Transformer-based deep learning for predicting protein properties in the life sciences

A Chandra, L Tünnermann, T Löfstedt, R Gratz - Elife, 2023 - elifesciences.org
Recent developments in deep learning, coupled with an increasing number of sequenced
proteins, have led to a breakthrough in life science applications, in particular in protein …

Unsupervised and semi‐supervised learning: The next frontier in machine learning for plant systems biology

J Yan, X Wang - The Plant Journal, 2022 - Wiley Online Library
Advances in high‐throughput omics technologies are leading plant biology research into the
era of big data. Machine learning (ML) performs an important role in plant systems biology …

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 …

DiscoTope-3.0: improved B-cell epitope prediction using inverse folding latent representations

MH Høie, FS Gade, JM Johansen, C Würtzen… - Frontiers in …, 2024 - frontiersin.org
Accurate computational identification of B-cell epitopes is crucial for the development of
vaccines, therapies, and diagnostic tools. However, current structure-based prediction …

Mgcnss: mirna–disease association prediction with multi-layer graph convolution and distance-based negative sample selection strategy

Z Tian, C Han, L Xu, Z Teng… - Briefings in …, 2024 - academic.oup.com
Identifying disease-associated microRNAs (miRNAs) could help understand the deep
mechanism of diseases, which promotes the development of new medicine. Recently …

Predicting microbe–drug associations with structure-enhanced contrastive learning and self-paced negative sampling strategy

Z Tian, Y Yu, H Fang, W **e, M Guo - Briefings in bioinformatics, 2023 - academic.oup.com
Motivation Predicting the associations between human microbes and drugs (MDAs) is one
critical step in drug development and precision medicine areas. Since discovering these …

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 …

Sequencing and characterizing human mitochondrial genomes in the biobank-based genomic research paradigm

L Luo, M Wang, Y Liu, J Li, F Bu, H Yuan… - Science China Life …, 2025 - Springer
Human mitochondrial DNA (mtDNA) harbors essential mutations linked to aging,
neurodegenerative diseases, and complex muscle disorders. Due to its uniparental and …

[HTML][HTML] Drug repositioning by multi-aspect heterogeneous graph contrastive learning and positive-fusion negative sampling strategy

J Liu, F Hu, Q Zou, P Tiwari, H Wu, Y Ding - Information Fusion, 2024 - Elsevier
Drug repositioning (DR) is a promising approach for identifying novel indications of existing
drugs. Computational methods for drug repositioning have been recognised as effective …

Bioinformatics approaches for unveiling virus-host interactions

H Iuchi, J Kawasaki, K Kubo, T Fukunaga… - Computational and …, 2023 - Elsevier
Abstract The coronavirus disease-2019 (COVID-19) pandemic has elucidated major
limitations in the capacity of medical and research institutions to appropriately manage …