Pre-training graph neural networks for link prediction in biomedical networks

Y Long, M Wu, Y Liu, Y Fang, CK Kwoh, J Chen… - …, 2022 - academic.oup.com
Motivation Graphs or networks are widely utilized to model the interactions between different
entities (eg proteins, drugs, etc.) for biomedical applications. Predicting potential …

Comprehensive pan-cancer analysis reveals CCDC58 as a carcinogenic factor related to immune infiltration

H Wu, Q Geng, W Shi, C Qiu - Apoptosis, 2024 - Springer
CCDC58, a member of the CCDC protein family, has been primarily associated with the
malignant progression of hepatocellular carcinoma (HCC) and breast cancer, with limited …

Multimorbidity prediction using link prediction

F Aziz, VR Cardoso, L Bravo-Merodio, D Russ… - Scientific Reports, 2021 - nature.com
Multimorbidity, frequently associated with aging, can be operationally defined as the
presence of two or more chronic conditions. Predicting the likelihood of a patient with …

Comprehensive pan-cancer analysis reveals NTN1 as an immune infiltrate risk factor and its potential prognostic value in SKCM

F Luan, Y Cui, R Huang, Z Yang, S Qiao - Scientific Reports, 2025 - nature.com
Abstract Netrin-1 (NTN1) is a laminin-related secreted protein involved in axon guidance
and cell migration. Previous research has established a significant connection between …

Fairness-aware Maximal Biclique Enumeration on Bipartite Graphs

Z Yin, Q Zhang, W Zhang, RH Li… - 2023 IEEE 39th …, 2023 - ieeexplore.ieee.org
Maximal biclique enumeration is a fundamental problem in bipartite graph data analysis.
Existing biclique enumeration methods mainly focus on non-attributed bipartite graphs and …

Snowflake: visualizing microbiome abundance tables as multivariate bipartite graphs

J Peeters, DM Bot, G Rovelo Ruiz, J Aerts - Frontiers in Bioinformatics, 2024 - frontiersin.org
Current visualizations in microbiome research rely on aggregations in taxonomic
classifications or do not show less abundant taxa. We introduce Snowflake: a new …

Consensus clustering for robust bioinformatics analysis

B Yousefi, B Schwikowski - bioRxiv, 2024 - biorxiv.org
Clustering plays an important role in a multitude of bioinformatics applications, including
protein function prediction, population genetics, and gene expression analysis. The results …

Integrating single-cell RNA-seq and bulk RNA-seq to construct a neutrophil prognostic model for predicting prognosis and immune response in oral squamous cell …

J Wang, Z Cui, Q Song, K Yang, Y Chen, S Peng - Human Genomics, 2024 - Springer
Background Oral squamous cell carcinoma (OSCC) is an aggressive malignancy with poor
prognosis. Neutrophil infiltration has been associated with unfavorable outcomes in OSCC …

[HTML][HTML] Maximum Butterfly Generators Search in Bipartite Networks

J Huang, G Pang, F Hao - Mathematics, 2024 - mdpi.com
Bipartite graphs are widely used for modelling various real-world scenarios characterized
with binary relations, such as, scholarly articles recommendation with author-paper …

Glioblastoma vulnerability to neddylation inhibition is dependent on PTEN status, and dysregulation of the cell cycle and DNA replication

B Taylor, N Tang, Y Hao, M Lee, S Peng… - Neuro-Oncology …, 2024 - academic.oup.com
Background Neddylation (NAE) inhibition, affecting posttranslational protein function and
turnover, is a promising therapeutic approach to cancer. We report cytotoxic vulnerability to …