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 …

Positive-unlabeled learning in bioinformatics and computational biology: a brief review

F Li, S Dong, A Leier, M Han, X Guo, J Xu… - Briefings in …, 2022 - academic.oup.com
Conventional supervised binary classification algorithms have been widely applied to
address significant research questions using biological and biomedical data. This …

Benchmarks in antimicrobial peptide prediction are biased due to the selection of negative data

K Sidorczuk, P Gagat, F Pietluch, J Kała… - Briefings in …, 2022 - academic.oup.com
Antimicrobial peptides (AMPs) are a heterogeneous group of short polypeptides that target
not only microorganisms but also viruses and cancer cells. Due to their lower selection for …

IPMiner: hidden ncRNA-protein interaction sequential pattern mining with stacked autoencoder for accurate computational prediction

X Pan, YX Fan, J Yan, HB Shen - BMC genomics, 2016 - Springer
Abstract Background Non-coding RNAs (ncRNAs) play crucial roles in many biological
processes, such as post-transcription of gene regulation. ncRNAs mainly function through …

Long noncoding RNA: a crosslink in biological regulatory network

Y Zhang, Y Tao, Q Liao - Briefings in bioinformatics, 2018 - academic.oup.com
Long noncoding RNAs (lncRNAs) had been defined as a novel class of functional RNAs
longer than 200 nucleotides around a decade ago. It is widely acknowledged that lncRNAs …

Positive-unlabeled learning identifies vaccine candidate antigens in the malaria parasite Plasmodium falciparum

RT Chou, A Ouattara, M Adams, AA Berry… - NPJ Systems Biology …, 2024 - nature.com
Malaria vaccine development is hampered by extensive antigenic variation and complex life
stages of Plasmodium species. Vaccine development has focused on a small number of …

RBPPred: predicting RNA-binding proteins from sequence using SVM

X Zhang, S Liu - Bioinformatics, 2017 - academic.oup.com
Motivation Detection of RNA-binding proteins (RBPs) is essential since the RNA-binding
proteins play critical roles in post-transcriptional regulation and have diverse roles in various …

Recent methodology progress of deep learning for RNA–protein interaction prediction

X Pan, Y Yang, CQ **a, AH Mirza… - Wiley Interdisciplinary …, 2019 - Wiley Online Library
Interactions between RNAs and proteins play essential roles in many important biological
processes. Benefitting from the advances of next generation sequencing technologies …

[HTML][HTML] Computational prediction of RNA-binding proteins and binding sites

J Si, J Cui, J Cheng, R Wu - International journal of molecular sciences, 2015 - mdpi.com
Proteins and RNA interaction have vital roles in many cellular processes such as protein
synthesis, sequence encoding, RNA transfer, and gene regulation at the transcriptional and …

Roles of emerging RNA-binding activity of cGAS in innate antiviral response

Y Ma, X Wang, W Luo, J **ao, X Song, Y Wang… - Frontiers in …, 2021 - frontiersin.org
cGAS, a DNA sensor in mammalian cells, catalyzes the generation of 2'-3'-cyclic AMP-GMP
(cGAMP) once activated by the binding of free DNA. cGAMP can bind to STING, activating …