Parallel computation of genome-scale RNA secondary structure to detect structural constraints on human genome

Global Analysis of the RNA-Protein Interaction and RNA Secondary Structure Landscapes of the Arabidopsis Nucleus

(2015) Sager J. Gosai et al.   MOLECULAR CELL

Ensembl Genomes 2016: more genomes, more complexity

(2015) Paul Julian Kersey et al.   NUCLEIC ACIDS RESEARCH

Mechanical force releases nascent chain-mediated ribosome arrest in vitro and in vivo

(2015) D. H. Goldman et al.   SCIENCE

Gateways to the FANTOM5 promoter level mammalian expression atlas

(2015) Marina Lizio et al.   GENOME BIOLOGY

GSDS 2.0: an upgraded gene feature visualization server

(2014) Bo Hu et al.   BIOINFORMATICS

RNA Bind-n-Seq: Quantitative Assessment of the Sequence and Structural Binding Specificity of RNA Binding Proteins

(2014) Nicole Lambert et al.   MOLECULAR CELL

Landscape and variation of RNA secondary structure across the human transcriptome

(2014) Yue Wan et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

The UCSC Genome Browser database: 2015 update

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

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

The human splicing code reveals new insights into the genetic determinants of disease

(2014) H. Y. Xiong et al.   SCIENCE

CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data

(2014) Tsukasa Fukunaga et al.   GENOME BIOLOGY

Alternative splicing: a pivotal step between eukaryotic transcription and translation

(2013) Alberto R. Kornblihtt et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

RefSeq: an update on mammalian reference sequences

(2013) Kim D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

Widespread recognition of 5' splice sites by noncanonical base-pairing to U1 snRNA involving bulged nucleotides

(2012) X. Roca et al.   GENES & DEVELOPMENT

Global or local? Predicting secondary structure and accessibility in mRNAs

(2012) Sita J. Lange et al.   NUCLEIC ACIDS RESEARCH

RNA secondary structure mediates alternative 3'ss selection in Saccharomyces cerevisiae

(2012) M. Plass et al.   RNA

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

(2011) Hisanori Kiryu et al.   BIOINFORMATICS

GC content around splice sites affects splicing through pre-mRNA secondary structures

(2011) Jing Zhang et al.   BMC GENOMICS

Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43

(2011) Magdalini Polymenidou et al.   NATURE NEUROSCIENCE

Understanding the transcriptome through RNA structure

(2011) Yue Wan et al.   NATURE REVIEWS GENETICS

RNA secondary structure in mutually exclusive splicing

(2011) Yun Yang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Secondary structure is required for 3′ splice site recognition in yeast

(2011) Ondřej Gahura et al.   NUCLEIC ACIDS RESEARCH

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz et al.   NATURE

Translation efficiency is determined by both codon bias and folding energy

(2010) Tamir Tuller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNAslider: a faster engine for consecutive windows folding and its application to the analysis of genomic folding asymmetry

(2009) Yair Horesh et al.   BMC BIOINFORMATICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Role of RNA structure in regulating pre-mRNA splicing

(2009) M. Bryan Warf et al.   TRENDS IN BIOCHEMICAL SCIENCES

Polypyrimidine-tract-binding protein: a multifunctional RNA-binding protein

(2008) Kirsty Sawicka et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Alternative splicing and disease

(2008) Jamal Tazi et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

Prediction of RNA secondary structure using generalized centroid estimators

(2008) Michiaki Hamada et al.   BIOINFORMATICS

The impact of target site accessibility on the design of effective siRNAs

(2008) Hakim Tafer et al.   NATURE BIOTECHNOLOGY

The Vienna RNA Websuite

(2008) A. R. Gruber et al.   NUCLEIC ACIDS RESEARCH

RNA landscape of evolution for optimal exon and intron discrimination

(2008) C. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conserved RNA secondary structures promote alternative splicing

(2008) P. J. Shepard et al.   RNA