From Structure Prediction to Genomic Screens for Novel Non-Coding RNAs

A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression

(2011) Kevin C. Wang et al.   NATURE

Long noncoding RNA in genome regulation

(2011) Tiffany Hung et al.   RNA Biology

Long Noncoding RNAs with Enhancer-like Function in Human Cells

(2010) Ulf Andersson Ørom et al.   CELL

Advances in RNA structure analysis by chemical probing

(2010) Kevin M Weeks   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz et al.   NATURE

FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing

(2010) Jason G Underwood et al.   NATURE METHODS

Genome-wide computational identification and manual annotation of human long noncoding RNA genes

(2010) H. Jia et al.   RNA

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

(2010) M.-C. Tsai et al.   SCIENCE

Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies

(2009) Parvez Anandam et al.   BIOINFORMATICS

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

The long noncoding RNA Kcnq1ot1 organises a lineage-specific nuclear domain for epigenetic gene silencing

(2009) L. Redrup et al.   DEVELOPMENT

Emerging similarities in epigenetic gene silencing by long noncoding RNAs

(2009) Takashi Nagano et al.   MAMMALIAN GENOME

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

(2009) Mitchell Guttman et al.   NATURE

Architecture and secondary structure of an entire HIV-1 RNA genome

(2009) Joseph M. Watts 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

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

(2009) Ahmad M. Khalil et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The tedious task of finding homologous noncoding RNA genes

(2009) P. Menzel et al.   RNA

De novo prediction of structured RNAs from genomic sequences

(2009) Jan Gorodkin et al.   TRENDS IN BIOTECHNOLOGY

A global view of genomic information – moving beyond the gene and the master regulator

(2009) John S. Mattick et al.   TRENDS IN GENETICS

MicroRNAs: A new class of gene regulators

(2008) Douglas J. Guarnieri et al.   ANNALS OF MEDICINE

Dinucleotide controlled null models for comparative RNA gene prediction

(2008) Tanja Gesell et al.   BMC BIOINFORMATICS

De novo search for non-coding RNA genes in the AT-rich genome of Dictyostelium discoideum: Performance of Markov-dependent genome feature scoring

(2008) P. Larsson et al.   GENOME RESEARCH

The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs

(2008) Katsutomo Okamura et al.   NATURE

Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight?

(2008) Witold Filipowicz et al.   NATURE REVIEWS GENETICS

Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments

(2008) Stefan E. Seemann et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser Database: update 2009

(2008) R. M. Kuhn et al.   NUCLEIC ACIDS RESEARCH

Rfam: updates to the RNA families database

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

Predicted Functional RNAs within Coding Regions Constrain Evolutionary Rates of Yeast Proteins

(2008) Charles D. Warden et al.   PLoS One

Accurate SHAPE-directed RNA structure determination

(2008) K. E. Deigan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Support Vector Machines and Kernels for Computational Biology

(2008) Asa Ben-Hur et al.   PLoS Computational Biology

Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions

(2007) E. Torarinsson et al.   GENOME RESEARCH