Binding site discovery from nucleic acid sequences by discriminative learning of hidden Markov models

RBM10 regulates alternative splicing

(2014) Akira Inoue et al.   FEBS LETTERS

Advancing the functional utility of PAR-CLIP by quantifying background binding to mRNAs and lncRNAs

(2014) Matthew B Friedersdorf et al.   GENOME BIOLOGY

Integrative analysis revealed the molecular mechanism underlying RBM10-mediated splicing regulation

(2013) Yongbo Wang et al.   EMBO Molecular Medicine

RBM5, 6, and 10 Differentially Regulate NUMB Alternative Splicing to Control Cancer Cell Proliferation

(2013) Elias G. Bechara et al.   MOLECULAR CELL

RBM5 promotes exon 4 skipping ofAIDpre-mRNA by competing with the binding of U2AF65 to the polypyrimidine tract

(2012) Wenxing Jin et al.   FEBS LETTERS

Systematic discovery of structural elements governing stability of mammalian messenger RNAs

(2012) Hani Goodarzi et al.   NATURE

CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex

(2012) Jérôme Saulière et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Inferring direct DNA binding from ChIP-seq

(2012) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

DECOD: fast and accurate discriminative DNA motif finding

(2011) Peter Huggins et al.   BIOINFORMATICS

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

Predicting sequence and structural specificities of RNA binding regions recognized by splicing factor SRSF1

(2011) Xin Wang et al.   BMC GENOMICS

Characterization of a Family of RanBP2-Type Zinc Fingers that Can Recognize Single-Stranded RNA

(2011) Cuong D. Nguyen et al.   JOURNAL OF MOLECULAR BIOLOGY

A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins

(2011) Shivendra Kishore et al.   NATURE METHODS

doRiNA: a database of RNA interactions in post-transcriptional regulation

(2011) Gerd Anders et al.   NUCLEIC ACIDS RESEARCH

De-Novo Discovery of Differentially Abundant Transcription Factor Binding Sites Including Their Positional Preference

(2011) Jens Keilwagen et al.   PLoS Computational Biology

Identification of Context-Dependent Motifs by Contrasting ChIP Binding Data

(2010) Mike J. Mason et al.   BIOINFORMATICS

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities

(2010) A. Jolma et al.   GENOME RESEARCH

Large-Scale Discovery and Characterization of Protein Regulatory Motifs in Eukaryotes

(2010) Daniel S. Lieber et al.   PLoS One

Genome-wide analysis of mRNA targets for Caenorhabditis elegans FBF, a conserved stem cell regulator

(2010) Aaron M. Kershner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

The zinc fingers of the SR-like protein ZRANB2 are single-stranded RNA-binding domains that recognize 5' splice site-like sequences

(2009) F. E. Loughlin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discovery of Regulatory Elements is Improved by a Discriminatory Approach

(2009) Eivind Valen et al.   PLoS Computational Biology

Connecting microRNA Genes to the Core Transcriptional Regulatory Circuitry of Embryonic Stem Cells

(2008) Alexander Marson et al.   CELL

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

Tcf3 is an integral component of the core regulatory circuitry of embryonic stem cells

(2008) M. F. Cole et al.   GENES & DEVELOPMENT

Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts

(2008) J. R. Sanford et al.   GENOME RESEARCH

Ribonomic Analysis of Human Pum1 Reveals cis-trans Conservation across Species despite Evolution of Diverse mRNA Target Sets

(2008) A. R. Morris et al.   MOLECULAR AND CELLULAR BIOLOGY

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

(2008) Donny D. Licatalosi et al.   NATURE

A core Klf circuitry regulates self-renewal of embryonic stem cells

(2008) Jianming Jiang et al.   NATURE CELL BIOLOGY

Comparative Analysis of mRNA Targets for Human PUF-Family Proteins Suggests Extensive Interaction with the miRNA Regulatory System

(2008) Alessia Galgano et al.   PLoS One

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE

T-Cell Factor 3 Regulates Embryonic Stem Cell Pluripotency and Self-Renewal by the Transcriptional Control of Multiple Lineage Pathways

(2008) Wai-Leong Tam et al.   STEM CELLS

Tcf3 Functions as a Steady-State Limiter of Transcriptional Programs of Mouse Embryonic Stem Cell Self-Renewal

(2008) Fei Yi et al.   STEM CELLS