ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data

2008, RNA-binding proteins and post-transcriptional gene regulation, FEBS Lett., 582, 1977, 10.1016/j.febslet.2008.03.004

2012, Insights into RNA biology from an atlas of mammalian mRNA-binding proteins, Cell, 149, 1393, 10.1016/j.cell.2012.04.031

2014, CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data, Genome Biol., 15, R16, 10.1186/gb-2014-15-1-r16

2010, RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins, PLoS Comput. Biol., 6, e1000832, 10.1371/journal.pcbi.1000832

2006, How does DNA sequence motif discovery work?, Nat. Biotechnol., 24, 959, 10.1038/nbt0806-959

2003, YMF: a program for discovery of novel transcription factor binding sites by statistical overrepresentation, Nucleic Acids Res., 31, 3586, 10.1093/nar/gkg618

2008, RSAT: regulatory sequence analysis tools, Nucleic Acids Res., 36, W119, 10.1093/nar/gkn304

2010, Evidence-ranked motif identification, Genome Biol., 11, R19, 10.1186/gb-2010-11-2-r19

2006, What are DNA sequence motifs?, Nat. Biotechnol., 24, 423, 10.1038/nbt0406-423

1994, Fitting a mixture model by expectation maximization to discover motifs in bipolymers, Proc. Int. Conf. Intell. Syst. Mol. Biol., 2, 28

1993, Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment, Science, 262, 208, 10.1126/science.8211139

2007, A systems approach to measuring the binding energy landscapes of transcription factors, Science, 315, 233, 10.1126/science.1131007

2007, Predicting transcription factor affinities to DNA from a biophysical model, Bioinformatics, 23, 134, 10.1093/bioinformatics/btl565

2010, Determining the specificity of protein–DNA interactions, Nat. Rev. Genet., 11, 751, 10.1038/nrg2845

2013, SELEX to identify protein-binding sites on RNA, Cold Spring Harb. Protoc., 2013, 156

2009, Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins, Nat. Biotechnol., 27, 667, 10.1038/nbt.1550

2003, CLIP identifies Nova-regulated RNA networks in the brain, Science, 302, 1212, 10.1126/science.1090095

2010, Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP, Cell, 141, 129, 10.1016/j.cell.2010.03.009

2010, iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution, Nat. Struct. Mol. Biol., 17, 909, 10.1038/nsmb.1838

2012, Site identification in high-throughput RNA–protein interaction data, Bioinformatics, 28, 3013, 10.1093/bioinformatics/bts569

2011, PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data, Genome Biol., 12, R79, 10.1186/gb-2011-12-8-r79

2014, Advancing the functional utility of PAR-CLIP by quantifying background binding to mRNAs and lncRNAs, Genome Biol., 15, R2, 10.1186/gb-2014-15-1-r2

1998, Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies, J. Mol. Biol., 281, 827, 10.1006/jmbi.1998.1947

2016, AptaTRACE Elucidates RNA Sequence-Structure Motifs from Selection Trends in HT-SELEX Experiments, Cell Syst., 3, 62, 10.1016/j.cels.2016.07.003

1998, Predicting Gene Regulatory Elements in Silico on a Genomic Scale, Genome Res., 8, 1202, 10.1101/gr.8.11.1202

2006, MEME: discovering and analyzing DNA and protein sequence motifs, Nucleic Acids Res., 34, W369, 10.1093/nar/gkl198

2006, Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE, Bioinformatics, 22, e141, 10.1093/bioinformatics/btl223

2002, A Gibbs Sampling Method to Detect Overrepresented Motifs in the Upstream Regions of Coexpressed Genes, J. Comput. Biol., 9, 447, 10.1089/10665270252935566

2001, BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes, Pac. Symp. Biocomput., 127

2006, GibbsST: a Gibbs sampling method for motif discovery with enhanced resistance to local optima, BMC Bioinformatics, 7, 486, 10.1186/1471-2105-7-486

2006, Using RNA secondary structures to guide sequence motif finding towards single-stranded regions, Nucleic Acids Res., 34, e117, 10.1093/nar/gkl544

2015, Leveraging cross-link modification events in CLIP-seq for motif discovery, Nucleic Acids Res., 43, 95, 10.1093/nar/gku1288

2014, GraphProt: modeling binding preferences of RNA-binding proteins, Genome Biol., 15, R17, 10.1186/gb-2014-15-1-r17

2015, Transcription factor trapping by RNA in gene regulatory elements, Science, 350, 978, 10.1126/science.aad3346

2006, RNAshapes: an integrated RNA analysis package based on abstract shapes, Bioinformatics, 22, 500, 10.1093/bioinformatics/btk010

2010, RNAstructure: software for RNA secondary structure prediction and analysis, BMC Bioinformatics, 11, 129, 10.1186/1471-2105-11-129

2015, DoRiNA 2.0 - upgrading the doRiNA database of RNA interactions in post-transcriptional regulation, Nucleic Acids Res., 43, D160, 10.1093/nar/gku1180

1995, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society. Series B (Methodological), 57, 289, 10.1111/j.2517-6161.1995.tb02031.x

2000, Nova-1 Regulates Neuron-Specific Alternative Splicing and Is Essential for Neuronal Viability, Neuron, 25, 359, 10.1016/S0896-6273(00)80900-9

2008, New implications for the QUAKING RNA binding protein in human disease, J. Neurosci. Res., 86, 233, 10.1002/jnr.21485

2005, The contributions of dsRNA structure to Dicer specificity and efficiency, RNA, 11, 674, 10.1261/rna.7272305

2012, DGCR8 HITS-CLIP reveals novel functions for the Microprocessor, Nat. Struct. Mol. Biol., 19, 760, 10.1038/nsmb.2344

2013, The core microprocessor component DiGeorge syndrome critical region 8 (DGCR8) is a nonspecific RNA-binding protein, J. Biol. Chem., 288, 26785, 10.1074/jbc.M112.446880

2004, The Drosha-DGCR8 complex in primary microRNA processing, Genes Dev., 18, 3016, 10.1101/gad.1262504

2013, Beyond secondary structure: primary-sequence determinants license pri-miRNA hairpins for processing, Cell, 152, 844, 10.1016/j.cell.2013.01.031

2014, Microprocessor activity controls differential miRNA biogenesis in vivo, Cell Rep., 9, 542, 10.1016/j.celrep.2014.09.007

2011, YY1 tethers Xist RNA to the inactive X nucleation center, Cell, 146, 119, 10.1016/j.cell.2011.06.026

1986, Information content of binding sites on nucleotide sequences, J. Mol. Biol., 188, 415, 10.1016/0022-2836(86)90165-8

2007, Effect of target secondary structure on RNAi efficiency, RNA, 13, 1631, 10.1261/rna.546207

2007, The role of site accessibility in microRNA target recognition, Nat. Genet., 39, 1278, 10.1038/ng2135