Computational identification of miRNAs, their targets and functions in three-spined stickleback (Gasterosteus aculeatus)

RNA sequencing reveals small RNAs differentially expressed between incipient Japanese threespine sticklebacks

(2013) Jun Kitano et al.   BMC GENOMICS

A gene with major phenotypic effects as a target for selection vs. homogenizing gene flow

(2013) Joost A. M. Raeymaekers et al.   MOLECULAR ECOLOGY

The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Large scale chromosomal mapping of human microRNA structural clusters

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Genetic Variations Creating MicroRNA Target Sites in the FXN 3′-UTR Affect Frataxin Expression in Friedreich Ataxia

(2013) Simonetta Bandiera et al.   PLoS One

Identifying miRNAs, targets and functions

(2012) B. Liu et al.   BRIEFINGS IN BIOINFORMATICS

Genome divergence during evolutionary diversification as revealed in replicate lake-stream stickleback population pairs

(2012) MARIUS ROESTI et al.   MOLECULAR ECOLOGY

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

A travel guide to Cytoscape plugins

(2012) Rintaro Saito et al.   NATURE METHODS

A fast ab-initio method for predicting miRNA precursors in genomes

(2012) Sébastien Tempel et al.   NUCLEIC ACIDS RESEARCH

Transcriptional regulation of brain gene expression in response to a territorial intrusion

(2012) Y. O. Sanogo et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

(2012) Jingjing Li et al.   PLoS Genetics

MiRPara: a SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences

(2011) Yonggan Wu et al.   BMC BIOINFORMATICS

Functional Divergences of GAPDH Isoforms During Early Development in Two Perciform Fish Species

(2011) Elena Sarropoulou et al.   MARINE BIOTECHNOLOGY

MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data

(2010) Anthony Mathelier et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

MapMi: automated mapping of microRNA loci

(2010) Jose Afonso Guerra-Assuncao et al.   BMC BIOINFORMATICS

Evolution of MicroRNAs and the Diversification of Species

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

Identification of homologous microRNAs in 56 animal genomes

(2010) Sung-Chou Li et al.   GENOMICS

miRBase: integrating microRNA annotation and deep-sequencing data

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

Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

(2010) Daniele Merico et al.   PLoS One

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe et al.   PLoS Genetics

JBrowse: A next-generation genome browser

(2009) M. E. Skinner et al.   GENOME RESEARCH

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Deep Sequencing of Chicken microRNAs

(2008) Joan Burnside et al.   BMC GENOMICS

Differential modulations of two glyceraldehyde 3-phosphate dehydrogenase mRNAs in response to bacterial and viral challenges in a marine teleost Oplegnathus fasciatus (Perciformes)

(2008) Y CHO et al.   FISH & SHELLFISH IMMUNOLOGY

MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation

(2008) Yvonne Tay et al.   NATURE

Discovering microRNAs from deep sequencing data using miRDeep

(2008) Marc R Friedländer et al.   NATURE BIOTECHNOLOGY

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

miROrtho: computational survey of microRNA genes

(2008) D. Gerlach et al.   NUCLEIC ACIDS RESEARCH

MicroRNA target site polymorphisms and human disease

(2008) Praveen Sethupathy et al.   TRENDS IN GENETICS