RNA‐protein interactions in an unstructured context

B Zagrovic, L Bartonek, AA Polyansky - FEBS letters, 2018 - Wiley Online Library
Despite their importance, our understanding of noncovalent RNA–protein interactions is
incomplete. This especially concerns the binding between RNA and unstructured protein …

[HTML][HTML] Interactions between long non‑coding RNAs and RNA‑binding proteins in cancer

H Huang, L Li, K Wen - Oncology reports, 2021 - spandidos-publications.com
Long non‑coding RNAs (lncRNAs) fulfill important roles in the majority of cellular processes.
Previous studies have demonstrated that lncRNAs are involved in the pathogenesis of …

Screening for small-molecule modulators of long noncoding RNA-protein interactions using AlphaScreen

R Pedram Fatemi, S Salah-Uddin… - Journal of …, 2015 - journals.sagepub.com
Long non–protein coding RNAs (lncRNAs) are an important class of molecules that help
orchestrate key cellular events. Although their functional roles in cells are not well …

[HTML][HTML] EDLMFC: an ensemble deep learning framework with multi-scale features combination for ncRNA–protein interaction prediction

J Wang, Y Zhao, W Gong, Y Liu, M Wang, X Huang… - BMC …, 2021 - Springer
Abstract Background Non-coding RNA (ncRNA) and protein interactions play essential roles
in various physiological and pathological processes. The experimental methods used for …

Widespread autogenous mRNA–protein interactions detected by CLIP-seq

TH Kapral, F Farnhammer, W Zhao, ZJ Lu… - Nucleic Acids …, 2022 - academic.oup.com
Autogenous interactions between mRNAs and the proteins they encode are implicated in
cellular feedback-loop regulation, but their extent and mechanistic foundation are unclear. It …

RCK: accurate and efficient inference of sequence-and structure-based protein–RNA binding models from RNAcompete data

Y Orenstein, Y Wang, B Berger - Bioinformatics, 2016 - academic.oup.com
Motivation: Protein–RNA interactions, which play vital roles in many processes, are
mediated through both RNA sequence and structure. CLIP-based methods, which measure …

Dissecting noncoding and pathogen RNA–protein interactomes

RA Flynn, L Martin, RC Spitale, BT Do, SM Sagan… - Rna, 2015 - rnajournal.cshlp.org
RNA–protein interactions are central to biological regulation. Cross-linking
immunoprecipitation (CLIP)-seq is a powerful tool for genome-wide interrogation of RNA …

[HTML][HTML] Unveiling the hidden function of long non-coding RNA by identifying its major partner-protein

Y Yang, L Wen, H Zhu - Cell & bioscience, 2015 - Springer
Tens of thousands of long non-coding RNAs (lncRNAs) have been discovered in eukarya,
but their functions are largely unknown. Fortunately, lncRNA–protein interactions may offer …

RPI-EDLCN: An ensemble deep learning framework based on capsule network for ncRNA–protein interaction prediction

X Li, W Qu, J Yan, J Tan - Journal of Chemical Information and …, 2023 - ACS Publications
Noncoding RNAs (ncRNAs) play crucial roles in many cellular life activities by interacting
with proteins. Identification of ncRNA-protein interactions (ncRPIs) is key to understanding …

Multimodal long noncoding RNA interaction networks: control panels for cell fate specification

KN Smith, SC Miller, G Varani, JM Calabrese… - Genetics, 2019 - academic.oup.com
Lineage specification in early development is the basis for the exquisitely precise body plan
of multicellular organisms. It is therefore critical to understand cell fate decisions in early …