Advances in the characterization of RNA‐binding proteins

D Marchese, NS de Groot… - Wiley …, 2016 - Wiley Online Library
From transcription, to transport, storage, and translation, RNA depends on association with
different RNA‐binding proteins (RBPs). Methods based on next‐generation sequencing and …

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

F Agostini, A Zanzoni, P Klus, D Marchese… - …, 2013 - academic.oup.com
Here we introduce cat RAPID omics, a server for large-scale calculations of protein–RNA
interactions. Our web server allows (i) predictions at proteomic and transcriptomic level;(ii) …

Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins

M Stražar, M Žitnik, B Zupan, J Ule, T Curk - Bioinformatics, 2016 - academic.oup.com
Motivation: RNA binding proteins (RBPs) play important roles in post-transcriptional control
of gene expression, including splicing, transport, polyadenylation and RNA stability. To …

Non-coding RNAs in lung cancer: contribution of bioinformatics analysis to the development of non-invasive diagnostic tools

M Kunz, B Wolf, H Schulze, D Atlan, T Walles, H Walles… - Genes, 2016 - mdpi.com
Lung cancer is currently the leading cause of cancer related mortality due to late diagnosis
and limited treatment intervention. Non-coding RNAs are not translated into proteins and …

Protein complex scaffolding predicted as a prevalent function of long non-coding RNAs

DM Ribeiro, A Zanzoni, A Cipriano… - Nucleic acids …, 2018 - academic.oup.com
The human transcriptome contains thousands of long non-coding RNAs (lncRNAs).
Characterizing their function is a current challenge. An emerging concept is that lncRNAs …

A large-scale assessment of nucleic acids binding site prediction programs

Z Miao, E Westhof - PLoS computational biology, 2015 - journals.plos.org
Computational prediction of nucleic acid binding sites in proteins are necessary to
disentangle functional mechanisms in most biological processes and to explore the binding …

Prediction of protein-RNA interactions from single-cell transcriptomic data

J Fiorentino, A Armaos, A Colantoni… - Nucleic Acids …, 2024 - academic.oup.com
Proteins are crucial in regulating every aspect of RNA life, yet understanding their
interactions with coding and noncoding RNAs remains limited. Experimental studies are …

Long intergenic non-coding RNAs (LincRNAs) identified by RNA-seq in breast cancer

X Ding, L Zhu, T Ji, X Zhang, F Wang, S Gan, M Zhao… - PloS one, 2014 - journals.plos.org
In an attempt to find the correlation of aberrant expression of long intergenic noncoding
RNAs (lincRNAs) with cancer, twenty-five samples of breast cancer tissue and respective …

Principles of self-organization in biological pathways: a hypothesis on the autogenous association of alpha-synuclein

A Zanzoni, D Marchese, F Agostini… - Nucleic acids …, 2013 - academic.oup.com
Previous evidence indicates that a number of proteins are able to interact with cognate
mRNAs. These autogenous associations represent important regulatory mechanisms that …

Constitutive patterns of gene expression regulated by RNA-binding proteins

D Cirillo, D Marchese, F Agostini, CM Livi, T Botta-Orfila… - Genome biology, 2014 - Springer
Background RNA-binding proteins regulate a number of cellular processes, including
synthesis, folding, translocation, assembly and clearance of RNAs. Recent studies have …