[HTML][HTML] dPromoter-XGBoost: Detecting promoters and strength by combining multiple descriptors and feature selection using XGBoost

H Li, L Shi, W Gao, Z Zhang, L Zhang, Y Zhao, G Wang - Methods, 2022 - Elsevier
Promoters play an irreplaceable role in biological processes and genetics, which are
responsible for stimulating the transcription and expression of specific genes. Promoter …

Protein function analysis through machine learning

C Avery, J Patterson, T Grear, T Frater, DJ Jacobs - Biomolecules, 2022 - mdpi.com
Machine learning (ML) has been an important arsenal in computational biology used to
elucidate protein function for decades. With the recent burgeoning of novel ML methods and …

[HTML][HTML] Computational analysis and prediction of PE_PGRS proteins using machine learning

F Li, X Guo, D Xiang, ME Pitt, A Bainomugisa… - Computational and …, 2022 - Elsevier
Mycobacterium tuberculosis genome comprises approximately 10% of two families of poorly
characterised genes due to their high GC content and highly repetitive nature. The largest …

BBPpredict: a web service for identifying blood-brain barrier penetrating peptides

X Chen, Q Zhang, B Li, C Lu, S Yang, J Long… - Frontiers in …, 2022 - frontiersin.org
Blood-brain barrier (BBB) is a major barrier to drug delivery into the brain in the treatment of
central nervous system (CNS) diseases. Blood-brain barrier penetrating peptides (BBPs), a …

Handcrafted versus non-handcrafted (self-supervised) features for the classification of antimicrobial peptides: complementary or redundant?

CR García-Jacas, LA García-González… - Briefings in …, 2022 - academic.oup.com
Antimicrobial peptides (AMPs) have received a great deal of attention given their potential to
become a plausible option to fight multi-drug resistant bacteria as well as other pathogens …

ExamPle: explainable deep learning framework for the prediction of plant small secreted peptides

Z Li, J Jin, Y Wang, W Long, Y Ding, H Hu… - Bioinformatics, 2023 - academic.oup.com
Abstract Motivation Plant Small Secreted Peptides (SSPs) play an important role in plant
growth, development, and plant–microbe interactions. Therefore, the identification of SSPs is …

Application of artificial intelligence for detection of chemico-biological interactions associated with oxidative stress and DNA damage

LM Davidovic, D Laketic, J Cumic, E Jordanova… - Chemico-Biological …, 2021 - Elsevier
In recent years, various AI-based methods have been developed in order to uncover
chemico-biological interactions associated with DNA damage and oxidative stress. Various …

6mA-RicePred: A Method for Identifying DNA N 6-Methyladenine Sites in the Rice Genome Based on Feature Fusion

Q Huang, J Zhang, L Wei, F Guo, Q Zou - Frontiers in plant science, 2020 - frontiersin.org
Motivation The biological function of N 6-methyladenine DNA (6mA) in plants is largely
unknown. Rice is one of the most important crops worldwide and is a model species for …

PredLLPS_PSSM: a novel predictor for liquid–liquid protein separation identification based on evolutionary information and a deep neural network

S Zhou, Y Zhou, T Liu, J Zheng… - Briefings in …, 2023 - academic.oup.com
The formation of biomolecular condensates by liquid–liquid phase separation (LLPS) has
become a universal mechanism for spatiotemporal coordination of biological activities in …

Multifactorial feature extraction and site prognosis model for protein methylation data

M Khandelwal, R Kumar Rout, S Umer… - Briefings in …, 2023 - academic.oup.com
Integrated studies (multi-omics studies) comprising genetic, proteomic and epigenetic data
analyses have become an emerging topic in biomedical research. Protein methylation is a …