MicroRNA duplication accelerates the recruitment of new targets during vertebrate evolution

SNPs in microRNA target sites and their potential role in human disease

(2017) Adrianna Moszyńska et al.   Open Biology

Evolutionary patterns of metazoan microRNAs reveal targeting principles in the let-7 and miR-10 families

(2016) Justin M. Wolter et al.   GENOME RESEARCH

microRNAs in the Same Clusters Evolve to Coordinately Regulate Functionally Related Genes

(2016) Yirong Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution by gene loss

(2016) Ricard Albalat et al.   NATURE REVIEWS GENETICS

MicroRNA evolution, expression, and function during short germband development inTribolium castaneum

(2015) Maria Ninova et al.   GENOME RESEARCH

miRNA–target chimeras reveal miRNA 3′-end pairing as a major determinant of Argonaute target specificity

(2015) Michael J. Moore et al.   Nature Communications

Predicting effective microRNA target sites in mammalian mRNAs

(2015) Vikram Agarwal et al.   eLife

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Genomic evidence for adaptation by gene duplication

(2014) Wenfeng Qian et al.   GENOME RESEARCH

Functional Conservation of Both CDS- and 3′-UTR-Located MicroRNA Binding Sites between Species

(2014) Guojing Liu et al.   MOLECULAR BIOLOGY AND EVOLUTION

3′LIFE: a functional assay to detect miRNA targets in high-throughput

(2014) Justin M. Wolter et al.   NUCLEIC ACIDS RESEARCH

Fast-evolving microRNAs are highly expressed in the early embryo of Drosophila virilis

(2014) M. Ninova et al.   RNA

Diverse modes of evolutionary emergence and flux of conserved microRNA clusters

(2014) Jaaved Mohammed et al.   RNA

Adaptive evolution of testis-specific, recently evolved, clustered miRNAs inDrosophila

(2014) Jaaved Mohammed et al.   RNA

New MicroRNAs in Drosophila—Birth, Death and Cycles of Adaptive Evolution

(2014) Yang Lyu et al.   PLoS Genetics

Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding

(2013) Aleksandra Helwak et al.   CELL

The evolution of evolvability in microRNA target sites in vertebrates

(2013) Jin Xu et al.   GENOME RESEARCH

Diverse functions of miR-125 family in different cell contexts

(2013) Yu-Meng Sun et al.   Journal of Hematology & Oncology

Clusters of microRNAs emerge by new hairpins in existing transcripts

(2013) Antonio Marco 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

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Neofunctionalization of young duplicate genes in Drosophila

(2013) R. Assis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The impact of age, biogenesis, and genomic clustering on Drosophila microRNA evolution

(2013) J. Mohammed et al.   RNA

Functional microRNA targets in protein coding sequences

(2012) Martin Reczko et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Impact of microRNA regulation on variation in human gene expression

(2012) J. Lu et al.   GENOME RESEARCH

Birth and expression evolution of mammalian microRNA genes

(2012) J. Meunier et al.   GENOME RESEARCH

Evolution of the let-7 microRNA Family

(2012) Jana Hertel et al.   RNA Biology

Evidence for Positive Selection on a Number of MicroRNA Regulatory Interactions during Recent Human Evolution

(2012) Jingjing Li et al.   PLoS Genetics

Evidence for post-transcriptional regulation of clustered microRNAs in Drosophila

(2011) Sergei S Ryazansky et al.   BMC GENOMICS

Inference of Gain and Loss Events from Phyletic Patterns Using Stochastic Mapping and Maximum Parsimony—A Simulation Study

(2011) Ofir Cohen et al.   Genome Biology and Evolution

Genome-wide identification of SNPs in microRNA genes and the SNP effects on microRNA target binding and biogenesis

(2011) Jing Gong et al.   HUMAN MUTATION

Evolution of microRNA diversity and regulation in animals

(2011) Eugene Berezikov   NATURE REVIEWS GENETICS

Argonaute protein identity and pairing geometry determine cooperativity in mammalian RNA silencing

(2011) J. A. Broderick et al.   RNA

PHAST and RPHAST: phylogenetic analysis with space/time models

(2010) M. J. Hubisz et al.   BRIEFINGS IN BIOINFORMATICS

Weighted Gene Coexpression Network Analysis: State of the Art

(2010) Wei Zhao et al.   Journal of Biopharmaceutical Statistics

Expanding the MicroRNA Targeting Code: Functional Sites with Centered Pairing

(2010) Chanseok Shin et al.   MOLECULAR CELL

The evolution of gene duplications: classifying and distinguishing between models

(2010) Hideki Innan et al.   NATURE REVIEWS GENETICS

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

(2010) Doron Betel et al.   GENOME BIOLOGY

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

Origins and Mechanisms of miRNAs and siRNAs

(2009) Richard W. Carthew et al.   CELL

The deep evolution of metazoan microRNAs

(2009) Benjamin M. Wheeler et al.   EVOLUTION & DEVELOPMENT

Lowly Expressed Human MicroRNA Genes Evolve Rapidly

(2009) Han Liang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolutionary flux of canonical microRNAs and mirtrons in Drosophila

(2009) Eugene Berezikov et al.   NATURE GENETICS

Reexamining microRNA Site Accessibility in Drosophila: A Population Genomics Study

(2009) Kevin Chen et al.   PLoS One

Genome-Wide Identification of Human RNA Editing Sites by Parallel DNA Capturing and Sequencing

(2009) J. B. Li et al.   SCIENCE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

The evolution and functional diversification of animal microRNA genes

(2008) Na Liu et al.   CELL RESEARCH

Chromatin structure analyses identify miRNA promoters

(2008) F. Ozsolak et al.   GENES & DEVELOPMENT

High-resolution human core-promoter prediction with CoreBoost_HM

(2008) X. Wang et al.   GENOME RESEARCH

Most mammalian mRNAs are conserved targets of microRNAs

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

Molecular Evolution of a Primate-Specific microRNA Family

(2008) R. Zhang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Adaptive Evolution of Newly Emerged Micro-RNA Genes in Drosophila

(2008) J. Lu et al.   MOLECULAR BIOLOGY AND EVOLUTION

The impact of microRNAs on protein output

(2008) Daehyun Baek et al.   NATURE

The birth and death of microRNA genes in Drosophila

(2008) Jian Lu et al.   NATURE GENETICS

RNA-based gene duplication: mechanistic and evolutionary insights

(2008) Henrik Kaessmann et al.   NATURE REVIEWS GENETICS

The let-7 family of microRNAs

(2008) Sarah Roush et al.   TRENDS IN CELL BIOLOGY

MicroRNA target site polymorphisms and human disease

(2008) Praveen Sethupathy et al.   TRENDS IN GENETICS