SAFPred: synteny-aware gene function prediction for bacteria using protein embeddings

A Urhan, BM Cosma, AM Earl, AL Manson… - …, 2024 - academic.oup.com
Motivation Today, we know the function of only a small fraction of the protein sequences
predicted from genomic data. This problem is even more salient for bacteria, which …

In silico and gene expression analysis of the acute inflammatory response of gilthead seabream (Sparus aurata) after subcutaneous administration of carrageenin

JC Campos-Sánchez, J Mayor-Lafuente… - Fish Physiology and …, 2021 - Springer
Inflammation is one of the main causes of loss of homeostasis at both the systemic and
molecular levels. The aim of this study was to investigate in silico the conservation of …

SAP: Synteny-aware gene function prediction for bacteria using protein embeddings

A Urhan, BM Cosma, AM Earl, AL Manson, T Abeel - bioRxiv, 2023 - pmc.ncbi.nlm.nih.gov
Motivation: Today, we know the function of only a small fraction of the protein sequences
predicted from genomic data. This problem is even more salient for bacteria, which …

[HTML][HTML] Network analysis in the identification of genes conferring metastatic potential in hepatocellular carcinoma

HD Tan, HJY Leong, WH Yap, AYY Chia… - Eurasian Journal of …, 2022 - accscience.com
Objectives: Hepatocellular carcinoma (HCC) is a common liver cancer accounting with high
mortality rate owing to metastasis. Anti-metastatic treatment is scant while proposed …

Pre-stabilization strategies for systems-wide in situ crosslinking mass spectrometry

AR Michael - 2025 - prism.ucalgary.ca
Understanding the associations proteins form within a network of protein-protein interactions
(PPIs) provides insight into the functions that drive cellular processes. These networks have …