Comprehensive prediction of lncRNA–RNA interactions in human transcriptome

High-throughput characterization of protein-RNA interactions

(2014) K. B. Cook et al.   Briefings in Functional Genomics

RNA-RNA Interactions Enable Specific Targeting of Noncoding RNAs to Nascent Pre-mRNAs and Chromatin Sites

(2014) Jesse M. Engreitz et al.   CELL

Elements and machinery of non-coding RNAs: toward their taxonomy

(2014) T. Hirose et al.   EMBO REPORTS

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification

(2014) Jeffrey J Quinn et al.   NATURE BIOTECHNOLOGY

Noncoding RNA and its associated proteins as regulatory elements of the immune system

(2014) Martin Turner et al.   NATURE IMMUNOLOGY

The rise of regulatory RNA

(2014) Kevin V. Morris et al.   NATURE REVIEWS GENETICS

7SL RNA represses p53 translation by competing with HuR

(2014) Kotb Abdelmohsen et al.   NUCLEIC ACIDS RESEARCH

CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains

(2014) Patrick R. Wright et al.   NUCLEIC ACIDS RESEARCH

The Intertwining of Transposable Elements and Non-Coding RNAs

(2013) Michael Hadjiargyrou et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The UCSC Genome Browser database: 2014 update

(2013) Donna Karolchik et al.   NUCLEIC ACIDS RESEARCH

Comparative genomics boosts target prediction for bacterial small RNAs

(2013) P. R. Wright et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Paraspeckle formation during the biogenesis of long non-coding RNAs

(2013) Takao Naganuma et al.   RNA Biology

Parameters for accurate genome alignment

(2012) Martin C Frith et al.   BMC BIOINFORMATICS

Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins

(2012) Alfredo Castello et al.   CELL

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

A Classification of Bioinformatics Algorithms from the Viewpoint of Maximizing Expected Accuracy (MEA)

(2012) Michiaki Hamada et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Control of somatic tissue differentiation by the long non-coding RNA TINCR

(2012) Markus Kretz et al.   NATURE

LncRNADisease: a database for long-non-coding RNA-associated diseases

(2012) Geng Chen et al.   NUCLEIC ACIDS RESEARCH

Accessibility and conservation: General features of bacterial small RNA–mRNA interactions?

(2012) Andreas Richter et al.   RNA Biology

A detailed investigation of accessibilities around target sites of siRNAs and miRNAs

(2011) Hisanori Kiryu et al.   BIOINFORMATICS

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements

(2011) Chenguang Gong et al.   NATURE

PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences

(2010) Stefan E. Seemann et al.   BIOINFORMATICS

RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming

(2010) Yuki Kato et al.   BIOINFORMATICS

A new repeat-masking method enables specific detection of homologous sequences

(2010) Martin C. Frith   NUCLEIC ACIDS RESEARCH

MENε/β noncoding RNAs are essential for structural integrity of nuclear paraspeckles

(2009) Yasnory T. F. Sasaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions

(2008) Anke Busch et al.   BIOINFORMATICS