miRge - A Multiplexed Method of Processing Small RNA-Seq Data to Determine MicroRNA Entropy

Chimira: analysis of small RNA sequencing data and microRNA modifications: Fig. 1.

(2015) Dimitrios M. Vitsios et al.   BIOINFORMATICS

Next-generation sequencing reveals novel differentially regulated mRNAs, lncRNAs, miRNAs, sdRNAs and a piRNA in pancreatic cancer

(2015) Sören Müller et al.   Molecular Cancer

sRNAtoolbox: an integrated collection of small RNA research tools

(2015) Antonio Rueda et al.   NUCLEIC ACIDS RESEARCH

Entropy-Based Model for MiRNA Isoform Analysis

(2015) Shengqin Wang et al.   PLoS One

A challenge for miRNA: multiple isomiRs in miRNAomics

(2014) Li Guo et al.   GENE

Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study

(2014) Pieter Mestdagh et al.   NATURE METHODS

Sequencing depth and coverage: key considerations in genomic analyses

(2014) David Sims et al.   NATURE REVIEWS GENETICS

5′ isomiR variation is of functional and evolutionary importance

(2014) Geok Chin Tan et al.   NUCLEIC ACIDS RESEARCH

Lessons from miR-143/145: the importance of cell-type localization of miRNAs

(2014) Oliver A. Kent et al.   NUCLEIC ACIDS RESEARCH

A Critical Evaluation of microRNA Biomarkers in Non-Neoplastic Disease

(2014) Baqer A. Haider et al.   PLoS One

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

(2013) Sören Müller et al.   BIOINFORMATICS

Genetic regulation of human adipose microRNA expression and its consequences for metabolic traits

(2013) Mete Civelek et al.   HUMAN MOLECULAR GENETICS

Kraken: A set of tools for quality control and analysis of high-throughput sequence data

(2013) Matthew P.A. Davis et al.   METHODS

Identification of differentially expressed microRNAs across the developing human brain

(2013) M N Ziats et al.   MOLECULAR PSYCHIATRY

Lack of detectable oral bioavailability of plant microRNAs after feeding in mice

(2013) Brent Dickinson et al.   NATURE BIOTECHNOLOGY

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

The miRNA Profile of Human Pancreatic Islets and Beta-Cells and Relationship to Type 2 Diabetes Pathogenesis

(2013) Martijn van de Bunt et al.   PLoS One

Consistent isomiR expression patterns and 3′ addition events in miRNA gene clusters and families implicate functional and evolutionary relationships

(2012) Li Guo et al.   MOLECULAR BIOLOGY REPORTS

High-throughput assessment of microRNA activity and function using microRNA sensor and decoy libraries

(2012) Gavriel Mullokandov et al.   NATURE METHODS

MicroRNA profiling: approaches and considerations

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

Identification of miRNA Signatures during the Differentiation of hESCs into Retinal Pigment Epithelial Cells

(2012) Ganlu Hu et al.   PLoS One

MicroRNA profiling of diverse endothelial cell types

(2011) Matthew N McCall et al.   BMC Medical Genomics

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

miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades

(2011) Marc R. Friedländer et al.   NUCLEIC ACIDS RESEARCH

miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression

(2009) Wei-Chi Wang et al.   BMC BIOINFORMATICS

miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments

(2009) Michael Hackenberg et al.   NUCLEIC ACIDS RESEARCH

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

GtRNAdb: a database of transfer RNA genes detected in genomic sequence

(2008) P. P. Chan et al.   NUCLEIC ACIDS RESEARCH