scAAGA: Single cell data analysis framework using asymmetric autoencoder with gene attention

R Meng, S Yin, J Sun, H Hu, Q Zhao - Computers in biology and medicine, 2023 - Elsevier
In recent years, single-cell RNA sequencing (scRNA-seq) has emerged as a powerful
technique for investigating cellular heterogeneity and structure. However, analyzing scRNA …

Gene function and cell surface protein association analysis based on single-cell multiomics data

H Hu, Z Feng, H Lin, J Cheng, J Lyu, Y Zhang… - Computers in Biology …, 2023 - Elsevier
Single-cell transcriptomics provides researchers with a powerful tool to resolve the
transcriptome heterogeneity of individual cells. However, this method falls short in revealing …

Stgnnks: identifying cell types in spatial transcriptomics data based on graph neural network, denoising auto-encoder, and k-sums clustering

L Peng, X He, X Peng, Z Li, L Zhang - Computers in Biology and Medicine, 2023 - Elsevier
Background: Spatial transcriptomics technologies fully utilize spatial location information,
tissue morphological features, and transcriptional profiles. Integrating these data can greatly …

[HTML][HTML] Hepatic encephalopathy post-TIPS: current status and prospects in predictive assessment

X Xu, Y Yang, X Tan, Z Zhang, B Wang, X Yang… - Computational and …, 2024 - Elsevier
Transjugular intrahepatic portosystemic shunt (TIPS) is an essential procedure for the
treatment of portal hypertension but can result in hepatic encephalopathy (HE), a serious …

Multidimensional computational study to understand non-coding RNA interactions in breast cancer metastasis

S Chakraborty, S Banerjee - Scientific Reports, 2023 - nature.com
Metastasis is a major breast cancer hallmark due to which tumor cells tend to relocate to
regional or distant organs from their organ of origin. This study is aimed to decipher the …

SUnet: A multi-organ segmentation network based on multiple attention

X Li, X Qin, C Huang, Y Lu, J Cheng, L Wang… - Computers in Biology …, 2023 - Elsevier
Organ segmentation in abdominal or thoracic computed tomography (CT) images plays a
crucial role in medical diagnosis as it enables doctors to locate and evaluate organ …

Casual effects of gut microbiota on risk of infections: a two-sample Mendelian randomization study

B Lyu, J Ma, Y Bai, Z Feng - Frontiers in Microbiology, 2023 - frontiersin.org
Background The correlation between gut microbiota and infections has garnered significant
attention in previous studies; nevertheless, our understanding of the causal relationships …

Predicting drug-induced liver injury using graph attention mechanism and molecular fingerprints

J Wang, L Zhang, J Sun, X Yang, W Wu, W Chen… - Methods, 2024 - Elsevier
Drug-induced liver injury (DILI) is a significant issue in drug development and clinical
treatment due to its potential to cause liver dysfunction or damage, which, in severe cases …

Leveraging a meta-learning approach to advance the accuracy of Nav blocking peptides prediction

W Shoombuatong, N Homdee, N Schaduangrat… - Scientific Reports, 2024 - nature.com
The voltage-gated sodium (Nav) channel is a crucial molecular component responsible for
initiating and propagating action potentials. While the α subunit, forming the channel pore …

The metabolism-related lncRNA signature predicts the prognosis of breast cancer patients

X Ge, S Lei, P Wang, W Wang, W Wang - Scientific Reports, 2024 - nature.com
Long non-coding RNAs (lncRNAs) involved in metabolism are recognized as significant
factors in breast cancer (BC) progression. We constructed a novel prognostic signature for …