Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins

Data Fusion by Matrix Factorization

(2015) Marinka Zitnik et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

The cleverSuite approach for protein characterization: predictions of structural properties, solubility, chaperone requirements and RNA-binding abilities

(2014) Petr Klus et al.   BIOINFORMATICS

Protein-specific prediction of mRNA binding using RNA sequences, binding motifs and predicted secondary structures

(2014) Carmen M Livi et al.   BMC BIOINFORMATICS

CPSF30 and Wdr33 directly bind to AAUAAA in mammalian mRNA 3′ processing

(2014) Serena L. Chan et al.   GENES & DEVELOPMENT

Competition between target sites of regulators shapes post-transcriptional gene regulation

(2014) Marvin Jens et al.   NATURE REVIEWS GENETICS

Transcriptome-wide Discovery of microRNA Binding Sites in Human Brain

(2014) Ryan L. Boudreau et al.   NEURON

Crosslinking-immunoprecipitation (iCLIP) analysis reveals global regulatory roles of hnRNP L

(2014) Oliver Rossbach et al.   RNA Biology

GraphProt: modeling binding preferences of RNA-binding proteins

(2014) Daniel Maticzka et al.   GENOME BIOLOGY

RNA Protein Interaction in Neurons

(2013) Robert B. Darnell   Annual Review of Neuroscience

Direct Competition between hnRNP C and U2AF65 Protects the Transcriptome from the Exonization of Alu Elements

(2013) Kathi Zarnack et al.   CELL

Predicting Protein–Protein Interactions from Multimodal Biological Data Sources via Nonnegative Matrix Tri-Factorization

(2013) Hua Wang et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

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

(2013) Chaolin Zhang et al.   NUCLEIC ACIDS RESEARCH

NSun2-Mediated Cytosine-5 Methylation of Vault Noncoding RNA Determines Its Processing into Regulatory Small RNAs

(2013) Shobbir Hussain et al.   Cell Reports

Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins

(2012) Alfredo Castello et al.   CELL

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

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

Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data

(2012) Cem Sievers et al.   NUCLEIC ACIDS RESEARCH

Discovery of multi-dimensional modules by integrative analysis of cancer genomic data

(2012) Shihua Zhang et al.   NUCLEIC ACIDS RESEARCH

Predictions of protein-RNA interactions

(2012) Davide Cirillo et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Differential GC Content between Exons and Introns Establishes Distinct Strategies of Splice-Site Recognition

(2012) Maayan Amit et al.   Cell Reports

Online Nonnegative Matrix Factorization With Robust Stochastic Approximation

(2012) Naiyang Guan et al.   IEEE Transactions on Neural Networks and Learning Systems

Computational biology of RNA interactions

(2012) Christoph Dieterich et al.   Wiley Interdisciplinary Reviews-RNA

Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions

(2012) Yoichiro Sugimoto et al.   GENOME BIOLOGY

A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules

(2011) Shihua Zhang et al.   BIOINFORMATICS

Computational methods for prediction of protein–RNA interactions

(2011) Tomasz Puton et al.   JOURNAL OF STRUCTURAL BIOLOGY

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

(2011) Shivendra Kishore et al.   NATURE METHODS

Characterizing the RNA targets and position-dependent splicing regulation by TDP-43

(2011) James R Tollervey et al.   NATURE NEUROSCIENCE

RNA targets of wild-type and mutant FET family proteins

(2011) Jessica I Hoell et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2011) Gerd Anders et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Markus Hafner et al.   CELL

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution

(2010) Julian König et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2010) X. Li et al.   RNA

Integrative Modeling Defines the Nova Splicing-Regulatory Network and Its Combinatorial Controls

(2010) C. Zhang et al.   SCIENCE

iCLIP Predicts the Dual Splicing Effects of TIA-RNA Interactions

(2010) Zhen Wang et al.   PLOS BIOLOGY

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

(2010) Hilal Kazan et al.   PLoS Computational Biology

Predictor correlation impacts machine learning algorithms: implications for genomic studies

(2009) K. K. Nicodemus et al.   BIOINFORMATICS

Position-dependent motif characterization using non-negative matrix factorization

(2008) Lucie N. Hutchins et al.   BIOINFORMATICS

A systematic analysis of intronic sequences downstream of 5' splice sites reveals a widespread role for U-rich motifs and TIA1/TIAL1 proteins in alternative splicing regulation

(2008) I. Aznarez et al.   GENOME RESEARCH

Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts

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

Convex and Semi-Nonnegative Matrix Factorizations

(2008) C.H.Q. Ding et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE