Accurate transcriptome-wide prediction of microRNA targets and small interfering RNA off-targets with MIRZA-G

Online GESS: prediction of miRNA-like off-target effects in large-scale RNAi screen data by seed region analysis

(2014) Bahar Yilmazel et al.   BMC BIOINFORMATICS

ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs

(2014) P. J. Balwierz et al.   GENOME RESEARCH

Global Analyses of the Effect of Different Cellular Contexts on MicroRNA Targeting

(2014) Jin-Wu Nam et al.   MOLECULAR CELL

Unambiguous Identification of miRNA:Target Site Interactions by Different Types of Ligation Reactions

(2014) Stefanie Grosswendt et al.   MOLECULAR CELL

Identification and consequences of miRNA–target interactions — beyond repression of gene expression

(2014) Jean Hausser et al.   NATURE REVIEWS GENETICS

Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding

(2013) Aleksandra Helwak et al.   CELL

Analysis of CDS-located miRNA target sites suggests that they can effectively inhibit translation

(2013) J. Hausser et al.   GENOME RESEARCH

An siRNA screen for NFAT activation identifies septins as coordinators of store-operated Ca2+ entry

(2013) Sonia Sharma et al.   NATURE

A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets

(2013) Mohsen Khorshid et al.   NATURE METHODS

DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows

(2013) Maria D. Paraskevopoulou et al.   NUCLEIC ACIDS RESEARCH

SeedSeq: Off-Target Transcriptome Database

(2013) Shaoli Das et al.   Biomed Research International

An alternative mode of microRNA target recognition

(2012) Sung Wook Chi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

MicroRNA-106b-25 cluster expression is associated with early disease recurrence and targets caspase-7 and focal adhesion in human prostate cancer

(2012) R S Hudson et al.   ONCOGENE

Genome-Wide RNAi Screens Identify Genes Required for Ricin and PE Intoxications

(2011) Dimitri Moreau et al.   DEVELOPMENTAL CELL

microRNA-101 is a potent inhibitor of autophagy

(2011) Lisa B Frankel et al.   EMBO JOURNAL

Gene silencing by microRNAs: contributions of translational repression and mRNA decay

(2011) Eric Huntzinger et al.   NATURE REVIEWS GENETICS

Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs

(2011) David M Garcia et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Ruffus: a lightweight Python library for computational pipelines

(2010) Leo Goodstadt   BIOINFORMATICS

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

miRBase: integrating microRNA annotation and deep-sequencing data

(2010) A. Kozomara et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Doron Betel et al.   GENOME BIOLOGY

Lost in translation: an assessment and perspective for computational microRNA target identification

(2009) Panagiotis Alexiou et al.   BIOINFORMATICS

Relative contribution of sequence and structure features to the mRNA binding of Argonaute/EIF2C-miRNA complexes and the degradation of miRNA targets

(2009) J. Hausser et al.   GENOME RESEARCH

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

(2009) Da Wei Huang et al.   Nature Protocols

Protein lysate microarray analysis to identify microRNAs regulating estrogen receptor signaling in breast cancer cell lines

(2009) S-K Leivonen et al.   ONCOGENE

Genome-Scale RNAi Screen for Host Factors Required for HIV Replication

(2008) Honglin Zhou et al.   Cell Host & Microbe

MicroRNA target prediction by expression analysis of host genes

(2008) V. A. Gennarino et al.   GENOME 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

Detecting microRNA binding and siRNA off-target effects from expression data

(2008) Stijn van Dongen et al.   NATURE METHODS

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

MicroRNA Expression and Identification of Putative miRNA Targets in Ovarian Cancer

(2008) Neetu Dahiya et al.   PLoS One