Non-coding transcription characterization and annotation

The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA

(2011) Philipp Kapranov et al.   BMC BIOLOGY

Deep sequencing analysis of the developing mouse brain reveals a novel microRNA

(2011) King-Hwa Ling et al.   BMC GENOMICS

Long noncoding intronic RNAs are differentially expressed in primary and metastatic pancreatic cancer

(2011) Ana C Tahira et al.   Molecular Cancer

The functional role of long non-coding RNA in human carcinomas

(2011) Ewan A Gibb et al.   Molecular Cancer

Molecular Mechanisms of Long Noncoding RNAs

(2011) Kevin C. Wang et al.   MOLECULAR CELL

Targeted RNA sequencing reveals the deep complexity of the human transcriptome

(2011) Tim R Mercer et al.   NATURE BIOTECHNOLOGY

NONCODE v3.0: integrative annotation of long noncoding RNAs

(2011) D. Bu et al.   NUCLEIC ACIDS RESEARCH

dPORE-miRNA: Polymorphic Regulation of MicroRNA Genes

(2011) Sebastian Schmeier et al.   PLoS One

Deep sequencing-based identification of small non-coding RNAs inStreptomyces coelicolor

(2011) Michael-Paul Vockenhuber et al.   RNA Biology

RNAcentral: A vision for an international database of RNA sequences

(2011) A. Bateman et al.   RNA

The Emergence of lncRNAs in Cancer Biology

(2011) J. R. Prensner et al.   Cancer Discovery

Genomewide characterization of non-polyadenylated RNAs

(2011) Li Yang et al.   GENOME BIOLOGY

The NetAge database: a compendium of networks for longevity, age-related diseases and associated processes

(2010) Robi Tacutu et al.   BIOGERONTOLOGY

PuTmiR: A database for extracting neighboring transcription factors of human microRNAs

(2010) Sanghamitra Bandyopadhyay et al.   BMC BIOINFORMATICS

CircuitsDB: a database of mixed microRNA/transcription factor feed-forward regulatory circuits in human and mouse

(2010) Olivier Friard et al.   BMC BIOINFORMATICS

A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response

(2010) Maite Huarte et al.   CELL

MicroRNAs, epigenetics and disease

(2010) Asli Silahtaroglu et al.   Essays in Biochemistry

Large non-coding RNAs: missing links in cancer?

(2010) M. Huarte et al.   HUMAN MOLECULAR GENETICS

The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation

(2010) Vidisha Tripathi et al.   MOLECULAR CELL

Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis

(2010) Rajnish A. Gupta et al.   NATURE

miRGator v2.0 : an integrated system for functional investigation of microRNAs

(2010) S. Cho et al.   NUCLEIC ACIDS RESEARCH

Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics

(2010) Z. Fei et al.   NUCLEIC ACIDS RESEARCH

miRTarBase: a database curates experimentally validated microRNA–target interactions

(2010) Sheng-Da Hsu et al.   NUCLEIC ACIDS RESEARCH

starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data

(2010) Jian-Hua Yang et al.   NUCLEIC ACIDS RESEARCH

miRBase: integrating microRNA annotation and deep-sequencing data

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

lncRNAdb: a reference database for long noncoding RNAs

(2010) Paulo P. Amaral et al.   NUCLEIC ACIDS RESEARCH

sRNATarBase: A comprehensive database of bacterial sRNA targets verified by experiments

(2010) Y. Cao et al.   RNA

ncRNAimprint: A comprehensive database of mammalian imprinted noncoding RNAs

(2010) Y. Zhang et al.   RNA

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

(2010) M.-C. Tsai et al.   SCIENCE

A transcriptional sketch of a primary human breast cancer by 454 deep sequencing

(2009) Alessandro Guffanti et al.   BMC GENOMICS

An Ariadne's thread to the identification and annotation of noncoding RNAs in eukaryotes

(2009) G. Solda et al.   BRIEFINGS IN BIOINFORMATICS

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure

(2009) Douglas H. Turner et al.   NUCLEIC ACIDS RESEARCH

deepBase: a database for deeply annotating and mining deep sequencing data

(2009) Jian-Hua Yang et al.   NUCLEIC ACIDS RESEARCH

Conserved tissue expression signatures of intronic noncoding RNAs transcribed from human and mouse loci

(2008) Rodrigo Louro et al.   GENOMICS

Noncoding RNA in development

(2008) Paulo P. Amaral et al.   MAMMALIAN GENOME

Identification of protein-coding and intronic noncoding RNAs down-regulated in clear cell renal carcinoma

(2008) Glauber Costa Brito et al.   MOLECULAR CARCINOGENESIS

Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation

(2008) Jiong-Tang Li et al.   NUCLEIC ACIDS RESEARCH

sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes

(2008) Hsi-Yuan Huang et al.   NUCLEIC ACIDS RESEARCH

NRED: a database of long noncoding RNA expression

(2008) Marcel E. Dinger et al.   NUCLEIC ACIDS RESEARCH

BPS: a database of RNA base-pair structures

(2008) Y. Xin et al.   NUCLEIC ACIDS RESEARCH

miRecords: an integrated resource for microRNA-target interactions

(2008) F. Xiao et al.   NUCLEIC ACIDS RESEARCH

Rfam: updates to the RNA families database

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

miRDB: A microRNA target prediction and functional annotation database with a wiki interface

(2008) X. Wang   RNA