Dynamics Simulation and Binding Energy Calculation for Estimation of Oligonucleotide Duplex Thermostability in RNA-Based Therapeutics

(2011) Lingling Shen et al.   Journal of Chemical Information and Modeling

A molecular dynamics study of a miRNA:mRNA interaction

(2011) Giulia Paciello et al.   JOURNAL OF MOLECULAR MODELING

RNA and protein 3D structure modeling: similarities and differences

(2011) Kristian Rother et al.   JOURNAL OF MOLECULAR MODELING

Cross-linking, ligation, and sequencing of hybrids reveals RNA-RNA interactions in yeast

(2011) G. Kudla et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

(2010) Chen Li et al.   BMC Systems Biology

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

The road toward microRNA therapeutics

(2010) Anita G. Seto   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

NUPACK: Analysis and design of nucleic acid systems

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

miRTarBase: a database curates experimentally validated microRNA–target interactions

(2010) Sheng-Da Hsu et al.   NUCLEIC ACIDS RESEARCH

A Viral microRNA Down-Regulates Multiple Cell Cycle Genes through mRNA 5′UTRs

(2010) Finn Grey et al.   PLoS Pathogens

Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites

(2010) Doron Betel et al.   GENOME BIOLOGY

VARNA: Interactive drawing and editing of the RNA secondary structure

(2009) Kévin Darty et al.   BIOINFORMATICS

Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM

(2009) Pavel Banáš et al.   METHODS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

DOCK 6: Combining techniques to model RNA-small molecule complexes

(2009) P. T. Lang et al.   RNA

Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases

(2008) Xi Chen et al.   CELL RESEARCH

Most mammalian mRNAs are conserved targets of microRNAs

(2008) R. C. Friedman et al.   GENOME RESEARCH

Widespread changes in protein synthesis induced by microRNAs

(2008) Matthias Selbach et al.   NATURE

The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data

(2008) Marc Parisien et al.   NATURE

Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex

(2008) Yanli Wang et al.   NATURE

mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein–enriched transcripts

(2008) Molly Hammell et al.   NATURE METHODS

miR2Disease: a manually curated database for microRNA deregulation in human disease

(2008) Q. Jiang et al.   NUCLEIC ACIDS RESEARCH

Circulating microRNAs as stable blood-based markers for cancer detection

(2008) P. S. Mitchell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computational analysis of miRNA-mediated repression of translation: Implications for models of translation initiation inhibition

(2008) T. Nissan et al.   RNA