Emergence of power law distributions in protein-protein interaction networks through study bias

DB Blumenthal, M Lucchetta, L Kleist, SP Fekete, M List… - eLife, 2024 - elifesciences.org
Degree distributions in protein-protein interaction (PPI) networks are believed to follow a
power law (PL). However, technical and study biases affect the experimental procedures for …

Communicability cosine distance: similarity and symmetry in graphs/networks

E Estrada - Computational and Applied Mathematics, 2024 - Springer
A distance based on the exponential kernel of the adjacency matrix of a graph and
representing how well two vertices connect to each other in a graph is defined and studied …

[HTML][HTML] Multi-level biological network analysis and drug repurposing based on leukocyte transcriptomics in severe COVID-19: in silico systems biology to precision …

P Sagulkoo, H Chuntakaruk, T Rungrotmongkol… - Journal of personalized …, 2022 - mdpi.com
The coronavirus disease 2019 (COVID-19) pandemic causes many morbidity and mortality
cases. Despite several developed vaccines and antiviral therapies, some patients …

Emergence of power-law distributions in protein-protein interaction networks through study bias

M Lucchetta, M List, DB Blumenthal, MH Schaefer - bioRxiv, 2023 - biorxiv.org
Protein-protein interaction (PPI) networks have been found to be power-law-distributed, ie,
in observed PPI networks, the fraction of nodes with degree k often follows a power-law (PL) …

[HTML][HTML] Gene association classification for autism spectrum disorder: Leveraging gene embedding and differential gene expression profiles to identify disease-related …

A Suratanee, K Plaimas - Applied Sciences, 2023 - mdpi.com
Identifying genes associated with autism spectrum disorder (ASD) is crucial for
understanding the underlying mechanisms of the disorder. However, ASD is a complex …

Heterogeneous network propagation with forward similarity integration to enhance drug–target association prediction

P Tangmanussukum, T Kawichai, A Suratanee… - PeerJ Computer …, 2022 - peerj.com
Identification of drug–target interaction (DTI) is a crucial step to reduce time and cost in the
drug discovery and development process. Since various biological data are publicly …

NIAPU: network-informed adaptive positive-unlabeled learning for disease gene identification

P Stolfi, A Mastropietro, G Pasculli, P Tieri… - …, 2023 - academic.oup.com
Motivation Gene–disease associations are fundamental for understanding disease etiology
and develo** effective interventions and treatments. Identifying genes not yet associated …

Integration of various protein similarities using random forest technique to infer augmented drug-protein matrix for enhancing drug-disease association prediction

S Kitsiranuwat, A Suratanee, K Plaimas - Science Progress, 2022 - journals.sagepub.com
Identifying new therapeutic indications for existing drugs is a major challenge in drug
repositioning. Most computational drug repositioning methods focus on known targets …

Identification of Tumor Budding-Associated Genes in Breast Cancer through Transcriptomic Profiling and Network Diffusion Analysis

P Janyasupab, K Singhanat, M Warnnissorn… - …, 2024 - pmc.ncbi.nlm.nih.gov
Breast cancer has the highest diagnosis rate among all cancers. Tumor budding (TB) is
recognized as a recent prognostic marker. Identifying genes specific to high-TB samples is …

[HTML][HTML] Immune-related protein interaction network in severe COVID-19 patients toward the identification of key proteins and drug repurposing

P Sagulkoo, A Suratanee, K Plaimas - Biomolecules, 2022 - mdpi.com
Coronavirus disease 2019 (COVID-19) is still an active global public health issue. Although
vaccines and therapeutic options are available, some patients experience severe conditions …