miRspongeR: an R/Bioconductor package for the identification and analysis of miRNA sponge interaction networks and modules

miRNACancerMAP: an integrative web server inferring miRNA regulation network for cancer

(2018) Yin Tong et al.   BIOINFORMATICS

JAMI: fast computation of conditional mutual information for ceRNA network analysis

(2018) Andrea Hornakova et al.   BIOINFORMATICS

The epithelial-to-mesenchymal transition activator ZEB1 initiates a prometastatic competing endogenous RNA network

(2018) Xiaochao Tan et al.   JOURNAL OF CLINICAL INVESTIGATION

LncCeRBase: a database of experimentally validated human competing endogenous long non-coding RNAs

(2018) Cong Pian et al.   Database-The Journal of Biological Databases and Curation

LncACTdb 2.0: an updated database of experimentally supported ceRNA interactions curated from low- and high-throughput experiments

(2018) Peng Wang et al.   NUCLEIC ACIDS RESEARCH

miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions

(2017) Chih-Hung Chou et al.   NUCLEIC ACIDS RESEARCH

DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA–gene interactions

(2017) Dimitra Karagkouni et al.   NUCLEIC ACIDS RESEARCH

microRNA target prediction programs predict many false positives

(2016) Natalia Pinzón et al.   GENOME RESEARCH

spongeScan: A web for detecting microRNA binding elements in lncRNA sequences

(2016) Pedro Furió-Tarí et al.   NUCLEIC ACIDS RESEARCH

miRNAsong: a web-based tool for generation and testing of miRNA sponge constructs in silico

(2016) Tomas Barta et al.   Scientific Reports

miRWalk2.0: a comprehensive atlas of microRNA-target interactions

(2015) Harsh Dweep et al.   NATURE METHODS

The mRNA related ceRNA–ceRNA landscape and significance across 20 major cancer types

(2015) Juan Xu et al.   NUCLEIC ACIDS RESEARCH

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

CircInteractome: A web tool for exploring circular RNAs and their interacting proteins and microRNAs

(2015) Dawood B. Dudekula et al.   RNA Biology

miRSponge: a manually curated database for experimentally supported miRNA sponges and ceRNAs

(2015) Peng Wang et al.   Database-The Journal of Biological Databases and Curation

Predicting effective microRNA target sites in mammalian mRNAs

(2015) Vikram Agarwal et al.   eLife

Computational analysis identifies a sponge interaction network between long non-coding RNAs and messenger RNAs in human breast cancer

(2014) Paola Paci et al.   BMC Systems Biology

Construction and investigation of breast-cancer-specific ceRNA network based on the mRNA and miRNA expression data

(2014) Xionghui Zhou et al.   IET Systems Biology

The multilayered complexity of ceRNA crosstalk and competition

(2014) Yvonne Tay et al.   NATURE

Natural RNA circles function as efficient microRNA sponges

(2013) Thomas B. Hansen et al.   NATURE

Circular RNAs are a large class of animal RNAs with regulatory potency

(2013) Sebastian Memczak et al.   NATURE

starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data

(2013) Jun-Hao Li et al.   NUCLEIC ACIDS RESEARCH

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

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

linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type

(2011) Alex T. Kalinka et al.   BIOINFORMATICS

An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma

(2011) Pavel Sumazin et al.   CELL

Coding-Independent Regulation of the Tumor Suppressor PTEN by Competing Endogenous mRNAs

(2011) Yvonne Tay et al.   CELL

A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA

(2011) Marcella Cesana et al.   CELL

A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language?

(2011) Leonardo Salmena et al.   CELL

A coding-independent function of gene and pseudogene mRNAs regulates tumour biology

(2010) Laura Poliseno et al.   NATURE

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

(2010) Doron Betel et al.   GENOME BIOLOGY

Genome-wide identification of post-translational modulators of transcription factor activity in human B cells

(2009) Kai Wang et al.   NATURE BIOTECHNOLOGY