The Role of microRNAs in the Repeated Parallel Diversification of Lineages of Midas Cichlid Fish from Nicaragua

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets

(2015) Gregory J. Hogan et al.   PLOS BIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Comprehensive overview and assessment of computational prediction of microRNA targets in animals

(2014) Xiao Fan et al.   BRIEFINGS IN BIOINFORMATICS

Microevolution of Nematode miRNAs Reveals Diverse Modes of Selection

(2014) Richard Jovelin et al.   Genome Biology and Evolution

The genomic substrate for adaptive radiation in African cichlid fish

(2014) David Brawand et al.   NATURE

Genomics and the origin of species

(2014) Ole Seehausen et al.   NATURE REVIEWS GENETICS

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

(2014) Jean Hausser et al.   NATURE REVIEWS GENETICS

A census of human RNA-binding proteins

(2014) Stefanie Gerstberger et al.   NATURE REVIEWS GENETICS

Evolution of transcription factor binding in metazoans — mechanisms and functional implications

(2014) Diego Villar et al.   NATURE REVIEWS GENETICS

Regulation of microRNA biogenesis

(2014) Minju Ha et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

The Gut Microbial Community of Midas Cichlid Fish in Repeatedly Evolved Limnetic-Benthic Species Pairs

(2014) Paolo Franchini et al.   PLoS One

Parallel evolution of Nicaraguan crater lake cichlid fishes via non-parallel routes

(2014) Kathryn R. Elmer et al.   Nature Communications

Evolution of mir-92a Underlies Natural Morphological Variation in Drosophila melanogaster

(2013) Saad Arif et al.   CURRENT BIOLOGY

Genomic architecture of ecologically divergent body shape in a pair of sympatric crater lake cichlid fishes

(2013) Paolo Franchini et al.   MOLECULAR ECOLOGY

The miR-30 MicroRNA Family Targets smoothened to Regulate Hedgehog Signalling in Zebrafish Early Muscle Development

(2013) Ami Ketley et al.   PLoS One

Molecular and fossil evidence place the origin of cichlid fishes long after Gondwanan rifting

(2013) M. Friedman et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Review of Computational Tools in microRNA Discovery

(2013) Clarissa P. C. Gomes et al.   Frontiers in Genetics

Impact of microRNA regulation on variation in human gene expression

(2012) J. Lu et al.   GENOME RESEARCH

Origins of Shared Genetic Variation in African Cichlids

(2012) Yong-Hwee E. Loh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic signatures of divergent selection and speciation patterns in a ‘natural experiment’, the young parallel radiations of Nicaraguan crater lake cichlid fishes

(2012) Andreas F. Kautt et al.   MOLECULAR ECOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Comparative studies of gene expression and the evolution of gene regulation

(2012) Irene Gallego Romero et al.   NATURE REVIEWS GENETICS

MicroRNA profiling: approaches and considerations

(2012) Colin C. Pritchard et al.   NATURE REVIEWS GENETICS

A Cross-Species Analysis of MicroRNAs in the Developing Avian Face

(2012) Kara E. Powder et al.   PLoS One

miRNA regulatory variation in human evolution

(2012) Jingjing Li et al.   TRENDS IN GENETICS

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

(2012) Jingjing Li et al.   PLoS Genetics

PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)

(2011) R. Kofler et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Evolution of microRNA diversity and regulation in animals

(2011) Eugene Berezikov   NATURE REVIEWS GENETICS

Adaptation in the age of ecological genomics: insights from parallelism and convergence

(2011) Kathryn R. Elmer et al.   TRENDS IN ECOLOGY & EVOLUTION

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Insights into the role of differential gene expression on the ecological adaptation of the snail Littorina saxatilis

(2010) Mónica Martínez-Fernández et al.   BMC EVOLUTIONARY BIOLOGY

Phylogeography, colonization and population history of the Midas cichlid species complex (Amphilophus spp.) in the Nicaraguan crater lakes

(2010) Marta Barluenga et al.   BMC EVOLUTIONARY BIOLOGY

Discovery and characterization of medaka miRNA genes by next generation sequencing platform

(2010) Sung-Chou Li et al.   BMC GENOMICS

Evolution of MicroRNAs and the Diversification of Species

(2010) Yong-Hwee E. Loh et al.   Genome Biology and Evolution

Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes

(2010) K. R. ELMER et al.   MOLECULAR ECOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

miRBase: integrating microRNA annotation and deep-sequencing data

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

Local variation and parallel evolution: morphological and genetic diversity across a species complex of neotropical crater lake cichlid fishes

(2010) K. R. Elmer et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

MicroRNAs and metazoan macroevolution: insights into canalization, complexity, and the Cambrian explosion

(2009) Kevin J. Peterson et al.   BIOESSAYS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Many roads to maturity: microRNA biogenesis pathways and their regulation

(2009) Julia Winter et al.   NATURE CELL BIOLOGY

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

(2009) Samuel Hiard et al.   NUCLEIC ACIDS RESEARCH

Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer

(2009) Y. F. Chan et al.   SCIENCE

Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

(2008) Sean B. Carroll   CELL

Most mammalian mRNAs are conserved targets of microRNAs

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

Regulatory changes underlying expression differences within and between Drosophila species

(2008) Patricia J Wittkopp et al.   NATURE GENETICS