To clarify the mechanisms of diseases, such as cancer, studies analyzing genetic mutations have been actively conducted for a long time, and a large number of achievements have already been reported. Indeed, genomic medicine is considered the core di...
BACKGROUND: RNA secondary structure prediction is an important issue in structural bioinformatics, and RNA pseudoknotted secondary structure prediction represents an NP-hard problem. Recently, many different machine-learning methods, Markov models, a...
The majority of our human genome transcribes into noncoding RNAs with unknown structures and functions. Obtaining functional clues for noncoding RNAs requires accurate base-pairing or secondary-structure prediction. However, the performance of such p...
IEEE/ACM transactions on computational biology and bioinformatics
Nov 4, 2019
Aptamers are short single-stranded nucleic acids that bind to target molecules with high affinity and selectivity. Aptamers are generally identified in vitro by performing SELEX (systematic evolution of ligands by exponential enrichment). Complementi...
Protein-RNA interaction plays important roles in post-transcriptional regulation. However, the task of predicting these interactions given a protein structure is difficult. Here we show that, by leveraging a deep learning model NucleicNet, attributes...
Journal of visualized experiments : JoVE
Oct 11, 2019
Differential gene expression analysis is an important technique for understanding disease states. The machine learning algorithm CorEx has shown utility in analyzing differential expression of groups of genes in tumor RNA-seq in a way that may be hel...
IEEE/ACM transactions on computational biology and bioinformatics
Sep 24, 2019
RNA-Protein binding is involved in many different biological processes. With the progress of technology, more and more data are available for research. Based on these data, many prediction methods have been proposed to predict RNA-Protein binding pre...
RNA binding proteins (RBPs) determine RNA process from synthesis to decay, which play a key role in RNA transport, translation and degradation. Therefore, exploring RBPs' function from the amino acid sequence using computational methods has become on...
Emerging RNA-based approaches to disease detection and gene therapy require RNA sequences that fold into specific base-pairing patterns, but computational algorithms generally remain inadequate for these secondary structure design tasks. The Eterna p...