Distance-based support vector machine to predict DNA N6-methyladenine modification

H Zhang, Q Zou, Y Ju, C Song, D Chen - Current Bioinformatics, 2022 - ingentaconnect.com
Background: DNA N6-methyladenine plays an important role in the restriction-modification
system to isolate invasion from adventive DNA. The shortcomings of the high time …

Sequence representation approaches for sequence-based protein prediction tasks that use deep learning

F Cui, Z Zhang, Q Zou - Briefings in Functional Genomics, 2021 - academic.oup.com
Deep learning has been increasingly used in bioinformatics, especially in sequence-based
protein prediction tasks, as large amounts of biological data are available and deep learning …

Application of machine learning for drug–target interaction prediction

L Xu, X Ru, R Song - Frontiers in genetics, 2021 - frontiersin.org
Exploring drug–target interactions by biomedical experiments requires a lot of human,
financial, and material resources. To save time and cost to meet the needs of the present …

CRBPDL: Identification of circRNA-RBP interaction sites using an ensemble neural network approach

M Niu, Q Zou, C Lin - PLoS computational biology, 2022 - journals.plos.org
Circular RNAs (circRNAs) are non-coding RNAs with a special circular structure produced
formed by the reverse splicing mechanism. Increasing evidence shows that circular RNAs …

A method for identifying vesicle transport proteins based on LibSVM and MRMD

Z Tao, Y Li, Z Teng, Y Zhao - Computational and Mathematical …, 2020 - Wiley Online Library
With the development of computer technology, many machine learning algorithms have
been applied to the field of biology, forming the discipline of bioinformatics. Protein function …

iTTCA-RF: a random forest predictor for tumor T cell antigens

S Jiao, Q Zou, H Guo, L Shi - Journal of translational medicine, 2021 - Springer
Background Cancer is one of the most serious diseases threatening human health. Cancer
immunotherapy represents the most promising treatment strategy due to its high efficacy and …

iThermo: a sequence-based model for identifying thermophilic proteins using a multi-feature fusion strategy

Z Ahmed, H Zulfiqar, AA Khan, I Gul, FY Dao… - Frontiers in …, 2022 - frontiersin.org
Thermophilic proteins have important application value in biotechnology and industrial
processes. The correct identification of thermophilic proteins provides important information …

ProtFold-DFG: protein fold recognition by combining Directed Fusion Graph and PageRank algorithm

J Shao, B Liu - Briefings in Bioinformatics, 2021 - academic.oup.com
As one of the most important tasks in protein structure prediction, protein fold recognition has
attracted more and more attention. In this regard, some computational predictors have been …

An analysis of protein language model embeddings for fold prediction

A Villegas-Morcillo, AM Gomez… - Briefings in …, 2022 - academic.oup.com
The identification of the protein fold class is a challenging problem in structural biology.
Recent computational methods for fold prediction leverage deep learning techniques to …

Identify DNA-binding proteins through the extreme gradient boosting algorithm

Z Zhao, W Yang, Y Zhai, Y Liang, Y Zhao - Frontiers in Genetics, 2022 - frontiersin.org
The exploration of DNA-binding proteins (DBPs) is an important aspect of studying
biological life activities. Research on life activities requires the support of scientific research …