Toward the human cellular microRNAome

Complex Sources of Variation in Tissue Expression Data: Analysis of the GTEx Lung Transcriptome

(2016) Matthew N. McCall et al.   AMERICAN JOURNAL OF HUMAN GENETICS

OUP accepted manuscript

(2016)   NUCLEIC ACIDS RESEARCH

Distribution of miRNA expression across human tissues

(2016) Nicole Ludwig et al.   NUCLEIC ACIDS RESEARCH

Re-evaluation of the roles ofDROSHA,Exportin 5, andDICERin microRNA biogenesis

(2016) Young-Kook Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Toward the promise of microRNAs – Enhancing reproducibility and rigor in microRNA research

(2016) Kenneth W. Witwer et al.   RNA Biology

Cultured networks of excitatory projection neurons and inhibitory interneurons for studying human cortical neurotoxicity

(2016) Jin-Chong Xu et al.   Science Translational Medicine

A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome

(2015) Bastian Fromm et al.   Annual Review of Genetics

Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms

(2015) Tsung-Cheng Chang et al.   GENOME RESEARCH

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

Prioritizing and selecting likely novel miRNAs from NGS data

(2015) Christina Backes et al.   NUCLEIC ACIDS RESEARCH

dbSUPER: a database of super-enhancers in mouse and human genome

(2015) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs

(2015) Eric Londin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicting effective microRNA target sites in mammalian mRNAs

(2015) Vikram Agarwal et al.   eLife

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

(2015) Alexander S. Baras et al.   PLoS One

A genome-wide screen for non-template nucleotides and isomiR repertoires in miRNAs indicates dynamic and versatile microRNAome

(2014) Li Guo et al.   MOLECULAR BIOLOGY REPORTS

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

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

(2014) Pieter Mestdagh et al.   NATURE METHODS

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

YM500v2: a small RNA sequencing (smRNA-seq) database for human cancer miRNome research

(2014) Wei-Chung Cheng et al.   NUCLEIC ACIDS RESEARCH

A Critical Evaluation of microRNA Biomarkers in Non-Neoplastic Disease

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

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

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

(2013) Mete Civelek et al.   HUMAN MOLECULAR GENETICS

Treatment of HCV Infection by Targeting MicroRNA

(2013) Harry L.A. Janssen et al.   NEW ENGLAND JOURNAL OF MEDICINE

The Gene Expression Barcode 3.0: improved data processing and mining tools

(2013) Matthew N. McCall et al.   NUCLEIC ACIDS RESEARCH

DEXUS: identifying differential expression in RNA-Seq studies with unknown conditions

(2013) Günter Klambauer et al.   NUCLEIC ACIDS RESEARCH

The role of miR-150 in normal and malignant hematopoiesis

(2013) Y He et al.   ONCOGENE

MicroRNAs in Stress Signaling and Human Disease

(2012) Joshua T. Mendell et al.   CELL

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

(2012) Gavriel Mullokandov et al.   NATURE METHODS

Inhibition of miR-9 de-represses HuR and DICER1 and impairs Hodgkin lymphoma tumour outgrowth in vivo

(2012) E Leucci et al.   ONCOGENE

IsomiRs – the overlooked repertoire in the dynamic microRNAome

(2012) Corine T. Neilsen et al.   TRENDS IN GENETICS

MicroRNA profiling of diverse endothelial cell types

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

Dopamine neurons derived from human ES cells efficiently engraft in animal models of Parkinson’s disease

(2011) Sonja Kriks et al.   NATURE

miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments

(2011) M. Hackenberg et al.   NUCLEIC ACIDS RESEARCH

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

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

PHAST and RPHAST: phylogenetic analysis with space/time models

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

The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes

(2010) Matthew N. McCall et al.   NUCLEIC ACIDS RESEARCH

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

DICER1 Mutations in Familial Pleuropulmonary Blastoma

(2009) D. A. Hill et al.   SCIENCE

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells

(2008) R. D. Morin et al.   GENOME RESEARCH

Circulating microRNAs as stable blood-based markers for cancer detection

(2008) P. S. Mitchell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA