[HTML][HTML] CLIP and complementary methods

M Hafner, M Katsantoni, T Köster, J Marks… - Nature Reviews …, 2021 - nature.com
RNA molecules start assembling into ribonucleoprotein (RNP) complexes during
transcription. Dynamic RNP assembly, largely directed by cis-acting elements on the RNA …

Revealing protein–lncRNA interaction

F Ferre, A Colantoni… - Briefings in …, 2016 - academic.oup.com
Long non-coding RNAs (lncRNAs) are associated to a plethora of cellular functions, most of
which require the interaction with one or more RNA-binding proteins (RBPs); similarly, RBPs …

Sequences enriched in Alu repeats drive nuclear localization of long RNAs in human cells

Y Lubelsky, I Ulitsky - Nature, 2018 - nature.com
Long noncoding RNAs (lncRNAs) are emerging as key parts of multiple cellular pathways,
but their modes of action and how these are dictated by sequence remain unclear. lncRNAs …

Dynamic characterization and interpretation for protein-RNA interactions across diverse cellular conditions using HDRNet

H Zhu, Y Yang, Y Wang, F Wang, Y Huang… - Nature …, 2023 - nature.com
RNA-binding proteins play crucial roles in the regulation of gene expression, and
understanding the interactions between RNAs and RBPs in distinct cellular conditions forms …

Prediction of RNA-protein sequence and structure binding preferences using deep convolutional and recurrent neural networks

X Pan, P Rijnbeek, J Yan, HB Shen - BMC genomics, 2018 - Springer
Background RNA regulation is significantly dependent on its binding protein partner, known
as the RNA-binding proteins (RBPs). Unfortunately, the binding preferences for most RBPs …

A deep learning framework for modeling structural features of RNA-binding protein targets

S Zhang, J Zhou, H Hu, H Gong, L Chen… - Nucleic acids …, 2016 - academic.oup.com
RNA-binding proteins (RBPs) play important roles in the post-transcriptional control of
RNAs. Identifying RBP binding sites and characterizing RBP binding preferences are key …

Specificity and nonspecificity in RNA–protein interactions

E Jankowsky, ME Harris - Nature reviews Molecular cell biology, 2015 - nature.com
To fully understand the regulation of gene expression, it is critical to quantitatively define
whether and how RNA-binding proteins (RBPs) discriminate between alternative binding …

Predicting dynamic cellular protein–RNA interactions by deep learning using in vivo RNA structures

L Sun, K Xu, W Huang, YT Yang, P Li, L Tang, T Xiong… - Cell research, 2021 - nature.com
Interactions with RNA-binding proteins (RBPs) are integral to RNA function and cellular
regulation, and dynamically reflect specific cellular conditions. However, presently available …

Predicting RNA–protein binding sites and motifs through combining local and global deep convolutional neural networks

X Pan, HB Shen - Bioinformatics, 2018 - academic.oup.com
Motivation RNA-binding proteins (RBPs) take over 5–10% of the eukaryotic proteome and
play key roles in many biological processes, eg gene regulation. Experimental detection of …

The lncRNA landscape of breast cancer reveals a role for DSCAM-AS1 in breast cancer progression

YS Niknafs, S Han, T Ma, C Speers, C Zhang… - Nature …, 2016 - nature.com
Molecular classification of cancers into subtypes has resulted in an advance in our
understanding of tumour biology and treatment response across multiple tumour types …