Principles of miRNA–mRNA interactions: beyond sequence complementarity

mrSNP: Software to detect SNP effects on microRNA binding

(2014) Mehmet Deveci et al.   BMC BIOINFORMATICS

Driving glioblastoma growth by alternative polyadenylation

(2014) Ting Han et al.   CELL RESEARCH

The panorama of miRNA-mediated mechanisms in mammalian cells

(2014) Anna Stroynowska-Czerwinska et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

miR-1, miR-10b, miR-155, and miR-191 are novel regulators of BDNF

(2014) Kärt Varendi et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

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

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

New Links between mRNA Polyadenylation and Diverse Nuclear Pathways

(2014) Dafne Campigli Di Giammartino et al.   MOLECULES AND CELLS

Role of Virus-Encoded microRNAs in Avian Viral Diseases

(2014) Yongxiu Yao et al.   Viruses-Basel

APADB: a database for alternative polyadenylation and microRNA regulation events

(2014) S. Muller et al.   Database-The Journal of Biological Databases and Curation

8.2% of the Human Genome Is Constrained: Variation in Rates of Turnover across Functional Element Classes in the Human Lineage

(2014) Chris M. Rands et al.   PLoS Genetics

Identification of distinct miRNA target regulation between breast cancer molecular subtypes using AGO2-PAR-CLIP and patient datasets

(2014) Thalia A Farazi et al.   GENOME BIOLOGY

In silico analysis of regulatory networks underlines the role of miR-10b-5p and its target BDNF in huntington’s disease

(2014) Sören Müller   Translational Neurodegeneration

omiRas: a Web server for differential expression analysis of miRNAs derived from small RNA-Seq data

(2013) Sören Müller et al.   BIOINFORMATICS

mirCoX: a database of miRNA-mRNA expression correlations derived from RNA-seq meta-analysis

(2013) Cory B Giles et al.   BMC BIOINFORMATICS

The nucleosome regulates the usage of polyadenylation sites in the human genome

(2013) Huan Huang et al.   BMC GENOMICS

Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding

(2013) Aleksandra Helwak et al.   CELL

Massive analysis of cDNA Ends (MACE) and miRNA expression profiling identifies proatherogenic pathways in chronic kidney disease

(2013) Adam M Zawada et al.   Epigenetics

Widespread and extensive lengthening of 3' UTRs in the mammalian brain

(2013) P. Miura et al.   GENOME RESEARCH

Identification of microRNA targets in tomato fruit development using high-throughput sequencing and degradome analysis

(2013) Rumyana Karlova et al.   JOURNAL OF EXPERIMENTAL BOTANY

Improved genome-wide mapping of uncapped and cleaved transcripts in eukaryotes—GMUCT 2.0

(2013) Matthew R. Willmann et al.   METHODS

Rapid construction of parallel analysis of RNA end (PARE) libraries for Illumina sequencing

(2013) Jixian Zhai et al.   METHODS

Alternative cleavage and polyadenylation: extent, regulation and function

(2013) Ran Elkon et al.   NATURE REVIEWS GENETICS

A Polymorphic 3’UTR Element in ATP1B1 Regulates Alternative Polyadenylation and Is Associated with Blood Pressure

(2013) Megana K. Prasad et al.   PLoS One

Alternative cleavage and polyadenylation: the long and short of it

(2013) Bin Tian et al.   TRENDS IN BIOCHEMICAL SCIENCES

MicroRNA-target interactions: new insights from genome-wide approaches

(2012) Dooyoung Lee et al.   Annals of the New York Academy of Sciences

CPSS: a computational platform for the analysis of small RNA deep sequencing data

(2012) Yuanwei Zhang et al.   BIOINFORMATICS

ncPRO-seq: a tool for annotation and profiling of ncRNAs in sRNA-seq data

(2012) Chong-Jian Chen et al.   BIOINFORMATICS

miRdSNP: a database of disease-associated SNPs and microRNA target sites on 3'UTRs of human genes

(2012) Andrew E Bruno et al.   BMC GENOMICS

Identification of soybean seed developmental stage-specific and tissue-specific miRNA targets by degradome sequencing

(2012) Md Shamimuzzaman et al.   BMC GENOMICS

MirSNP, a database of polymorphisms altering miRNA target sites, identifies miRNA-related SNPs in GWAS SNPs and eQTLs

(2012) Chenxing Liu et al.   BMC GENOMICS

Joint analysis of miRNA and mRNA expression data

(2012) A. Muniategui et al.   BRIEFINGS IN BIOINFORMATICS

U1 snRNP Determines mRNA Length and Regulates Isoform Expression

(2012) Michael G. Berg et al.   CELL

Kinetic analysis reveals successive steps leading to miRNA-mediated silencing in mammalian cells

(2012) Julien Béthune et al.   EMBO REPORTS

Extensive alternative polyadenylation during zebrafish development

(2012) I. Ulitsky et al.   GENOME RESEARCH

A quantitative atlas of polyadenylation in five mammals

(2012) Adnan Derti et al.   GENOME RESEARCH

Discovery of hundreds of mirtrons in mouse and human small RNA data

(2012) E. Ladewig et al.   GENOME RESEARCH

MicroRNA 218 Acts as a Tumor Suppressor by Targeting Multiple Cancer Phenotype-associated Genes in Medulloblastoma

(2012) Sujatha Venkataraman et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Analysis of alternative cleavage and polyadenylation by 3′ region extraction and deep sequencing

(2012) Mainul Hoque et al.   NATURE METHODS

Mass spectrometry–based targeted proteomics

(2012) Allison Doerr   NATURE METHODS

PAREsnip: a tool for rapid genome-wide discovery of small RNA/target interactions evidenced through degradome sequencing

(2012) Leighton Folkes et al.   NUCLEIC ACIDS RESEARCH

Large-Scale Identification of Mirtrons in Arabidopsis and Rice

(2012) Yijun Meng et al.   PLoS One

miRNA-Mediated Gene Silencing by Translational Repression Followed by mRNA Deadenylation and Decay

(2012) S. Djuranovic et al.   SCIENCE

Ribosome Profiling Shows That miR-430 Reduces Translation Before Causing mRNA Decay in Zebrafish

(2012) A. A. Bazzini et al.   SCIENCE

Single Nucleotide Polymorphisms Can Create Alternative Polyadenylation Signals and Affect Gene Expression through Loss of MicroRNA-Regulation

(2012) Laurent F. Thomas et al.   PLoS Computational Biology

E2F mediates enhanced alternative polyadenylation in proliferation

(2012) Ran Elkon et al.   GENOME BIOLOGY

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

(2011) Leonardo Salmena et al.   CELL

Ending the message: poly(A) signals then and now

(2011) N. J. Proudfoot   GENES & DEVELOPMENT

Identification of putative miRNAs from the deep-branching unicellular flagellates

(2011) Po-Jung Huang et al.   GENOMICS

miRWalk – Database: Prediction of possible miRNA binding sites by “walking” the genes of three genomes

(2011) Harsh Dweep et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Mechanisms and Consequences of Alternative Polyadenylation

(2011) Dafne Campigli Di Giammartino et al.   MOLECULAR CELL

Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data

(2011) Chaolin Zhang et al.   NATURE BIOTECHNOLOGY

TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support

(2011) T. Vergoulis et al.   NUCLEIC ACIDS RESEARCH

Experimental strategies for microRNA target identification

(2011) D. W. Thomson et al.   NUCLEIC ACIDS RESEARCH

miRConnect: Identifying Effector Genes of miRNAs and miRNA Families in Cancer Cells

(2011) Youjia Hua et al.   PLoS One

Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq

(2011) P. J. Shepard et al.   RNA

Vive la différence: biogenesis and evolution of microRNAs in plants and animals

(2011) Michael J Axtell et al.   GENOME BIOLOGY

Single-Nucleotide Polymorphisms Inside MicroRNA Target Sites Influence Tumor Susceptibility

(2010) Milena S. Nicoloso et al.   CANCER RESEARCH

The Promise of MicroRNA Replacement Therapy

(2010) A. G. Bader et al.   CANCER RESEARCH

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

(2010) Markus Hafner et al.   CELL

MicroSNiPer: a web tool for prediction of SNP effects on putative microRNA targets

(2010) Maxim Barenboim et al.   HUMAN MUTATION

Diverse Pathways Generate MicroRNA-like RNAs and Dicer-Independent Small Interfering RNAs in Fungi

(2010) Heng-Chi Lee et al.   MOLECULAR CELL

U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation

(2010) Daisuke Kaida et al.   NATURE

Formation, regulation and evolution of Caenorhabditis elegans 3′UTRs

(2010) Calvin H. Jan et al.   NATURE

Small RNA sorting: matchmaking for Argonautes

(2010) Benjamin Czech et al.   NATURE REVIEWS GENETICS

Desperately seeking microRNA targets

(2010) Marshall Thomas et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Molecular mechanisms of eukaryotic pre-mRNA 3′ end processing regulation

(2010) Stefania Millevoi et al.   NUCLEIC ACIDS RESEARCH

Origin, Biogenesis, and Activity of Plant MicroRNAs

(2009) Olivier Voinnet   CELL

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells

(2009) Christine Mayr et al.   CELL

Origins and Mechanisms of miRNAs and siRNAs

(2009) Richard W. Carthew et al.   CELL

Molecular Architecture of the Human Pre-mRNA 3′ Processing Complex

(2009) Yongsheng Shi et al.   MOLECULAR CELL

MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression

(2009) Seungyoon Nam et al.   NUCLEIC ACIDS RESEARCH

Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates

(2009) Samuel Hiard et al.   NUCLEIC ACIDS RESEARCH

Reprogramming of 3′ Untranslated Regions of mRNAs by Alternative Polyadenylation in Generation of Pluripotent Stem Cells from Different Cell Types

(2009) Zhe Ji et al.   PLoS One

Progressive lengthening of 3' untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development

(2009) Z. Ji et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

miRo: a miRNA knowledge base

(2009) A. Lagana et al.   Database-The Journal of Biological Databases and Curation

Conserved Expression Patterns Predict microRNA Targets

(2009) William Ritchie et al.   PLoS Computational Biology

A PROBABILISTIC FRAMEWORK TO IMPROVE MICRORNA TARGET PREDICTION BY INCORPORATING PROTEOMICS DATA

(2009) JINGJING LI et al.   Journal of Bioinformatics and Computational Biology

CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets

(2008) C. Addo-Quaye et al.   BIOINFORMATICS

Polymorphisms in microRNA targets: a gold mine for molecular epidemiology

(2008) K. Chen et al.   CARCINOGENESIS

Endogenous siRNA and miRNA Targets Identified by Sequencing of the Arabidopsis Degradome

(2008) Charles Addo-Quaye et al.   CURRENT BIOLOGY

A Link between RNA Metabolism and Silencing Affecting Arabidopsis Development

(2008) Brian D. Gregory et al.   DEVELOPMENTAL CELL

A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains

(2008) Q.-H. Zhu et al.   GENOME RESEARCH

Most mammalian mRNAs are conserved targets of microRNAs

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

Global identification of microRNA–target RNA pairs by parallel analysis of RNA ends

(2008) Marcelo A German et al.   NATURE BIOTECHNOLOGY

Primary microRNA transcripts are processed co-transcriptionally

(2008) Mariangela Morlando et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

miRecords: an integrated resource for microRNA-target interactions

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

Proliferating Cells Express mRNAs with Shortened 3' Untranslated Regions and Fewer MicroRNA Target Sites

(2008) R. Sandberg et al.   SCIENCE

Widespread Translational Inhibition by Plant miRNAs and siRNAs

(2008) P. Brodersen et al.   SCIENCE

Experimental validation of miRNA targets

(2007) Donald E. Kuhn et al.   METHODS