catRAPID omics v2.0: going deeper and wider in the prediction of protein–RNA interactions

A large-scale binding and functional map of human RNA-binding proteins

(2020) Eric L. Van Nostrand et al.   NATURE

HOTAIRM1 regulates neuronal differentiation by modulating NEUROGENIN 2 and the downstream neurogenic cascade

(2020) Jessica Rea et al.   Cell Death & Disease

FMRP promotes RNA localization to neuronal projections through interactions between its RGG domain and G-quadruplex RNA sequences

(2020) Raeann Goering et al.   eLife

UniProt: the universal protein knowledgebase in 2021

(2020) et al.   NUCLEIC ACIDS RESEARCH

Modeling RNA-Binding Protein Specificity In Vivo by Precisely Registering Protein-RNA Crosslink Sites

(2019) Huijuan Feng et al.   MOLECULAR CELL

Axonal localization of the Fragile X family of RNA binding proteins is conserved across mammals

(2019) Katherine A. Shepard et al.   JOURNAL OF COMPARATIVE NEUROLOGY

EuRBPDB: a comprehensive resource for annotation, functional and oncological investigation of eukaryotic RNA binding proteins (RBPs)

(2019) Jian-You Liao et al.   NUCLEIC ACIDS RESEARCH

A brave new world of RNA-binding proteins

(2018) Matthias W. Hentze et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

SAMMSON fosters cancer cell fitness by concertedly enhancing mitochondrial and cytosolic translation

(2018) Roberto Vendramin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RNAct: Protein–RNA interaction predictions for model organisms with supporting experimental data

(2018) Benjamin Lang et al.   NUCLEIC ACIDS RESEARCH

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

An Integrative Study of Protein-RNA Condensates Identifies Scaffolding RNAs and Reveals Players in Fragile X-Associated Tremor/Ataxia Syndrome

(2018) Fernando Cid-Samper et al.   Cell Reports

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

Quantitative predictions of protein interactions with long noncoding RNAs

(2017) Davide Cirillo et al.   NATURE METHODS

ncRNA orthologies in the vertebrate lineage

(2016) Miguel Pignatelli et al.   Database-The Journal of Biological Databases and Curation

ATtRACT—a database of RNA-binding proteins and associated motifs

(2016) Girolamo Giudice et al.   Database-The Journal of Biological Databases and Curation

Ensembl comparative genomics resources

(2016) Javier Herrero et al.   Database-The Journal of Biological Databases and Curation

catRAPIDsignature: identification of ribonucleoproteins and RNA-binding regions

(2015) Carmen Maria Livi et al.   BIOINFORMATICS

Functional Insights into Chromatin Remodelling from Studies on CHARGE Syndrome

(2015) M. Albert Basson et al.   TRENDS IN GENETICS

A census of human RNA-binding proteins

(2014) Stefanie Gerstberger et al.   NATURE REVIEWS GENETICS

RBPmap: a web server for mapping binding sites of RNA-binding proteins

(2014) Inbal Paz et al.   NUCLEIC ACIDS RESEARCH

Constitutive patterns of gene expression regulated by RNA-binding proteins

(2014) Davide Cirillo et al.   GENOME BIOLOGY

catRAPID omics: a web server for large-scale prediction of protein-RNA interactions

(2013) F. Agostini et al.   BIOINFORMATICS

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

System-wide identification of RNA-binding proteins by interactome capture

(2013) Alfredo Castello et al.   Nature Protocols

FMRP targets distinct mRNA sequence elements to regulate protein expression

(2012) Manuel Ascano et al.   NATURE

APPRIS: annotation of principal and alternative splice isoforms

(2012) Jose Manuel Rodriguez et al.   NUCLEIC ACIDS RESEARCH

X-inactivation: quantitative predictions of protein interactions in the Xist network

(2012) Federico Agostini et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Neurodegenerative diseases: Quantitative predictions of protein-RNA interactions

(2012) D. Cirillo et al.   RNA

Predicting protein associations with long noncoding RNAs

(2011) Matteo Bellucci et al.   NATURE METHODS

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Fragile X and autism: Intertwined at the molecular level leading to targeted treatments

(2010) Randi Hagerman et al.   Molecular Autism

A Direct Role for FMRP in Activity-Dependent Dendritic mRNA Transport Links Filopodial-Spine Morphogenesis to Fragile X Syndrome

(2008) Jason B. Dictenberg et al.   DEVELOPMENTAL CELL