Computational methods for identifying miRNA sponge interactions

Parameter optimization for constructing competing endogenous RNA regulatory network in glioblastoma multiforme and other cancers

(2015) Yu-Chiao Chiu et al.   BMC GENOMICS

Identification of module biomarkers from the dysregulated ceRNA–ceRNA interaction network in lung adenocarcinoma

(2015) Tingting Shao et al.   Molecular BioSystems

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

Identification of lncRNA-associated competing triplets reveals global patterns and prognostic markers for cancer

(2015) Peng Wang et al.   NUCLEIC ACIDS RESEARCH

Lnc2Cancer: a manually curated database of experimentally supported lncRNAs associated with various human cancers

(2015) Shangwei Ning et al.   NUCLEIC ACIDS RESEARCH

miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database

(2015) Chih-Hung Chou et al.   NUCLEIC ACIDS RESEARCH

Model-guided quantitative analysis of microRNA-mediated regulation on competing endogenous RNAs using a synthetic gene circuit

(2015) Ye Yuan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulation of circRNA biogenesis

(2015) Ling-Ling Chen 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

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

Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks

(2014) Hua-Sheng Chiu et al.   GENOME RESEARCH

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

DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions

(2014) Ioannis S. Vlachos et al.   NUCLEIC ACIDS RESEARCH

lnCeDB: Database of Human Long Noncoding RNA Acting as Competing Endogenous RNA

(2014) Shaoli Das et al.   PLoS One

HumanViCe: host ceRNA network in virus infected cells in human

(2014) Suman Ghosal et al.   Frontiers in Genetics

MicroRNAs as a Selective Channel of Communication between Competing RNAs: a Steady-State Theory

(2013) Matteo Figliuzzi et al.   BIOPHYSICAL JOURNAL

Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding

(2013) Aleksandra Helwak et al.   CELL

Endogenous miRNA Sponge lincRNA-RoR Regulates Oct4, Nanog, and Sox2 in Human Embryonic Stem Cell Self-Renewal

(2013) Yue Wang et al.   DEVELOPMENTAL CELL

The Imprinted H19 LncRNA Antagonizes Let-7 MicroRNAs

(2013) Amanda N. Kallen et al.   MOLECULAR CELL

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

Modelling Competing Endogenous RNA Networks

(2013) Carla Bosia et al.   PLoS One

Integrated transcriptional and competitive endogenous RNA networks are cross-regulated in permissive molecular environments

(2013) U. Ala et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

miRcode: a map of putative microRNA target sites in the long non-coding transcriptome

(2012) Ashwini Jeggari et al.   BIOINFORMATICS

Versican 3′-untranslated region (3′-UTR) functions as a ceRNA in inducing the development of hepatocellular carcinoma by regulating miRNA activity

(2012) Ling Fang et al.   FASEB JOURNAL

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

The non-coding 3' UTR of CD44 induces metastasis by regulating extracellular matrix functions

(2012) Z. J. Rutnam et al.   JOURNAL OF CELL SCIENCE

Regulatory long non-coding RNA and its functions

(2012) Yong Huang et al.   JOURNAL OF PHYSIOLOGY AND BIOCHEMISTRY

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

LncRNADisease: a database for long-non-coding RNA-associated diseases

(2012) Geng Chen et al.   NUCLEIC ACIDS RESEARCH

Evidence for conserved post-transcriptional roles of unitary pseudogenes and for frequent bifunctionality of mRNAs

(2012) Ana C Marques et al.   GENOME BIOLOGY

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

In Vivo Identification of Tumor- Suppressive PTEN ceRNAs in an Oncogenic BRAF-Induced Mouse Model of Melanoma

(2011) Florian A. Karreth et al.   CELL

An atlas of tissue-specific conserved coexpression for functional annotation and disease gene prediction

(2011) Rosario Michael Piro et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

A multilevel data integration resource for breast cancer study

(2010) Ettore Mosca et al.   BMC Systems Biology

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

(2010) Laura Poliseno et al.   NATURE

Expression of CD44 3′-untranslated region regulates endogenous microRNA functions in tumorigenesis and angiogenesis

(2010) Zina Jeyapalan et al.   NUCLEIC ACIDS RESEARCH

CREB up-regulates long non-coding RNA, HULC expression through interaction with microRNA-372 in liver cancer

(2010) Jiayi Wang et al.   NUCLEIC ACIDS RESEARCH

Expression of Versican 3′-Untranslated Region Modulates Endogenous MicroRNA Functions

(2010) Daniel Y. Lee et al.   PLoS One

Redefining MicroRNA Targets

(2009) Hervé Seitz   CURRENT BIOLOGY

A 3′-Untranslated Region (3′UTR) Induces Organ Adhesion by Regulating miR-199a* Functions

(2009) Daniel Y. Lee et al.   PLoS One

Molecular Titration and Ultrasensitivity in Regulatory Networks

(2008) Nicolas E. Buchler et al.   JOURNAL OF MOLECULAR BIOLOGY

miRecords: an integrated resource for microRNA-target interactions

(2008) F. Xiao et al.   NUCLEIC ACIDS RESEARCH