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 …

Prediction of anticancer peptides based on an ensemble model of deep learning and machine learning using ordinal positional encoding

Q Yuan, K Chen, Y Yu, NQK Le… - Briefings in …, 2023 - academic.oup.com
Anticancer peptides (ACPs) are the types of peptides that have been demonstrated to have
anticancer activities. Using ACPs to prevent cancer could be a viable alternative to …

[HTML][HTML] Mini-review: recent advances in post-translational modification site prediction based on deep learning

L Meng, WS Chan, L Huang, L Liu, X Chen… - Computational and …, 2022 - Elsevier
Post-translational modifications (PTMs) are closely linked to numerous diseases, playing a
significant role in regulating protein structures, activities, and functions. Therefore, the …

Deepm5C: a deep-learning-based hybrid framework for identifying human RNA N5-methylcytosine sites using a stacking strategy

MM Hasan, S Tsukiyama, JY Cho, H Kurata, MA Alam… - Molecular Therapy, 2022 - cell.com
As one of the most prevalent post-transcriptional epigenetic modifications, N5-
methylcytosine (m5C) plays an essential role in various cellular processes and disease …

Alterations of the gut microbiota in patients with severe chronic heart failure

W Sun, D Du, T Fu, Y Han, P Li, H Ju - Frontiers in microbiology, 2022 - frontiersin.org
Chronic heart failure (CHF) is the final outcome of almost all forms of cardiovascular
diseases, remaining the main cause of mortality worldwide. Accumulating evidence is …

Deep-STP: a deep learning-based approach to predict snake toxin proteins by using word embeddings

H Zulfiqar, Z Guo, RM Ahmad, Z Ahmed, P Cai… - Frontiers in …, 2024 - frontiersin.org
Snake venom contains many toxic proteins that can destroy the circulatory system or
nervous system of prey. Studies have found that these snake venom proteins have the …

StackedEnC-AOP: prediction of antioxidant proteins using transform evolutionary and sequential features based multi-scale vector with stacked ensemble learning

G Rukh, S Akbar, G Rehman, FK Alarfaj, Q Zou - BMC bioinformatics, 2024 - Springer
Background Antioxidant proteins are involved in several biological processes and can
protect DNA and cells from the damage of free radicals. These proteins regulate the body's …

iRNA-ac4C: a novel computational method for effectively detecting N4-acetylcytidine sites in human mRNA

W Su, XQ Xie, XW Liu, D Gao, CY Ma, H Zulfiqar… - International Journal of …, 2023 - Elsevier
Abstract RNA N4-acetylcytidine (ac4C) is the acetylation of cytidine at the nitrogen-4
position, which is a highly conserved RNA modification and involves a variety of biological …

iACVP: markedly enhanced identification of anti-coronavirus peptides using a dataset-specific word2vec model

H Kurata, S Tsukiyama… - Briefings in bioinformatics, 2022 - academic.oup.com
The COVID-19 pandemic caused several million deaths worldwide. Development of anti-
coronavirus drugs is thus urgent. Unlike conventional non-peptide drugs, antiviral peptide …

NmRF: identification of multispecies RNA 2'-O-methylation modification sites from RNA sequences

C Ao, Q Zou, L Yu - Briefings in bioinformatics, 2022 - academic.oup.com
O-methylation (Nm) is a post-transcriptional modification of RNA that is catalyzed by 2'-O-
methyltransferase and involves replacing the H on the 2′-hydroxyl group with a methyl …