A novel method for the identification of conserved structural patterns in RNA: From small scale to high-throughput applications

A New Method to Predict RNA Secondary Structure Based on RNA Folding Simulation

(2016) Yuanning Liu et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Lin28A Binds Active Promoters and Recruits Tet1 to Regulate Gene Expression

(2016) Yaxue Zeng et al.   MOLECULAR CELL

RNA motif discovery: a computational overview

(2015) Avinash Achar et al.   Biology Direct

Revealing protein–lncRNA interaction

(2015) Fabrizio Ferrè et al.   BRIEFINGS IN BIOINFORMATICS

Web-Beagle: a web server for the alignment of RNA secondary structures: Figure 1.

(2015) Eugenio Mattei et al.   NUCLEIC ACIDS RESEARCH

AREsite2: an enhanced database for the comprehensive investigation of AU/GU/U-rich elements

(2015) Jörg Fallmann et al.   NUCLEIC ACIDS RESEARCH

Towards an improved apple reference transcriptome using RNA-seq

(2014) Yang Bai et al.   MOLECULAR GENETICS AND GENOMICS

A novel approach to represent and compare RNA secondary structures

(2014) Eugenio Mattei et al.   NUCLEIC ACIDS RESEARCH

Leveraging cross-link modification events in CLIP-seq for motif discovery

(2014) Emad Bahrami-Samani et al.   NUCLEIC ACIDS RESEARCH

DoRiNA 2.0—upgrading the doRiNA database of RNA interactions in post-transcriptional regulation

(2014) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

GraphProt: modeling binding preferences of RNA-binding proteins

(2014) Daniel Maticzka et al.   GENOME BIOLOGY

Classification and assessment tools for structural motif discovery algorithms

(2013) Ghada Badr et al.   BMC BIOINFORMATICS

Prediction of clustered RNA-binding protein motif sites in the mammalian genome

(2013) Chaolin Zhang et al.   NUCLEIC ACIDS RESEARCH

RBPmotif: a web server for the discovery of sequence and structure preferences of RNA-binding proteins

(2013) Hilal Kazan et al.   NUCLEIC ACIDS RESEARCH

Finding the target sites of RNA-binding proteins

(2013) Xiao Li et al.   Wiley Interdisciplinary Reviews-RNA

LIN28A Is a Suppressor of ER-Associated Translation in Embryonic Stem Cells

(2012) Jun Cho et al.   CELL

Efficient motif search in ranked lists and applications to variable gap motifs

(2012) Limor Leibovich et al.   NUCLEIC ACIDS RESEARCH

Rfam 11.0: 10 years of RNA families

(2012) Sarah W. Burge et al.   NUCLEIC ACIDS RESEARCH

RNA–protein interactions in vivo: global gets specific

(2012) Minna-Liisa Änkö et al.   TRENDS IN BIOCHEMICAL SCIENCES

Deciphering the role of RNA-binding proteins in the post-transcriptional control of gene expression

(2011) S. Kishore et al.   Briefings in Functional Genomics

Molecular Basis for Interaction of let-7 MicroRNAs with Lin28

(2011) Yunsun Nam et al.   CELL

Genomic Analyses of the RNA-binding Protein Hu Antigen R (HuR) Identify a Complex Network of Target Genes and Novel Characteristics of Its Binding Sites

(2011) Philip J. Uren et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure

(2010) X. Li et al.   RNA

RNAcontext: A New Method for Learning the Sequence and Structure Binding Preferences of RNA-Binding Proteins

(2010) Hilal Kazan et al.   PLoS Computational Biology

Between a chicken and a grape: estimating the number of human genes

(2010) Mihaela Pertea et al.   GENOME BIOLOGY

A local multiple alignment method for detection of non-coding RNA sequences

(2009) Yasuo Tabei et al.   BIOINFORMATICS

TUT4 in Concert with Lin28 Suppresses MicroRNA Biogenesis through Pre-MicroRNA Uridylation

(2009) Inha Heo et al.   CELL

RNA processing and its regulation: global insights into biological networks

(2009) Donny D. Licatalosi et al.   NATURE REVIEWS GENETICS

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Evaluation of time profile reconstruction from complex two-color microarray designs

(2008) Ana C Fierro et al.   BMC BIOINFORMATICS

The Vienna RNA Websuite

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

Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes

(2008) M. Rabani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA