Protein–RNA interaction prediction with deep learning: structure matters
Protein–RNA interactions are of vital importance to a variety of cellular activities. Both
experimental and computational techniques have been developed to study the interactions …
experimental and computational techniques have been developed to study the interactions …
Dynamic m6A methylation facilitates mRNA triaging to stress granules
M Anders, I Chelysheva, I Goebel… - Life science …, 2018 - life-science-alliance.org
Reversible post-transcriptional modifications on messenger RNA emerge as prevalent
phenomena in RNA metabolism. The most abundant among them is N6-methyladenosine …
phenomena in RNA metabolism. The most abundant among them is N6-methyladenosine …
The NSUN5-FTH1/FTL pathway mediates ferroptosis in bone marrow-derived mesenchymal stem cells
J Liu, Z Ren, L Yang, L Zhu, Y Li, C Bie, H Liu, Y Ji… - Cell Death …, 2022 - nature.com
Ferroptosis is a type of cell death induced by the iron-dependent accumulation of lipid
hydroperoxides and reactive oxygen species (ROS) in cells. Inhibiting ferroptosis is …
hydroperoxides and reactive oxygen species (ROS) in cells. Inhibiting ferroptosis is …
DeepCLIP: predicting the effect of mutations on protein–RNA binding with deep learning
Nucleotide variants can cause functional changes by altering protein–RNA binding in
various ways that are not easy to predict. This can affect processes such as splicing, nuclear …
various ways that are not easy to predict. This can affect processes such as splicing, nuclear …
Deep neural networks for interpreting RNA-binding protein target preferences
M Ghanbari, U Ohler - Genome research, 2020 - genome.cshlp.org
Deep learning has become a powerful paradigm to analyze the binding sites of regulatory
factors including RNA-binding proteins (RBPs), owing to its strength to learn complex …
factors including RNA-binding proteins (RBPs), owing to its strength to learn complex …
Positional motif analysis reveals the extent of specificity of protein-RNA interactions observed by CLIP
Background Crosslinking and immunoprecipitation (CLIP) is a method used to identify in
vivo RNA–protein binding sites on a transcriptome-wide scale. With the increasing amounts …
vivo RNA–protein binding sites on a transcriptome-wide scale. With the increasing amounts …
Deciphering human ribonucleoprotein regulatory networks
RNA-binding proteins (RBPs) control and coordinate each stage in the life cycle of RNAs.
Although in vivo binding sites of RBPs can now be determined genome-wide, most studies …
Although in vivo binding sites of RBPs can now be determined genome-wide, most studies …
Interrelationship between miRNA and splicing factors in pancreatic ductal adenocarcinoma
IGP Supadmanaba, G Mantini, O Randazzo… - Epigenetics, 2022 - Taylor & Francis
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers because of
diagnosis at late stage and inherent/acquired chemoresistance. Recent advances in …
diagnosis at late stage and inherent/acquired chemoresistance. Recent advances in …
Long noncoding RNA MAPKAPK5‐AS1 promotes colorectal cancer proliferation by partly silencing p21 expression
H Ji, B Hui, J Wang, Y Zhu, L Tang, P Peng… - Cancer …, 2019 - Wiley Online Library
Colorectal cancer (CRC) is the third most common malignancy in the world, and long
noncoding RNA (lncRNA) plays a critical role in carcinogenesis. Here, we report a novel …
noncoding RNA (lncRNA) plays a critical role in carcinogenesis. Here, we report a novel …
Expectation pooling: an effective and interpretable pooling method for predicting DNA–protein binding
Abstract Motivation Convolutional neural networks (CNNs) have outperformed conventional
methods in modeling the sequence specificity of DNA–protein binding. While previous …
methods in modeling the sequence specificity of DNA–protein binding. While previous …