Large-scale profiling of microRNAs for The Cancer Genome Atlas

Comprehensive genomic characterization of head and neck squamous cell carcinomas

(2015)   NATURE

Integrated Genomic Characterization of Papillary Thyroid Carcinoma

(2014) Nishant Agrawal et al.   CELL

Comprehensive molecular characterization of gastric adenocarcinoma

(2014) Adam J. Bass et al.   NATURE

Comprehensive molecular profiling of lung adenocarcinoma

(2014) Eric A. Collisson et al.   NATURE

Comprehensive molecular characterization of urothelial bladder carcinoma

(2014)   NATURE

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

(2014) Jean Hausser et al.   NATURE REVIEWS GENETICS

The UCSC Genome Browser database: 2015 update

(2014) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

The Role of miRNAs in Regulating Gene Expression Networks

(2013) Allan M. Gurtan et al.   JOURNAL OF MOLECULAR BIOLOGY

Comprehensive molecular characterization of clear cell renal cell carcinoma

(2013)   NATURE

Integrated genomic characterization of endometrial carcinoma

(2013) Gad Getz et al.   NATURE

Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia

(2013)   NEW ENGLAND JOURNAL OF MEDICINE

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

ShortStack: Comprehensive annotation and quantification of small RNA genes

(2013) M. J. Axtell   RNA

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Comprehensive genomic characterization of squamous cell lung cancers

(2012)   NATURE

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

(2012) Gavriel Mullokandov et al.   NATURE METHODS

Finding consistent patterns: A nonparametric approach for identifying differential expression in RNA-Seq data

(2011) Jun Li et al.   STATISTICAL METHODS IN MEDICAL RESEARCH

A flexible R package for nonnegative matrix factorization

(2010) Renaud Gaujoux et al.   BMC BIOINFORMATICS

Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries

(2010) M. J.L. de Hoon et al.   GENOME RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Discovering microRNAs from deep sequencing data using miRDeep

(2008) Marc R Friedländer et al.   NATURE BIOTECHNOLOGY